1	11117257_MI:0004	Copurification of LOX2 with eIF4E by m7GTP-Sepharose affinity chromatography.
2	11500378_MI:0004	UAF, a yeast RNA polymerase I transcription factor, contains Rrn5p, Rrn9p, Rrn10p, histones H3 and H4, and uncharacterized protein p30.
3	11739376_MI:0004	Following co-incubation of two further, similar aliquots of the same preparations of apoPacSN and copper-Atx1, the amount of copper associated with Atx1 declined and, most importantly, copper became associated with apoPacSN.
4	12376572_MI:0004	Subunit identification of human 20S proteasome purified from erythrocytes.
5	12482983_MI:0004	ADA2b-containing Hep0.5-derived fraction, we detected more GCN5 together with TAF1, TAF4, TAF9, TAF10, TAF10b, and TBP.
6	12482983_MI:0004	In the ADA2a-containing Hep0.24-derived fraction, we also detected some GCN5, TAF9, and TBP.
7	12637749_MI:0004	Purification of the TIM22 complex from yeast mitochondria.
8	14657239_MI:0004	Therefore, these data show that the human unknown KIAA1684 protein corresponds to the p140 band selectively eluted from MBP-p130Cas column, suggesting that the two proteins might associate into the cells.
9	15024052_MI:0004	A large-scale purification of the Isw2 complex by FLAG immunoaffinity chromatography followed by a Source Q anionic-exchange column showed Isw2p to copurify with two previously unidentified proteins (Fig. 1A).
10	15024052_MI:0004	To further confirm the association of Dpb4p and Yjl065cp with Isw2, we directly purified Yjl065cp via FLAG immunoaffinity chromatography followed by a Source Q anionic-exchange column (Fig. 1B), which yielded a four-subunit Isw2 complex (Itc1p, Isw2p, Dpb4p, and Yjl065cp) and no other proteins at a detectable level.
11	15491154_MI:0004	In addition to the nonhydrogenase-related contaminants also observed in the purification of HypE, there are two bands visible at the masses expected for HypD, HypE, or HypF1, as well as some strong bands in the region expected for HoxH
12	15506919_MI:0004	Additionally, we found that IgG pulldown of Rtt102 also revealed an interaction with Sth1, the catalytic subunit of the Rsc chromatin-remodelling complex,
13	15506919_MI:0004	To determine whether SGF11 is a stable component of SAGA and SLIK, we reciprocally tagged SGF11 using the standard tandem-affinity tag and purified the complexes associated with SGF11. The proteins purified from the Sgf11TAP strain were identified using MudPIT MS.
14	15506919_MI:0004	Using whole-cell extract derived from the Rtt102TAP-tagged strain and IgG resin, we were first able to show that Swi3, a component of the Swi/Snf complex, was pulled down with the Rtt102TAP tag
15	15506919_MI:0004	we purified the Swi/Snf complex from a yeast strain containing the TAP tag on the Snf6 subunit. MudPIT analysis of the purified Swi/Snf complex revealed a number of peptide hits for RTT102, which had not been previously characterized as a subunit of Swi/Snf
16	15506919_MI:0004	we separated and individually purified the two complexes (Figures 1A and 1B). This purification was followed by MudPIT of both SAGA and SLIK, in which we identified a previously uncharacterized open reading frame, YPL047W, present in both the SAGA and SLIK HAT complexes
17	16230339_MI:0004	Chromatography of an equimolar mixture of ProT and Met- SC-(1-325), in contrast, resulted in depletion of the free ProT and Met- SC-(1-325) peaks and appearance of a new Met-SC-(1-325)
ProT peak eluted with NaSCN
18	16314420_MI:0004	The 67-kDa Spliced Variant of 
-Galactosidase That Binds Elastin Also Forms a Cell Membrane-targeted Complex with Neu1 and PPCA
19	16339759_MI:0004	Sp3 protein isoforms co-purify with KCS DNA binding activity.
20	16339759_MI:0004	The Sp1 protein also co-purified with KBP activity (Fig. 1B)
21	16354655_MI:0004	S105-RNase specifically interacts with NaTrxh.
22	16816426_MI:0004	Get3 biochemically copurifies with Get2 and Get1.
23	17000644_MI:0004	Proteins identified by at least two arginine-containing peptides with a minimum SILAC cutoff ratio of 1.5 are presented here and include 25 SUMO-1 targets (top part), 19 SUMO-2 targets (middle part), and nine proteins conjugated to both SUMO family members (bottom part).
24	17000644_MI:0004	RanGAP1 is preferentially conjugated to SUMO-1,
25	17000644_MI:0004	SART1 is conjugated to both SUMOs at similar levels.
26	17000644_MI:0004	Sp100 is conjugated to SUMO-2
27	18065690_MI:0004	Copurified HSC70 protein amounts were too low to perform the analysis with SGT1a-Strep. For SGT1b-Strep, HSC70-1 and HSC70-3 remained the principal interactors of SGT1b expressed under the control of its native promoter in both samples (Figure 2C; see Supplemental Figure 2 online). Weak but reproducible signals were also unambiguously identified as HSC70 isoforms 2 (CAB85986) and 4 (BAB02269) in the pathogen-treated samples only.
28	18065690_MI:0004	SGT1a accumulated to similar levels as SGT1b in N. benthamiana extracts but bound lower amounts of HSC70-1 protein
29	18065690_MI:0004	The association between SGT1 and HSC70s was confirmed and analyzed further using Agrobacterium tumefaciens-mediated transient coexpression of Arabidopsis SGT1 (Strep-tagged) and HSC70-1 (hemagglutinin [HA]-tagged) domains in Nicotiana benthamiana followed by detection of StrepII copurified protein on immunoblots
30	18065690_MI:0004	Therefore, HSC70-1 and HSC70-3 are two novel SGT1b-Strep interactors in healthy leaf tissue.
31	18160036_MI:0004	A dual Flag- and [HA]2-tagged Tel2 protein (FH2-Tel2) was expressed in HeLa S3 cells and sequentially immunoprecipitated using anti-Flag and anti-HA antibody conjugated beads followed by MALDI-TOF mass spectrometric analysis of associated proteins. This analysis revealed DNA-PKcs and ATR in the Tel2 complex
32	18160036_MI:0004	Immunoblotting analysis showed that ATM, mTOR, and SMG1 were also present in the Tel2 complex derived from HeLa cells (Figure 6B)
33	18425733_MI:0004	We have not identified multiple peptides from the same protein family as match. After analysis of their polypeptide sequences (http://pfam.janelia.org/) four of them were considered protein candidates for further studies: the proteins encoded by the ORFs NCU01021, NCU03876, NCU03482, and NCU06679 (Table 1).
34	18571510_MI:0004	NPR1 binds preferentially to the DNA-inactive form of TGA2.
35	18571510_MI:0004	The following experimental strategy was used to investigate this question (Fig. 1). Recombinant histidine-tagged TGA2 (35 μg input, I) was applied to a DNA-affinity column containing the double-stranded LS7 cis-element. LS7 is an activating sequence [24] previously shown to be bound in vitro by TGA2 [23]. In our experiments, as expected, the flowthrough (FT) fraction (not, vert, similar50% total input) consists of the DNA-inactive form of TGA2, while the eluted (E) fraction is highly enriched for the fraction of TGA2 that is competent to bind DNA.
36	18805096_MI:0004	To test whether the FMRP-CYFIP1 complex simultaneously interacts with PABP, we used poly(A)-Sepharose beads to isolate PABP and associated factors from brain extracts.
37	7925282_MI:0004	The final fraction (lane 8) consisted of six proteins in approximately equimolar amounts: a doublet of bands migrating at 66 kDa (Srp68p and Srp72p) and single bands at 60 (Srp54p), 34 (Sec65p), 21 (Srp2lp) and 19 kDa (Srpl4p). The identification of an additional protein, Srp2lp, in this purification, not seen in the immunoprecipitations of [35S]methionine-labeled proteins, suggested that it lacked methionine residues and was therefore not visible in Figure lB.
38	8372350_MI:0004	MBF contains Swi6 and a 120-kilodalton protein (p120). MBF was purified and the gene encoding p120 (termed MBPI) was cloned.
39	9173976_MI:0004	chromatography fractions from 0 0.9 M NH42SO4 gradient indicate that hSUG1 co-elutes with XPB in Heparin 5PW fractions 10 14.
40	imex:IM-11896_MI:0004	As shown in Fig. 1C, larger bands were observed prior to heating indicating the presence of supramolecular complexes. In the case of CcpC the complexes were subjected to MS and found to be identical to CcpC demonstrating the presence of CcpC dimers as previously suggested
41	imex:IM-11896_MI:0004	Figure 1A shows the SDS-PAGE analysis of the eluted proteins. In the absence of a Strep-tagged protein (empty vector), no proteins were purified, as expected from the initial test experiments. The purification of GltC resulted in the coelution of one single protein which was identified by MS (LCQ-DecaXPlus mass spectrometer, Thermo Finnigan, San Jose, USA) as the glutamate dehydrogenase RocG
42	imex:IM-11896_MI:0004	Moreover, this finding confirms the specificity of the interaction between GltC and RocG since both CcpC and GltC are members of the LysR family of transcriptional regulators. The identity of the eluted proteins was confirmed byWestern blot analysis using antibodies raised against B. subtilis GltC [14], CcpC [21], and RocG [19]
43	imex:IM-11919_MI:0004	Gel filtration profile of FimD2:CHis:F:G:H complexes.
44	imex:IM-11935_MI:0004	Identification of SET-binding proteins.
45	imex:IM-11935_MI:0004	Mass spectrometric SET-interacting proteins in mouse liver cells
46	imex:IM-11935_MI:0004	SET binds to the active form of GP
47	imex:IM-11935_MI:0004	To identify some of the high affinity SET-binding proteins, the 300 mM KCl eluates from the SET columns were analyzed by MS using a MALDI-TOF. From these analyseswe identified 19 SET-binding proteins that have been listed in Table 2.
48	imex:IM-11935_MI:0004	Western blot validation of the association of several different proteins with SET.
49	imex:IM-11998_MI:0004	A glutathione S-transferase (GST)-fusion protein containing a 472 aa C-terminal fragment of dCAMTA bound to calmodulin-agarose beads,
50	imex:IM-12014_MI:0004	Fractionation of Raji mitochondrial extracts over Shepherdin-Sepharose resulted in the specific elution of both TRAP-1 and Hsp90
51	imex:IM-12024_MI:0004	Addition of Rab6 enhanced the ability of GCC185 to bind Arl1
52	imex:IM-12024_MI:0004	C-110 bound Rab6-GTP with a 5-fold preference over Rab6-GDP, which defines GCC185 as a Rab6 effector.
53	imex:IM-12024_MI:0004	Rab6 and Rab9 compete for GCC185 binding both specifically and efficiently.
54	imex:IM-12024_MI:0004	Rab6 and Rab9 C-terminal hypervariable domains contributed to GCC185 binding
55	10068665_MI:0006	The Grb2 immunoprecipitation experiments required longer exposure times than the Shc or SHIP experiments, suggesting a weaker interaction of Grb2 with SHIP.
56	10075709_MI:0006	Fine mapping, however, revealed that aa 313-420 of p160, an N-terminal region in close proximity to the KOW motifs, is sufficient for pol II binding (lane 23). aa 420-757 of p160, which contains all four of the KOW motifs, also bound to pol II weakly
57	10087265_MI:0006	Vik1p coimmunoprecipitates with Kar3p.
58	10207046_MI:0006	Antibodies raised against cpSecY were used to immunoprecipitate the digitonin-solubilized complex, and cpSecY and cpSecE in the supernatant and precipitate were detected by immunoblot analysis.
59	10209119_MI:0006	A specific interaction was readily detectable in lysates from cells co-overexpressing Pop1p and Pop2p, however. Histidine (His)-tagged Pop1p co-purified with hemagglutinin (HA)-epitope-tagged Pop2p (HA-Pop2p) on Ni-agarose beads, but not on control beads (Figure 2a). In the reciprocal experiment, anti-Pop2p antisera, but not pre-immune sera, co-precipitated Myc-tagged Pop1p along with HA-Pop2p (Figure 2a).
60	10209119_MI:0006	Both Pop1p and Pop2p interact with their substrate Cdc18p in vivo [10,12]. To test whether the Cdc18p-Pop2p interaction depends on Pop1p, Mycepitope-tagged GFP-Cdc18p was expressed in wild-type cells, Dpop1 and Dpop2 mutant cells. Anti-Myc immunoprecipitates were tested for the presence of endogenous Pop2p with anti-Pop2p antisera. Although the interaction between Pop2p and GFP-Cdc18p was detected in lysates from wild-type cells, it was undetectable in lysates from Dpop1 mutants, suggesting that Pop1p-Pop2p heterooligomers cooperate in substrate binding.
61	10209119_MI:0006	To map the region in Pop2p required for the interaction with Pop1p, we analyzed various Pop2p truncation mutants (Figure 2b). Pop1p bound to full-length Pop2p as well as to amino-terminal Pop2p fragments containing residues 2-344 or 2-241(Figure 2b). In contrast, deletion of the amino-terminal 171 or 344 amino acids of Pop2p abolished the interaction with Pop1p (Figure 2b). These carboxy-terminal fragments were expressed at lower levels than the amino terminal fragments, however, so the carboxyl terminus of Pop2p may contain an independent Pop1p interaction motif not detected in this assay.
62	10329624_MI:0006	However, while anti-Tpd3 antibodies precipitated Tpd3 as well as Pph21, Pph22 and Cdc55, the anti-Tpd3 antibodies did not precipitate Tap42 (Figure 3B).
63	10369680_MI:0006	Ring1 binds RYBP and M33 through the same C-terminal domain, whereas the RYBP-M33 interaction takes place through an M33 domain not involved in Ring1 binding.
64	10369680_MI:0006	We have identified a new Zn finger protein, RYBP, which interacts directly with both Ring1 proteins (Ring1A and Ring1B) and with M33, two mutually interacting sets of proteins of the mammalian Polycomb complex.
65	10383400_MI:0006	Co-immunoprecipitation from T-cells of theta PKC and p59fyn.
66	10383417_MI:0006	Association of endogenous AMSH with STAM.
67	10436016_MI:0006	Figure 3A shows that anti-Mad2p immunoprecipitates contained Mad1p.
68	10436016_MI:0006	When the two proteins were transiently expressed in COS7 cells by co-transfection, Mad1p was found in Mad2p immunoprecipitates (Figure 6).
69	10536025_MI:0006	This provides additional evidence for the association of CHS and F3H with CHI in the plant cell.
70	10611319_MI:0006	Reciprocal coimmunoprecipitation of IP3R and TRP. T3 9 or T6 12 cells
71	10648604_MI:0006	and immunoblotting. HA-tagged Tim18p coimmunoprecipitated with Tim12p, with all of Tim22p, and with a portion of Tim54p (Fig. 4B; not shown)
72	10648604_MI:0006	In addition to Tim10p and Tim22p, a band of ~18 kDa was seen that was absent from the control precipitates with nonimmune serum
73	10656681_MI:0006	In contrast, TRX SET was readily detected in the pellet when either of two different anti-TRX antibodies directed against the N-terminal (N1) or the central (N4) regions of the TRX molecule (Kuzin et al., 1994) were used for
74	10677492_MI:0006	interaction with Stt3p was impaired only when the mutation in Ost4p occurred in position 18, 21, or 24 (Fig. 5C).
75	10704439_MI:0006	Fig 6 a shows that there was no difference in the amount of Bub3p associated with Mad3p at different points in the cell cycle.
76	10704439_MI:0006	Fig 7 a reveals that Cdc20-HAp was present in Mad3p immunoprecipitates at wild-type levels in bub2 extracts, but at reduced levels or was entirely absent in mad1, mad2, bub1, bub3, and mps1 extracts.
77	10704439_MI:0006	However, in both wild-type and bub2 strains, where nocodazole treatment would lead to an inhibition of Cdc20p-dependent APC activity, Mad3p was stably associated with both Cdc20p and Mad2p.
78	10704439_MI:0006	Levels of Mad3p-Cdc20p and Mad3p-Mad2p interaction vary through the cell cycle,
79	10704439_MI:0006	These experiments show that Mad3p was not required for Mad2p-Cdc20p complex formation, in fact in some experiments the Mad2p-Cdc20p complex was found at slightly higher levels in mad3 than in wild-type extracts.
80	10713067_MI:0006	The Lcb1p-GST fusion protein restores SPT activity (data not shown) and coimmunoprecipitates with Lcb2p (Fig. 5A, lanes 6 and 7).
81	10713067_MI:0006	The rabbit polyclonal antibodies to either Lcb1p or Lcb2p coimmunoprecipitate both Lcb1p and Lcb2p, indicating that the two proteins are associated (Fig. 5A).
82	10713067_MI:0006	The rabbit polyclonal antibodies to either Lcb1p or Lcb2p coimmunoprecipitated Tsc3p-HA along with Lcb1p/Lcb2p (Fig. 6C)
83	10727209_MI:0006	12-LOX and lamin A coimmunoprecipitated from nuclear extracts of untransfected A431 cells.
84	10727209_MI:0006	12-LOX antibody co-immunoprecipitated keratin with 12-LOX in A431 cells and transfectants.
85	10727209_MI:0006	keratin antibody co-immunoprecipitated 12-LOX with keratin in A431 cells and transfectants
86	10801826_MI:0006	an increase in PECAM-1/gamma -catenin association occurred between days 7.5 and 9.5 p.c.
87	10801826_MI:0006	A two-fold decrease in PECAM-1/gamma -catenin association was noted in the glucose-treated samples
88	10801826_MI:0006	exposure of EOMA cells to bisindolylmaleimide GF-109203x (bis), a potent and selective PKC inhibitor (21), resulted in a substantial increase in PECAM-1/gamma -catenin association (Fig. 2E, top panel). Interestingly, the increase in gamma -catenin binding was accompanied by a comparable decrease in beta -catenin association with PECAM-1 (Fig. 2E, middle panel)
89	10801826_MI:0006	exposure of HUVEC to a physiologic PKC inducer, diacylglycerol analog, significantly decreased PECAM-1/gamma -catenin interactions (Fig. 2C), more than 3-fold based on densitometric analysis (Fig. 2D). Staurosporine, a potent PKC inhibitor, did not affect PECAM-1/gamma -catenin interactions (Fig. 2C), further supporting the concept that PKC activity in HUVEC is low.
90	10801826_MI:0006	Interestingly, low but detectable levels of desmoplakin were co-IP with PECAM-1 independently of gamma -catenin phosphotyrosine state,
91	10801826_MI:0006	not only beta -catenin but also gamma -catenin is a PECAM-1 partner and that PECAM-1 interaction with the two catenins is differentially regulated
92	10801826_MI:0006	PECAM-1/gamma -catenin association showed the exact opposite phenotype, being highest in HUVEC
93	10805743_MI:0006	Rai1p binds to Rat1p.
94	10809665_MI:0006	The identity of the OSA protein in the core BRM complex was confirmed by Western blot analysis (Fig. 3E).
95	10888666_MI:0006	AtTLG2a, AtTLG2b, and AtVTI1b coimmunoprecipitate with the use of AtVPS45 antibodies.
96	10888666_MI:0006	AtTLG2a coprecipitated with AtVPS45, whereas AtPEP12 and AtVAM3 did not.
97	10918185_MI:0006	when 293T cells were co-transfected with wild-type Fas, but not mutant Fas (tPLV), FAP-1 was co-precipitated with the anti-Fas MAb
98	10954706_MI:0006	and double-stained with anti-Mrj polyclonal antibody and anti-K18 monoclonal antibody. Mrj was present in both the cytoplasm and nucleus (Fig. 4a). In the cytoplasm, Mrj was dispersed mainly in the perinuclear area and showed some filamentous patterns. There was a significant overlap between filamentous Mrj and K18 (Fig. 4, a-d), where Mrj was more remarkably associated with K8/18 filament bundles around perinuclear areas than with finer filament structures in the cell periphery.
99	10954706_MI:0006	Hsp/c70 was indeed detected in the Mrj immune complex. These results indicate that Mrj is associated with K18 and Hsp/c70 in vivo.
100	10987273_MI:0006	b-catenin was coimmunoprecipitated with AR in the absence of hormone.
101	11003656_MI:0006	In extracts from mammalian cells transfected with Myc-tagged FBD and HaHSP27, Myc-tagged FBD could be coimmunoprecipitated by HSP27 antibody L2R3
102	11022036_MI:0006	immune complexes of peptides corresponding to PCNA N-terminal (1-46 aa) and middle (87-127 aa) but not the C-terminal (224-261 aa) domains also contained CR6.
103	11022036_MI:0006	PCNA immune complexes contained the CR6/76-159 peptide
104	11022036_MI:0006	the CR6 immune complex contained p21.
105	11022036_MI:0006	the CR6 immune complex contained PCNA
106	11022036_MI:0006	the p21 immune complex obtained from cell lysate after 48 h of IL-6 treatment contained CR6.
107	11022036_MI:0006	the PCNA immune complex, obtained from M1 cell extracts contained CR6.
108	11022036_MI:0006	Transfection of 293T with pcDNA3.1(2) encoding for either C-terminal or N-terminal HA-CR6 peptides has demonstrated that PCNA immune complexes contained C-terminal but not N-terminal CR6 peptide.
109	11029466_MI:0006	As seen in Fig. 1A, eIF3c coimmunoprecipitated with eIF3e and eIF3b, indicating that these three proteins are components of the same protein complex,
110	11029466_MI:0006	eIF3c also coimmunoprecipitated with CSN8
111	11029466_MI:0006	eIF3c also coimmunoprecipitated with CSN8 and CSN1.
112	11029466_MI:0006	eIF3e coimmunoprecipitated a core component of the COP9 signalosome, CSN7, in extracts from both wild type and cop9 mutants,
113	11029584_MI:0006	In addition p300 and Brn-2 proteins were able to be coimmunoprecipitated when challenged with an anti-(Brn-2) Ig
114	11030144_MI:0006	Both non-phosphorylated and phosphorylated BUBR1 were co-immunoprecipitated by the anti-p55CDC antibody
115	11030144_MI:0006	were immunoprecipitated with the anti-p55CDC antibody followed by Western blot analysis using the anti-BUBR1 antibody.
116	11046044_MI:0006	Coimmunoprecipitation of RACK-1 with IFN-RßL is independent of IFN stimulation.
117	11096103_MI:0006	The eluted Cdc2a immunoprecipitates were immunoblotted with anti-CycD2 antiserum (Fig. 6C, a and b). CycD2 was efficiently coimmunoprecipitated by the anti-Cdc2a antiserum from exponential cells (
118	11096103_MI:0006	The PSTAIRE CDK Cdc2a coimmunoprecipitates with CycD2 and CycD3 from Arabidopsis cell extracts, but the non-PSTAIRE Cdc2b does not.
119	11106648_MI:0006	expression of PTP1B carrying both the C215S and the Y152F mutations does not alter the association of endogenous PTP1B with N-cadherin.
120	11106648_MI:0006	Expression of the dominant-negative C215S mutant PTP1B in LN-cells prevents the association of endogenous PTP1B with N-cadherin
121	11117257_MI:0006	Co-immunopurification of LOX2 with eIF(iso)4E.
122	11117257_MI:0006	Co-immunopurification of the eIF(iso)4E-LOX2 complex with anti LOX2 antibodies.
123	11139495_MI:0006	Figure 7 demonstrates that immuno-precipitation of Mms4-HA results in the coprecipitation of Slx3-V5.
124	11139495_MI:0006	The reciprocal experiment confirms that Mms4-HA coprecipitates with Slx3-V5
125	11154276_MI:0006	Endogenous association of Akt and ASK1 in L929 cells.
126	11154276_MI:0006	We verified that transfected Akt and ASK1 interact in 293 cells by coimmunoprecipitation (Fig. 2B).
127	11169732_MI:0006	As shown in Figure 2b, p150 was found only in the immunoprecipitates with antigen affinity-purified anti-K7 and anti-hPrt1 (lanes 3 and 5 from the left), but not in the immunoprecipitates obtained with preimmune sera (lanes 2 and 4 from the left).
128	11259609_MI:0006	We show here that an anti-AhR antibody can coprecipitate pRb and the Arnt protein in a TCDD-dependent manner from the virally infected BP8 cells (compare lanes 3 and 4). In contrast, although the mutant AhR in BP8-E333A cells binds the Arnt protein, it failed to associate with pRb.
129	11274188_MI:0006	antibodies against the PMCA were able to coimmunoprecipitate SAP93 together with either PMCA2b or PMCA4b
130	11274188_MI:0006	SAP102 only coimmunoprecipitated well with PMCA4b but not with PMCA2b
131	11276259_MI:0006	Radiolabeled Tom40 accumulated in the 400K complex of wild type mitochondria was efficiently coprecipitated by anti-Tom5
132	11276259_MI:0006	Significant amounts of Tom40 were also coprecipitated by anti-Tom20 and anti-Tom22 (Fig. 6a, lanes 8 and 9).
133	11279037_MI:0006	immunoprecipitation of TAF72 or TAF73 with TBP.
134	11356864_MI:0006	Neurofibromin antibodies precipitated over 50% of neurofibromin from Triton X-100- solubilized rat brain and coprecipitated  about 5-10% of syndecan-3. In addition, a small fraction of CASK was coimmunoprecipitated by neurofibromin antibody
135	11388671_MI:0006	The his273 p53 protein was about 75% less efficient in forming complexes with PIASy, and the ala143 mutant did not appear to bind at all.
136	11401320_MI:0006	As shown in Figure 6B, FGFR-1 comigrated with E-cadherin immunoprecipitates as a fainter signal (lane 2), and with b-catenin (lane 3).
137	11401320_MI:0006	E-cadherin was detected as a faint band in FGFR-1 immunoprecipitates.
138	11477570_MI:0006	The binding of SART3 to RNPS1 was observed in the cell extract from the coexpressed cells.
139	11483513_MI:0006	The imported Tim10 and the endogenous Tim9 formed a complex and were co-immunoprecipitated (Figure 3, lanes IP10 and IP9).
140	11495919_MI:0006	ASK1 was associated with Daxx.
141	11495919_MI:0006	Daxx was recruited to Fas in the cells co-expressing both of Daxx and ASK1 whereas it was not in the cells expressing either one of the two proteins, suggesting that the molecular interaction between Daxx and Fas requires ASK1.
142	11495919_MI:0006	more ASK1 was recruited to Fas after Fas ligation in the cells with Daxx and ASK1 than in the cells with ASK1 alone, implying that Daxx is a mediator for helping the recruitment of ASK1 to Fas after Fas ligation.
143	11560889_MI:0006	We used anti-Rhp57p antibodies for immunoprecipitation and showed that Rhp55 and Rhp57 proteins can be coprecipitated (Figure 1B, lanes 6).
144	11574472_MI:0006	Immunoprecipitation of EDS1 protein from extracts of the Myc::PAD4 line using the anti-EDS1 antiserum, followed by detection on western blots using the anti-c-Myc antibody, showed that the EDS1 and PAD4 proteins interact in healthy plant tissue
145	11577348_MI:0006	We next tested GST-IBtk fusion proteins for binding to endogenous Btk using a pull-down assay. Btk proteins were specifically recovered from MC3 lysates after binding to GST-IBtk
146	11577348_MI:0006	we subjected cell lysates of DeFew and MC3 B cells to immunoprecipitation with IBtk antiserum to peptide 1 followed by immunoblotting with anti-Btk. Btk was detected in the immunoprecipitated proteins, indicating that IBtk associated with Btk in B cells under physiologic conditions
147	11606059_MI:0006	Endogenous ALG-2 was present in the immunoprecipitates of Jurkat cels which received up to 1 h of CH11 anti-Fas Ab treatment
148	11701877_MI:0006	To further substantiate this observation, we performed coimmunoprecipitation experiments with antibodies against CSN5 and CSN6. As shown in Figure 3B, CSN6 coimmunoprecipitated with CSN1 and CSN5 from total protein extracts with antibodies against both CSN1 and CSN5,
149	11713520_MI:0006	To examine whether SCFTIR1 physically interacts with AUX/ IAA proteins, the AXR2 antibody was used in immunoprecipitation experiments with extracts prepared from seedlings expressing the c-myc epitope-tagged TIR1 derivative. TIR1 Myc was readily detected in anti-AXR2 immunoprecipitates but was absent from control precipitations using the AXR2 pre-immune serum
150	11731480_MI:0006	Asf1 was coimmunoprecipitated with both Sas2 and Sas4 (Fig. 7A).
151	11731480_MI:0006	For coimmunoprecipitation of myc-Sas4 with Sas2,
152	11731480_MI:0006	In coimmunoprecipitation experiments, Cac1 immunoprecipitated with both Sas2 and Sas4 (Fig. 5A).
153	11731480_MI:0006	myc-Sas4 coimmunoprecipitated with Sas2
154	11786550_MI:0006	NHERF2 was only coprecipitated by anti-PMCA antibodies when coexpressed with full-length PMCA2b
155	11823419_MI:0006	An aliquot of the samples in (A) was used for western blotting with antibodies to Vtc1p and Nyv1p
156	11823419_MI:0006	The major co-precipitated bands were identified by MALDI mass spectrometry as Vtc2p, Vtc3p and Vtc4p
157	11877381_MI:0006	Immunoprecipitation with the GEX-3 antibody coprecipitates a protein that is recognized by the GEX-2 antibody.
158	11903063_MI:0006	TACC1 speci®cally co-immunoprecipitated with the EGGAS41 fusion protein, using an antibody raised against the GFP moiety
159	11907036_MI:0006	PEK co-immunoprecipitated with GRP78 and GRP94
160	11907036_MI:0006	PEK co-immunoprecipitated with GRP78 and GRP94. PEK deleted for region 4, which had no impact on PEK dimerization, significantly reduced GRP78
161	11919189_MI:0006	nly in ICAP-1alpha -transfected cells, immunoprecipitation of ICAP-1alpha  using the anti-ICAP-1alpha  9B10 monoclonal antibody resulted in a co-immunoprecipitation of endogenous nm23-H2 as detected by Western blot analysis using an affinity-purified polyclonal antibody (Fig. 2D).
162	12006645_MI:0006	In a reciprocal experiment using an anti-SpCdc45 antibody, SpSld3-FLAG coprecipitated with SpCdc45 (Figure 3A, lane 8).
163	12011449_MI:0006	Additionally, we detected a significant presence of BCL-XL in anti-Siva immunoprecipitates but not in other control immunoprecipitations (Lower).
164	12011449_MI:0006	The kinetics of natural Siva-1/BCL-XL complexes in murine thymocytes after CD3 crosslinking is shown.
165	12011449_MI:0006	With untreated HUT78 cells (Fig. 3C), we observed that a significant amount of Siva-1 coprecipitated with BCL-XL but not with BCL-2 or with the secondary antibody-conjugated beads (Upper).
166	12032852_MI:0006	In vivo interaction was verified by co-immunoprecipitation from HEK 293 cells transfected with the human homologues of TRC8 and VHL. HA-tagged VHL was co-precipitated with the anti-TRC8 antibody, 645/646
167	12032852_MI:0006	Transfection of a GFP fusion gene encoding the C-terminus and RING-H2 domain (C-ter, including aa491 - 664), although expressed at low levels, nevertheless co-precipitated more VHL (lane 3) than endogenous TRC8
168	12039038_MI:0006	In reciprocal experiments, anti-dSAP18 antibodies were found to co-immunoprecipitate E(Z).
169	12039038_MI:0006	The resulting western blot was probed with rabbit anti-dSAP18 antibodies, revealing co-immunoprecipitation of dSAP18 by anti-E(Z) antibodies
170	12065423_MI:0006	Figure 6B shows that clearly, a band corresponding to the size of ScpA (black arrowhead in lower magnification) co-precipitated with SMC (arrowhead, upper magnification) in wild-type but not in smc mutant (Δsmc) cells. A band corresponding to ScpB (open arrowhead) was extremely faint but detected reproducibly.
171	12071968_MI:0006	Co-immunoprecipitation of UP12 with GroEL from cell extracts.
172	12082530_MI:0006	Endogenous JAB1-p27Kip1 complexes were immunoprecipitated from H1299 cell lysate with anti-JAB1 antibody and detected anti- p27Kip1 antibod
173	12082530_MI:0006	PGP9.5 and JAB1 proteins coprecipitated when the JAB1 antibody was used
174	12082530_MI:0006	PGP9.5 is in the same complex with p27Kip1 in H1299 cell lysate as detected by immunoprecipitation using K25020 anti-p27Kip1 (K25020), but not M197 antibody
175	12107167_MI:0006	50% or greater of polysomal LDH is bound to AUF1 in the CB3 and THP-1 cell lines. Immunoprecipitation of LDH from THP-1 polysomes demonstrated the presence of AUF1 and hsp-70, which were shown previously to interact in HeLa cytosols (31).
176	12107167_MI:0006	LDH and AUF1 associate in vivo and in vitro. A, coimmunoprecipitation of LDH and AUF1.CB3 erythroleukemia and THP-1 monocyte polysomes (0.5 A260) were immunoprecipitated (IP) with 
-AUF1 antibody and then analyzed by immunoblotting using AB1222.
177	12119386_MI:0006	Erg25p also coimmunoprecipitated with Erg27p and Erg28p by using rabbit anti-Erg25p (Fig. 5D).
178	12150928_MI:0006	BRI1 Is Capable of Interacting with BAK1 in Plants
179	12165861_MI:0006	proteins from Cos-1 cells cotransfected by HA-tagged TACC1l with myc-tagged LSM7 or Myc-tagged SmG were immunoprecipitated with either anti-myc or anti-TACC1-C antibody and Western blotted. In both cases, blotting with the anti-HA antibody revealed TACC1l protein and blotting with the myc antibody revealed LSM7 or SmG.
180	12165861_MI:0006	proteins from Cos-1 cells cotransfected by HA-tagged TACC1l with myc-tagged LSM7 or myc-tagged SmG were immunoprecipitated with either anti-myc or anti-TACC1l-C antibody and Western blotted. In both cases, blotting with the anti-HA antibody revealed LSM or SmG
181	12165861_MI:0006	Proteins from Cos-1 cells cotransfected with myc-tagged TACC1s and myc-tagged LSM7 or myc-tagged SmG were immunoprecipitated by anti-TACC1-C antibody and Western blotted. Blotting with anti-myc antibody revealed LSM7 or SmG
182	12167173_MI:0006	Co-immunoprecipitation experiments using affinity purified rabbit antisera confirmed these interactions at the level of the endogenous proteins. While each of the five antisera co-precipitated at least one of the other subunits, Pip1p, Pop1p, and Pop2p antisera co-precipitated all five proteins from wild-type cell lysate (Fig. 1A).
183	12167173_MI:0006	Pip1p immunoprecipitates were prepared from lysates of these four strains and appropriate controls, and co-purification of SCF components was determined by immunoblotting. These experiments showed that both F-box proteins, in the absence of their respective heterooligomerization partner, could individually bind to Pip1p in complexes that also contained Psh1p and Pcu1p (Fig. 7A). These findings indicate the existence of distinct SCFPop1p and SCFPop2p complexes in vivo.
184	12167173_MI:0006	Size fractionation of total cell lysates prior to immunoprecipitation revealed co-elution of Pip1p with Pop1p, Pop2p, Pcu1p, and Psh1p in a high molecular weight complex of approximately 500 kDa, which we refer to as SCFPop1p-Pop2p (Fig. 1B).
185	12167173_MI:0006	The composition of the core complex Pip1p/Pcu1p/ Psh1p did not undergo major variations during the cell cycle (Fig. 1C). We have carefully reexamined potential cell cycle variations of Pcu1p neddylation apparent in the IP/ immunoblotting experiment in Fig. 1C. These variations were not seen when samples were denatured in SDS immediately following extract preparation (data not shown), suggesting that they arise from varying degrees of deneddylation presumably occuring during the immunoprecipitation step. In addition, in a separate experiment, Pop1p-Pop2p heterooligomerization was largely constant during the cell cycle (Fig. 1C).
186	12217076_MI:0006	Co-immunoprecipitation of ALB3 and cpSecY
187	12223483_MI:0006	To examine the binding of AAT-1alpha  to S-AKAP84 or AKAP149 in a physiological condition, the proteins in the extracts prepared from rat testes were first immunoprecipitated with an anti-AAT-1alpha  serum or preimmune serum.
188	12379796_MI:0006	The proteins encoded by AtCstF-64 and AtCstF-77 interact with each other. 35[S]-methionine-labelled in vitro translation products were immunoprecipitated as previously described
189	12419231_MI:0006	A crude DE400 fraction was incubated with anti-Cet1p antibodies immobilized on protein-A beads, and the supernatant was recovered. An equal volume of load (DE400) and supernatant (DE400[ΔCet1/Ceg1]) was analyzed by Western blotting.
190	12421467_MI:0006	In vitro interaction of psoriasin and RanBPM as determined by co-immunoprecipitation.
191	12421915_MI:0006	Furthermore, immunoprecipitation assays confirmed the association between the endogenous motor protein and chemokine receptor in T lymphocytes.
192	12434308_MI:0006	While PP1alpha co-immunoprecipitated with an anti-pRb antibody
193	12437990_MI:0006	As with mArpNα, hArpNα was also co-immunoprecipitated with BRM
194	12437990_MI:0006	HA-tagged mArpNα was co-immunoprecipitated with BRM but not with preimmune serum
195	12441347_MI:0006	The results demonstrated that KaiC interacts rhythmically with KaiA, KaiB, and SasA (Fig. 1B).
196	12482983_MI:0006	dmTAF1 (dTAFII230), dmTAF4 (dTAFII110), dmTAF6 (dTAFII80), dmTAF9 (dTAFII40), and dTBP were specifically coimmunoprecipitated with both dmTAF10 and dmTAF10b
197	12482983_MI:0006	In the anti-dmTAF10 IP, dADA2b could be found associated with dmTAF10 together with GCN5 (Fig. 4A, lane 2), indicating that dADA2b is associated with a dmTAF10-containing multiprotein complex.
198	12482983_MI:0006	IP experiments were carried out with the purified antisera raised against either dADA2a or dADA2b. Both antibodies coimmunoprecipitated dADA2b, GCN5, and TAF9 from the nuclear extract (lanes 6 and 8); however, the anti-dADA2b PAb also coimmunoprecipitated dTAF10 and dTAF4
199	12493754_MI:0006	and endogenous Chk2 and Plk1 co-immunoprecipitated from 293T cells
200	12525503_MI:0006	the endogenous gankyrin was co-immunoprecipitated with MAGE proteins by anti-MAGE antibody.
201	12527904_MI:0006	As seen in Figure 4b, when the BRCA2 protein present in HeLa cell extracts was immunoprecipitated with anti-BRCA2 antibodies, hRPA was also present in this immunoprecipitate
202	12527904_MI:0006	hRPA was coimmunoprecipitated with XPA by anti-XPA antibodies
203	12529400_MI:0006	Endogenous Daxx coimmunoprecipitated with endogenous HIPK1
204	12529400_MI:0006	overexpressed HIPK1 coimmunoprecipitated with endogenous Daxx
205	12529400_MI:0006	overexpressed HIPK1 coimmunoprecipitated with endogenous Daxx and to a much greater degree with overexpressed Daxx
206	12529400_MI:0006	Western blots containing Daxx immunoprecipitates and probed for HDAC1 showed that a Daxx-HDAC1 association was present in all samples.
207	12529400_MI:0006	Western blots containing Daxx or HIPK1 immunoprecipitates and probed for HIPK1 or Daxx, respectively, showed that Daxx interacted with HIPK1 to a much greater degree than with K219A (Fig. 6C). This was the case for both endogenous and overexpressed Daxx.
208	12566426_MI:0006	To determine whether Mgm1p also is present in a complex containing Ugo1p, we performed immunoprecipitations using anti-Mgm1p antibodies from cross-linked Ugo1:3XHA-tagged mitochondria.
209	12711603_MI:0006	MBD is an interacting surface to Suv39h1-HP1{alpha}
210	12711603_MI:0006	MBD is an interacting surface to Suv39h1-HP1{alpha}.
211	12724312_MI:0006	1-MMP-9 was co-immunoprecipitated with integrin 51 from cells grown in the presence (Fig. 9A) or absence (Fig. 9B) of FN.
212	12724535_MI:0006	Coimmunoprecipitation Analysis of the Physical Association of CSN and SCFCOI1 in Vivo.
213	12757932_MI:0006	a strong interaction exists in vivo between soluble ataxin-1 and p80 coilin.
214	12788081_MI:0006	Similar results were obtained when anti-Fyn immunoprecipitates were probed with anti-p250GAP antibodies ( Fig. 3B).
215	12805220_MI:0006	Endogenous LKB1 (55 kDa) interacts with STRAD (45-48 kDa) in Rat-2 and HEK-293T cells.
216	12857813_MI:0006	To test whether CDKA;1 or CDKB2;1 makes protein complexes with CYCD4;1, protein extract was immunoprecipitated with anti-CDKA;1 or anti- CDKB2;1 antibody and assayed by western blotting. As shown in Figure 4, His-CDKA;1 or His-CDKB2;1 was equally immunoprecipitated with the antibody, and FLAG-CYCD4;1 was included in the immunoprecipitates in the case of co-expression. These results indicate that His-CDKA;1 or His-CDKB2;1 formed a complex with FLAG-CYCD4;1 in insect cells.
217	12864730_MI:0006	DDC co-immunoprecipitated with AR in the presence and absence of R1881 (compare lanes 4 and 6 in Figure 4B), but the association seems to be stronger with the androgen treatment.
218	12874027_MI:0006	Fig. 1CCitation  shows that FANCD2 was specifically immunoprecipitated by the antimenin antibody but not by the control IgG.
219	12917342_MI:0006	Consistent with the constitutive activation seen in these cells, the GR1-556 protein interacted with the steroid receptor coactivator SRC-1 in the absence of hormone (Fig. 1B). In addition, we also observed GR1-556 interactions with chromatin-remodeling proteins BRG1 and BAF155 in the absence of hormone (Fig.1B)
220	12917342_MI:0006	In order to determine how BAF60a4-140 inhibits GR-activated chromatin remodeling, we investigated the protein-protein interactions with the BRG1 complex in both UL3 and 60N.17 cells. The BRG1 complex in UL3 and 60N.17 cells treated with vehicle or hormone was immunoprecipitated with an antibody against BRG1. In agreement with earlier studies, the GR shows a hormone-dependent interaction with BRG1 in UL3 cells such that the GR is enriched in BRG1 complex upon hormone treatment (Fig. 6A, compare lanes 5 and 6). In contrast, hormone treatment does not enrich GR in the BRG1 complex in 60N.17 cells (Fig. 6A, compare lanes 7 and 8).
221	12917342_MI:0006	We next directly investigated BRG1 complex interactions with the GR mutants by coimmunoprecipitation assays. As the results show, BRG1 interacts with GRwt in addition to GR(R488Q) and GR1-556 mutants (Fig. 4B).
222	12947415_MI:0006	The anti-Yfh1 immunoprecipitate contained significant amounts of Isu1 and Ssq1
223	14508515_MI:0006	The resulting immunoprecipitate was enriched not only in menin but also in NMHC II-A
224	14521924_MI:0006	Association of hAATYKs or KIAA0641 was also observed in the immunoprecipitate of the HEK293 cell extract with anti-Cdk5 antibody ( Fig. 5B)
225	14521924_MI:0006	p35 was detected in the anti-hAATYK immunoprecipitate of the cell lysate cotransfected with hAATYKs (Fig. 5A).
226	14521924_MI:0006	The cell extracts were immunoprecipitated with anti-p35 antibody, followed by immunoblotting with anti-hAATYK antibody
227	14550308_MI:0006	The PKCl-MT 2A interaction in PC cells was confirmed by full-length PKCl co-IP with MT 2A
228	14557665_MI:0006	As shown in Fig. 2C, Daxx was coprecipitated with the E1B 55-kDa protein, indicating a direct interaction in vitro.
229	14557665_MI:0006	Daxx was present in the anti-E1B immunocomplexes
230	14557665_MI:0006	In a reciprocal IP, the E1B 55-kDa protein was precipitated by anti-Daxx M112 antibody
231	14563843_MI:0006	only the larger molecular form of NKCC1, which represents phosphorylated NKCC1, interacts with pp38
232	14563843_MI:0006	the amount of SPAK coprecipitated with NKCC1 does not change significantly with stress.
233	14563843_MI:0006	The figure panel also shows that the amount of NKCC1 and SPAK coprecipitated with pp38 decreases with cellular stress.
234	14612908_MI:0006	While FADD was found to associate with caspase-8 in Jurkat cells incubated with anti-Fas IgM, no interaction was evident in DU 145 cells
235	14627983_MI:0006	Coimmunoprecipitation of Carom with MAGI-1 from MDCK cells.
236	14627983_MI:0006	When the lysates of MDCK cells were incubated with the anti-Carom antibody, the immunoprecipitate contained CASK (Figure 5B).
237	14627987_MI:0006	Endogenous levels of PARP-1 bound to E2F-1 was first evident at 5 h, and increased thereafter up to 16 h after S-phase re-entry
238	14627987_MI:0006	Immunoblot analysis of the precipitates with anti-Myc revealed that, while full-length PARP-1 as well as mutants lacking either the active site or the DBD equally bound E2F-1 (Figure 6c, lanes 1-3, respectively), the mutant lacking the DBD-AD did not (Figure 6c, lane 4), indicating that the protein interaction site is located in the central AD.
239	14627987_MI:0006	immunoblot analysis of the precipitates with anti-PARP-1 showed binding of PARP-1 to GST-p53 in vitro
240	14627987_MI:0006	Immunoblot analysis of the resulting precipitates with anti-PARP-1 revealed binding of PARP-1 to E2F-1 in vitro
241	14645241_MI:0006	endogenous Rb and ASC-2 were co-immunoprecipitated from HL60 cells
242	14645241_MI:0006	from whole cell lysates of HEK293 cells cotransfected with expression vector for AR, AR and ASC-2 antibodies co-immunoprecipitated ASC-2 and AR, respectively
243	14653779_MI:0006	By Western blotting, we showed that the decreasing amount of RIP bound to IKKg
244	14653779_MI:0006	By Western blotting, we showed that the decreasing amount of RIP bound to IKKg was correlated with the increasing level of ABIN-2 (Figure 6C)
245	14653779_MI:0006	only IKKg, but not IKKa or IKKb, was co-immunoprecipitated with ABIN-2.
246	14657239_MI:0006	As shown in Figure 4A, antibodies to p140Cap were able to immunoprecipitate p130Cas and vice versa, indicating that the endogenous proteins associate in an immunoprecipitable complex in ECV304 cells.
247	14657239_MI:0006	In addition p140Cap and p130Cas immunocomplexes also contained the adaptor protein Crk, a known interactor of p130Cas, indicating that p140Cap and p130Cas take part in a macromolecular complex.
248	14685242_MI:0006	IkappaB-alpha antibody also pulled down RelA and Murr1.
249	14685242_MI:0006	Murr1 interacted biochemically with the Cul1 and not the Skp1 component of the E3 ligase complex
250	14685242_MI:0006	RelA antibody immunoprecipitated IkappaB-alpha, IkappaB-beta and Murr1
251	14690608_MI:0006	Interestingly, anti-Bdf1 also coprecipitated the histone H2A variant, Htz1, as well as histones H3 and H4 (Figure 2C).
252	14701856_MI:0006	BAF60c, PPAR{gamma}, and BRG1 are present in the same complex in vivo.
253	14715275_MI:0006	pull down the endogenous hRpp20 and hSMN complex from HeLa cells.
254	14726512_MI:0006	Immunoblot analysis of precipitated material showed that antibodies against Tim9 precipitated both Tim9 and Tim10a; likewise, both proteins were precipitated using antibodies against Tim10a indicating that both proteins interact in a complex (Fig. 2).
255	14726512_MI:0006	Western blot analysis of the immunoprecipitated material showed that both anti-Tim9 and anti-Tim10b were able to co-precipitate Tim22
256	14726512_MI:0006	Western blot analysis of the immunoprecipitated material showed that both anti-Tim9 and anti-Tim10b were able to co-precipitate Tim22 (Fig. 4).
257	14729613_MI:0006	immunoprecipitation was performed using human breast carcinoma cell line MCF7 (RASSF1A negative) and non-small cell lung tumor cell line NCI-H1792 (RASSF1A positive). Cell lysates were prepared and subjected to immunoprecipitation with RASSF1A-specific polyclonal antibody. As shown in Fig. 2B endogenous levels of RASSF1A interact with p120E4F in vivo.
258	14729613_MI:0006	p120E4F-HA was efficiently coprecipitated in both NIH 3T3 and A549 cells with RASSF1A but not control IgG
259	14764652_MI:0006	The in vivo interaction between endogenous PP5 and ER in human breast cancer MCF7 cells was also shown by coimmunoprecipitation study
260	14960328_MI:0006	Endogenous CaM co-immunoprecipitates with EGFR.
261	15016378_MI:0006	antibodies to APPL1 but not preimmune serum efficiently and specifically coimmunoprecipitated PID/MTA2 protein and, to a lesser extent, also RbAp46.
262	15016378_MI:0006	we undertook a search for interacting partners by coimmunoprecipitation experiments from cytosol and detergent extracts of HeLa cells. Whereas no proteins were coimmunoprecipitated with APPL1 from cytosol (data not shown), a number of proteins were recovered from the detergent extract (Figure 6B). Surprisingly, mass spectrometry sequencing revealed the presence of PID/MTA2, p66, HDAC1, and/or HDAC2 (identified through common peptides) RbAp46, RbAp48, and MBD3, namely 6 out of 10 components of the nucleosome remodeling and histone deacetylase NuRD/MeCP1 complex
263	15044383_MI:0006	Co-immunprecipitation of aprataxin with PARP-1, p53 and XRCC1
264	15047801_MI:0006	Cell lysates were immunoprecipitated with an NSP3-specific MAb, and RoXaN I was detected by immunoblotting using a T7tag-specific MAb (Fig. 3C).
265	15047801_MI:0006	To investigate the presence of a RoXaN I-NSP3-eIF4G I complex during rotavirus infection, COS-7 cells were transfected with T7tag-RoXaN I and infected with rotavirus RF, and the cell lysates were immunoprecipitated with an eIF4G I-specific antiserum (Fig. 6).
266	15047801_MI:0006	Transfected and infected cell lysates were immunoprecipitated with either an NSP1- or NSP3-specific MAb, and Flag-RoXaN I:1-387 was detected by immunoblotting using the Flag-specific MAb (Fig. 3B).
267	15078334_MI:0006	In vitro coimmunoprecipitation amoung the subunits of the G protein complexes.
268	15146192_MI:0006	we showed that the matrix metalloproteinase MMP2 co-immunoprecipitates with hsp90alpha from HT-1080-conditioned medium
269	15147268_MI:0006	In order to verify this and to examine the effects of mutation on Skp1 interactions we carried out a binding analysis of mutant Skp1tsA7 with F-box proteins and Pcu1 by immunoprecipitation. Each F-box protein was tagged with a myc epitope at its C-terminus. Immunoprecipitations were carried out using a polyclonal anti-Skp1 antibody.
270	15147268_MI:0006	In order to verify this and to examine the effects of mutation on Skp1 interactions we carried out a binding analysis of mutant Skp1tsA7 with F-box proteins and Pcu1 by immunoprecipitation. Each F-box protein was tagged with a myc epitope at its C-terminus. Immunoprecipitations were carried out using a polyclonal anti-Skp1 antibody. In cases where the C-terminus could not be tagged due to loss of protein function, GFP (green fluorescence protein) was used to tag the N-terminus of the protein under the thiamine repressible nmt promoter (e.g. GFP-Pof6 and GFP-Fdh1).
271	15155892_MI:0006	As shown in Figure 2, GCR1 and GPA1 can be coimmunoprecipitated.
272	15159385_MI:0006	HAX-1 associates with cortactin in the apical membrane of hepatocytes.
273	15159385_MI:0006	HAX-1 co-immunoprecipitates with BSEP, MDR1, and MDR2 from transfected cells and hepatocytes.
274	15169888_MI:0006	Immunoprecipitation and Western blot analysis confirmed that both p105 and TPL-2 copurified with ABIN-2 in these cells (Fig. 4A).
275	15174051_MI:0006	Proteins associated with six high abundance serum proteins identified by μLCMS/MS.
276	15177031_MI:0006	Tea2p/Tip1p/Mal3p Coimmunoprecipitations
277	15182174_MI:0006	Anti-caveolin-1 antibody successfully precipitated caveolin-1 (Figure 8B, lane 3) and coprecipitated SCP-2
278	15182174_MI:0006	Anti-SCP-2 antibody successfully coimmunoprecipitated caveolin-1
279	15225636_MI:0006	Immunoblot analysis of α4-precipitated proteins revealed bands of approximately 27 and 28 kDa predominately in fractions 5 and 6 corresponding to the α7 subunit
280	15248212_MI:0006	Western blot analysis demonstrated the presence of latent and active MMP-2 in the immunoprecipitate from both RA and OA synovial fluid
281	15250827_MI:0006	For all cell lines, three complex I subunits, the 23, 30 and 49 kDa subunits, were shown by Western blotting to be in the immunopurified samples.
282	15250827_MI:0006	Therefore MS analysis of the subcomplex fractions, independently immunopurified with the 30- or 49-kDa subunit antibody, confirmed the presence of the 49, 30 and 23 kDa subunits in a complex I subfraction.
283	15272023_MI:0006	Both MAGE-D1 and Msx2 bound to immunopurified necdin, and both necdin and Msx2 bound to immunopurified MAGE-D1.
284	15272023_MI:0006	FLAG-Msx1 and FLAG-Msx2 were co-immunoprecipitated with endogenous MAGE-D1. Conversely, endogenous MAGE-D1 was co-immunoprecipitated with FLAG-Msx1 and FLAG-Msx2.
285	15272023_MI:0006	Full-length MAGE-D1 and MAGE-D1{Delta}N was co-immunoprecipitated with necdin
286	15272023_MI:0006	Msx1 was co-immunoprecipitated with necdin in the presence and absence of MAGE-D1 (Fig. 4A).
287	15272023_MI:0006	Msx2 was co-immunoprecipitated with necdin (Fig. 4B).
288	15280210_MI:0006	both OLIG1 and OLIG2 interact with the E2A proteins, E12 and E47
289	15280210_MI:0006	OLIG1 and OLIG2 complexed with both ID2 and ID4
290	15280210_MI:0006	we observed similar interactions between endogenous levels of OLIG and ID2 or ID4 proteins in E17 progenitor cells
291	15293782_MI:0006	Caveolin-1 α and β were the major proteins in addition to the 50 kDa band.
292	15350535_MI:0006	Coprecipitation of Wrch1 with PAK1 and NCKbeta.
293	15364927_MI:0006	Daxx was coprecipitated with WT p53 (Fig. 4B, lane 2) and to a lesser extent with p53 K381A/K382A (lane 6), K381R/K382R (lane 8), S376A (lane 10), and p53 S376E
294	15364927_MI:0006	When the extract of insect Sf9 cells expressing Daxx was mixed with purified WT p53, Daxx was precipitated along with p53 in an IP assay using DO-1
295	15364927_MI:0006	When the extract of insect Sf9 cells expressing Daxx was mixed with purified WT p53, Daxx was precipitated along with p53 in an IP assay using DO-1 (Fig. 1A, lane 3). Reciprocally, p53 was precipitated from the same mixture using anti-Daxx antibody M112
296	15377662_MI:0006	The PDGFR typically binds p85 in a PDGF-dependent manner, as shown by the presence of p85 in anti-PDGFR immunoprecipitates from PDGF-treated NIH 3T3 cell lysates
297	15377662_MI:0006	we find that anti-PDGFR immunoprecipitates contain FLAG-p85 proteins (both wild type and BH mutants BH and R274A) after PDGF stimulation.
298	15451437_MI:0006	CAML was immunoprecipitated with IEX-1 and was detected with an anti-CAML antibody.
299	15456783_MI:0006	immunoprecipitation of Dvl2 with anti-Dvl2 antibodies captures both Vangl1 and Vangl2 expressed in HEK293 cells
300	15456783_MI:0006	immunoprecipitation of Vangl1 from HEK293 cell lysates also captured Dvl2
301	15467741_MI:0006	Magicin and Grb2 co-immunoprecipitate.
302	15467741_MI:0006	Magicin binds to merlin in vivo
303	15503857_MI:0006	By immunoprecipitation with antiserum against HSPB9 between 10 and 20%HSPB9 was precipitated (data not shown) and about 0.5% VSV-tagged TCTEL1 could be co-precipitated and immunodetected
304	15542844_MI:0006	VRK1 promotes the formation of a p53-p300 complex.
305	15555586_MI:0006	Furthermore, Pmh1 was found to associate with a Mcs6-Mcs2 complex in insect cells infected with Mcs6,Mcs2, and FLAG-Pmh1 baculoviruses as seen by co-immunoprecipitation of FLAG-Pmh1 with anti-Mcs6 antibodies (Fig. 2B).
306	15652749_MI:0006	Stathmin and p27 associated in adult pork brain
307	15652749_MI:0006	Stathmin and p27 associated in adult pork brain, in mouse fibroblasts adherent to FN but not in serum-starved cells
308	15652749_MI:0006	stathmin was readily co-IP with p27 from mouse fetal brain (day 18 p.c.)
309	15674350_MI:0006	anti-ER-a IP co-precipitated smaller smaller quantities of the FLAG-BRCA1 1-100 mutant 1 than any of the other BRCA1 1-100 proteins
310	15674350_MI:0006	the amount of ER-a precipitated by anti-BRCA1 and the amount of BRCA1 precipitated by anti-ER-a were significantly lower for BRCA1-NES mutant than for wtBRCA1
311	15674350_MI:0006	we performed immunoprecipitation (IP)-Western blotting assays to determine if ER-a binding BRCA1 protein fragments identified above associate with the endogenous ER-a protein in MCF-7 cells. MCF-7 cells were transfected with FLAG-tagged BRCA1 proteins encompassing aa 1-100, 101-200, and 201-300. Each of the FLAG-BRCA1 proteins was expressed well. Consistent with the GST capture assays, we found that IP of FLAG-BRCA1 1-100 and 101-200, but not 201-300, co-precipitated ER-a (Figure 3a) and vice versa
312	15674350_MI:0006	Western blotting of HCC1937 cells showed a significantly reduced steady-state association of BRCA1 1- 1863 mutant 1 with ER-a, as compared with that of wtBRCA1, mutant 2, or mutant 3
313	15684389_MI:0006	The data also demonstrate three-way complex formation between Nm23-H1, KSR1, and Hsp90 with either anti-HA-KSR1 or anti-Nm23 as immunoprecipitating antibodies
314	15694377_MI:0006	Furthermore, endogenous CASK and Id1 proteins were co-precipitated from the lysates of ECV304 cells by immunoprecipitation.
315	15695390_MI:0006	Furthermore, we carried out the immunoprecipitation experiments with [35S]-labeled methionine and cysteine LNCaP cell protein lysate, followed by analysis of all the immunoprecipitated proteins on SDS-PAGE and autoradiography. Under these conditions, relatively few proteins coimmunoprecipitated [(Fig. 2A(3) lane 1)] which provided additional evidence for specificity of the PKD1/E-cadherin interaction.
316	15695390_MI:0006	Immunoblot analysis using E-cadherin-specific antibody showed the coimmunoprecipitation of E-cadherin with PKD1 in LNCaP cells
317	15695390_MI:0006	we also did reciprocal immunoprecipitation assays with E-cadherin antibody and immunoblotted for PKD1. PKD1 was also immunoprecipitated with the E-cadherin antibody
318	15696166_MI:0006	MeCP2 was present in immunoprecipitates of antibody to Brm, as shown by immunoblot assay using an MeCP2-specific antibody3 (Fig. 1g). In a reciprocal assay, MeCP2 was copurified from Brm isolates
319	15696166_MI:0006	we carried out reciprocal immunopurifications using glycerol-gradient fractions 17−20 followed by western-blot analysis using antibodies to MeCP2 and Brm (Fig. 1b). Results of these analyses are consistent with the existence of a complex containing MeCP2, Brm and BAF57.
320	15799966_MI:0006	precipitation of endogenous COMMD1 with the use of rabbit polyclonal sera against COMMD1 resulted in the co-precipitation of endogenous RelA and c-Rel
321	15805117_MI:0006	In contrast, the CAF-1 complex immunoprecipitated from cells transfected by the R5A/K110A mutant construct did not contain pol {delta} (Fig. 4E, lane 8),
322	15805117_MI:0006	To determine whether PCNA can physically bind to pol {delta} and CAF-1 simultaneously, extracts prepared from cells transfected by wild-type PCNA were subjected to DNase I digestion and immunoprecipitated with PC10.
323	15827353_MI:0006	CHO cells were transfected with SPAG6/pTarget and PF6/pEGFP-N2 plasmids, and co-immunoprecipitation studies were performed.
324	15855171_MI:0006	immunoprecipitation of FAK detected p53 in the complex with FAK
325	15855171_MI:0006	Immunoprecipitation of p53 detected FAK in the complex with p53
326	15855171_MI:0006	we immunoprecipitated p53 in these cells without and with doxorubicin treatment and performed Western blot with FAK antibody (Fig. 2E, lower panel). The FAK-p53 complex was detected in NHF-1 fibroblasts and increased in doxorubicin-treated cells with increased level of p53.
327	15855171_MI:0006	We performed immunoprecipitation of FAK from cytoplasmic and nuclear fractions in these cells and detected binding of p53 protein and FAK proteins in both nuclear and cytoplasmic fractions
328	15855171_MI:0006	we performed immunoprecipitation of p53 in colon cancer HCT116 cells, followed by Western blot with FAK antibody (Fig. 2D). We detected FAK protein in the complex with p53 protein in HCT116 cells
329	15886098_MI:0006	Anti-Flag (ABL2)-immunoprecipitated material was immunobloted with anti-RIN1 (left), and anti-RIN1-immunoprecipitated material was immunobloted with anti-Flag (right).
330	15886098_MI:0006	Expression of HRASG12V (activated RAS), RIN1, and ABL2 resulted in the formation of a complex including all three proteins, as detected by immunoprecipitation of either ABL2 or HRAS (Figure 6A).
331	15886098_MI:0006	RIN1 binding to ABL1 was assessed with anti-RIN1 or anti-ABL1 immunoprecipitation from extracts of transfected 293 cells.
332	15886098_MI:0006	The right side shows immunoprecipitation of endogenous RIN1 with endogenous ABL1 from MCF10A cells when anti-ABL1 but not anti-Flag (control) was used
333	15887118_MI:0006	nuclear proteins were extracted from KMC-1 cells and then used in immunoprecipitation. The results con-firmed binding of HHM to Jab1
334	15896299_MI:0006	Fig. 8A shows that PLD2 was immunoprecipitated with Grb2-specific antibodies; an interaction that was stimulated by addition of recombinant Grb2 to the lysates prior to immunoprecipitation.
335	15896299_MI:0006	Fig. 9B shows that PTP1B and PLD2 were reciprocally co-immunoprecipitable.
336	15896299_MI:0006	Similarly, PTP1B and Grb2 were reciprocally pulled down with Grb2 and PTP1B-specific antibodies, respectively (Fig. 9A).
337	15907477_MI:0006	In reciprocal experiments E1B-AP5 was immunoprecipitated with a rabbit polyclonal antibody. Coimmunoprecipitating p53 was detected using the monoclonal antibody D01 in Western blots
338	15907477_MI:0006	p53 was immuno-precipitated from cell lysates of MCF7 and Ad12E1HER2 cells using a rabbit polyclonal antibody. Co-precipitated E1B-AP5 was identified by Western blotting
339	15917470_MI:0006	Antibody against Oct-4 (C-10, Santa Cruz Biotechnology), and not control serum, coprecipitated EWS
340	15917470_MI:0006	EWS was found to specifically coprecipitate with Oct-4
341	15917470_MI:0006	whereas anti-EWS (C-19, Santa Cruz Biotechnology) coprecipitated Oct-4
342	15976083_MI:0006	FasII and APPL coimmunoprecipitate from body-wall muscle extracts
343	15976083_MI:0006	Furthermore, because the coprecipitation between FasII and dX11
344	15976083_MI:0006	Furthermore, because the coprecipitation between FasII and dX11 is stronger in the absence of APPL, these results suggest that APPL may negatively regulate the binding between dX11 and FasII.
345	15976083_MI:0006	However, similar levels of FasII were coprecipitated by APPL antibodies
346	15976083_MI:0006	We also confirmed that the interaction between APPL and dX11 depended on the PTB domain in vivo,
347	15976083_MI:0006	We found that antibodies against APPL strongly coprecipitated both FasII and dX11 in cells double transfected with FasII and dX11, and no such coprecipitation was observed in untransfected cells (Fig. 7C).
348	15990873_MI:0006	In addition, the anti-MPK4 antibody preferentially precipitated, from wild type versus mpk4, MPK4 that phosphorylated the N-terminal regions of W25 and W33
349	15990873_MI:0006	These results indicate that MKS1 and MPK4 interact in vivo, and that MPK4 is the major kinase activity that phosphorylates MKS1 under default conditions.
350	16049941_MI:0006	Summary of Proteins Identified as co-immunoprecipitants with Amyloid Precursor Protein
351	16049941_MI:0006	the adaptor protein Fe65 was found in complexes with APP-immunoreactive material only when CT15, but not APPNeo, was used as the immunoprecipitating antibody
352	16053918_MI:0006	To determine whether KIAA0649 and 1A6/DRIM could interact at their endogenous levels, we performed an endogenous co-immunoprecipitation assay using BGC823 nuclear extract and anti-1A6/DRIM monoclonal antibody. The result showed that KIAA0649 protein could be co-precipitated by the anti-1A6/DRIM antibody,
353	16055635_MI:0006	The epitope-tagged E2FB and DPA proteins are likely to be functional in BY-2 cells because they form heterodimers (Figure 3C)
354	16061848_MI:0006	BxPc3 cell lysates were immunoprecipitated with anti-RAGE antibody and S100P was identified in the precipitate by Western blotting.
355	16091426_MI:0006	We were able to co-immunoprecipitate hSec23Ap with PCTAIRE-3 from MDCK cell lysates (Fig. 3B, lanes 1-3), as well as with PCTAIRE-1 from HeLa cell lysates (Fig. 3B, lanes 4-6).
356	16120479_MI:0006	However, some -co-precipitating/interacting proteins- were also identified at low to very low abundance levels in regions of the gel lane where the protein dye stain was barely visible.
357	16120479_MI:0006	Proteins identified by ESI-MS/MS from immunocaptured bovine heart Complex II
358	16120479_MI:0006	Proteins identified by ESI-MS/MS from immunocaptured bovine heart Complex III
359	16120479_MI:0006	Proteins identified by ESI-MS/MS from immunocaptured mouse heart Complex II
360	16120479_MI:0006	Proteins identified by ESI-MS/MS from immunocaptured mouse heart Complex III
361	16142218_MI:0006	Purified TRBP (human immunodeficiency virus (HIV-1) transactivating response (TAR) RNA-binding protein) and Dicer interact with each other.Interaction of TRBP with Dicer studied with purified proteins
362	16142218_MI:0006	Purified TRBP (human immunodeficiency virus (HIV-1) transactivating response (TAR) RNA-binding protein) and Dicer interact with each other.Interaction of TRBP with Dicer studied with purified proteins.
363	16142218_MI:0006	TRBP and Dicer co-immunoprecipitation.Anti-Dicer antibodies (Abs) pull down endogenous TRBP (human immunodeficiency virus (HIV-1) transactivating response (TAR) RNA-binding protein) in extracts of human embryonic kidney (HEK)293 cells.
364	16183855_MI:0006	to verify the existence of the physical association between caspase-8 small subunit and Bcl-2. In CHO cells, the endogenous Bcl-2 was found to coimmunoprecipitate with the ectopically expressed EGFP-fused p10 subunit
365	16203867_MI:0006	LPA2 forms a macromolecular complex with CFTR mediated through NHERF2
366	16203867_MI:0006	LPA2 forms a macromolecular complex with CFTR mediated through NHERF2.
367	16204054_MI:0006	Although the overall expression level of actinin-4 was unaffected by E-cadherin transfection (Fig. 3C, left), the amount of actinin-4 protein present in the immunoprecipitants with anti-beta-catenin antibody was significantly reduced.
368	16204054_MI:0006	An f100-kDa protein and a few other proteins were constantly coimmunoprecipitated with anti-h-catenin antibody but not with normal control IgG (Fig. 2A). Peptide mass fingerprinting (Fig. 2B) and a protein database search revealed that the protein was actinin-4
369	16205631_MI:0006	The same protein lysates in which PDGF b receptor hadbeen detected(Figure 1) were immunoprecipitatedeither with anti-E5 antibody or with anti-PDGF b receptor antibody #1. The immunoprecipitates were probedfor the presence of the PDGF b receptor or of E5 by Western blotting with the respective antibodies. PDGF b receptor was detected in E5 immunoprecipitates
370	16205631_MI:0006	The same protein lysates in which PDGF b receptor hadbeen detected(Figure 1) were immunoprecipitatedeither with anti-E5 antibody or with anti-PDGF b receptor antibody #1. The immunoprecipitates were probedfor the presence of the PDGF b receptor or of E5 by Western blotting with the respective antibodies. PDGF b receptor was detected in E5 immunoprecipitates (Figure 3a) and, conversely, E5 was detected in PDGF b receptor immunoprecipitates
371	16221674_MI:0006	Using FLN29 overexpressing RAW cells, we were also able to detect FLN29 protein associated with endogenous TRAF6, indicating that FLN29 interacted with TRAF6 in these cells (Fig. 5C).
372	16227626_MI:0006	Detection of immunoprecipitated samples with C/EBP{beta} antibody revealed the presence of LIP-FLAG in those cases where WT p53 or p53.M175 had been co-transfected
373	16227626_MI:0006	p53 and C/EBP
 interact in vivo.
374	16229834_MI:0006	By employing the anti-Amida antibody, we could coprecipitate endogenous Par-4 protein
375	16230351_MI:0006	endogenous SIAH1 and POSH interact with each other. PC12 cells
376	16253998_MI:0006	Co-immunoprecipitation of-catenin and
-catenin together with different cadherins.
377	16253999_MI:0006	COS-7 cell lysates were immunoprecipitated with anti-Arp3 antibody and immunoblotted (IB) with rabbit anti-SPIN90 antibody.
378	16257958_MI:0006	A, endogenous Kv4.2 coimmunoprecipitates with Kiv17 from brain lysate.
379	16257961_MI:0006	Grp78 co-immunoprecipitated with the G544V mutant LDLR from cells treated with or without crosslinker.
380	16257961_MI:0006	The chaperones Grp94, ERp72, and calnexin were only co-immunoprecipitated with G544V mutant LDLR in cells pretreated with cross-linker.
381	16260785_MI:0006	Detergent- solubilized extracts from yeast cells expressing the N-terminally HA-tagged Gef1p channel were immunoprecipitated using an antiserum that we raised against Arr4p.
382	16267043_MI:0006	the increase in Crk Tyr221 phosphorylation in response to inhibition of the 26 S proteasome was associated with a 50% decrease in CAS-Crk coupling
383	16275645_MI:0006	By using these anti-Fbx4 antibodies, we found that endogenous Fbx4 was immunoprecipitated with anti-Pin2/TRF1 antibodies but not the preimmune controls.
384	16275649_MI:0006	Recombinant WNV E DIII Protein Interacts with 
V3 Integrin
385	16280327_MI:0006	Next, reciprocal co-immunoprecipitation, followed by Western blotting, demonstrated that the Bcl10-Bcl3 complex existed in the nucleus after TNFalpha treatment.
386	16280327_MI:0006	The possible interaction between Bcl10 and Akt1 was identified by reciprocal co-immunoprecipitation, followed by Western blotting.
387	16282323_MI:0006	Akt stimulation promotes BimEL binding to 14-3-3 proteins.
388	16282325_MI:0006	RING mutation does not affect interaction of cIAP1 with TRAF2 or SMAC
389	16286464_MI:0006	Phosphorylated 7B2 fails to interact with pro-PC2.
390	16286467_MI:0006	and the recruitment of TRAF6 and NIK to IL-1R1 following IL-1beta stimulation
391	16286467_MI:0006	H2O2 Modulates \nik association with TRAF6
392	16286467_MI:0006	However, because IKKalpha and IKKbeta form a complex in vivo (as evident by immunoprecipitation of IKKalpha with an IKK-beta-specific antibody, Fig 3C),
393	16286467_MI:0006	NIK inhibition does not alter TRAF6 recruitment to IL-1R1 following IL-1beta stimulation
394	16286470_MI:0006	As shown in Fig. 8A, endogenous Skp2 coexisted with MKP-1 containing phospho-Ser296 in an immunocomplex derived from H293 cells during forced expression of MKK1-CA or MKK2-CA;
395	16286470_MI:0006	The DEF motif is involved in ERK-directed MKP-1 degradation via the ubiquitin-proteasome pathway in vivo, whereas the N-terminal domain is not essential.
396	16286470_MI:0006	The Skp2/ MKP-1 immunocomplex also contained the other SCF subunits Skp1 and Cul1 and the accessory protein Cks1 (Fig. 8A).
397	16286473_MI:0006	pRB co-immunoprecipitates with endogenous DGK, and vice versa.
398	16291744_MI:0006	Cell lysates were subjected to coimmunoprecipitation with an antibody to Src and probed with antibodies to FAK or to alpha-antinin.
399	16291753_MI:0006	Complex formation of ATF3Zip2 with p65 in vivo and in vitro.
400	16291755_MI:0006	A, endogenous RIP1 and Tpl2 co-precipitate in TNF-alpha-stimulated macrophages.
401	16291755_MI:0006	B, endogenous RIP1 co-precipitate with overexpressed Tpl2.
402	16291755_MI:0006	C, endogenous RIP1 co-precipitate with overexpressed Myc-tagged NF-kappaB1.
403	16293618_MI:0006	the PDZ domain of Shank2 showed a potent induction of both HIS3 and -galactosidase reporter genes in yeast, indicating a direct protein-protein interaction between the carboxyl terminus of NHE3 and the PDZdomain of Shank2.
404	16298995_MI:0006	Cell lysates were subjected to immunoprecipitation against EphB2 and were probed via Western blot for FAK. FAK was found to associate with EphB2 following EphB2 activation
405	16298995_MI:0006	Cell lysates were subjected to immunoprecipitation against EphB2 and were probed via Western blot for FAK. FAK was found to associate with EphB2 following EphB2 activation, a finding also confirmed by FAK immunoprecipitation followed by EphB2 immunoblotting
406	16298995_MI:0006	Further reciprocal co-immunoprecipitation study identified the non-receptor tyrosine kinase Src (Fig. 1B) and the adaptor protein Grb2 (Fig. 1B, right panel) in the EphB2 immunoreactive complex following EphB activation.
407	16298995_MI:0006	Immunoprecipitations against FAK and immunoblotting against paxillin showed that FAK association with paxillin was also induced following EphB2 activation
408	16298995_MI:0006	Reciprocal co-immunoprecipitations identified Src and Grb2 as FAK binding partners following EphB2 activation as well
409	16301118_MI:0006	The transglutaminase-AKAP13 interaction was confirmed by tTG co-immunoprecipitation with AKAP13 antibody
410	16301319_MI:0006	Erbin was detected in Sur-8 precipitates, suggesting that endogenous Erbin and Sur-8 may interact in cells.
411	16306047_MI:0006	The possibility that inhibition was related to the interaction of 
-catenin with PS1 was also investigated. Both proteins were co-immunoprecipitated either in SW-480 cells or in RWP1 cells
412	16306047_MI:0006	The possibility that inhibition was related to the interaction of 
-catenin with PS1 was also investigated. Both proteins were co-immunoprecipitated either in SW-480 cells or in RWP1 cells (Fig. 3). We detected that PS1 also interacted with the 
-catenin homologue plakoglobin in both cell lines.
413	16306047_MI:0006	Transfection of PS1 increased the amount of 
-catenin that could be precipitated with wild-type Tcf-4, but the increase was only very modest with Tcf-4 S60E (Fig. 6C). Better PS1 stimulation was observed when binding of Tcf-4 to plakoglobin was analyzed. Surprisingly, PS1 also up-regulated binding of plakoglobin to Tcf-4 S60E,
414	16316992_MI:0006	Beta1AR and MAGI-3 interact in native tissues.
415	16316995_MI:0006	As shown in Fig. 5A (lower panel), an antibody to Lyn (lanes 1-3) co-immunoprecipitated [35S]methionine-labeled SphK2 only when both purified human recombinant Lyn and [35S]methionine-labeled SphK2, which was in vitro transcribed/translated, were present.
416	16316995_MI:0006	Fyn interacts with SphK1 and SphK2.
417	16316995_MI:0006	Fyn or Lyn was immunoprecipitated where indicated, and the presence of SphK1 (upper panel) or SphK2 (lower panel) was demonstrated by Western blotting using anti-V5 and anti-SphK2 (Ct), respectively.
418	16316995_MI:0006	Fyn was immunoprecipitated from nonstimulated or Ag-stimulated (2 min) WT BMMC lysates mixed with lysates from HEK293 cells overexpressing FLAG-SphK2.
419	16316995_MI:0006	To verify that the interaction between SphK and Fyn was not an artifact of the in vitro system or the overexpression of these proteins in cells, we tested the association of endogenous SphK2 (Fig. 5C), which was the weaker interacting SphK, with Fyn in BMMC from WT and Fyn-deficient mice.
420	16316995_MI:0006	We further confirmed the interaction of SphK1 with Fyn by co-immunoprecipitation analysis using purified human recombinant Fyn and [35S]methionine-labeled SphK1, transcribed/translated in an in vitro TNT T7 reticulocyte system (Fig. 5A, upper panel).
421	16319058_MI:0006	A constitutive association of IKK and IKK with IKK was detected, and TNF stimulation resulted in similar cosedimentation levels (Fig. 7, B and C).
422	16319068_MI:0006	Association of prohibitin with CRM-1 in vivo.
423	16319076_MI:0006	As shown in Fig. 1A, dynamin 1 can be co-immunoprecipitated with profilin 2 from brain lysates using a profilin 2-specific antibody.
424	16326698_MI:0006	Therefore, BRCA1 associated with endogenous P-ACCA in mammalian cells.
425	16326701_MI:0006	Vaccinia virus UDG protein is an early protein that interacts with A20 in vivo.
426	16326706_MI:0006	TIMP-2 increases p27Kip1 association with Cdk4 and Cdk2.
427	16330542_MI:0006	Co-immunoprecipitation assay of CREB and CARM1 endogenous proteins in H4IIE hepatocytes.
428	16330544_MI:0006	We first demonstrated that covalent coupling did not disrupt the ability of Hsp90 to co-precipitate Raf-1, a bona fide Hsp90 client
429	16332682_MI:0006	anti-ApoEr2 co-precipitated NR1 in transfected COS7 cells
430	16332682_MI:0006	ApoEr2 and NR1 co-immunoprecipitated
431	16332682_MI:0006	immunoprecipitation of ApoEr2 from primary neuronal cultures resulted in precipitation of NR1
432	16332688_MI:0006	After eukaryotic expression plasmid encoding FLAG-tagged Parkin was transfected into the SH-SY5Y cells (Fig. 1B), the immunoprecipitation was performed with either anti-RanBP2 or anti-FLAG antibodies. As shown in Fig. 1B, Parkin selectively binds to endogenous RanBP2.
433	16332688_MI:0006	After the rat and mouse brain cortex were isolated and homogenized, Western blot analysis revealed that significant levels of Parkin are present (Fig. 1F, left). The cell extracts were then immunoprecipitated with anti-RanBP2 antibodies, followed by the immunoblot analysis with either anti-Parkin or anti-RanBP2 antibodies.
434	16332688_MI:0006	As shown in Fig. 1A, the transfected FLAG-tagged Parkin was able to bind to endogenous RanBP2 in the HEK293 cells.
435	16332688_MI:0006	C, where specified, dopaminergic MN9D cells were transfected with 3 µg of mammalian plasmid encoding GFP-tagged IR1 + 2 mutant of RanBP2 (IR) or co-transfected with FLAG-Parkin plus GFP-IR1 + 2 (IR+P), as indicated. The cells were immunoprecipitated with anti-FLAG antibodies, followed by immunoblot analysis with anti-GFP IgG.
436	16338934_MI:0006	GluR1, but not NR1 or synaptotagmin I (Syt I), co-immunoprecipitated (IP) with myosin Vb
437	16338934_MI:0006	myosin Vb and GluR2, but not NR1, co-immunoprecipitated with GluR1
438	16339760_MI:0006	As expected, immunoprecipitation of either HAP1-A or HAP1-B from PC12 cells pulled down both HAP1-A and HAP1-B. Because PC12 cells express more HAP1-B than HAP1-A, the HAP1-B immunoprecipitation yielded a much greater amount of HAP1-B than HAP1-A.
439	16339760_MI:0006	Only when HAP1 was present did HAP1 immunoprecipitation coprecipitate kinesin (Fig. 1D), indicating that KLC associates with HAP1 in vivo.
440	16341228_MI:0006	Brm also immunoprecipitated along with the U5 snRNP subunit PRP6 in the absence of cross-linking, confirming the contact of Brm with the U5-associated complex (Fig. 2c). The interaction with PRP6 was weakened in the presence of RNase A, suggesting that RNA components were required either as interaction intermediates or for the stabilization of the complex.
441	16341228_MI:0006	Co-immunoprecipitation experiments from HeLa cell extracts revealed an association of Brm with Sam68
442	16344550_MI:0006	Anti--catenin antibody effectively precipitated CoCoA (lane 5), even in the absence of exogenously expressed -catenin (lane 7).
443	16344550_MI:0006	CoCoA interacts with -catenin in vitro and in vivo.
444	16352593_MI:0006	Although Miz-1 coimmunoprecipitated with wild-type c-Myc, it was not bound by the V394D mutant.
445	16352593_MI:0006	As shown in Fig. 3B, both c-Myc proteins interact with endogenous Max
446	16364915_MI:0006	As shown in Figure 1C,endogenous Helds and hEdc3 both exist in complex with hDcp1a.
447	16365431_MI:0006	After treatment of THP-1 cells with PMA for 3 days, the cells were lysed and immunoprecipitated with a control Ab or anti-STAP-2 Ab. The immunoprecipitate with the anti-STAP-2 Ab contained IKK-
448	16369483_MI:0006	Pull down showing CgA and CgB interacted with mutant SOD1
449	16369483_MI:0006	Western analysis of the immunoprecipitates demonstrated that both G37R and G93A SOD1 co-precipitated with TNG38
450	16373488_MI:0006	The 68-kDa band appears as a doublet and yielded five peptides that all correspond to Vg1RBP/Vera. Western blotting confirmed the presence of Vg1RBP/Vera in the immunoprecipitated fraction (Fig. 3C).
451	16373488_MI:0006	We searched for 40LoVe interaction partners by immunoprecipitation from the YPW fraction. Using affinity purified 40LoVe antibodies we observed three copurifying species (Fig. 3A).
452	16390871_MI:0006	Another possible explanation for the reduced activity of Cdc2 in cdc37ts mutants at 36c is that the ability of Cdc2 to form a stable complex with the mitotic Cdc13 might be impaired. Formation of a complex between Cdc13 and Cdc2 is essential for Cdc2 activity and entry into mitosis (Nurse, 1997). Native protein extracts were prepared from cdc37-184, cdc37-681 and cdc37+ strains cultured at 28 and 36c. For comparison, a cdc25-22 strain was treated in the same way. Immunoprecipitations were carried out with the anti-Cdc13 antibody. Western blot analysis with the anti-PSTAIR antibody revealed that the level of Cdc2 that co-precipitated with Cdc13 was reduced in cdc37ts mutants incubated at 36c (Fig. 6A,B).
453	16390871_MI:0006	To investigate this possibility further, the biochemical interaction between Cdc2 and Cdc37 was investigated by immunoprecipitation experiments. Immunoprecipitates of Cdc37 from cdc37+, cdc37-681 and cdc37-184 cells grown at 28 and 36c contained Cdc2, identifying a biochemical interaction between the Cdk and the molecular chaperone protein (Fig. 6C). The level of Cdc2 bound to Cdc37 was reduced in cdc37-681 and cdc37-184 protein extracts from cells cultured at both 28 and 36c compared with immunoprecipitation experiments with the cdc37+ strain ED1022 (Fig. 6C). In the reverse immunoprecipitation experiment using a Cdc2-HA-tagged strain ED1576, we were unable to detect a biochemical interaction between Cdc2 and Cdc37. It is possible that the HA tag subtly affects stability of the complex, making it harder to detect by immunoprecipitation.
454	16403913_MI:0006	MyH9{Delta}N-GFP was pulled down by antinucleolin Ab, which suggests that the c-terminal of MyH9 is indeed the binding site for nucleolin
455	16403913_MI:0006	We found that MyH9 can bind to nucleolin from cell surface and cytoplasm but not from nucleus
456	16407827_MI:0006	Mutant plasmids were expressed in COS-7 cells, immunoprecipitated with an anti-Grb2 antibody, and the immunological presence of mycPLD2 was analysed by Westernblot. As shown in Figures 3a and d, a B70% reduction in the coimmunoprecipitated mycPLD2 could be achieved with mycPLD2 Y179F and DY179, suggesting that PLD2 Y179 is involved in Grb2 binding in vivo.
457	16415858_MI:0006	Western blot analysis showing co-immunoprecipitation and interaction of endogenous Arf6 with the c-subunit of V-ATPase.
458	16415858_MI:0006	Western blot showing immunoprecipitation of ARNO (upper panel) but not of Arf6 (lower panel) with the a2-isoform of vesicles isolated from MTC, HeLa and HEK cells.
459	16415858_MI:0006	Western blot (WB) showing immunoprecipitation (IP) of ARNO with the a2-isoform from proximal tubule post-mitochondrial supernatant (PMS)
460	16473966_MI:0006	Reciprocal coimmunoprecipitation with anti-BRI1 antibodies revealed the presence of SERK1-CFP in the coimmunoprecipitated proteins
461	16473966_MI:0006	To confirm the in vivo interaction of CDC48A with SERK1, we coimmunoprecipitated SERK1 from Arabidopsis tissue-cultured cells with anti-GST-SERK1 kinase antibodies (Rienties et al., 2005). The precipitated proteins were analyzed by immunoblotting using anti-CDC48 antibodies (Rancour et al., 2002). A band with the expected mobility for monomeric CDC48A was detected in the total protein extract (Figure 4A, lane 1) and in the immunoprecipitated sample (Figure 4A, lane 3), showing that Arabidopsis CDC48A indeed coimmunoprecipitates with SERK1.
462	16480949_MI:0006	Results shown in Fig. 4 reveal that flotillin-1 could be coprecipitated with APP and/or APP C-terminal fragment(s) and vice versa.
463	16490787_MI:0006	Clones of the prostate cancer cell lines LNCaP, Du145, and PC3 were generated through retrovirus transformation using the full-length rat C/EBP cDNA inserted into the retrovirus vector PLNCX. The increased expression of C/EBP was seen in all transduced cell lines. Although the p42 isoform was the predominant isoform, the p30 isoform was detected in transduced LNCaP cells (Fig. 2D, right panel). As shown in Fig. 2E, in all three lines Ku70, Ku80, and PARP-1 co-precipitated with C/EBP
464	16490787_MI:0006	Ku70, Ku80, and PARP-1 also co-precipitated with endogenous C/EBP as was demonstrated in LNCaP cells
465	16490787_MI:0006	Ku70, Ku80, and PARP-1 also co-precipitated with endogenous C/EBP
 as was demonstrated in LNCaP cells (Fig. 2F, top panel) and in human prostate cancer tissue
466	16501604_MI:0006	A commercial antiprocaspase-3 antibody was used to precipitate procaspase-3 and the precipitate was found to contain GFP-WNK3 (Figure 5b)
467	16517759_MI:0006	Immunoprecipitation (IP) of CYCD3;1 followed by protein gel blot detection of CYCD3;1 and CDKA (PSTAIRE).
468	16525419_MI:0006	Identification of a phosphotyrosine-dependent interaction between nephrin and the Nck SH2/SH3 adaptor.
469	16525474_MI:0006	ClC-7 was efficiently co-immunoprecipitated from the brain with Ostm1, and vice versa (Fig. 3d).
470	16525474_MI:0006	Co-immunoprecipitation performed with transfected cells in which only the large form of Ostm1 could be detected showed that this putative ER form also interacted with ClC-7 (Supplementary Fig. S2).
471	16525503_MI:0006	Cell extracts were prepared from transiently transfected COS-1 cells and treated with antisera raised against Atx-3 or Htt. VCP was selectively precipitated by an anti-Atx-3
472	16525503_MI:0006	VCP was co-immunoprecipitated from mouse and human brain extracts using an anti-Atx-3 antibody
473	16537908_MI:0006	Based upon coimmunoprecipitations from soluble extracts (Fig. 5D) and analysis of a recombinant ESCL-E(Z) complex (see below), this close tracking likely reflects a complex containing both ESCL and E(Z).
474	16541025_MI:0006	Here we find a specific subtype of serine/threonine protein phosphatase 2A (PP2A) associating with human shugoshin.
475	16543236_MI:0006	Immunoprecipitation revealed that the fraction of total HIF-1{alpha} co-precipitated with p300
476	16567647_MI:0006	We could pull down PR130 (Fig. 1D Right) with the anti-Nkd antibody, but not with preimmune serum (PI).
477	16600381_MI:0006	CIITA co-immunoprecipitated with the endogenous ZXDC protein (Fig. 5A).
478	16603732_MI:0006	Here we describe the identification of a novel protein complex, the MLL2 complex, consisting of MLL2, ASH2, RBQ3, and WDR5, which is required for ligand-dependent ER{alpha} transactivation
479	16612387_MI:0006	IKK-b was also co-immunoprecipitatied in anti-IRF-7 immunoprecipitates, and the co-immunoprecipitated amount increased after stimulation
480	16612387_MI:0006	IKK-b was also co-immunoprecipitatied in anti-IRF-7 immunoprecipitates, and the co-immunoprecipitated amount increased after stimulation; in contrast, IKK-g was hardly detected.
481	16612387_MI:0006	in Flt3L-induced BMDCs and IRF-7- expressing BMDCs induced with granulocyte-macrophage colonystimulating factor (GM-CSF), IKK-a was detected in IRF-7 immunoprecipitates, but not in control immunoprecipitates (Fig. 3d and Supplementary Fig. 5a). This association was observed before stimulation; after stimulation with TLR7/9 agonists, the amount of co-immunoprecipitated IKK-a increased, and was accompanied by an increase in IRF-7 protein levels
482	16616919_MI:0006	Full-length PRMT2 interacted with RB, while the deletion mutant did not
483	16616919_MI:0006	HA-tagged PRMT2 expression vectors or control vectors were transfected into 293 cells, and immunoprecipitation of endogenous RB was followed by a Western blot analysis using an anti-HA antibody. PRMT2 directly interacted with RB in contrast to control vectors
484	16616919_MI:0006	In cells transfected with E2F1, PRMT2 and RB, PRMT2 co-immunoprecipitated with E2F1
485	16616919_MI:0006	We observed the presence of RB in immunoprecipitates of endogenous PRMT2 from PRMT2+/+ MEFs
486	16619302_MI:0006	MVP co-immunoprecipitates with GR.
487	16619302_MI:0006	Silver stained 2-D gels of GR interacting proteins. Immunopurified GR from (A) liganded/activated and (B) nonliganded/ non-activated rat liver were separated on 2-D gels (18 cm IPG strips 3-10 non-linear in the first dimension followed by a gradient slab gel, T = 5-20%, in the second dimension). The protein patterns from both states were reproduced on five independent 2-D gels. Identified proteins have been marked and are listed in Table 1.
488	16622416_MI:0006	Immunoprecipitated APPL1 and coimmunoprecipitated AdipoR1 were detected with the antibodies to the proteins.
489	16636664_MI:0006	A weak interaction between GSTP1-1 and p38, which was unaffected by TNF, was also observed
490	16636664_MI:0006	The results from imunoblot analysis using anti-GSTP1-1 antibody of the TRAF2 of TRAF6 immunoprecipitates revealed that GSTP1-1 specifically associated with TRAF2
491	16636664_MI:0006	The results showed that GSTP1-1 associated with JNK1 in unstimulated cells,
492	16641999_MI:0006	All four known constituents of the PS1 complex (nicastrin3, aph-1 (refs 4, 5), pen-2 (ref. 5) and PS1 (ref. 1)) were present only in the co-precipitates from wild-type cells.
493	16641999_MI:0006	endogenous TMP21 from mouse brain, neuron-like SHSY-5Y cells and human embryonic kidney (HEK-293) cells could be co-immunoprecipitated with endogenous nicastrin, aph-1, pen-2 and PS1
494	16641999_MI:0006	p24a, another member of the p24 cargo protein family, does not interact with any members of the presenilin complex but does co-precipitate TMP21.
495	16641999_MI:0006	TMP21 also interacts with the p24 cargo protein p24a, but as a component of a separate complex.
496	16648843_MI:0006	Mud and Pins immunoprecipitated (IP) from wild-type embryonic lysates with anti-Pins antibody but not with non-specific control antibodies.
497	16648845_MI:0006	To determine whether Nek2A interacts directly with the APC/C, a human APC/C preparation that was immunopurified using an anti-Apc3 antibody was first western blotted with antibodies against APC/C subunits and Nek2. Nek2A was clearly detected in the purified APC/C preparation, but not in the control immunoprecipitation sample
498	16648845_MI:0006	To verify that interaction between the APC/C and Nek2A is dependent on its destruction motifs, radiolabelled Nek2A, Nek2AΔK−ΔD and both full-length (Cdc13) and nondegradable (Cdc13Δ67) fission yeast cyclin B were incubated with HeLa nuclear extracts before APC/C immunopurification. Nek2A co-purified with the APC/C, whereas only trace amounts of Nek2AΔK−ΔD, Cdc13 or Cdc13Δ67 were co-purified and Nek2. Nek2A was clearly detected in the purified APC/C preparation, but not in the control immunoprecipitation sample
499	16648845_MI:0006	We added 35Slabelled Nek2AΔK and Nek2AΔK−ΔMR to CSF extracts and immunopurified the APC/C to assess their ability to bind the Xenopus APC/C. Nek2A-ΔK, but not Nek2AΔK−ΔMR, bound to the APC/C in mock-treated CSF extractsand, equally well, to the APC/C in CSF extracts from which Cdc20 (Fizzy) had been depleted
500	16652156_MI:0006	Interaction of caspase-2, RAIDD and PIDD.
501	16672379_MI:0006	We next tested whether endogenous cytLEK1/SNAP-25 complexes could be isolated from cells. A series of coimmunoprecipitation studies, with the same NIH 3T3 cell line that demonstrated immunofluorescent colocalization, was conducted with an antibody previously used to recover SNAP-25 and its interacting partners (Kolk et al., 2000). As seen in Figure 2D (lane 2), SNAP-25 forms an endogenous complex containing cytLEK1.
502	16675552_MI:0006	GFP-DdVASP was coimmunoprecipitated with dDia2,
503	16682412_MI:0006	anti-SETDB1 antibody specifically co-immunoprecipitated endogenous DNMT3A
504	16702408_MI:0006	Coimmunoprecipitation assays using two distinct antibodies revealed that, as expected, K17, K16, and K14 are present in endogenous TRADD immunopreciptates obtained from primary cultures of mouse skin keratinocytes (Fig. 3A,A').
505	16713564_MI:0006	Reduced interaction between Net1 and Cdc14 in the absence of Cdc55.
506	16713564_MI:0006	Separase and Cdc55 interact.
507	16713566_MI:0006	This study has shown thatOCA-B also functions in the pre-B1-to-pre-B2 cell transition and,most surprisingly, that it directly interacts with SYK, a tyrosine kinase critical for pre-BCR and BCR signaling.
508	16740636_MI:0006	CatSper1 was detected in the proteins immunoprecipitated by anti-Cav3.3 antibody only when Cav3.3 and CatSper1 co-expressed in the cells.
509	16740636_MI:0006	similar co-immunoprecipitation experiments demonstrating the association of CatSper2 with Cav3.3 in HEK cells.
510	16760425_MI:0006	Flag-1-991123 exhibited significantly reduced  affinity for CaM compared with the wild-type control in coimmunoprecipitation experiments (Figure 9D).
511	16760425_MI:0006	In addition, endogenous CP110 from 293T cell extracts binds specifically to a CaM agarose conjugate under low calcium (Figure 1D). Furthermore, we showed that CP110 and CaM interact in the presence or absence of calcium from extracts supplemented with either EGTA (-Ca2+) or calcium (+Ca2+), suggesting that CP110 may contain both Ca2+-dependent and Ca2+-independent CaM-binding domains (Figure 1E).
512	16760425_MI:0006	Interestingly, both the wild type and CaM-binding mutant proteins interacted equally well with centrin (Figure 9C), rendering less likely the possibility that the mutant protein fails to interact with CaM owing to global misfolding.
513	16760425_MI:0006	We demonstrated that endogenous CP110 and centrin interact in cells by showing that both proteins coimmunoprecipated from 293T cell extracts with anti-centrin antibody but not with an irrelevant antibody (Figure 5C).
514	16766265_MI:0006	HDAC1 was partially or completely displaced by the binding to pRB in the presence of 5 mg and 10 mg of HMGA2, respectively. This result demonstrates that HMGA2 directly interferes with the binding between HDAC1 and pRB. Moreover, to correlate the effect of HMGA2 on HDAC1 displacement from pRB with the HMGA2/pRB interaction, we also performed the experiment by using the A2(1-44) mutant, unable to bind pRB. As shown in the same Figure 4B, the binding between HDAC1 and pRB was not affected at all by the HMGA2 mutant,
515	16766265_MI:0006	HEK293 cells were transiently cotransfected with hemagglutinin (HA)-tagged-HMGA2 and pRB expression vectors. Protein lysates were immunoprecipitated with antipRB or anti-HA antibodies and immunoblotted with anti-HA or anti-pRB, respectively (Figure 2A, right panels). Coexpression of pRB and HMGA2 resulted in coimmunoprecipitation of the two proteins.
516	16766265_MI:0006	we coimmunoprecipitated protein lysates from two HMGA2 pituitary adenomas and from a pool of pituitary glands from control mice. Immunoprecipitation of the protein lysates with anti-pRB antibodies resulted in the coimmunoprecipitation of HMGA2 from pituitary adenomas
517	16766265_MI:0006	we performed coimmunoprecipitation experiments with HEK293 cells transiently cotransfected with pRB and E2F1 expression plasmids in the presence of E1A or HMGA2 recombinant proteins (Figure 4A). As previously reported (Putzer et al., 1997), E1A prevented the binding between pRB and E2F1 (lane 2), whereas HMGA2 did not
518	16767099_MI:0006	Association of erbB4 with NMDAR is enhanced in PFCs of SCZ subjects.
519	16767099_MI:0006	Association of erbB4 with PSD-95 is enhanced in the PFC of schizophrenic subjects.
520	16767099_MI:0006	NRG1 treatment attenuated the NMDA-induced enhancement of NMDAR2A tyrosine phosphorylation as well as the recruitment of PIPLC-g1 by NMDAR1.
521	16767099_MI:0006	These enhancements were accompanied by parallel increases in the activation of ERK and AKT, downstream signaling molecules, as well as in the formation of erbB4 and erbB2 heterodimers
522	16775625_MI:0006	Interaction of hPFTAIRE1 with 14-3-3 proteins in HeLa cells
523	16777605_MI:0006	We isolated SIR-2.1 protein complexes by coprecipitation with the anti-SIR-2.1 antibody and analyzed the complexes by mass spectrometry.
524	16777849_MI:0006	As shown in Fig. 1A, Fyn was co-immunoprecipitated with TCGAP.
525	16777849_MI:0006	Moreover, Fyn was co-immunoprecipitated with TCGAP from brain lysates of wild-type mice (Fig. 1D).
526	16792691_MI:0006	Immunoprecipitation assays using a CUL4- specific antibody demonstrate co-precipitation of myc-tDET1 and CUL4.
527	16799092_MI:0006	Comparison of the temporal changes of the EGFR interaction partners by Western blotting.
528	16799092_MI:0006	Identification of EGFR interaction partners by mass spectrometry: proteins that decrease upon EGF stimulation
529	16809346_MI:0006	These results showed that the endogenous FoxM1 and FoxO3a proteins coprecipitated with one another in MCF-7 cells, thus confirming in vivo interaction between FoxM1 and FoxO3a.
530	16845383_MI:0006	A sequential immunoprecipitation assay showed that Daxx, Mdm2 and Hausp were present in the same complex
531	16845383_MI:0006	Deletion analyses revealed that the main binding domain for Mdm2 resides in a small region of Daxx (amino acids 157-260)
532	16845383_MI:0006	Deletion analyses revealed two regions in Daxx that associate with Hausp: the N-terminal 160 amino acids, which contain the first paired amphipathic helix domain (PAH1), and amino acids 347-570, which encompass the acid-rich region
533	16845383_MI:0006	The Daxx- Hausp interaction was not dependent on either Mdm2 or p53, as it occurred in HCT116 (p53-/-) and Mdm2-/-p53-/- MEF cells (Fig. 3b).
534	16845383_MI:0006	The disruption of the binary Mdm2- Daxx interaction by DNA-damage signals seemed to be persistent and was not restored 4 h after treatment with etoposide (see Supplementary Information, Fig. S4b), whereas the binary Daxx-Hausp interaction was partially recovered by this time (see Supplementary Information, Fig. S4c). In contrast, the Daxx-p53 interaction was affected to a lesser extent
535	16845383_MI:0006	the Hausp-Mdm2 interaction was significantly enhanced by exogenous Daxx in a cotransfection assay
536	16845383_MI:0006	the Hausp-Mdm2 interaction was significantly enhanced by exogenous Daxx in a cotransfection assay (Fig. 4a), whereas this interaction was reduced in Daxx-deficient ES cells
537	16845383_MI:0006	the Hausp-Mdm2 interaction was significantly enhanced by exogenous Daxx in a cotransfection assay (Fig. 4a), whereas this interaction was reduced in Daxx-deficient ES cells (Fig. 4b) and Daxx siRNA-treated U2OS cells
538	16845383_MI:0006	The interaction between endogenous Daxx and Hausp was verified using both a coimmunoprecipitation assay with anti-Daxx (Fig. 3b) and a reciprocal assay with anti-Hausp antibodies
539	16845383_MI:0006	The interaction between endogenous Daxx and Hausp was verified using both a coimmunoprecipitation assay with anti-Daxx (Fig. 3b) and a reciprocal assay with anti-Hausp antibodies (see Supplementary Information, Fig. S2e). The Daxx- Hausp interaction was not dependent on either Mdm2 or p53, as it occurred in HCT116 (p53-/-) and Mdm2-/-p53-/- MEF cells (Fig. 3b).
540	16845383_MI:0006	Using a coimmunoprecipitation assay, the interaction between endogenous Daxx and Mdm2 was detected in several of the human cell lines examined, regardless of the status of p53
541	16862148_MI:0006	Endogenous FilGAP associates with endogenous FLNa.
542	16885985_MI:0006	MYPT-1 preferred the phosphorylated form of merlin, because fulllength S518D or wild type merlin compared to S518A merlin coprecipitated with MYPT-1
543	16885985_MI:0006	PP1d and MYPT-1 were co-precipitated with endogenous merlin from lysates of both RT4 and NIH 3T3 cells
544	16887178_MI:0006	physical binding occurs between endogenous DmIKK3 and endogenous DIAP1 in S2 cells
545	16888242_MI:0006	We found that treatment of neonatal rat cardiomyocytes with ET-1 (100 nmol/L, 30 minutes) decreased FHL2 interaction with SK1
546	16888242_MI:0006	we performed immunoprecipitation with anti-FHL2 antibody using lysates obtained from murine heart. SK1 coprecipitated with the anti-FHL2 antibody
547	16892067_MI:0006	in the mouse pro-B cell line BAF stably expressing a constitutively active mutant form of Rap1 (Rap1V12) or vector alone (as a control). RAPL and Mst1 were associated each other in the absence of exogenous stimuli.
548	16899217_MI:0006	Coimmunoprecipitations performed with Fyn, Lck or anti-magicin (Tim3) antibodies revealed anin vivo association of magicin with both Fyn and Lck at the endogenous levels in Jurkat cells (Fig. 4B).
549	16899217_MI:0006	Pull-down (Fig 2A) and coimmunoprecipitation (Fig. 2B) experiments in CAD cells confirmed the interaction of CAD and Fyn
550	16901789_MI:0006	The B form of CFTR coimmunoprecipitates with HA-Derlin-1.
551	16902409_MI:0006	14-3-3sigma interacts primarily with the p37 isoform of AUF1.
552	16919237_MI:0006	BRMS1 and FLAG-epitope tagged HDAC-cDNAs were co-transfected in COS7. The immunoprecipitations by anti- FLAG antibodies showed BRMS1 co-immunoprecipitation (Fig. 5A). The reverse co-immunoprecipitation further confirmed these interactions
553	16919237_MI:0006	BRMS1 was co-immunoprecipitated with mSDS3, NMI, MRJ, and BAF57 from whole cell lysates (1 mg) of COS7 transient co-transfections.
554	16936772_MI:0006	Immunoprecipitation experiments showed that ILK merely recruited caspase-8 upon irradiation on FN (Figure 6b).
555	16936772_MI:0006	In contrast, ILK exclusively interacted with caspase-9 in suspension cultures (Figure 6b)
556	16936772_MI:0006	In contrast to paxillin, ILK was detectable in caspase-8 or -9 precipitates after irradiation under adhesion or suspension, respectively.
557	16938345_MI:0006	By reciprocal immunoprecipitation, LAT was co-precipitated with PLC-g1 in J2.LAT cells but not in the other two cell lines (Fig. 2c, middle panel).
558	16938345_MI:0006	However, Grb2 was co-precipitated with LAT, but not with LATF171F191, in the presence of Fyn, mLckKA or Syk (Fig. 1g).
559	16938345_MI:0006	Indeed, in the pervanadate-stimulated Jurkat cells, both Lck and PLC-g1 were co-precipitated with LAT (Fig. 1f).
560	16949368_MI:0006	Complex formation of endogenous CTCF and CHD8 in HeLa cells.
561	16951195_MI:0006	Immunoprecipitation of a cytoplasmic extract from TG2-rich Panc28 cells with an anti-InBa antibody revealed the presence of a 66-kDa dimeric InBa band (Fig. 4D, left) in addition to the 33-kDa monomeric InBa band. Treatment of cells with A23187 further augmented the formation of dimeric bands and resulted in the appearance of another polymeric InBa band.
562	16951195_MI:0006	Immunoprecipitation of Panc28 cytoplasmic extracts with anti-InBa antibody effectively pulled down the TG2 protein in addition to the InBa and p65 proteins, suggesting that TG2 forms a part of the complex between p65/p50 and InBa
563	16951195_MI:0006	We confirmed this association by immunoprecipitating TG2 and showing the presence of p65 and InBa in the immune complex
564	16959610_MI:0006	Laforin-GSK-3β association was unaffected by PDGF stimulation and did not require phosphastase activity of laforin
565	16959610_MI:0006	we precipitated the GSK-3b in untransfected NIH3T3 cells and probed the precipitates with antibody specific for laforin. As shown in the lower panel of Figure 7E, significant amounts of laforin were coprecipitated with GSK-3b.
566	16959611_MI:0006	Immunodepletion experiment was carried out immunoprecipitating 300μg of SKBR3 total cell extracts. Three rounds of immunoprecipitation were performed using 3μl of sheep serum α-p53 Ab7 antibody each round. The mutant p53 immunodeprivation was monitorated round by round with western blotting (lanes 4- 6). The immunocomplexes of the three rounds were collected and 1/3 of these (i.e. 100μg of total cell extracts; lane 2) was analyzed by western blotting.
567	16959611_MI:0006	Reciprocal protein complexes involving mutant p53, NF-YA, and NF-YB were found in cells whose exogenous expression of mutant p53His175 (H-175#41) or wtp53 (H-wtp53#23) was under the control of ponasterone A
568	16959611_MI:0006	To evaluate in a more physiological context the existence of mutant p53/NF-Y/p300 protein complexes, we performed coprecipitation experiments in SKBR3 cells. Interestingly, this complex was found predominantly in cells treated with ADR
569	16959611_MI:0006	To evaluate in a more physiological context the existence of mutant p53/NF-Y/p300 protein complexes, we performed coprecipitation experiments in SKBR3 cells. Interestingly, this complex was found predominantly in cells treated with ADR (Figure 5C, lanes 5 and 6). We also found that the presence of a protein complex involving mutant p53 and HDAC1, unlike that containing p300, can be detected predominantly in the absence of ADR
570	16959611_MI:0006	we performed coimmunoprecipitation experiments, employing cell extracts derived from tumor cells (SKBR3, HT29, and SW480) harboring endogenous mutant p53His175, p53His273, and p53His273/Ser309 proteins, respectively. As shown in Figure 1A (lanes 5 and 6), we found the presence of protein complexes between mutant p53 and NF-YA and NF-YB.
571	16959611_MI:0006	we transiently overexpressed NF-YA and p300 in H1299 cells expressing ponasterone-inducible mutant p53His175. We found that reciprocal protein complexes involving NF-YA, mutp53, and p300 were present in ponasterone-treated cells (Figure 5A, upper panels). Furthermore, mutant p53 and NF-Y are necessary for the binding of p300
572	16959611_MI:0006	wtp53 interacted preferentially with HDAC1 and not p300 in ADR-treated MCF10
573	17000644_MI:0006	The SUMO-1 target protein RanGAP1 and the SUMO-2 target protein Sp100 were immunoprecipitated from HeLa cell lysates, transferred to a membrane, and probed using antibody 21C7 directed against SUMO-1 or antibody AV-SM23-0100 directed against SUMO-2/3.
574	17041588_MI:0006	Endogenous WDR proteins interact with the CUL4-DDB1 complexes
575	17041588_MI:0006	Endogenous WDR proteins such as TLE2 and L2DTL were observed in complexes with the CUL4-DDB1 E3 ligases (Fig. 3a-d).
576	17041588_MI:0006	The proteins associated with the CUL4B complexes were identified by mass spectrometry. This led to the identification of a novel WD40-repeat protein, human L2DTL, in the CUL4B-DDB1 complex8, which regulates CDT1 proteolysis in response to DNA damage8. Using similar purifications from293 cells, several other WD40-repeat proteins were identified, including WDR26, WD40 repeat-transducin-like enhancer proteins 1-3 (TLE1-3), WDR82, glutamate-rich WD40-repeat protein 1 (GRWD1) and Suppressor of mec-8 and unc-52 (SMU1), in addition to L2DTL, DDB1 and components of the COP9-signalosome complex (CSN; Fig. 1)
577	17041588_MI:0006	To confirm these interactions, these WDR proteins were tagged with a Flag-epitope tag and expressed in human cells by transfection (Fig. 2). Our studies confirmed that these WDR proteins interact with the CUL4-DDB1 complexes in vivo
578	17041588_MI:0006	WDR proteins were tagged with a Flag-epitope tag and expressed in human cells by transfection (Fig. 2). Our studies confirmed that these WDR proteins interact with the CUL4-DDB1 complexes in vivo
579	17055998_MI:0006	Interaction of glycogenin and glycogen synthase expressed in COS cells.
580	17088979_MI:0006	These results suggest that RNF2 interacts with Pgp and the interactions between these proteins were not affected by the NP-40 and Triton X-100 detergents.
581	17092940_MI:0006	Our results demonstrate that ErbB2 (Fig. 2A, panel b, lane 1) is complexed with both CD44 (Fig. 2A, panel c, lane 1) and N-WASP
582	17092940_MI:0006	we have demonstrated that HA induces recruitment of Arp2 (Fig. 1B-(I), panel b, lane 2) and Arp3 (Fig. 1B-(I), panel c, lane 2) into CD44-N-WASP complexes
583	17098746_MI:0006	We also investigated the interaction between endogenous p53 and FBXO11 protein in a coimmunoprecipitation assay (Fig. 3B).
584	17112726_MI:0006	Remarkably, however, we found that, when Wapl was co-expressed with Scc1 and SA1 together, the three proteins formed a very robust complex in a near-stoichiometric fashion (Figure 7B, lanes 8-10).
585	17113138_MI:0006	Consistent with this possibility we detected more Pds5A in Wapl IPs than in cohesin IPs by MS and immunoblotting
586	17113138_MI:0006	Immunoblot experiments confirmed that cohesin subunits were present in Wapl IPs and that Wapl was present in cohesin but not in condensin samples
587	17137291_MI:0006	Complexes between endogenous MAGE-C1 and NY-ESO-1 proteins were precipitated when both anti-NY-ESO-1 antibodies (NY-41 and E978) were used
588	17137291_MI:0006	MAGE-C1 and NY-ESO-1 were also co-precipitated when the anti-NY-ESO-1 antibodies were used in two additional cells lines: SK-LC-17, a NSCLC cell line (data not shown) and U266, a multiple myeloma cell line
589	17137291_MI:0006	MAGE-C1 and NY-ESO-1 were line (data not shown) and U266, a multiple myeloma cell line also co-precipitated when the anti-NY-ESO-1 antibodies were used in two additional cells lines: SK-LC-17, a NSCLC cell
590	17137291_MI:0006	NY-ESO-1 was detected in Western blots by anti-CT7 mAb CT7-33, although with much lower effciency.
591	17137328_MI:0006	Further, Co-IP indicated that OmpW, FrdB and Odp1 could be complexed
592	17157259_MI:0006	binding of Fbw7 to c-Myc was unaffected by overexpressing SNIP1
593	17157259_MI:0006	HEK293 cell transfection experiments using c-Myc deletion mutants showed that D43 and DS c-Myc mutants interacted with endogenous SNIP1, whereas D147 c-Myc again failed to interact
594	17157259_MI:0006	Overexpression of SNIP1 reduced Skp2 bound to c-Myc, concomitant with formation of a SNIP1/c-Myc complex
595	17157259_MI:0006	the amounts of both the exogenous (lane 4 versus lane 8, short exposure) and endogenous (lane 2 versus lane 6, longer exposure) c-Myc/p300 complexes were enhanced by ectopic expression of SNIP1.
596	17157259_MI:0006	The Max protein, a major component of the c-Myc transactivation complex
597	17157259_MI:0006	The Max protein, a major component of the c-Myc transactivation complex (Bouchard et al., 1998), also bound SNIP1,
598	17157259_MI:0006	This suggests Skp2 and SNIP1 compete for binding to c-Myc.
599	17157259_MI:0006	We confirmed the interaction between c-Myc and SNIP1 in HEK293 cells using transiently overexpressed c-Myc and HA-tagged SNIP1
600	17157259_MI:0006	We confirmed the interaction between c-Myc and SNIP1 in HEK293 cells using transiently overexpressed c-Myc and HA-tagged SNIP1 (Figure 1A) as well as endogenous proteins
601	17157788_MI:0006	A strong interaction between Che-1 and Chk2 was detected after DNA damage
602	17157788_MI:0006	coimmunoprecipitation of Che-1 with antip65 Ab demonstrated increased amounts of Che-1 associated to p65 after DNA damage.
603	17157788_MI:0006	low levels of Che-1 coprecipitated with ATM in control cells, increasing amounts of Che-1 were coprecipitated after Dox treatment
604	17157788_MI:0006	Myc-Che-1 strongly interacted with p65 whereas Myc-Che-1S4A did not bind this protein,
605	17157790_MI:0006	we used an antibody specific to Mdm2 to coimmunoprecipitate p53ERTAM from the p53KI/KI MEF lysates used in Figure 1A. p53ERTAM was clearly coimmunoprecipitated along with Mdm2 (Figure 1C).
606	17157790_MI:0006	we used an antibody specific to Mdm2 to coimmunoprecipitate p53ERTAM from the p53KI/KI MEF lysates used in Figure 1A. p53ERTAM was clearly coimmunoprecipitated along with Mdm2 (Figure 1C). The reverse experiment, using an antibody against p53 (Pab246), gave the converse result.
607	17158449_MI:0006	After IL-1 stimulation, L929 cells expressing GFP showed increased amounts of TAK1 co-precipitating with TAB2, butTAK1was absent in the anti-TAB2 complex from cells expressing TAK1-C100
608	17158449_MI:0006	Analysis of these TAK1 deletion mutants indicated that TAB2 appears to interact with residues 479-547 of TAK1, because TAK1-{Delta}5 and TAK1-{Delta}6 both interacted with TAB2, but not TAK1-{Delta}1-{Delta}4 or TAK1-{Delta}7.
609	17158449_MI:0006	The interaction between the TAB2-TAK1 complex was significantly impaired in cells expressing TAK1-C100 compared with the cells expressing only GFP
610	17159996_MI:0006	we identified PIAS1 as a PTP1B-interacting protein and confirmed this interaction by coimmunoprecipitation studies using PTP1B-null and similar mouse embryonic fibroblasts (MEFs) reconstituted with wild-type PTP1B8 (Fig. 1a).
611	17170761_MI:0006	Consequently, we found that Mdm2 and JMY occurred in the same immunoprecipitate when either Mdm2 or JMY antibodies were used (Fig 2E).
612	17183697_MI:0006	The co-IPs from embryonic lysates showed different sizes of the Cno proteins coimmunoprecipitated with either Dsh or N
613	17189269_MI:0006	When coimmunoprecipitation was performed in reverse with anti-Fyn antibodies, followed by immunoblotting with anti-HA antibodies, the result was the same (Fig. 2C, lane 3).
614	17202144_MI:0006	FLAG-Foxo1 bands were detected in anti-AR antibody-precipitated immune complexes from cells treated with DHT
615	17202144_MI:0006	we further verified that endogenous AR and Foxo1 interacted in an androgen-dependent manner
616	17205597_MI:0006	Using coimmunoprecipitation we have shown that Aminopeptidase N interacts with Aminopeptidase A
617	17210579_MI:0006	Cell lysates from MEFs were subjected to immunoprecipitation with the ASK1 antibody, and endogenous ASK2 co-purified with ASK1 was clearly detected by immunoblotting with the ASK2 antibody (Fig. 1F).
618	17210637_MI:0006	To demonstrate that endogenous NGB and NF2 interact, a coimmunoprecipitation experiment was performed using both 82HTB cells and fresh skeletal muscle tissues with antibodies against NF2 and NGB. The specificity of anti-NGB antibody was demonstrated by Western and immunoprecipitation (IP)-Western blot analysis (Fig. 2C and D). Figure 2E shows that NGB was immunoprecipitated with anti-NF2 antibody but not with preimmune serum.
619	17210637_MI:0006	To demonstrate that endogenous NGB and NF2 interact, a coimmunoprecipitation experiment was performed using both 82HTB cells and fresh skeletal muscle tissues with antibodies against NF2 and NGB. The specificity of anti-NGB antibody was demonstrated by Western and immunoprecipitation (IP)-Western blot analysis (Fig. 2C and D). Figure 2E shows that NGB was immunoprecipitated with anti-NF2 antibody but not with preimmune serum. Moreover, the immunoprecipitation of NGB was competed by GST-NF2 fusion protein, which was used as an antigen to generate the anti-NF2 antibody. Further, merlin was detected in NGB immunoprecipitates
620	17220200_MI:0006	Protein gel blot analysis detected the presence of CINV1 in the immunoprecipitated PIP5K9 complex
621	17220478_MI:0006	although NDRG1 is dramatically increased after R1881 treatment, the levels of E-cadherin and beta-catenin in the NDRG1-IP complex did not increase after exposure to R1881.
622	17220478_MI:0006	Both Ku70 and CANX were detected in the NDRG1 IP complex but not in the IgY and IgG contro
623	17220478_MI:0006	E-cadherin was detected in beta-catenin IP complexes and beta-catenin was detected in E-cadherin IP complexes. We showed that NDRG1 was detected in both E-cadherin and beta-catenin IP complexes, suggesting that these three proteins form a complex.
624	17220478_MI:0006	Furthermore, some of the NDRG1 interacting proteins are also involved in the regulation of cell differentiation and tumor progression. Transducin-like enhancer protein 3 (TLE3) is a member of Notch signaling pathway (63). This pathway controls the prostate epithelial cell differentiation and also involves in the prostate cancer progression.
625	17220478_MI:0006	many proteins that were identified from the NDRG1 complex are also known androgen-regulated proteins such as heat shock protein 90 alpha (HSPCA), beta-catenin (CTNNB1), calnexin (CANX), SEC23, 26S protease regulatory subunit 7 (PSMC2), and 26S protease regulatory subunit 6A (PSMC3).
626	17220478_MI:0006	NDRG1 was postulated to play a role in ER stress response (39) and some NDRG1 interacting proteins that we identified were also involved in the ER stress response (Table 1).
627	17220478_MI:0006	Since this study was performed under androgen-stimulated conditions, many proteins that were identified from the NDRG1 complex are also known androgen-regulated proteins such as heat shock protein 90 alpha (HSPCA),
628	17220478_MI:0006	Since this study was performed under androgen-stimulated conditions, many proteins that were identified from the NDRG1 complex are also known androgen-regulated proteins such as heat shock protein 90 alpha (HSPCA), beta-catenin (CTNNB1), calnexin (CANX), SEC23, 26S protease regulatory subunit 7 (PSMC2), and 26S protease regulatory subunit 6A (PSMC3).
629	17220478_MI:0006	The identified proteins can be classified into several functional categories such as ER chaperons, vesicle-mediated protein trafficking, DNA repair and transcription, cell adhesion and cytoskeleton organization, signal transduction, RNA processing, protein translation, and metabolism
630	17220478_MI:0006	The identified proteins can be classified into several functional categories such as ER chaperons, vesicle-mediated protein trafficking, DNA repair and transcription, cell adhesion and cytoskeleton organization, signal transduction, RNA processing, protein translation, and metabolism (Table 1).
631	17220478_MI:0006	This pathway controls the prostate epithelial cell differentiation and also involves in the prostate cancer progression. 17beta-hydroxysteroid dehydrogenase 4 (HSD17B4) catalyzes branched chain fatty acid beta-oxidation in the peroxisome and works in the downstream from alpha-methylacyl-CoA racemase (AMACR). Both enzymes have been found to be upregulated in human prostate cancer and the selective upregulation of peroxisomal branched chain fatty acid beta-oxidation may involve in the progression of prostate cancer (64). Further investigation of the interaction between NDRG1 and these proteins may uncover the mechanisms by which NDRG1-induced differentiation.
632	17220478_MI:0006	Using coimmunoprecipitation and mass spectrometry analysis, we identified fifty-eight proteins that interact with NDRG1 in prostate cancer cells. These proteins include nuclear proteins, adhesion molecules, ER chaperons, proteasome subunits, and signaling proteins.
633	17220478_MI:0006	We also identified ER stress response proteins in the NDRG1 complex including HSPA5, CANX, and transitional endoplasmic reticulum ATPase (VCP) in NDRG1 complex (Table 1).
634	17220478_MI:0006	we also identified PPP2R2A (Serine\threonine protein phosphatase 2A) as an NDRG1 interacting protein
635	17220478_MI:0006	We also identified several nucleoproteins such as XRCC6 and RuvB like-2 (RUVBL2) in the NDRG1 complex.
636	17220478_MI:0006	We identified a transcriptional factor NFAT90 (ILF3) in the NDRG1 complex.
637	17220478_MI:0006	We identified fifty-eight novel NDRG1-interacting proteins by IP-LC/MS/MS and demonstrated that NDRG1 directly binds to beta-catenin and E-cadherin.
638	17220478_MI:0006	we were able to detect Ku70 and CANX when the IP was performed by the anti-NDRG1 antibody
639	17222790_MI:0006	in the presence of VEGF, NRP1 can be coimmunoprecipitated from HUVEC lysate with anti- VEGFR2 antibodies (Figure 4F, lane 2). This interaction was reduced by anti-VEGF (Figure 4F, lane 3). Interestingly, both anti-NRP1A and anti-NRP1B strongly inhibit the formation of the NRP1/VEGFR2 complex
640	17234752_MI:0006	Endogenous NKX3.1 and Topo I from LNCaP cells could be coprecipitated with NKX3.1 antibody.
641	17237231_MI:0006	When endogenous murine SR-A was precipitated by rat antimouse SR-A monoclonal antibody 2F8 and probed with anti- HK3 antibody, endogenous murine HK3 was clearly detected
642	17237354_MI:0006	Microsomal proteins from Pro35S:PGP19-HA transformants were incubated with PIN1 antiserum, and protein gel blots showed an ;136-kD signal with anti-HA, indicating that PGP19-HA coimmunoprecipitated with PIN1
643	17237354_MI:0006	PIN1 coimmunoprecipitated with anti-PGP1/19.
644	17254966_MI:0006	Lyn binds to a p27 mutant protein lacking all three tyrosines.
645	17254966_MI:0006	pY88-p27 binds cyclin D and cyclin E complexes in vivo.
646	17254966_MI:0006	Y88-phosphorylated p27 is a superior substrate for Cdk2.
647	17254967_MI:0006	Equal amounts of p27 from (B) were incubated with cyclin E-Cdk2. (C) p27, (D) Cdk2, and (E) cyclin E were precipitated and associated proteins blotted.
648	17254967_MI:0006	Similarly, Src transfection modestly reduced p27 in Cdk2 precipitates, while Cdk2- bound cyclin E was unaffected (Figure 3E).
649	17254967_MI:0006	YFPp27WT immunoprecipitates contained less bound cyclin E and Cdk2 following Src transfection, and this was abrogated by PP1 (Figure 3D).
650	17274640_MI:0006	Although all three isoforms were physically associated with pRb during the G1 phase of the cell cycle
651	17274640_MI:0006	exposure of A549 cells to nicotine appeared to induce binding between PP1R and Bad
652	17274640_MI:0006	Figure 5A shows that PP1R also associated with cullin 1
653	17274640_MI:0006	PP1 overlay experiments indicated that purified PP1R was unable to bind directly to p19Skp1, suggesting that there is another protein in the SCF complex that directly binds to PP1R
654	17274640_MI:0006	Seven previously unknown PIPs, that is, APAF-1, E-cadherin, HSP-70, Id2, p19Skp1, PCNA, and PTEN, could be precipitated with the PP1alpha antibody,
655	17274640_MI:0006	Seven previously unknown PIPs, that is, APAF-1, E-cadherin, HSP-70, Id2, p19Skp1, PCNA, and PTEN, could be precipitated with the PP1alpha antibody, whereas one more, p53, could be precipitated with the PP1gamma antibody
656	17274640_MI:0006	The association between p19Skp1 and PP1R was readily detectable at the G1/S transition and during S phase, but barely in G2/M and not at all during G1
657	17276458_MI:0006	PLD2 WT interacts with Grb2/Sos
658	17283121_MI:0006	FLAG-tagged TCF-4 (FLAG), Ku80, and PARP-1 were also detected in the immunoprecipitate with anti-Ku70 antibody
659	17283121_MI:0006	Ku70 and Ku80 were also coimmunoprecipitated with PARP-1
660	17283121_MI:0006	Ku70, Ku80, and FLAG-tagged TCF-4 proteins were detected in the immunoprecipitate with anti-PARP-1 antibody
661	17283121_MI:0006	Ku70, Ku80, PARP-1, and beta-catenin proteins were coimmunoprecipitated with endogenous TCF-4 from a lysate of colorectal cancer HCT116 cells
662	17283121_MI:0006	Nuclear extracts from DLD-1 cells untreated or treated with bleomycin were immunoprecipitated with anti-TCF-4 antibody. Although the total amount of Ku70 in the nucleus was not affected by bleomycin treatment (Fig. 5D, Nuclear), the amount of Ku70 coimmunoprecipitated with the anti-TCF-4 antibody was significantly increased (Fig. 5D, *). On the other hand, the amounts of PARP-1 and beta-catenin coimmunoprecipitated with anti-TCF-4 antibody were decreased
663	17296600_MI:0006	Anti-Ring1B antibodies specifically immunoprecipitated, Fbxl10/Jmjd1B, BcoR, LSD1/Aof2, Skp1 and Ck2a1.
664	17296600_MI:0006	coimmunoprecipitations, with anti-Skp1 and anti-CK2a antibodies also precipitated complexes containing Ring1B/Rnf2.
665	17296600_MI:0006	immunoprecipitation using anti-LSD1/Aof2 antibodies clearly brings down an appreciable amount of Ring1B.
666	17297443_MI:0006	GRIM-19:HtrA2 interactions also occur in non-tumorigenic mammary epithelial cells
667	17297443_MI:0006	To determine if endogenous proteins also interact, MCF-7 cell extracts were IPed using GRIM-19-specific (Figure 1e) or isotype control antibodies, and the products were subjected to WB analysis with HtrA2-specific antibodies. The GRIM-19 antibody, but not the isotype control, IPed endogenous HtrA2. Conversely, GRIM-19 was coIPed by HtrA2-specific
668	17308091_MI:0006	Complementary immunoprecipitation using Ku80 (Fig. 3D, lanes 4-6) or DNA-PKcs (Fig. 3D, lanes 7-9) antibodies confirmed the presence of HOXB7-YFP in their complexes
669	17308091_MI:0006	depletion of DNA in the extracts using ethidium bromide did not reduce the interactions between endogenous HOXB7 and Ku70 or Ku80
670	17308091_MI:0006	treatment with an intercalating agent (ethidium bromide) effectively blocked the interaction between Ku70/80 and DNA-PK because this reaction was completely dependent on the presence of DNA
671	17310983_MI:0006	Under normal physiological conditions, there was an interaction between endogenous MDM2 and S7, as indicated by immunoprecipitation using an MDM2 antibody (H221, Figure 1d1) or S7 antibody (Figure 1d2) followed by immunoblotting with an antibody against S7 (Figure 1d1) or MDM2 (SMP14, Figure 1d2).
672	17310983_MI:0006	We also observed binding between MDM2 and p53 and between MDM2 and S7 when cells were exposed to low concentrations of actinomycin D (Act D) (5nM), which disrupts ribosomal biogenesis (Figure 3d). This likely results from the formation of a ternary complex among S7, MDM2 and p53 following the release of S7 in response to ribosomal stress.
673	17310990_MI:0006	a low amount of MCM7 was coprecipitated with INT6 in the nucleoplasmic fraction and this was increased following proteasome inhibition (Supplementary Figure S1b, lanes 2 and 5). Using the chromatin fraction, INT6 was also found to bind MCM7, but mainly when cells were treated with MG132
674	17310990_MI:0006	Extracts of Jurkat (Figure 1d, lanes 1-3) and HeLa cells (Figure 1d, lanes 4-6) were immunoprecipitated with an antibody directed against INT6 or the corresponding preimmune serum. Immunoblot analysis of MCM7 revealed that the protein which appears as a double band was clearly coprecipitated with INT6 in both cell types, although slightly more efficiently in Jurkat (Figure 1d, compare lanes 2 and 5), showing that the interaction occurs between endogenous proteins.
675	17310990_MI:0006	immunoprecipitation using the HA antibody showed that MCM7 is polyubiquitylated, but this was not seen for MCM4 and MCM6
676	17310990_MI:0006	MCM7 was immunoprecipitated and analysed using an antibody recognizing polyubiquitylated proteins, a weak smear of bands above the position of unmodified MCM7 was observed and its intensity was reinforced by a proteasome inhibitor treatment (Figure 2a, compare lanes 2 and 4), strongly suggesting that endogenous MCM7 is polyubiquitylated and that these polyubiquitylated forms are processed by the proteasome.
677	17314099_MI:0006	NM23-H1 was present in anti-STRAP immune complexes from all cell lines examined, including 293T, Hep3B, and SK-N-BE(2)C (18) cells (Fig. 1B), demonstrating that NM23-H1 physically interacts with STRAP in vivo.
678	17314099_MI:0006	To determine whether the interaction of NM23-H1 and STRAP was redox-dependent, we examined complex formation in 293T cells transiently expressing FLAG-STRAP using in vivo binding assays.
679	17314511_MI:0006	For two selected proteins (DBC‑1 and MCM7), the interaction was verified on the level of endogenous proteins
680	17324924_MI:0006	In support of our results in yeast, HIF-2 was coprecipitated with Int6 under normoxia (Fig. 2B). For further confirmation, the endogenous binding was examined and also observed in HeLa, MCF7, and 786-O cell lines, even under normoxia (Fig. 2C).
681	17329248_MI:0006	Immunoblotting of the XAP2 precipitates with a PDE2A antibody revealed the presence of endogenous PDE2A
682	17329248_MI:0006	In a reverse experiment using anti-PDE2A for immunoprecipitation we could detect XAP2 in the precipitates by immunoblotting.
683	17329248_MI:0006	XAP2 was precipitated using anti-FLAG. Analysis of the precipitates by immunoblotting with anti-VSV revealed the presence of PDE2A
684	17333335_MI:0006	These coimmunoprecipitation experiments revealed a time-dependent increase in the amount of FXR/ER complexes in MCF-7 cells incubated with 50 lM farnesol,
685	17334399_MI:0006	Using immunoprecipitation assays, we find that cyclin D1 complexes with BRCA1 in MCF-7 and T47D cells
686	17334399_MI:0006	We next determined if cyclin D1 and BRCA1 complexed at various stages of cell cycle. A prominent complex was observed at the early G1 and some at the early S phase (panel d). This complex was specific since both BRCA1 and cyclin D1 peptides competed out the antibodies in the immunoprecipitation reaction (panel d).
687	17342744_MI:0006	reverse immunoprecipitations were performed using anti-HSP27 or anti-HSP70 with C4-2 cell extract. Western blot analysis of the protein complexes from the HSP27 and HSP70 immunoprecipitations confirmed the presence of CD10
688	17342744_MI:0006	Western blot analysis shows HSP70 and HSP27 to be co-precipitated with CD10 using anti-CD10 antibodies
689	17347654_MI:0006	CUEDC2 was immunoprecipitated with an anti-PR antibody from human T47D breast cancer cells, which express endogenous PR and CUEDC2, and the immunocomplexes were subjected to SDS-PAGE, followed by Western blot analysis. Figure 1C reveals that CUEDC2 is detected in the PR immunocomplexes in the presence or absence of 100 nM progesterone.
690	17349584_MI:0006	the different Cdc25C expression resulted in lower levels of endogenous Cdc25C associated with endogenous Cdk1 in mitotic Lzts1-/- MEFs
691	17349584_MI:0006	we precipitated the endogenous Cdc25C protein from mitotic or exponentially growing 293 cells known to express high levels of Lzts1 (Ishii et al., 2001). In these conditions, endogenous Lzts1 readily associated with Cdc25C protein, preferentially in mitotic cells
692	17350576_MI:0006	In the first step, anti-Coronin 1B (but not control IgG) immunoprecipitated both SSH1L-GFP and Arp2/3 complex.
693	17350576_MI:0006	SSH1L-myc interacted with endogenous Coronin 1B using reciprocal coimmunoprecipitations (Figure 4H). Arp2/3 complex (as reported by the p34 subunit) was detected in both the Coronin 1B and SSH1L immunoprecipitates.
694	17350576_MI:0006	We conclude that SSH1L, Coronin 1B and Arp2/3 exist in a ternary complex that is bridged by Coronin 1B.
695	17353262_MI:0006	More importantly, immunoprecipitation of endogenous XRCC1 from the human A549 cell extract, which we detected using both standard anti-XRCC1 polyclonal antibodies and antibodies specific for CK2-phosphorylated XRCC1(pS485/pT488) (21, 22), corecovered endogenous APLF,
696	17355907_MI:0006	Lysates from cells transfected with p75NTR and myc-NADE were subjected to immunoprecipitation using anti-p75NTR and p75NTR, NADE, hamartin and tuberin were found to co-immunoprecipitate
697	17373842_MI:0006	Analysis of the immunoprecipitates by SDS polyacrylamide gel electrophoresis and autoradiography (Figure 3A-C) showed that anti-HDM2 antibody coimmunoprecipitates EF1R in the presence of HDM2
698	17373842_MI:0006	Table 1A number of proteins were conclusively identified in the HDM2 immunoprecipitation fractions in addition to the bait protein HDM2 itself. The protein identified with the most number of unique peptide hits was the eukaryotic elongation factor EF1R, and this result was confirmed by manual examination of spectra identified as EF1R
699	17373842_MI:0006	The data show that anti-HDM2 rabbit antiserum coimmunoprecipitates EF1R (lane 2), whereas the preimmune serum cannot (lane 1).
700	17373842_MI:0006	The results (Figure 2A) show that anti-EF1R antibody coimmunoprecipitates HDM2 from HDM2 expression plasmid transfected cell extracts
701	17373842_MI:0006	We also detected interaction of HDM2 with tubulins R6, beta1, and 2 chains.
702	17373842_MI:0006	We also detected interaction of HDM2 with tubulins R6,beta1, and 2 chains.
703	17374643_MI:0006	binding of full-length HRSL3 to PR65alpha was confirmed
704	17376809_MI:0006	Full-length PHV protein can precipitate fulllength DRN (A) or DRNL (B).
705	17426252_MI:0006	As shown in Fig. 6A, when LNCaP cells were cultured under hypoxia in the presence of 10 nmol/L dihydrotestosterone, HIF-1a and the AR were coimmunoprecipitated with each other, indicating a potential physical interaction between HIF-1 (HIF-1a/arylhydrocarbon receptor nuclear translocator complex) and the AR.
706	17426253_MI:0006	Immunoprecipitation with anti-ErbB3 antibody revealed that B4G7 but not EGF stimulated heterodimeriztion between ErbB2 and ErbB3
707	17442384_MI:0006	Consistent with the in vivo localization data, Vps23M254D and Mvb12L47D/I57D mutations had the greatest effect on the incorporation of Mvb12 into the complex. Vps23M254D blocked the Vps23-Mvb12 interaction and reduced, but did not prevent, Vps23 binding to Vps37, whereas Mvb12L47D/I57D showed reduced binding to both Vps23 and Vps37
708	17442384_MI:0006	Consistent with the in vivo localization data, Vps23M254D and Mvb12L47D/I57D mutations had the greatest effect on the incorporation of Mvb12 into the complex. Vps23M254D blocked the Vps23-Mvb12 interaction and reduced, but did not prevent, Vps23 binding to Vps37, whereas Mvb12L47D/I57D showed reduced binding to both Vps23 and Vps37. Vps37L67D-containing complexes contained wild-type levels of Mvb12 and Vps23, in keeping with the MVB localization of both proteins.
709	17442384_MI:0006	Mvb12 and Vps23 copurified efficiently, with immunoprecipitation of 80 percent of the cellular Vps23 resulting in the coprecipitation of a nearly equal proportion 70 percent of cellular Mvb12
710	17446396_MI:0006	SHRGFP is detected in SCR immunoprecipitates (SCR-IP).
711	17460694_MI:0006	NP was further biochemically fractionated, immunoprecipitated using anti-FANCI or control IgG, and western blotted with anti-FANCI (lower gel) or anti-FANCD2 (upper gel).
712	17474147_MI:0006	An anti-PLCg1 antibody was used to precipitate PLCg1 from Jurkat T cells and the associated proteins were identified using an anti-SOS2 or anti-AGAP1 antibody on Western blots.
713	17474147_MI:0006	Interaction between endogenous HPK1 and PLCg1 in Jurkat T cells was independent of Tcell receptor activation by an anti-CD3 antibody.
714	17474147_MI:0006	Interaction between endogenous HPK1 and PLCg1 in Jurkat T cells was independent of Tcell receptor activation by an anti-CD3 antibody. (C) HA-HPK1 was overexpressed in HEK293T cells and IP-ed using anti-HA antibodies.
715	17482142_MI:0006	following immunoprecipitations the fibrosarcoma lysates were probed with either the p53 antibody (Fig. 3A) or with the PBK antibody (Fig. 3B). PBK was also coimmunoprecipitated by p53 antibody utilizing Jurkat T-leukemia cells which make endogenous PBK (Fig. 3C). These experiments suggested a direct interaction between PBK and p53.
716	17510388_MI:0006	Immunoprecipitation of endogenous AR pulled down DJ-1
717	17510388_MI:0006	In both LAPC4and LNCaP cells, antiandrogen treatment with either OH-flutamide or bicalutamide increased the amount of DJ-1 bound to AR
718	17511879_MI:0006	Protein was immunoprecipitated using antibodies against BRCA1, or an antibody against the Flag epitope to immunoprecipitate Flag epitope tagged PP1, , or. BRCA1 coimmunoprecipitated all three PP1 isoforms, and conversely, PP1 , and coimmunoprecipitated BRCA1
719	17513757_MI:0006	the reciprocal experiment using a KLF13 Ab pulled down PRP4 (Fig. 1B)
720	17517622_MI:0006	Endogenous interaction between PFTK1 and CCND3
721	17517622_MI:0006	In contrast, CDK6 was coimmunoprecipitated with both CCND1 and CCND3 (Fig 3C)
722	17517622_MI:0006	To examine the in vivo interaction and physiological relevance between PFTK1 and p21Cip1 identified in the yeast two-hybrid screening, we first conducted semiendogenous coimmunoprecipitation experiments.
723	17525340_MI:0006	Binding of ABRA1 to BRCA1 requires phosphorylation
724	17525340_MI:0006	RAP80 from extracts associates with GST-BRCA1-BRCT in vitro and BRCA1 in vivo in a phosphorylation dependent manner
725	17525340_MI:0006	The RAP80-ABRA1 interaction is BRCA1-independent, because the S406A ABRA1 mutant maintained RAP80 binding (fig. S9) and because RAP80-ABRA1 association was intact in HCC1937 cells
726	17525340_MI:0006	To determine the extent Abraxas and CtIP mediate RAP80 binding to BRCA1, we immunoprecipitated RAP80 from cells depleted for ABRA1, BACH1, or CtIP. The RAP80-BRCA1 interaction was decreased when ABRA1, but not BACH1 or CtIP, was depleted
727	17531812_MI:0006	A coupled IP-western blot assay using extracts prepared from synchronised cells confirmed interactions between p130 and LIN9, LIN37, LIN52, LIN54 and RBBP4 in G0
728	17531812_MI:0006	Antibodies against p130 coprecipitated LIN9, LIN37, LIN54 (Figure 1B) and LIN52 (Figure 1C) while the antibodies against pRB or p107 did not.
729	17531812_MI:0006	p130 also bound to LIN9, LIN54 and LIN37 in human LF1 primary fibroblast cells (Figure 1D)
730	17531812_MI:0006	This assay also revealed that the MuvB proteins LIN9, LIN37, LIN52 and  LIN54 remained associated in S phase and boud B-MYB
731	17535814_MI:0006	Immunoblotting with anti-CENP-E antibody confirmed a successful precipitation of CENP-E, and immunoblotting against HsNUF2 demonstrated that HsNUF2 was coprecipitated
732	17535814_MI:0006	Immunoprecipitation of HsNUF2 using a mouse antibody confirmed the presence of a complex of HsNUF2 and CENP-E
733	17560376_MI:0006	In order to further characterize the A. thaliana Mediator, the α-At1g11760 antibodies were affinity purified and used for immunoprecipitation experiments using the 200 mM potassium acetate eluate from the DEAE-Sephacel column. Figure 4C shows that both AtMed6 and AtMed7 are coimmunoprecipitated with At1g11760.
734	17560376_MI:0006	Mediator and RNA Polymerase Subunits of Arabidopsis thaliana Identified by LC-ESI-MS/MS
735	17560376_MI:0006	we decided to affinity purify the anti-AtMed6 antibodies to use them for immunoprecipitation of a possible A. thaliana Mediator complex directly from the 200 mM potassium acetate eluate of the DEAE-Sephacel column. Western blot analysis showed that AtMed7 partially coimmunoprecipitated with AtMed6
736	17565979_MI:0006	The interaction of both endogenous proteins was also assessed by immunoprecipitating mTOR, and detecting P-Rex1,
737	17577629_MI:0006	endogenous Akt1 protein could be co-immunoprecipitated with endogenous SETDB1 proteins
738	17587138_MI:0006	RAGE was present in the S100P complexes from SW480 cells incubated with exogenous S100P and precipitated with S100P antibody
739	17588663_MI:0006	Co-immunoprecipitation assays of Jurkat cells, transiently co-transfected with tagged PKCzeta and wildtype or catalytic fragment of PKCtheta or GFP expression control.
740	17592114_MI:0006	the amount of phosphorylated activating transcription factor (ATF) is reduced in the csrp1 morphants (Fig. 3D).
741	17620405_MI:0006	endogenous UXT was coimmunoprecipitated by p65 antibody from cells treated with TNF-
742	17635912_MI:0006	antibodies against Bax could precipitate Bax together with a lower, but significant, amount of Tom40
743	17635912_MI:0006	Antibodies against Tom22 allowed isolating Tom22 together with Tom40.
744	17635912_MI:0006	Antibodies against Tom22 allowed isolating Tom22 together with Tom40. Bax was only co-immunoprecipitated with the TOM complex from lysates of mitochondria that were exposed to Bax for 2 min but not from lysates of mitochondria that were incubated with Bax for 30 min
745	17635912_MI:0006	Antibodies against Tom40 recovered Tom40 and, to a lesser extent, Bax
746	17668322_MI:0006	an association between PKCe and Bax could be detected in MCF-7/PKCe cells but not in MCF-7/Neo cells and this interaction increased further by TNF treatment.
747	17681274_MI:0006	Immunoprecipitating Cdk1 and staining for Aurora B and survivin revealed a similar pattern to whole cell lysates. The amount of Aurora B (Fig. 4A c) and survivin (Fig. 4A d) binding to Cdk1 increased in cells arrested at the G2 checkpoint both at 24 (lane 2) and 48 h (lane 5) compared to controls (lanes 1 and 4).
748	17681274_MI:0006	The level of Survivin coimmunoprecipitated with Cdk1 was increased in cells arrested at G2 and cell that undergo mitotic catastrophe.
749	17681274_MI:0006	When Aurora B was immunoprecipitated it was demonstrated that survivin bound to Aurora B in control cells (Fig. 4A f lane 4). Survivin binding to Aurora B was increased in G2 cell cycle arrested cells (lane 5) and cells induced to die post genotoxic insult (lane 6).
750	17693255_MI:0006	Indeed, TNFalpha treatment, which induced IKKbeta to phosphorylate TSC1, interfered with TSC complex formation (Figure 5E).
751	17693255_MI:0006	In vitro transcribed TSC1 proteins were incubated with recombinant IKKbeta proteins and then pulled down by antibody to IKKbeta.
752	17693255_MI:0006	This interaction between IKKbeta and TSC1 was also observed with endogenous IKKbeta and TSC1
753	17693260_MI:0006	Furthermore, anti-rhodopsin antibody (Ab), but not control Ab, was able to coimmunoprecipitate endogenous SARA from mouse retinal extracts (Figure 1F), suggesting that SARA interacts with rhodopsin in vivo.
754	17702749_MI:0006	Interaction between snapin and UT-A1 analyzed by coimmunoprecipitations with indicated antibodies from adenovirus-mediated snapin overexpressing UT-A1-MDCK cell lysate.
755	17704303_MI:0006	We found that an antibody directed against TAF3 efficiently immunoprecipitates TRF3 from myotube extracts (Fig. 4B)..
756	17709393_MI:0006	The TAK1-JIP1 interaction increases within 20 min following DFO exposure
757	17709753_MI:0006	Immunoprecipitation and Western blotting (IP-WB) of HEK293 cells transfected with full-length APP (APP-FL) and CHT.
758	17709753_MI:0006	IP-WB analysis of HEK293 cells transfected with CHT and C-terminal fragment (CTF) of APP (APP-CTF), APLP1 (APLP1-CTF),
759	17719541_MI:0006	Treatment of U2OS cells with etoposide in the presence of MG132 revealed that endogenous Hzf undergoes extensive ubiquitination after prolonged exposure (72 hr) to genotoxic stress, while no such ubiquitinated forms were observed at 36 hr of treatment
760	17719541_MI:0006	We also immunoprecipitated p53 over the time course of etoposide treatment to examine the amount of Hzf bound to p53. We found that there was a sharp decline in the amount of p53-bound Hzf beyond the 36 hr time point to undetectable levels by 72 hr
761	17719542_MI:0006	Endogenous hCAS/CSE1L was detectable within anti-p53 immunoprecipitates, and this was markedly augmented when p53 levels were increased following DNA damage (Figure 2C).
762	17719542_MI:0006	Reciprocally, p53 could be detected in immunoprecipitates of hCAS/CSE1L in lysates of either H1299 cells expressing ectopic p53 (Figure 2D) or MCF-7 cells expressing endogenous p53 after adriamycin treatment (Figure 2E).
763	17719550_MI:0006	Endogenous alpha-chimerin and EphA4 interacted in neurons
764	17719550_MI:0006	Fig. 5A
765	17719550_MI:0006	Fig. 5A & Supp. Fig. S9
766	17719550_MI:0006	Finally, we prepared lysates from the developing motor cortex of WT mice and immunoprecipitated them with anti-alpha2-chimerin antibody. EphA4 was again precipitated with alpha2-chimerin (Figure 5D).
767	17727679_MI:0006	Coimmunoprecipitation of androgen receptor and ADAM-10 was detected in the nuclear fraction but not in the cell membrane and cytoplasmic fractions.
768	17728244_MI:0006	coimmunoprecipitated vIRF-3 strongly interacted with endogenous c-Myc
769	17728244_MI:0006	we detected the inter-action between endogenously expressed vIRF-3 and MM-1 proteins
770	17785436_MI:0006	-catenin coimmunoprecipitated only poorly with caveolin-1 from HT29(US) cells ectopically expressing the protein
771	17785436_MI:0006	Readily detectable amounts of -catenin coimmunoprecipitated with caveolin-1 from transfected HEK293T, DLD1, and HT29(ATCC) cells, as well as MDCK cells
772	17785436_MI:0006	Transiently expressed caveolin-1 was immunoprecipitated from cells either cotransfected with pBATEM2 for E-cadherin expression or not. In HEK293T cells with augmented E-cadherin levels, coimmunoprecipitation of E-cadherin and -catenin with caveolin-1 increased
773	17803907_MI:0006	Additionally, the isolated N-terminus of SOCS7 fused to GFP (GFP-SOCS7(1-124)) coprecipitated with the septin complex (Figure 4C).
774	17803907_MI:0006	endogenous SEPT6 was immunoprecipitated from HeLa cell lysate, and the precipitates were probed for endogenous SOCS7 and SEPT2.
775	17803907_MI:0006	Septins interact with longer-variant SOCS7, but not with the splice variant NAP4.
776	17803915_MI:0006	Endogenous RIM1 was coimmunoprecipitated with SCRAPPER.
777	17803915_MI:0006	Similarly, SCRAPPER formed an SCF complex with Skp1 and Cullin1 in mouse brain lysates (Figure 2A).
778	17855368_MI:0006	endogenous Id-1 was detected in the immunoprecipitates by an anti-Cav-1 antibody
779	17875708_MI:0006	HT-1080 cells prepared from monolayer cultures were immunoprecipitated with either anti-PGI/AMF polyclonal antibodies or preimmunized rabbit IgG and blotted with anti-PARP-14 or anti-PGI/AMF antibodies (Fig. 2E). The results clearly show that PARP-14 coprecipitated with PGI/AMF, suggesting that the two are complexed in vivo.
780	17887956_MI:0006	Cdc45 could be co-precipitated together with endogenous TopBP1 using anti-TopBP1 antibody bound to Sepharose beads in cell extracts from synchronized HeLa-S3 cells in early S-phase 3 h after release from the double TdR-block
781	17887956_MI:0006	TopBP1 could be co-precipitated with Cdc45
782	17893151_MI:0006	Increased levels of HAtagged ubiquitin were detected on PKC II in the presence of exogenous RINCK
783	17893151_MI:0006	RINCK was immunoprecipitated from tsA201 cells and probed for bound PKC ;. A discrete band co-migrating with PKC ; was visible in Western blots of immunoprecipitated RINCK (Figure 2B, lane 3), but not control beads incubated with pre-immune serum (Figure 2B, lane 2). Thus, RINCK forms a complex with PKC ; in cells.
784	17909018_MI:0006	2HA-tagged wild-type p16INK4a coprecipitated with both CDK4 and CDK6, whereas the A20P variant did not. In line with the in vitro binding data, the R24P variant coprecipitated with CDK6 but not with CDK4.
785	17909018_MI:0006	Induction of ARF was accompanied by a corresponding up-regulation of MDM2 and p53, and under these conditions it was possible to show an association between endogenous ARF and MDM2
786	17909018_MI:0006	In the normal HDFs, both CDK4 and CDK6 were present in the p16INK4a immunoprecipitates
787	17909018_MI:0006	In the normal HDFs, both CDK4 and CDK6 were present in the p16INK4a immunoprecipitates and endogenous p16INK4a was coprecipitated with CDK4 and CDK6
788	17909018_MI:0006	the 16INK4a immune complexes from Milan cells contained CDK6 but not CDK4
789	17909037_MI:0006	AR was coprecipitated with Prx1 after hypoxia/reoxygenation when a Prx1 antibody was used for immunoprecipitation.
790	17909037_MI:0006	Prx1 was coprecipitated with AR after hypoxia/reoxygenation when an AR antibody was used for immunoprecipitation
791	17922164_MI:0006	The lower unique band (asterisk) contained several peptides specific for rat SEPT2, while the upper band (<) contained peptides for rat SEPT7, SEPT9, and SEPT14
792	17928403_MI:0006	Human gastrin mRNA was detected in the hnRNP K and PCBP1 immunoprecipitation complexes under normal and EGF treatment at different time points
793	17928403_MI:0006	the in vivo association of nucleolin with gastrin mRNA was demonstrated by RNA-immunoprecipitation assay. We found that nucleolin bound to gastrin mRNA and slightly increased the binding amounts under EGF treatment for 4 hours
794	17928403_MI:0006	we found the hnRNP K immunoprecipitated complex contained the nucleolin protein, and vice versa.
795	17934516_MI:0006	DNMT1 and HDAC1 were present in immunoprecipitates obtained with anti-ICBP90 mAb, with higher amounts found in mimosine-treated cells
796	17934516_MI:0006	ICBP90, DNMT1 and HDAC1 were found co-immunoprecipitated by anti-HDAC1 and anti-DNMT1 Abs
797	17934516_MI:0006	Immunoprecipitation with the anti-ICBP90 mAb (Figure 3a) or anti-HDAC1 or with anti-DNMT1 (Figure 3b) showed bands for DNMT1, ICBP90 and HDAC1 in all experimental conditions, with the highest amount found in mimosine-treated cells
798	17934516_MI:0006	When using the anti-DNMT1 mAb, ICBP90 and HDAC1 were co-immunoprecipitated in proliferating VSMCs
799	17934516_MI:0006	when using the anti-ICBP90 mAb as the precipitating antibody, DNMT1 and HDAC1 were found to be co-immunoprecipitated in proliferating VSMCs but not in confluent cells as a consequence of the lack of ICBP90 expression at confluency
800	17936559_MI:0006	Overexpressed Wip1 resulted in increased p53 ubiquitination, while reduction of Wip1 via Wip1 siRNA suppressed p53 ubiquitination in both IR-treated and untreated cells
801	17936559_MI:0006	we showed that endogenous Wip1 binds to endogenous Mdm2 in U2OS cells as measured by reciprocal immunoprecipitation western blot analyses using Wip1 and Mdm2 antibodies
802	17936559_MI:0006	Wip1 enhances the HAUSP-Mdm2 interaction.
803	17944809_MI:0006	We observed co-immunoprecipitation of functional hemaglutinin (HA)-tagged HBT, as well as of CDC27A (Figure 4c) with APC2,
804	17965023_MI:0006	53BP2S was co-immunoprecipitated with IRS-1
805	17965023_MI:0006	immunoprecipitation of endogenous IRS-1 resulted in the co-immunoprecipitation of the endogenous 53BP2S in 3T3-L1 adipocytes
806	17967441_MI:0006	The physical interaction of hMLH1 with Tb4 was verified by coimmunoprecipitation in a mammalian system
807	17981125_MI:0006	As seen in Figure 2C, endogenous Sig-1Rs coimmunoprecipitated BiP, and conversely BiP coimmunoprecipitated endogenous Sig-1Rs.
808	17981125_MI:0006	Coimmmunoprecipitation of IP3R3 with endogenous immunoreactive Sig-1R or Sig-1R EYFP.
809	17981125_MI:0006	Stable association of Sig-1R-EYFP with BiP: pulse chase plus IP
810	17983804_MI:0006	Immunoblotting revealed that the TopoII protein was co-immunoprecipitated with anti-catenin and anti-TCF-4 antibodies, but not with control immunoglobulin (Ig)G.
811	17983804_MI:0006	the -catenin and TCF-4 proteins were co-immunoprecipitated with anti-Topo II antibody
812	18001824_MI:0006	Lysates from HEK293T cells were immunoprecipitated with control or RNF8-specific antibodies followed by immunoblotting with antibody to MDC1.
813	18024891_MI:0006	full-length XPC also was co-immunoprecipitated from wild-type BGLF4 and XPC-cotransfected 293T cells using anti-BGLF4 antibody
814	18024891_MI:0006	HA-XPC (aa 509-835) was precipitated specifically from BGLF4 (K102I) and HA-XPC (aa 509-835)-cotransfected 293T cells by using anti-BGLF4 antibody (Fig. 1b, lane 1).
815	18024891_MI:0006	we cotransfected NA cells with expression plasmids for full-length XPC, BGLF4 and Rta and immunoprecipitated BGLF4 from the derived extracts. Western blots showed that XPC was coprecipitated with BGLF4 (Fig. 3), indicating that BGLF4 interacts specifically with XPC in NA cells undergoing lytic DNA replication.
816	18025262_MI:0006	A strong interaction between endogenous ERa and BTF3 was observed in both estradiol-treated and untreated MCF-7 samples
817	18025262_MI:0006	This data clearly shows that ERa is specifically coimmunoprecipitated with BTF3b.
818	18029035_MI:0006	We also verified interaction between endogenous A20 and endogenous Ymer by anti-A20 and anti-Ymer antibodies
819	18045535_MI:0006	Conversely, endogenous RPS3 was precipitated with antibodies against endogenous p65 and p50 (Figure 1D)
820	18045535_MI:0006	Immunoprecipitation of endogenous RPS3 revealed a strong association with endogenous p65 in Jurkat cells (Figure 1C). We also detected p50 and I&#954;B&#945; in this immunoprecipitate (Figure 1C).
821	18045535_MI:0006	Lysates as in (C) were immunoblotted for RPS3 directly or after immunoprecipitation with p65
822	18045535_MI:0006	We found that the N-terminal portion (NTD, aa 21-186) of the Rel homology domain (RHD) of p65 was necessary for binding to RPS3
823	18055446_MI:0006	Coimmunoprecipitation analyses using the hemichannelcontaining fractions led to the conclusion that Cx31 and Cx43, as well as Cx43 and Cx45, form heteromeric connexin hemichannels.
824	18056116_MI:0006	Co-immunoprecipitation with AKR1B10 antibody and protein mass spectrometry analysis identified that AKR1B10 associates with acetyl-CoA carboxylase-&#945; (ACCA), a rate-limiting enzyme of de novo fatty acid synthesis.
825	18056116_MI:0006	In RAO-3 cells, AKR1B10 protein was specifically co-precipitated by ACCA antibody
826	18056989_MI:0006	the interaction between endogenous BCRP and Pim-1L in a prostate cancer cell line CWR-R1 was confirmed by the co-immunoprecipitation experiments shown in Fig. 1D.
827	18064632_MI:0006	the interaction between GRP78 and Raf-1 in H460 cells was demonstrated by coimmunoprecipitation analysis
828	18083099_MI:0006	Cps35's interaction with Dot1 was determined in strains bearing FLAG::Cps35 tag and Dot1::9Myc tag.
829	18093972_MI:0006	The association of endogenous HIPK2 with WSB-1 was also verified via co-immunoprecipitation with anti-HIPK2 antibody followed by Western blotting using anti-WSB-1 antibody
830	18160036_MI:0006	Endogenous human ATM, ATR, DNA-PKcs, mTOR, and TRRAP were recovered in IPs of the endogenous Tel2 but not in the IP of a control protein (TRF1) (Figure 6C
831	18165900_MI:0006	Myc-tagged ARAP1-CDexon30 co-immunoprecipitated with DR4
832	18165900_MI:0006	Myc-tagged ARAP1-CDexon30 co-immunoprecipitated with DR4 and, to lesser extent, DR5
833	18191226_MI:0006	Purified GST-&#946;Arr2 was incubated with the recombinant Akt1
834	18212739_MI:0006	BRCA2 co-immunoprecipitated using FANCD2 antisera in bothwi ld-type cells(HeLa and CRL-1583) and cells from groups FA-A/C/E/F
835	18212739_MI:0006	Coprecipitation of BRCA2 withFANCD2 was observed in wild-type cell lines
836	18212739_MI:0006	Coprecipitation of BRCA2 withFANCD2 was observed in wild-type cell lines and PD20-3-15 (functionally complemented withh uman chromosome 3p) and also in PD20K561R-FANCD2
837	18212739_MI:0006	Coprecipitation of BRCA2 withFANCD2 was observed in wild-type cell lines and PD20-3-15 (functionally complemented withh uman chromosome 3p) and also in PD20K561R-FANCD2 and an additional FA-A cell line (HCS72).
838	18212739_MI:0006	Introduction of wild-type FANCG (either human cDNA or genomic hamster for 40BP6), and expression of FANCG protein in the four cell lines restored the interaction of FANCD2-BRCA2.
839	18212739_MI:0006	The two isoforms of FANCD2 can be distinguished in the wild-type cells, but only FANCD2-S co-precipitated with BRCA2 in human cells of complementation groups FA-A/C/E/F as expected
840	18212739_MI:0006	The two isoforms of FANCD2 can be distinguished in the wild-type cells, but only FANCD2-S co-precipitated withBRC A2 in human cells of complementation groups FA-A/C/E/F as expected
841	18230339_MI:0006	As expected, p53 co-immunoprecipitated with PARC
842	18242510_MI:0006	We confirmed that CDK10 binds to ETS2 using coimmunoprecipitation
843	18245485_MI:0006	ARC was detected in caspase-8 complexes obtained with an antibody against caspase-8 in the whole lysates from Mel-RM and MM200 cells before and after exposure to thapsigargin or tunicamycin.
844	18250306_MI:0006	Anti-Drp1 antibody coprecipitated endogenous Bcl-xL protein from brain lysate, and conversely, anti-Bcl-xL antibody coprecipitated endogenous brain Drp1
845	18303029_MI:0006	After the treatment of doxorubicin to induce endogenous p53 in 293T cell line, the nuclear extracts were immunoprecipitated with anti-BAF60a antibody. As shown in Fig 2B, endogenous p53 as well as BRG1 and SRG3 co-immunoprecipitated with endogenous BAF60a.
846	18303029_MI:0006	FLAG-p53 specifically co-immunoprecipitated with both SRG3 and BRG1
847	18303029_MI:0006	When immunoprecipitation assay was performed with anti-p53 antibody, both BRG1 and SRG3 were co-purified with p53 which was endogenously induced by the treatment of doxorubicin, the DNA-damaging agent
848	18316612_MI:0006	Anti-AEG-1 and anti-CBP antibodies effectively immunoprecipitated CBP and AEG-1
849	18316612_MI:0006	the N3 to N6 NH2-terminal deletion mutants did not interact with p65, indicating that amino acids 101 to 205 mediate interaction of AEG-1 with p65.
850	18319262_MI:0006	Endogenous Fhit co-precipitated with Hsp10 and with Fdxr
851	18319262_MI:0006	endogenous Hsp60 co-immunoprecipitated Fhit and Hsp10 in absence of DSP
852	18319262_MI:0006	Hsp60 was immunoprecipitated from total cell lysates of these cells at 48 hr after PonA induction, with or without H2O2, and coprecipitated Fhit and Fdxr
853	18326491_MI:0006	Thus, our biochemical results support the conclusions from FRET analysis that the subunits of the Arabidopsis G protein form a heterotrimeric complex in vivo and that the interaction of G&#945; and G&#947;1 requires G&#946;.
854	18329368_MI:0006	Caspase-1 Binds to proIL-1&#945;
855	18329368_MI:0006	CoIP of endogenous FGF-2 and procaspase-1 from lysates of human primary fibroblasts.
856	18329368_MI:0006	Interestingly, the amount of caspase-1 bound to IL-1&#945; was clearly enhanced 30 min after irradiation (Figure 3A).
857	18329369_MI:0006	lysates of HEK293T cells were immunoprecipitated (IP) with either rabbit IgGs or anti-MKLP1 antibodies and analyzed by anti-BRUCE WB
858	18329369_MI:0006	Plk1 and MEK1 co-precipitate with BRUCE at endogenous levels.
859	18329369_MI:0006	Sec8 and BRUCE interact when expressed at endogenous levels.
860	18329370_MI:0006	Crtam was detected in Scrib, but not Dlg1, immunoprecipitates
861	18332111_MI:0006	When MTD-1A cell lysates were subjected to immunoprecipitation with anti-JRAB/MICAL-L2 antibody, endogenous actinin-4 was specifically precipitated with JRAB/MICAL-L2
862	18332867_MI:0006	we also observed an increased binding between Mdm2 and AR following isosilybin B treatment
863	18339839_MI:0006	Reciprocal immunoprecipitation experiments were done using MDA-MB-231 and PC3 cells (Fig. 1B,iii), confirming the presence of ILK in rictor immunoprecipitates.
864	18339839_MI:0006	we coimmunoprecipitated rictor and ILK from cytoskeletal extracts prepared from HeLa cells, a cell line used in the original identification and characterization of rictor (3), and MDA-MB-231 breast cancer cells. Rictor, but not mTOR, was clearly copurified when ILK was immunoprecipitated from these cells
865	18344519_MI:0006	Immunoprecipitation of cell lysates prepared from HEK293 with an anti-AGTR2 antibody showed that AGTR2 associated with TIMP-3
866	18347058_MI:0006	Immunoprecipitates from whole-cell lysates with an antibody specific for the RASSF1A isoform coprecipitated endogenous EWS
867	18358808_MI:0006	we measured the amount of TERC bound by TERT
868	18387811_MI:0006	Focusing initially on Homer3, we found that immunoprecipitation of APP751 with the R1(57) antibody (Fig. 1B, panel 1, lane 4) resulted in co-precipitation of Homer3 (Fig. 1B, panel 2, lane 4)
869	18394558_MI:0006	Wild-type, but not mutant, p18INK4C coimmunoprecipitated with CDK6
870	18408009_MI:0006	The result showed that Flag-USP11 was co-precipitated with Flag-HPV-16E7
871	18408009_MI:0006	USP11 was co-precipitated with HPV-16E7
872	18408765_MI:0006	Notably, FOXO1 proteins were detected in the protein complex immunoprecipitated by the anti-CDK1 antibody
873	18420585_MI:0006	In MCF7 breast cancer cells, endogenous RACK1 was able to be co-immunoprecipitated with anti-Bim antibody, which was greatly enhanced upon paclitaxel or staurosporine treatment
874	18420585_MI:0006	Little interaction between RACK1 and BimEL
875	18455983_MI:0006	Fas recruits FADD and caspase-8,
876	18455983_MI:0006	Total cell lysates of wild-type and TIPE2-knockdown RAW 264.7 cells were immunoprecipitated with an anti-TIPE2 rabbit polyclonal antibody
877	18502764_MI:0006	In addition, immunoblotting with an anti-EHD2 antibody confirmed that EHD2 was immunoprecipitated along with myoferlin in the presence of anti-myoferlin antibodies (Fig. 1D).
878	18504434_MI:0006	A weak but consistent band corresponding to TCTP was obtained in the Chfr immunoprecipitate from CSF and XL2 extracts
879	18504434_MI:0006	TCTP binds to Chfr in Xenopus egg extracts
880	18504434_MI:0006	The results showed that the focused band corresponded exclusively to Chfr, whereas Chfr and ubiquitin were present in all of the sequenced smeared bands, indicating that endogenous Chfr is continuously ubiquitinated in CSF extracts.
881	18550827_MI:0006	However, although unmodified CUL1 efficiently coprecipitated with CAND1 from wild-type extracts, little if any CUL1 was observed in CAND1 precipitates from eta2-1 extracts (Fig. 1A).
882	18550827_MI:0006	To investigate how axr6-1 and axr6-2 affect the CAND1-CUL1 interaction, we performed 
-CAND1 immunoprecipitations with wild-type and homozygous mutant seedling extracts. In both axr6 mutants, we detected a dramatic increase in the amount of CUL1 coprecipitating with CAND1
883	18557765_MI:0006	These results suggest that endogenous necdin interacts with EID-1.
884	18585357_MI:0006	As a control, the DN form of Met precipitated HGF but not netrin-1 (Figure 3C).
885	18585357_MI:0006	Both DSCAM and DCC can be detected in netrin-1 precipitates (Figure 3E).
886	18585357_MI:0006	Endogenous DSCAM and DCC proteins form a complex
887	18585357_MI:0006	Endogenous DSCAM and DCC proteins form a complex in the absence of netrin-1 but not in its presence.
888	18591351_MI:0006	Co-IP from the wild type and wit1-1 wit2-1 indicated that the interaction between endogenous RanGAP1 and WIP1 was not affected (
889	18591351_MI:0006	The Binding Affinity of WIT1 for RanGAP1 Is Increased in the Presence of WIP1.
890	18598942_MI:0006	LEDGF was detected in the endogenous MLL/menin complex in REH cells as well
891	18617507_MI:0006	endogenous VRK1 was immunoprecipitated and the Ran protein was detected in this specific immunoprecipitate, but not in the case of the control with an anti-Flag antibody
892	18617507_MI:0006	VRK1 was detected in the Ran immunoprecipitate, but not in the control with a non specific (anti AU5) antibody (Fig. 4C,
893	18653891_MI:0006	Antibodies to BSK1 (anti-BSK1) immunoprecipitated the BRI1-green fluorescent protein (GFP) protein expressed from the BRI1 promoter
894	18653891_MI:0006	Co-immunoprecipitation of BRI1 with BSK3
895	18676877_MI:0006	We conducted coimmunoprecipitation assays on the two most abundant recombinant Cys proteases (RD21 and CP43) isolated (Figure 7C). The PDI5 antiserumcoimmunoprecipitatedwithRD21 and CP43 only in the presence of recombinant PDI5
896	18692471_MI:0006	It thus appears that IKK2 regulates the formation of SNARE complex of SNAP-23/syntaxin 4/VAMP-2, resulting in the membrane fusions in the mast cells.
897	18805096_MI:0006	A specific interaction among FMRP, eIF4E, and CYFIP1 was detected in wild-type (Figure 1C, lane 4) but not in FMR1 knockout (KO) mice (Figure 1C, lane 3)
898	18805096_MI:0006	CYFIP1 was immunoprecipitated under control conditions (lane 2, bottom panel) or after BDNF treatment (lane 6), and its presence with eIF4E and FMRP was analyzed by western blotting.
899	18805096_MI:0006	indeed, around 80% of Map1b and BC1 RNAs, as measured by RT-Q-PCR, was released from the CYFIP1 complex after stimulation (Figure 6C).
900	18805096_MI:0006	We then stimulated cortical synaptoneurosomes with BDNF, immunoprecipitated CYFIP1, and examined coprecipitated eIF4E
901	18835031_MI:0006	HEK293T cells transfected with GFP-Nur77/489-497 or GFP-Nur77/478-504 (2 &#956;g) together with or without Bcl-2 expression plasmid (0.8 &#956;g) were analyzed by coimmunoprecipitation (CoIP) using anti-Bcl-2 antibody, followed by western blotting (WB) using either anti-GFP or anti-Bcl-2 antibody
902	18835031_MI:0006	Nur77 lacking its DNA-binding domain (DBD), Nur77/&#916;DBD, bound Bcl-2 (Lin et al., 2004 B. Lin, S.K. Kolluri, F. Lin, W. Liu, Y.H. Han, X. Cao, M.I. Dawson, J.C. Reed and X.K. Zhang, Conversion of Bcl-2 from protector to killer by interaction with nuclear orphan receptor Nur77/TR3, Cell 116 (2004), pp. 527-540. Article |  PDF (976 K)  | View Record in Scopus | Cited By in Scopus (157)Lin et al., 2004), and binding was inhibited by NuBCP-9 or D-NuBCP-9 (Figure 3B).
903	18984162_MI:0006	anti-NEDD9 immunoprecipitates from A375M2 cells transfected with HA-DOCK3 immunoblotted for HA-DOCK3
904	18984162_MI:0006	anti-NEDD9 immunoprecipitates immunoblotted for DOCK3.
905	19000167_MI:0006	Interaction of IBR5 with MPK12 in vivo.
906	19103756_MI:0006	In the VRK1 immunoprecipitate the Plk3 protein was detectable (Fig. 2B).
907	19135897_MI:0006	The endogenous motor/adaptor complex from HEK293T cells was immunoprecipitated with anti-hMiro1 and probed with anti-KHC, anti-hMiro1, and anti-OIP106 (one of two human homologs of milton).
908	19167329_MI:0006	Antisera raised against the N-terminus of STT3B quantitatively precipitated STT3B from digitonin-high salt extracts under nondenaturing conditions, along with 40 +/- 5% of the ribophorin I (Figure 2B).
909	7568034_MI:0006	35S-labeled cyclins C and Dl were incubated with unlabeled in vitro-translated CDK4, and CDK4 was then immunoprecipitated with anti-CDK4 antibodies.
910	7568034_MI:0006	Among all cyclins tested, only cyclin C coprecipitated reproducibly with K35 (lane 4).
911	7916014_MI:0006	Tg antibodies coprecipitated a 75-kDa polypeptide (BiP), and BiP antibodies coprecipitated a 300-kDa polypeptide (Tg)
912	7916014_MI:0006	the same proteins appeared to be coimmunoprecipitated with anti-BiP antiserum (Fig. lA, lanes 5-8). The identities of Tg,
913	7925282_MI:0006	In addition to Sec65p and Srp54p proteins (identified by comigration of bands in non-native immunoprecipitations), novel species of 19 and 66 kDa were immunoprecipitated from 16S fractions of a gradient through which wild type cell extract was sedimented
914	8313896_MI:0006	In double infections of baculoviruses expressing p85a and p110, both proteins were detected in either anti-p85a or anti-p110 immunoprecipitates
915	8313896_MI:0006	Infected cells immunoprecipitated with antibodies directed to the p85 or the p1lO subunit, or if bound to Y751 phosphopeptide affinity beads, were found to contain both p850 and p110 proteins when analysed by SDS-PAGE
916	8334998_MI:0006	This specific immunoprecipitation of the SEC20 cytoplasmic domain with tagged Tip20p provides further evidence that the two proteins are present in a complex.
917	8521818_MI:0006	35S-labelled CDK7 and cyclin H were mixed with increasing quantities of purified GST-p36 expressed in Ecoli. Lysates were then incubated with anti-CDK7 antibodies and immune complexes were analysed
918	8521818_MI:0006	In contrast, a ternary complex consisting of CDK7, cyclin H and p36 could be readily precipitated from the lysate containing all three proteins (lane 7).
919	8521818_MI:0006	The p36 polypeptide co-immunoprecipitated with CDK7 and cyclin H from 35S-labelled HeLa cells using anti-CDK7 antibodies (lane 1) comigrates in a 10% polyacrylamide gel with p36 produced in reticulocyte lysate (lane 2).
920	8567678_MI:0006	freeze-thawing treatment which induces dissociation of synaptobrevin 2 from synaptophysin and V-ATPase also induces dissociation of synaptophysin from V-ATPase.
921	8567678_MI:0006	The c subunit of the V-ATPase was found to be associated with synaptobrevin 2 and synaptophysin also in freshly prepared Triton X-100 extracts of PC12 cells.
922	8567678_MI:0006	We confirmed the specificity of the association between synaptobrevin 2, synaptophysin, and the V-ATPase by performing immunoprecipitation experiments using monoclonal antibodies against synaptophysin (Cl 7.2) and syntaxin 1 (HPC-1) (Fig. 4).
923	8567678_MI:0006	when freshly made Triton X-100 extract was used, synaptophysin (Fig. 1, a and b, see also Fig. 3) and a protein migrating at approximately 80 kDa were the major bands visible by protein staining in the immunoprecipitates. In addition, a 10-kDa protein (p10) and several other minor bands of higher molecular mass were visible.
924	8567678_MI:0006	When frozen-thawed extract was used, the major proteins which coprecipitated with synaptobrevin 2 were SNAP-25 and syntaxin 1 (Fig. 1, a and b, and Fig. 3), in addition to a band of approximately 85 kDa
925	8657141_MI:0006	Sp1 was bound by antibody against E2F1, indicating that complexes of the two proteins exist in vivo.
926	8663349_MI:0006	Two polypeptides of approximately 30 kilodaltons that were recognized by anti-HP1 antibodies in cell extracts (Fig. 4b, lane 1) were present in immunoprecipitates obtained with the experimental antibodies
927	8816473_MI:0006	The coimmunoprecipitation of Msh2p and Msh6p was unaffected by the addition of NaCl to 1 M and ethylene glycol to 20% (vol/vol),
928	8862413_MI:0006	A reduced amount of p107 was coimmunopre-cipitated with E1A from both dlE105 (CR1D)- and dlE106 (CR3D)-infected cells (6 and 83% of wild-type, respec-tively, the mean of three experiments) compared to wild-type infected cells (Fig. 5, lanes 10, 12 and 18, 20). p107 was not coimmunoprecipitated from mock-, dlE102 (CR2D)-, or pmE109 (TTG)-infected cells
929	8862413_MI:0006	Both dlE105 (CR1D)- and dlE106 (CR3D)-infected showed coimmunoprecipitation of pRb and E1A, although to lower levels, 4% and 55% of wild-type, respectively. The low proportion of pRb coimmunoprecipitated from dlE105-infected cells compared to wild-type-infected cells may reflect a cooperative role for E1A CR1 in pRb association with E1A. expressed from dlE102 (CR2D) and dlE106 (CR3D) mi- pRb coimmunoprecipitation did not occur with mock-,dlE102 (CR2D)-,
930	8940073_MI:0006	These results indicate that both rtARNT proteins can associate with the mouse AHR
931	9139733_MI:0006	Co-immunoprecipitation of GAP-43 and PKC-delta.
932	9144171_MI:0006	The interaction of RAS with RIN1 was confirmed by copurification of activated RAS with an epitope tagged form of the carboxyl terminus of RIN1 (RIN1C) from cells expressing these proteins (Fig. 2B).
933	9144171_MI:0006	When RAS is immunoprecipitated from these cells (using antibody Y238), RIN1 was also present (Fig. 2A).
934	9173976_MI:0006	Even after extensive washing with buffer containing 500 mM KCl, mSUG1 still remained associated with XPB imidazole, immunoblot analysis indicated that XPB is retained onto the affinity column only in the presence of His-tagged mSUG1
935	9173976_MI:0006	Extract from insect cells co-infected with viruses expressing XPB and Hemagglutinin (HA)-tagged mSUG1 were immunoprecipitated with a MAb-XPB (1B3) or an anti MAb-SUG1 (2SU). Immunoprecipitates were analyzed on immunoblots with a MAb-HA (12CA5) (Fig. 4A) and MAb-XPB (1B3) (Fig. 4B).
936	9173976_MI:0006	immunoprecipitation of XPB from Heparin 5PW fraction 12 with a XPB monoclonal crosslinked to protein A-Sepharose specifically precipitates hSUG1.
937	9173976_MI:0006	Immunoprecipitations of hSUG1 from Heparin 5PW fraction 12 with the C-terminal-specific anti SUG1 MAb, 3SU or N-terminal-specific anti SUG1 MAb 2SU bound to protein G-Sepharose, specifically precipitate XPB
938	9214646_MI:0006	However, when the purified RLF-M complex was immunoprecipitated using anti-XMcm3 anti-bodies, a different pattern of MCM/P1 proteins was observed (Figure 2C): XMcms 3 and 5 were removed quantitatively from the supernatant,
939	9214646_MI:0006	The anti-XMcm3 antibodies co-precipitated all six MCM/P1 proteins from crude extract, removing the majority of each protein from the supernatants.
940	9214647_MI:0006	These results indicate that six immunologically distinct proteins; p112, p102, XMCM3, p98, p92 and p90, are present in the immunoprecipitates.
941	9223340_MI:0006	N-glycosylated APP was precipitated with PS1 by antibody 4627 in 293 cells stably expressing APP695 (Fig. 3  D, lane 2).
942	9223340_MI:0006	To confirm unequivocally the physiological occurrence of APP-PS complexes at endogenous protein levels, we used X81 or 4627 to precipitate a large amount of lysate from nontransfected CHO cells expressing only endogenous APP and PS and then blotted with 22C11, which recognizes human and hamster APP.
943	9223340_MI:0006	To determine whether APP and PS proteins interact in CHO cells, we performed immunoprecipitation/Western blotting using numerous distinct PS and APP antibodies.
944	9223340_MI:0006	To identify whether this region of APP is responsible for the interaction with PS, we analyzed PS1-APP complex formation in a stable CHO cell line (7W&#916;C) expressing APP751 truncated at residue 709 and thus lacking almost the entire cytoplasmic domain (710-751).
945	9223340_MI:0006	Using the same 22C11 antibody, endogenous hamster APP precipitated with transfected human PS2 in line C-PS2 (Fig. 3E, lane 3).
946	9223340_MI:0006	We also used the antibodies in reverse order: lysates were precipitated with APP antibody 8E5 and any PS1 then detected by blotting with N-terminal antibody 311/2a, -loop- antibody 4624 or C-terminal antibody 4627.
947	9223340_MI:0006	When cell lysates were precipitated with the polyclonal PS2 N-terminal antibody 2972, followed by Western blotting with APP antibody 8E5, APP was again found to coprecipitate
948	9303310_MI:0006	It can be seen that p25rum1 could form specific complexes with p56cdc13 and with p34cdc2/p56cdc13 complexes but not with p34cdc2 alone. We next tested whether the destruction box which is required for B-cyclin proteolysis in mitosis was required for p25rum1 binding. The cdc13D90 mutant lacks this destruction box, but the mutant protein could still form an in vitro complex with p25rum1 (Figure 4).
949	9303310_MI:0006	We first tested whether p25rum1 could bind either p56cdc13 alone or p56cdc13 complexed with p34cdc2.
950	9367441_MI:0006	We observed coimmunoprecipitation of Dorsal with both anti-Cactus and anti-Tube sera
951	9395480_MI:0006	Co-immunoprecipitation of Munc18-1 and syntaxin 1 with Mint proteins from rat brain homogenates.
952	9464541_MI:0006	Endogenous p107 or p130 was immunoprecipitated from C33A cells programmed to stably express an HA-tagged version of Pax-3. As Figure 3 clearly demonstrates, Pax-3 forms stable complexes with both of these pRB-family proteins in vivo.
953	9528852_MI:0006	Co-transfection of COS1 cells with BRCA1-D11 and BAP1 revealed that these proteins could be co-immunoprecipitated using either anti-BAP1 or anti-BRCA1 antibodies
954	9580671_MI:0006	Hamartin could be recovered from the immunoprecipitates of antisera specific for tuberin, while tuberin coimmunoprecipitated with hamartin when an antiserum specific for hamartin was used (Fig. 3).
955	9588209_MI:0006	35S Pex1p was detectable in immunoprecipitates from HsPEX6-transfected CHO-K1 cell lysates, with anti-Pex1p antibody.
956	9588209_MI:0006	Pex6p was recovered in immunoprecipitates by using anti-Pex1p antibody.
957	9603525_MI:0006	Many TAFIIs, including hTAFII20, hTAFII30, hTAFII55, hTAFII80, hTAFII100 and hTAFII135, are apparently common to both TFTC and TFIIDbeta. In contrast, hTAFII250 and hTAFII28, which strongly interact with TBP, were absent from the TFTC fraction (Fig. 1c). Moreover, recombinant TAFIIs (hTAFII18, hTAFII20, hTAFII31, hTAFII80, hTAFII100 and hTAFII135) can assemble into a stable complex, containing stoichiometric amounts of each of these TAFIIs.
958	9614144_MI:0006	we immunoprecipitated p60 from an S phase nuclear extract using pAb1 (Fig. 9) and analyzed the presence of all three subunits by Western blotting using monoclonal antibodies. All three subunits were immunoprecipitated by pAb1
959	9614176_MI:0006	Given these results, we used a rum1-HAcyr1Dsxa2D strain to test whether rum1p physically associated with cdc13p after pheromone addition. Immunoprecipitations of cdc13p and cig2p before and after addition of pheromone were analyzed by Western blotting with anti-HA antibodies. rum1p was found associated with cdc13p, and this association was increased after 3 h in P-factor (Figure 3B). rum1p was also found associated with cig2p, although the amount detected was lower (Figure 3B).
960	9635188_MI:0006	Cam1p interacts with Rng2p (b) but not with Myo2p
961	9670034_MI:0006	Mec1p is essential for phosphorylation of the yeast DNA damage checkpoint protein Ddc1p, which physically interacts with Mec3p
962	9674425_MI:0006	PCAF complex has a subset of histone-like TAFs, namely, hTAFII31, hTAFII20, and hTAFII15
963	9674425_MI:0006	While anti-PCAF antibody coprecipitated hTAFII31 along with PCAF, neither anti-p300 nor anti-CBP antibody coprecipitated hTAFII31
964	9697699_MI:0006	Altering a crucial leucine in the Rb binding site abolishes the ability of Bog to interact with Rb
965	9697699_MI:0006	Bog is present in complexes with all the Rb family members
966	9697699_MI:0006	Rb could be precipitated with both anti-Bog and anti-Rb
967	9697699_MI:0006	Rb could be precipitated with both anti-Bog and anti-Rb, but E2F-1 was detected only in samples precipitated with anti-Rb.
968	9697699_MI:0006	The Rb/E2F-1 complexes were immunoprecipitated with either anti-Rb or anti-E2F-1 antibodies, and incubated with the fusion protein MBP-Bog or the mutated MBP-BogDeltaQ.
969	9701578_MI:0006	These data demonstrate that KAPP and CLV1 associate in vivo as well as in vitro.
970	9756887_MI:0006	As shown in Fig. 2B, endogenous FAK was coprecipiated with endogenous Hic-5, indicating the FAK-Hic-5 interaction in vivo
971	9763420_MI:0006	Consistent with these results, a CENP-E immunoprecipitate was found to contain hBUBR1 (Fig. 8 a, lane 2
972	9763420_MI:0006	Immunoprecipitates obtained with hBUBR1 antibodies were found to contain hBUBR1 (Fig. 8 a, bottom panel of lane 1)
973	9774667_MI:0006	Coimmunoprecipitation of Tom70, Tom20, and Tom22 from digitonin-lysed mitochondria was performed with all available monospecific anti-Tom antibodies: anti-Tom70, anti-Tom20, anti-Tom22, anti-Tom40, and anti-Tom5.
974	9811788_MI:0006	Coimmunoprecipitation of the Arabidopsis JAB1 Homologs with COP9 and FUS6.
975	9840943_MI:0006	Cyclin E2 was readily detected in p27 immunocomplex (Figure 3b), demon- strating an in vivo association between cyclin E2 and CDK inhibitor.
976	9840943_MI:0006	The level of cyclin E2 protein as well as cyclin E2-CDK2 complexes in these cells were determined by IP-Western analysis (Figure 7a).
977	9840943_MI:0006	Total cell lysates were prepared from CT10 and HSF43 and sequentially immunoprecipitated with the cyclin E2 antibody and immunoblotted (IP-Western) with either anti-cyclin E2 or anti-CDK2 antibody (Figure 2b).
978	9989503_MI:0006	association of CBP with Stat5 proteins was enhanced by Nmi
979	9989503_MI:0006	Nmi was detected in anti-Stat5b immunoprecipitates
980	imex:IM-11846_MI:0006	PTEN was detected in an anti-CENP-C immunoprecipitated complex from Pten+/+ MEFs
981	imex:IM-11846_MI:0006	The results shown in Figures 3A and 3C indicate that the C-terminal domain of PTEN is required for its association with centromeres and CENP-C since the truncated mutant PTEN189 no longer interacts
982	imex:IM-11846_MI:0006	We wished to determine whether the PTEN-associated 140 kDa protein that was recognized by the anti-centromere antibody (Figure 2B) could in fact be CENP-C. This possibility was confirmed by using a CENP-C-specific antibody that detected the 140 kDa PTEN-associated protein in Pten+/+ MEFs
983	imex:IM-11847_MI:0006	immunoprecipitation of TPXL-1 resulted in copurification of the RSA complex, as judged by Western blot and mass spectrometry
984	imex:IM-11847_MI:0006	TPXL-1 and RSA-2 were immunoprecipitated with antibodies against the endogenous proteins.
985	imex:IM-11857_MI:0006	we observed that cyclin D1 KE-CDK4 complexes retained the ability to bind p27Kip1 (Figure 2D). Although less CDK4 was immunoprecipitated from the cyclin D1KE/KE lysates, as might be expected due to the decreased CDK4 expression in the knockin retinas, the relative amounts of cyclin D1 KE protein and p27Kip1 that coimmunoprecipitated with CDK4 were similar in the wild-type and cyclin D1KE/KE lysates. As expected, virtually no p27Kip1 coimmunoprecipitated with CDK4 from cyclin D12/2 retinas, confirming the requirement for cyclin D1 in p27Kip1 titration
986	imex:IM-11858_MI:0006	Immunoprecipitation analyses revealed the presence of abundant cyclin D1-CDK4 complexes in ErbB-2-driven mammary carcinomas
987	imex:IM-11858_MI:0006	In CDK4 null mammary glands that were stimulated by hormones to undergo lobuloalveolar development, cyclin D1 associated with CDK6, CDK2, and p27Kip1
988	imex:IM-11858_MI:0006	We found that, in wild-type glands, cyclin D1 associated with CDK4, CDK6, CDK2, and p27Kip1 (Figure 1B). In CDK4 null mammary glands that were stimulated by hormones to undergo lobuloalveolar development, cyclin D1 associated with CDK6, CDK2, and p27Kip1
989	imex:IM-11864_MI:0006	After further truncation up to Ser392 (265-392), the interaction with IRF9 was disrupted (Figure 3B, left panel) without apparently affecting its interaction with STAT2 (Figure 3B, right panel).
990	imex:IM-11864_MI:0006	Coimmunoprecipitation results revealed that IRF-DBD but not IRF9-DBD with K81R substitution associated with IRF9 either full-length or the C-terminal 118-393 fragment
991	imex:IM-11864_MI:0006	Consistently, IFNalpha failed to induce the interaction between IFNalphaR2 and IRF9 (Figure 3E) or IRF9 nuclear translocation (data not shown) in CBP-/- mouse embryonic fibroblast (MEF).
992	imex:IM-11864_MI:0006	IH2D (257-338) of IRF9 is responsible for IFNalphaR2 binding.
993	imex:IM-11864_MI:0006	In addition, both IFNalphaR2 and IFNalphaR1 were able to recruit p300 (Figures S1C and S1D).
994	imex:IM-11864_MI:0006	In contrast, STAT2 DBD acetylation seemed to be irrelevant to STAT2's interaction with IRF9 (Figure 6F, right panel)
995	imex:IM-11864_MI:0006	Indeed, we repeatedly detected a stable STAT1:STAT2 interaction, which was slightly diminished following IFNalpha treatment in HeLa cells (Figure 6H).
996	imex:IM-11864_MI:0006	In HeLa cells or mouse fibroblasts, CBP was associated with IFNalphaR2, and this association was enhanced upon IFNalpha treatment (Figures 1C and S1B).
997	imex:IM-11864_MI:0006	In HeLa cells or mouse fibroblasts, CBP was associated with IFNalphaR2, and this association was enhanced upon IFNalpha treatment (Figures 1C and S1B). Similarly, IRF9 and IFNalphaR2 also coprecipitated (Figure 1C).
998	imex:IM-11864_MI:0006	Myc-tagged forms of IFNalphaR2 C-terminal region as indicated were cotransfected with IRF9
999	imex:IM-11864_MI:0006	STAT2 DBD interacts with STAT1.
1000	imex:IM-11864_MI:0006	STAT3, which can also form heterodimer with STAT2 (Figure S3E).
1001	imex:IM-11864_MI:0006	The interaction between CBP and IFNalphaR2 detected in HeLa cells was confirmed by recovering IFNalphaR2 from anti-CBP precipitates prepared from 293T cells transiently transfected with HA-tagged IFNalphaR2 and HA-tagged CBP (Figure 1D)
1002	imex:IM-11864_MI:0006	this domain of STAT2 (1-314) and IRF9 coprecipitated
1003	imex:IM-11864_MI:0006	To estimate STAT2-K390R mutant on ISGF3 complex formation, Myc-tagged forms of IRF9 and STAT1 were cotransfected with Myc-tagged STAT2 wild-type or K390R mutant in STAT2 null U6A cells.
1004	imex:IM-11864_MI:0006	When both K399R and S400A were introduced, however, the activity of IFNalphaR2 in IRF9 interaction was severely affected (Figure 3C).
1005	imex:IM-11864_MI:0006	While STAT2 with a K384R or K419R substitution moderately weakened the STAT2 and STAT1 interactions, STAT2-K390R and to a lesser extent STAT2-K415R interacted more strongly with STAT1 (Figure 6F, left panel).
1006	imex:IM-11866_MI:0006	a high-molecular-weight ladder of p53-indicative of polyubiquitinated p53 species-was observed only in Mdm2+/+;p53/ MEFs, but not in Mdm2/;p53/ and Mdm2C462A/C462A;p53/MmEFs, indicating that theb Mdm2C462A mutant is unable to promote p53 polyubiquitination.
1007	imex:IM-11866_MI:0006	p53A135V was able to precipitate comparable amounts of wild-type and mutant Mdm2C462A protein. Thus, the mutant Mdm2C462A protein is fully capable of interacting physically with p53.
1008	imex:IM-11866_MI:0006	The p53ER protein, as well as L5 and L11, was clearly coimmunoprecipitated along with the Mdm2C462A protein
1009	imex:IM-11866_MI:0006	We believe that the high-molecular-weight ladders/smears observed in the Mdm2C462A mutant are polyubiquitinated Mdm2C462A protein, because they were identical to those from the wild-type Mdm2 and were enhanced by MG132 treatment.
1010	imex:IM-11867_MI:0006	Further immunoprecipitation experiments showed that RSUME could also interact with SUMO-1 (Figure 4B).
1011	imex:IM-11867_MI:0006	Immunoprecipitation experiments showed a direct interaction of RSUME with I&#954;B (Figure 5B).
1012	imex:IM-11875_MI:0006	Co-immunoprecipitation of CaM and rMBP with the BKCa channel from rat brain lysate.
1013	imex:IM-11875_MI:0006	Western blotting demonstrated rMBP co-precipitation with BKCa channel-specific antibody but not control IgG (Fig. 3B),
1014	imex:IM-11876_MI:0006	cyclin-dependent kinase 2 (CDK2) immunoprecipitations (IPs) were performed on hypoxic HCT116 and WT8 cells at 48 hr and tested for coprecipitated p21 and p27. We observed substantially increased levels of p21 associated with CDK2 in hypoxic HCT116 cells
1015	imex:IM-11876_MI:0006	cyclin-dependent kinase 2 (CDK2) immunoprecipitations (IPs) were performed on hypoxic HCT116 and WT8 cells at 48 hr and tested for coprecipitated p21 and p27. We observed substantially increased levels of p21 associated with CDK2 in hypoxic HCT116 cells, while less change was observed for p27.
1016	imex:IM-11876_MI:0006	cyclin-dependent kinase 2 (CDK2) immunoprecipitations (IPs) were performed on hypoxic HCT116 and WT8 cells at 48 hr and tested for coprecipitated p21 and p27. We observed substantially increased levels of p21 associated with CDK2 in hypoxic HCT116 cells, while less change was observed for p27. However, it should be noted that HCT116 cells express higher levels of p21 than p27. In direct contrast, p27 association with CDK2 was almost completely abrogated in hypoxic WT8 cells
1017	imex:IM-11876_MI:0006	hypoxic culture for 4 or 20 hr correlated with a substantial decrease in c-Myc coprecipitation with Sp1, Miz1, and Max in HCT116 cells and an increase in c-Myc coprecipitation with these proteins in WT8 cells, albeit less dramatically than the decrease seen in HCT116 cells
1018	imex:IM-11876_MI:0006	IP was also performed for Sp1, Miz1, and Max. As before, we observed decreased coprecipitation of these proteins with c-Myc in hypoxic HCT116 cells and increased coprecipitation in hypoxic WT8 cells
1019	imex:IM-11876_MI:0006	There was no difference in c-Myc/Max binding in any of these lines under normoxia
1020	imex:IM-11876_MI:0006	when HIF-2a overexpressing cell lines were incubated under hypoxia, a dose-dependent increase in c-Myc/Max binding was observed, correlating with the increase in HIF-2a/Max binding
1021	imex:IM-11876_MI:0006	When Mad1 IP was performed, the opposite result was observed: increased Mad1/Max association in hypoxic HCT116 cells and decreased association in hypoxic WT8 cells.
1022	imex:IM-11876_MI:0006	When the HIF-1a overexpressing cell lines and a vector control (V1) were incubated at 0.5% O2 for 20 hr, increasing levels of HIF-1a/Max binding correlated with decreasing c-Myc/ Max binding and HIF-2a/Max binding, despite similar levels of c-Myc and Max in whole-cell lysates.
1023	imex:IM-11877_MI:0006	However, among these proteins tested, only NALP1 associated with Bcl-XL and Bcl-2
1024	imex:IM-11877_MI:0006	When endogenous NALP1 was immunoprecipitated from untreated macrophages using anti-NALP1 antibody, endogenous Bcl-2 and Bcl-XL were associated with NALP1-containing immune complexes, while ASC was not (Figure 2B).
1025	imex:IM-11877_MI:0006	When endogenous NALP1 was immunoprecipitated from untreated macrophages using anti-NALP1 antibody, endogenous Bcl-2 and Bcl-XL were associated with NALP1-containing immune complexes, while ASC was not (Figure 2B). These macrophages evidently contain more Bcl-2 than Bcl-XL, which possibly accounts for the clearer association of Bcl-2 with NALP1 immunoprecipitates when compared to Bcl-XL. In contrast, when immunoprecipitated from MDP/ATP-treated (Figure 2B) or LPS/ATP-treated (Figure S1) macrophages, ASC was associated with NALP1-containing immune complexes, while Bcl-2 and Bcl-XL were not.
1026	imex:IM-11877_MI:0006	when immunoprecipitated from MDP/ATP-treated (Figure 2B) or LPS/ATP-treated (Figure S1) macrophages, ASC was associated with NALP1-containing immune complexes
1027	imex:IM-11881_MI:0006	immunoprecipitation using antibodies against either FcgRIIA, FcgRIIC, or CRP, but not IgG controls (data not shown) revealed that, on APR-1 cells that express both FcgRIIA and FcgRIIC, CRP was associated with both of these receptors
1028	imex:IM-11881_MI:0006	On MM1-144 cells that express FcgRIIB and FcgRIIC,CRPwas predominantly associated with FcgRIIC but not FcgIIB
1029	imex:IM-11882_MI:0006	Please note that the signals for tagged TAF3 are similar in the TBP and FLAG precipitates, while the signals for TAF1, TAF5 and TBP are weaker in the FLAG precipitates.
1030	imex:IM-11884_MI:0006	D645 cells transfected with &#916;C6 cIAP1 were treated with compound A for the indicated time in hours, and endogenous TNF-R1 immunoprecipitated from DISC lysates with Fc-TNF&#945; and bound proteins were examined by western blotting. Where indicated, blots were probed first with anti-cIAP1 and then reprobed with anti-RIP1.
1031	imex:IM-11891_MI:0006	After immunoaffinity purification of Flag-CP110, we eluted the resulting CP110-associated proteins with a Flag peptide, fractionated the eluate by SDS-PAGE (Figure 1A), and excised gel fragments which we subjected to proteolytic digestion and mass spectrometric (MS) sequencing. MS sequencing identified at least five known centrosomal and/or spindle pole proteins, including calmodulin (CaM).
1032	imex:IM-11891_MI:0006	To determine whether Cep97 and CP110 directly interact, we in vitro translated both proteins and performed CP110 immunoprecipitations, which resulted in very efficient recovery of both proteins, suggesting that the proteins most likely interact directly (Figure 1C). Since both CP110 and Cep97 are CaM-binding proteins, we tested the possibility that the CP110-Cep97 interaction was mediated by CaM in the reticulocyte lysate by performing in vitro binding assays with CP110 mutants harboring small deletions that abrogate CaM association (Tsang et al., 2006). These studies suggested that CaM was not required to bridge interactions between Cep97 and CP110, and likewise, Cep97 mutants that do not bind CaM retain the ability to interact with CP110 (Figure 1C, and data not shown).
1033	imex:IM-11891_MI:0006	To determine whether CP110 and Cep97 interact in vivo, we performed immunoprecipitations with affinity purified CP110 and Cep97 antibodies. Both CP110 and Cep97 were immunoprecipitated by CP110 antibodies, and reciprocal immunoprecipitations with Cep97 antibodies confirmed this physiological interaction(Figure 1E).
1034	imex:IM-11891_MI:0006	To determine whether CP110 and Cep97 interact in vivo, we performed immunoprecipitations with affinity purified CP110 and Cep97 antibodies. Both CP110 and Cep97 were immunoprecipitated by CP110 antibodies, and reciprocal immunoprecipitations with Cep97 antibodies confirmed this physiological interaction(Figure 1E). CP110 has been shown to associate with both CaM and centrin, and we therefore tested the ability of Cep97 to interact with a similar cohort of proteins. Although we readily detected CP110 in centrin immunoprecipitates, as expected (Tsang et al., 2006), we did not observe Cep97. Moreover, Cep97 failed to immunoprecipitate centrin, although CP110 and CaM were detected (Figure 1E, and data not shown), suggesting that CP110 associates with discrete centrin and Cep97 complexes.
1035	imex:IM-11891_MI:0006	We confirmed the interaction between Cep97 and CP110 by ectopically expressing Flag-tagged Cep97 and immunoprecipitating this protein using antibodies against CP110 (Figure S1B). Similarly, anti-Flag antibodies coprecipitated both Cep97 and CP110. In addition, Cep97 associates with CaM, an observation anticipated by the presence of an IQ domain.
1036	imex:IM-11893_MI:0006	Coimmunoprecipitation of p16 and MCM6 was observed when NP-18 cell extracts were immunoprecipitated with anti- MCM6, and immunoblotted with anti-p16 antibodies.
1037	imex:IM-11893_MI:0006	In vivo interaction of p16 with PCNA
1038	imex:IM-11902_MI:0006	Both endogenous CLOCK and BMAL1 coimmunoprecipitated with SIRT1 in extracts obtained from mouse liver nuclei (Figure 5A)
1039	imex:IM-11902_MI:0006	Fig. 5B
1040	imex:IM-11902_MI:0006	SIRT1 bound to CLOCK in a circadian manner with maximal binding around ZT4 (Figure 5F).
1041	imex:IM-11905_MI:0006	We confirmed that Cdh1 reassociates with Cdc27 (an APC/C core subunit) in human G2 cells subjected to genotoxic stresses,
1042	imex:IM-11909_MI:0006	Endogenous CLOCK:BMAL1 and SIRT1 interactions in the mice liver (B) and in cultured MEFs after serum shock
1043	imex:IM-11909_MI:0006	In coimmunoprecipitation experiments we reveal that SIRT1 interacts with CLOCK
1044	imex:IM-11911_MI:0006	Association of JAK2 with betac
1045	imex:IM-11911_MI:0006	We have determined the structure of the GM-CSF ternary complex revealing a 2:2:2 hexamer consisting of two Bc chains, two GMRa chains, and two GM-CSF molecules
1046	imex:IM-11914_MI:0006	Nectin1-Ig clearly precipitated gD
1047	imex:IM-11916_MI:0006	immunoprecipitation of EGFR with the C225 antibody coprecipitated SGLT1 with either WT-EGFR or kmtEGFR
1048	imex:IM-11916_MI:0006	we were able to coprecipitate SGLT1 with EGFR
1049	imex:IM-11918_MI:0006	GzmA interacts with Hsp70 and Hsp90,
1050	imex:IM-11923_MI:0006	Anti-Sec61&#946; immunoprecipitates were analyzed by immunoblotting with anti-BAP31 (top panel)
1051	imex:IM-11923_MI:0006	BAP31 associates with the MSD1 domain of CFTR
1052	imex:IM-11923_MI:0006	Endogenous BAP31 and Sec61&#946; were coimmunoprecipitated from both HeLa and KB cells
1053	imex:IM-11923_MI:0006	Interactions between TRAM and p20BAP31 were monitored in cotransfected cells as indicated.
1054	imex:IM-11923_MI:0006	The association of BAP31 with CFTR&#916;F508 was monitored by immunoblotting of anti-BAP31 immunoprecipitates with antibody against CFTR.
1055	imex:IM-11923_MI:0006	The associations between endogenous BAP31, Sec61&#946;, and CFTR were monitored by immunoblotting of anti-BAP31 immunoprecipitates,
1056	imex:IM-11924_MI:0006	Fmi coimmunoprecipitates Fz from inducible S2 cells.
1057	imex:IM-11934_MI:0006	Immunoblot analysis of anti-PML-RARa immunoprecipitates revealed the existence of endogenous complexes of PML-RARa with SUZ12, EZH2, and EED
1058	imex:IM-11934_MI:0006	We found that the PML-RARa AHT mutant retains the capability to interact with EZH2
1059	imex:IM-11935_MI:0006	In vivo interaction of SET with CK2, eIF2a, GP, and TCP-1b.
1060	imex:IM-11936_MI:0006	Co-precipitation of endogenous Mad2L2 and APC3.
1061	imex:IM-11953_MI:0006	Immunoblots of mitotic (M), G1, or G2 HeLa extracts subjected to immunoprecipitation with RanBP2 antibody and analyzed for coprecipitation of Topo IIalpha.
1062	imex:IM-11953_MI:0006	MEFs subjected to immunoprecipitation with RanBP2 antibody and analyzed for coimmunoprecipitation of Topo IIalpha
1063	imex:IM-11955_MI:0006	As shown in Figure 4C, eIF4AIII was coimmunoprecipitated with SKAR, and the interaction was not disrupted by RNase digestion.
1064	imex:IM-11955_MI:0006	SKAR coimmunoprecipitates endogenous CBP80
1065	imex:IM-11956_MI:0006	As expected if the increased reactivity of eIF3a with myc-Upf1R(G495R/G497E) relative to myc-Upf1R(WT) was due to Upf1 phosphorylation
1066	imex:IM-11959_MI:0006	the anti-Ub antibody precipitated a protein that can be detected by the anti-Myc antibody and comigrates with the modified Rad17-Myc band from the whole-cell extract
1067	imex:IM-11960_MI:0006	In cells that were stably transfected with a tetracycline-inducible RIPK1-shRNA construct, silencing of RIPK1 with tetracycline abolished the interaction between caspase-8 and FADD
1068	imex:IM-11960_MI:0006	Smac mimetic induces more FADD/caspase-8 complex formation than cycloheximide
1069	imex:IM-11960_MI:0006	We noticed that only a small fraction of RIPK1 and FADD from the total cellular pool was associated with caspase-8 after the TNF-a plus Smac mimetic treatment
1070	imex:IM-11962_MI:0006	To assess potential physical interactions among endogenous &#946;-catenin, Rac1, and JNK, coimmunoprecipitation experiments were performed using cytosolic versus nuclear fractions from ST2 cells
1071	imex:IM-11978_MI:0006	Consistent with all of these effects, we found that the R1 chain of the type I IFN receptor and Axl physically associate in BM-DCs, in a TAM-ligand-dependent fashion, and can be reciprocally coimmunoprecipitated (Figure 4J).
1072	imex:IM-11978_MI:0006	TRAF3 was immunoprecipitated, and its ubiquitylation was assessed by immunoblotting with ubiquitin (top blot) and TRAF3 (bottom blot) antibodies.
1073	imex:IM-11978_MI:0006	TRAF6 was immunoprecipitated and analyzed by immunoblotting with ubiquitin (top blot) and TRAF6 (bottom blot) antibodies.
1074	imex:IM-11980_MI:0006	RelA was detected in immunoprecipitates prepared from untransfected 293T cells using an anti-LZAP serum but not in precipitates using a preimmune rabbit serum
1075	imex:IM-11980_MI:0006	When coexpressed, LZAP was readily detected from RelA immunoprecipitates and RelA was reciprocally coprecipitated using LZAP antibody
1076	imex:IM-11982_MI:0006	Association of endogenous Jmjd3 with RbBP5-containing complexes.
1077	imex:IM-11982_MI:0006	RbBP5 coimmunoprecipitated about 10% of the endogenous Ash2L, irrespective of LPS stimulation. A comparable percentage of Jmjd3 was immunoprecipitated selectively from cells treated with LPS, indicating that newly synthesized Jmjd3 is incorporated in RbBP5-containing complexes
1078	imex:IM-11990_MI:0006	Although TPX2 was not enriched in anti-BRCA1 IPs (Figure 6A), an identical experiment performed with TPX2 Ab led to specific coimmunoprecipitation of BRCA1/BARD1 (Figure 6B, lanes 5 and 6 versus 1 and 2).
1079	imex:IM-11990_MI:0006	BRCA1/BARD1 Interacts with Spindle-Pole-Organizing Proteins
1080	imex:IM-11990_MI:0006	BRCA1 immunoprecipitates (IPs) for the presence of TPX2, NuMA, and XRHAMM. Both NuMA and XRHAMM were significantly enriched in these fractions compared to control IPs
1081	imex:IM-11990_MI:0006	These results imply that nearly all of the BRCA1 and BARD1 in Xenopus egg extracts exists in a heterodimeric complex throughout the cell cycle.
1082	imex:IM-11994_MI:0006	Substitution of either Y12 or T17 results in a dramatic reduction of covalent zz dimer formation.
1083	imex:IM-11995_MI:0006	Photocrosslinking analysis revealed that both ILMEKIHKV and IDMEKIHK peptides (high- and low-affinity peptides for A2.1, respectively) (Rammensee et al., 1999) can bind TAP, PDI, and PDI-abb0, but not PDI-ab
1084	imex:IM-11995_MI:0006	These results demonstrate that PDI is a component of the peptide-loading complex irrespective of cell type.
1085	imex:IM-11995_MI:0006	We confirmed the identity of the TAP-associated components by reprecipitating anti-TAP1 immunoprecipitates from digitonin lysates of radiolabeled HeLa cells with the indicated antibodies (Figure 1B). TAP1, TAP2, tapasin, class I heavy chain, calreticulin, ERp57, and PDI, but not calnexin, were positively identified by reprecipitation (Figure 1B).
1086	imex:IM-11995_MI:0006	we purified TAP complexes from digitonin lysates of HeLa cells. Both silver staining and subsequent analysis by tandem mass spectrometry (MS/MS) revealed that several proteins, including calreticulin, tapasin, MHC class I heavy chain, b2m, and Ig g H chain, specifically associated with TAP (Figure 1A). By MS/MS analysis of the 58 kDa protein band, we found that this band was a mixture of ERp57 and PDI.
1087	imex:IM-11999_MI:0006	An immunoprecipitation using an antibody against RORa coimmunoprecipitated ATXN1 from a lysate prepared from a normal mouse cerebellum
1088	imex:IM-11999_MI:0006	Coimmunoprecipitations using cerebella extracts from wild-type mice indicated that endogenous ATXN1 and Tip60 do interact
1089	imex:IM-11999_MI:0006	Figure 5E shows that more ATXN1[82Q] was coimmunoprecipitated with Tip60 than was ATXN1[30Q]
1090	imex:IM-11999_MI:0006	RORa coimmunoprecipitated with the anti-ATXN1 antibody 11750
1091	imex:IM-12000_MI:0006	CFTR immunoprecipitates that were not observed in control immunoprecipitates from cell lines lacking CFTR or in immunoprecipitates prepared from CFTR-expressing cell lines using nonspecific antibody provide us with a comprehensive network of CFTR-interacting components (Figure 1; see also Tables S1-S7 in the Supplemental Data available with this article online), which we refer to as the CFTR interactome.
1092	imex:IM-12000_MI:0006	The CFTR Interactome
1093	imex:IM-12001_MI:0006	when BIM or BAK was immunoprecipitated from OCI-AML3 cells, coimmunoprecipitation of MCL-1 was unimpaired in ABT-737-treated cells.
1094	imex:IM-12029_MI:0006	Caspase-8 recruitment to CD95 increased upon stimulation with CD95L-T4 in LN18 and J16 cells but not in T98G cells
1095	imex:IM-12029_MI:0006	we identified Yes as the Src family member that links CD95 to PI3K
1096	imex:IM-12029_MI:0006	Whereas upon stimulation with CD95L-T4 recruitment of FADD to CD95 increased in LN18 cells, no increase was detected in T98G cells
1097	imex:IM-12030_MI:0006	immunoblot analysis showed that Btk coimmunoprecipitated with BLNK in BMMs in the presence of RANKL, but the association was abrogated in DAP12&#8722;/&#8722;FcRgamma&#8722;/&#8722; cells (Figure 5B).
1098	imex:IM-12034_MI:0006	Coimmunoprecipitation experiments in primary keratinocytes revealed that TPA facilitated the association of endogenous Cyld with endogenous Bcl-3 already 15 min after TPA treatment
1099	imex:IM-12042_MI:0006	Coimmunoprecipitation assays demonstrated a TGFbdependent interaction between endogenous Smad4 and C/EBPb
1100	imex:IM-12048_MI:0006	Immunoblots of RelA coimmunoprecipitates prepared from wild-type (left panel) or I B / /var epsilon-deficient (right panel) MEF lysates revealed RelA association with I B , p50, p100, and p105 proteins.
1101	imex:IM-12048_MI:0006	Increased p52 association with p100 following LT R signaling.
1102	imex:IM-12048_MI:0006	RelA protein associated with p105 and p100 were examined by RelA immunoblotting of immunoprecipitates from wild type (left panel) or I B-deficient (right panel)
1103	imex:IM-12048_MI:0006	RelA protein associated with p105 and p100 were examined by RelA immunoblotting of immunoprecipitates from wild type (left panel) or I
 B deficient (right panel)
1104	imex:IM-12048_MI:0006	The fractions of cellular p100 or p105 bound to RelA or RelB were examined by immunoblots of RelA or RelB immunoprecipitate (IP)
1105	imex:IM-12055_MI:0006	analyzed the ubiquitination status of the immunoprecipitated Pax3 protein. In cell extracts, a small fraction of the protein was monoubiquitinated and, again, no polyubiquitination could be detected
1106	imex:IM-12056_MI:0006	BIM was present in high levels in SU-DHL4 and SU-DHL6, and it was likewise sequestered in a complex with BCL-2.
1107	imex:IM-12059_MI:0006	preliminary experiments suggest that the ability of Twist proteins to prevent the Ras-mediated activation of p16INK4A might be associated with their ability to interact with the Ras effector Ets2
1108	imex:IM-12065_MI:0006	Indeed, endogenous CIP2A and PP2Ac coimmunoprecipitated with the endogenous PR65 (Figure 1C).
1109	imex:IM-12128_MI:0006	The cell lysates from HeLa cells were prepared and immunoprecipitated with normal rabbit IgG or anti-NML antibody and immunoblotted using antibodies against SIRT1 and SUV39H1.
1110	imex:IM-12131_MI:0006	The Mre11+ and Mre11H129N proteins associate with equal quantities of endogenous NBS1 and Rad50.
1111	imex:IM-12133_MI:0006	Further, MRCK&#945; and &#946; from rat brain lysates coimmunoprecipitated with LRAP35a (Figure 2B).
1112	imex:IM-12133_MI:0006	Identification of MRCK-Interacting LRAP35a
1113	imex:IM-12133_MI:0006	The immunoprecipitates were immunoblotted with anti-MRCK&#946;, anti-MYO18A, or anti-LRAP35a antibody.
1114	imex:IM-12135_MI:0006	As shown in Figure4C, keratinocyte ACF7 specifically coimmunoprecipitated with +tip proteins EB1, Clasp1, and Clasp2,
1115	imex:IM-12136_MI:0006	To test whether the interaction of Baz with Par-6 and aPKC is inhibited by Lgl, we analyzed Par-6 immunoprecipitates from larval brains expressing Baz-GFP.
1116	imex:IM-12140_MI:0006	The 6S peak fraction, aside from pICln, contained the Sm proteins D1/D2 and E/F/G in apparently stoichiometric amounts
1117	imex:IM-12140_MI:0006	These approaches resolved the 20S peak as a complex formed by pICln, PRMT5, WD45, and all Sm proteins
1118	imex:IM-12145_MI:0006	Indeed, these immunoprecipitation studies demonstrated that E6 and CYLD interact weakly in SiHa and HeLa cells under normoxia (Figure 7B, lanes 2 and 6). Importantly, the interaction was markedly augmented by hypoxia (Figure 7B, compare lanes 2-4 and lanes 6-8). As a positive control, we coimmunoprecipitated p53 with the E6 antibody (Figure 7B)
1119	imex:IM-12146_MI:0006	Endogenous ternary complex of &#946;-catenin/TCF4/RUNX3 in HCT116 and SW620 cells
1120	imex:IM-12148_MI:0006	Scribble immunoprecipitants were analyzed for coimmunoprecipitated &#946;PIX and GIT1.
1121	imex:IM-12149_MI:0006	Coimmunoprecipitation of endogenous Nezha and PLEKHA7
1122	imex:IM-12156_MI:0006	conversely, SIRT6 was detected in IPs of endogenous RELA (Figure S1)
1123	imex:IM-12156_MI:0006	Endogenous SIRT6 and RELA proteins interact
1124	imex:IM-12166_MI:0006	Accordingly, HDAC6 interacted with Cdc20 endogenously in neurons (Figure 5C)
1125	imex:IM-9153_MI:0006	APPL1 presence within the ADIPOR1 collection and confirmed interaction
1126	10075709_MI:0007	HA-p14 was co-precipitated with Flag-p160 (lane 8), demonstrating their interaction in vivo.
1127	10078207_MI:0007	We could copurify untagged BAF155 and BAF170 via association with HA-INI1 following mixed infection (Figure 1A, lane 5), implying that these subunits can form a complex.
1128	10078207_MI:0007	we mixed an Sf9 nuclear extract containing Flag-tagged BRG1 (F-BRG1) with nuclear extract containing HA-INI1 and untagged BAF155 and BAF170 and found that we could copurify all four proteins by immunopurification based on the Flag epitope ( Figure 1B).
1129	10220385_MI:0007	HDAC4 coimmunoprecipitates with Rbp48 and HDAC3, while none of the other proteins were apparent.
1130	10220385_MI:0007	HDAC5 associates only with HDAC3, though it is possible that the expression levels were too low to detect other associated factors.
1131	10220385_MI:0007	To determine whether HDAC4, HDAC5, and HDAC6 associated with the same proteins in vivo, a series of coimmunoprecipitation experiments was performed. Immunoprecipitates were probed with alpha -CHD4, alpha -mSin3A, alpha -MTA, alpha -RbAp48, alpha -HDAC1, and alpha -HDAC3 antibodies (Fig. 5B). The HDAC1 sample contains bands corresponding to all proteins with the exception of HDAC3, as anticipated.
1132	10231394_MI:0007	mPER1 specifically co-immunoprecipitated with fulllength mTIM from nuclear extracts (Fig. 4B).
1133	10329624_MI:0007	Anti-Myc antibodies immunoprecipitated c-Myc-tagged Tap42, Pph21 and Pph22, but not Tpd3 or Cdc55 (Figure 3C).
1134	10409688_MI:0007	Co-immunoprecipitation of eIF4E with HA epitope-tagged eIF4G from crude lysates has been shown to be sensitive to mutations that disrupt this interaction.
1135	10436016_MI:0007	This experiment confirms the importance of the C terminus of Mad1p for its Mad2p interaction: the smallest fusion protein capable of binding to Mad2p contained residues 529-749 (pKH603), and deleting the last 35 amino acids (pKH609) abolished that ability.
1136	10542152_MI:0007	The NPH3C2-CBD-dependent immunoprecipitation of NPH1 was not the result of nonspecific interaction with CBD, as a BTB/ POZ-containing NPH3-CBD fusion protein did not promote a similar immunoprecipitation response
1137	10602478_MI:0007	To provide independent evidence of the PRUNE/ nm23-H1 interaction, in vitro translated and labelled HA tagged-PRUNE and FLAG tagged-nm23-H1 were mixed and a low stringency co-immunoprecipi-tation was performed using anti-HA or anti-FLAG antibody and proteinA-Sepharose.
1138	10611319_MI:0007	Reciprocal coimmunoprecipitation of IP3R and TRP. T3 9 or T6 12 cells
1139	10656681_MI:0007	radiolabeled TRX SET, ALL-1 SET and ASH1 SET polypeptides co-immunoprecipitated with the T7-tagged relevant SET fragments
1140	10656681_MI:0007	To demonstrate in vivo binding in transfected cells, TRX, ALL-1 and ASH1 SET polypeptides were tagged with the T7 and hemagglutinin (HA) epitopes, and plasmids encoding appropriate partners were transiently cotransfected into COS cells. The proteins produced were examined for co-precipitation by Western blotting. In each case, significant co-precipitation was observed
1141	10677492_MI:0007	As shown in Fig. 5B, wild-type Ost4HAp was found to have precipitated with the Ost3mycp.
1142	10704439_MI:0007	Fig 5 a shows that a Bub3p immunoprecipitate contained wild-type Mad3p, and that the homology region I mutation had no effect on this binding, but that the single amino acid change in the homology region II mutant was sufficient to abolish Bub3p binding.
1143	10704439_MI:0007	Wild-type, but not homology region I mutant, Mad3p was coimmunoprecipitated with Cdc20p
1144	10713067_MI:0007	or conversely, the monoclonal anti-HA antibodies coimmunoprecipitated Lcb1p and Lcb2p along with Tsc3p-HA (Fig. 6D).
1145	10733566_MI:0007	coimmunoprecipitation experiments were performed with HEK293 cells transiently transfected with IKKb, IKKa-DCm, or IKKa and NIK. As shown in Fig. 9A (top), NIK coimmunoprecipitated with each polypeptide
1146	10733566_MI:0007	HA epitope-tagged IKKa-DCm and FLAG epitope-tagged NIK were produced by in vitro translation in the presence of [35S]methionine. These proteins were preincubated for 15 min at 30 C prior to selective immunoprecipitation with either anti-HA or anti-FLAG antibodies. IKKa-DCm associates with NIK in this assay, irrespective of whether NIK or IKKa-DCm was immunoprecipitated first.
1147	10733566_MI:0007	IKKb coprecipitated with IKKa and its IKKa-DH isoform
1148	10747865_MI:0007	The ability of antibody against the Xpress epitope to precipitate a complex of THEG and CCTe suggests that the two proteins interact in the cytoplasm
1149	10749931_MI:0007	Immunoblotting with anti-HA antibody revealed specific coimmunoprecipitation of Brn1p with Smc2p only when Myc-tagged Smc2p was present (Figure 5).
1150	10757791_MI:0007	coenrichment of PcG proteins with HA-ESC by immunoaffinity chromatography
1151	10866661_MI:0007	Lysates were immunoprecipitated with anti-Gal4-DBD and then probed for the presence of p300. Immunoblotting revealed the association of p300 with the AD1-containing fragments (AIB1 556 to 1420 and 578 to 1131) but not with AIB1 1210 to 1420, expressing only the AD2 domain.
1152	10888666_MI:0007	The same result was obtained when T7- AtTLG2b was immunoprecipitated from transgenic plants with T7 antibodies (Figure 5C). Thus, it seems likely that AtVTI1b, and not AtVTI1a, is present in complexes containing AtVPS45 and AtTLG2a or -b.
1153	10899120_MI:0007	For Mpc54p, we identified conditions (salt concentration, ion chelators) for the SPB fraction under which only a subset of SPB components, in this case Nud1p, co-precipitated (Figure 4B). None of the other SPB components tested (Cnm67p, Spc42p, Kar1p, Spc72p, Spc97p, Spc98p) co-precipitated under these conditions (not shown). This confirms the two-hybrid interaction of Mpc54p with Nud1p and points to a direct interaction of Mpc54p with Nud1p.
1154	10915743_MI:0007	Myc-E12 was coprecipitated with full-length HHM
1155	10915743_MI:0007	Myc-E12 was coprecipitated with full-length HHM as well as positive controls (FLAG-Id2
1156	10915743_MI:0007	Myc-E12 was coprecipitated with full-length HHM as well as positive controls (FLAG-Id2 and FLAG-MyoD),
1157	10920254_MI:0007	Co-Precipitation of the AcrA and AcrB Proteins
1158	10930412_MI:0007	AR protein was detected in anti-FLAG immunoprecipitates from cells co-transfected with AR and FLAG-HBO1
1159	10984058_MI:0007	Finally, cells expressing an haemagglutinin (HA)-epitope-tagged copy of Kar9, revealed that endogeneous Myo2 co-immunoprecipitates with HA-Kar9 (Fig. 3b).
1160	11006275_MI:0007	co-immunoprecipitation of flag-HDAC and RIP140.
1161	11006275_MI:0007	where cells were co-transfected with HDAC3 plus an empty vector or a flag-RIP vector, the anti-HDAC3 antibody detected a band of approximately 52 kDa in the precipitate of the flag-RIP plus HDAC3- transfected culture
1162	11022036_MI:0007	CR6 C-terminal (76-159 aa) immune complexes contained PCNA.
1163	11022036_MI:0007	HA immunocomplexes brought down PCNA from cells transfected with pcDNA3.1(2) encoding for C-terminal but not N-terminal CR6
1164	11022036_MI:0007	immune complexes of peptides corresponding to PCNA N-terminal (1-46 aa) and middle (87-127 aa) but not the C-terminal (224-261 aa) domains also contained CR6.
1165	11084035_MI:0007	HA-tagged Dlxin-1 (HA-Dlxin1) was coimmunoprecipitated with FLAG-tagged Dlx5 (F-Dlx5), Dlx7 (F-Dlx7), Msx2 (F-Msx2), and Dlxin-1 (F-Dlxin1), but not when the FLAG peptide was included in the precipitation
1166	11106648_MI:0007	mutation at tyrosine residues 66 and 153 alone (Fig. 4A) or in combination (not shown) have no effect on binding of PTP1B to N-cadherin.
1167	11108847_MI:0007	However, both HA-AtE2F proteins co-precipitated reproducibly with c-myc-tagged AtDPa
1168	11108847_MI:0007	However, both HA-AtE2F proteins co-precipitated reproducibly with c-myc-tagged AtDPa (Fig. 2B, lanes 1 and 2) and AtDPb (Fig. 2C, lanes 3 and 4).
1169	11108847_MI:0007	These data indicate that other carboxyl-terminal regions of AtDPa are required for the stable interaction with AtE2Fb.
1170	11108847_MI:0007	To con¢rm this hypothesis, a deletion mutant of AtDPb (182^ 263) was constructed and, as expected, it could bind to AtE2Fb
1171	11112409_MI:0007	Daxx was detected as hyperphosphorylated 110 kDa band by Western blot analysis with rabbit anti-Daxx antibody after immunoprecipitation with anti-FLAG antibody in pFLAG-CMV-2/ sentrin transfected BOSC23 cells.
1172	11117257_MI:0007	Co-immunopurification of in vitro transcribed and translated T7 tagged-eIF(iso)4E-LOX2 complex with anti T7 tag antibody.
1173	11124122_MI:0007	In addition, when anti-E(Z), anti-RPD3 and anti-p55 antibodies were used for immunoprecipitation, FLAG-ESC was detected in the immunoprecipitates
1174	11124122_MI:0007	In contrast, the FLAG-ESC and E(Z) present in the transgenic extract (lane 4) were recovered by anti-FLAG affinity gel (lane 6). Although most of the p55 was present in the unbound fraction from the anti-FLAG affinity gel, a substantial amount of p55 was detected in the bound fraction eluted with FLAG peptide
1175	11124122_MI:0007	On an anti-FLAG M2 agarose affinity gel column, p55 is present in the bound fraction and is co-eluted by FLAG peptide along with FLAG-ESC and E(Z)
1176	11124122_MI:0007	We confirmed the presence of ESC and E(Z) in the complex both by western blot analysis of the purified fraction and by peptide sequencing. One of the new proteins identified was the histone-binding protein p55 (also known as CAF-1 p55 and Nurf-55).
1177	11156409_MI:0007	The caspase-2L-Pro/procaspase-2L interaction appeared weaker than the caspase-2L-Pro/RAIDD interaction, both in the yeast 2-hybrid assay and in cotransfected cells
1178	11163211_MI:0007	Immunoprecipitation analysis indicated that Cig2AAA was unable to bind Cdc2 (Figure 7A, lane 5).
1179	11163770_MI:0007	As shown in Fig. 1B, HA-LZK was co-immunoprecipitated with His-LZK, indicating that LZK forms homo-dimers or oligomers in cells.
1180	11274192_MI:0007	Immunoprecipitation of Ctr5-myc4 resulted in the co-immunoprecipitation of Ctr4-FLAG2 (Fig. 7B, top panel, lane 8) and immunoprecipitation of Ctr4-FLAG2 co-fractionated with Ctr5-myc4 (Fig. 7B, bottom panel, lane 8)
1181	11278694_MI:0007	The deletion of the C-terminal part of the STRA13 in the 1-299 mutant abolished the pSTRA13/pUBC9 interaction (Fig. 3B, line 7). Subsequent deletions of the N-terminal bHLH domain or three adjacent a-helices (Fig. 3, lines 3-6 and 8) did not lead to binding abrogation. Therefore, the region between amino acid residues 299 and 412 is absolutely required for the pSTRA13/pUBC9 interaction, whereas the bHLH domain and all three a-helices were dispensable.
1182	11279037_MI:0007	Association of TAF72 and TAF73 with TBP.
1183	11279037_MI:0007	Association of TAF72 with Gcn5.
1184	11279037_MI:0007	co-immunoprecipitation of TAF73 with TAF72.
1185	11328817_MI:0007	Western blot analysis of anti-FLAG M2-immunoprecipitated cell extracts, with anti-myc 9E10, detects the Evi1myc fusion protein only in cell extracts containing both Evi1myc and FLAGmCtBP2 epitope-tagged proteins (Fig. 2B), demonstrating the two proteins can interact in mammalian cells.
1186	11377421_MI:0007	Co-immunoprecipitation of CASK-GUK-Myc with rabphilin3a-FLAG.
1187	11431700_MI:0007	Tbx5 was co-immunoprecipitated with Nkx2-5
1188	11438682_MI:0007	Coimmunoprecipitation of FBP17 and SNX2.
1189	11448933_MI:0007	In these experiments, p6 cells were incubated for 6 h with CM containing 486/STOP as described for Fig. 7. Cell lysates were made and immunoprecipitated with anti-FLAG antibody, and the blots were developed with an antibody to the b subunit of the IGF-IR. Lanes 2 and 3 show that the b subunit of the IGF-IR coprecipitates with an anti-FLAG antibody, and the amount precipitated is proportional to the amount of 486/STOP in the CM
1190	11495919_MI:0007	ASK1 was associated with Daxx.
1191	11560889_MI:0007	Rhp55p:Rhp57 complexes were also identified in reciprocal immunoprecipitation experiments using anti-HA antibodies to precipitate Rhp55 protein (Figure 1C, lanes 6).
1192	11726501_MI:0007	As shown in Figure 1A, Bub3HA3 immunoprecipitates from extracts of the latter strain contained Cdc20myc18 and vice versa, suggesting that the two proteins physically interact in vivo.
1193	11726501_MI:0007	As shown in Figure 5B, HA-tagged Bub3-WDd mutant proteins were no longer able to interact with Mad2, Mad3 and Cdc20 in co-immunoprecipitation experiments, although the mutant protein levels were comparable to those of wild-type Bub3 (Figure 5B).
1194	11726501_MI:0007	Cdc20myc18, Mad2 and Mad3 co-immunoprecipitated with Bub3HA3 in all kinetochore mutants, whereas, as expected, Bub3HA3-Cdc20myc18 interaction was abolished by deletion of MAD2, which did not affect association of Bub3HA3 to Mad3, as previously shown
1195	11726501_MI:0007	Conversely, Cdc20myc18 immunoprecipitates contained Bub3HA3 and Mad2, but not Mad1, suggesting that either Mad1 is not part of the Cdc20-Bub3 complex, or the levels of Mad1 bound to Cdc20 are below the detection limit.
1196	11726501_MI:0007	We also found that, in addition to Cdc20myc18, both Mad1 and Mad2 associated with Bub3HA3 and inter action increased upon nocodazole treatment (Figure 1B).
1197	11731480_MI:0007	Asf1 was coimmunoprecipitated with both Sas2 and Sas4 (Fig. 7A).
1198	11731480_MI:0007	For coimmunoprecipitation of myc-Sas4 with HA-Sas5,
1199	11731480_MI:0007	In coimmunoprecipitation experiments, Cac1 immunoprecipitated with both Sas2 and Sas4 (Fig. 5A).
1200	11731480_MI:0007	myc-Sas4 coimmunoprecipitated with Sas2 and HA coimmunoprecipitated Sas5
1201	11731480_MI:0007	Sas2 coimmunoprecipitated with myc-Sas4 and HA-Sas5.
1202	11820777_MI:0007	We further confirmed these associations with a coimmunoprecipitation assay in fission yeast (Fig. 2C). Myc-tagged full-length Pof10 and a mutant Pof10 lacking the NH2-terminal domain (DN) or F-box domain (DF) were coexpressed with HA-tagged Skp1 in S. pombe, and cell lysates were subsequently subjected to immunoprecipitation with antibodies to the HA tag.
1203	11823419_MI:0007	We also performed immunoprecipitation with an HA-tagged version of Vph1p, an integral component of the V0 sector of the V-ATPase. Vtc1p and Vtc4p were recovered in association with Vph1p (Figure 1C).
1204	11877381_MI:0007	An interaction between GEX-2 and GEX-3 was also observed in yeast cells expressing HA-GEX-2 and myc-GEX-3 by reciprocal coimmunoprecipitation experiments (Fig. 6B).
1205	11907036_MI:0007	Deletion of either regions 1, 2, or 3 reduced co-immunoprecipitation with c-Myc-tagged PEK-Delta C to between 10 and 22% of that measured for full-length PEK.
1206	11909965_MI:0007	Mad3-GFP was immunoprecipitated from strains containing Bub3-Myc.
1207	11909965_MI:0007	Mad3p interacts with Mad2p and the Cdc20p homologue Slp1p in checkpoint-arrested cells.
1208	11959851_MI:0007	Msx2, Praja1, and Dlxin-1 form molecular complexes in the cells and that endogenous Dlxin-1 may participate in the formation of this complex
1209	11959851_MI:0007	Praja1 was co-precipitated with Msx2 either with (lane 5) or without (lane 4) Dlxin-1 transfection.
1210	11959851_MI:0007	Wild-type Praja1 bound to Dlxin-1 in vivo when overexpressed in HEK293 cells (Fig. 3B, lanes 1 and 2).
1211	11976948_MI:0007	Co-immunoprecipitation of FLAG-Dcyp33 with GAL4-trxPHD1-3 from SL1 Drosophila cell extracts using an anti-GAL4 antibody,
1212	11988016_MI:0007	After immunoprecipitation using anti-FLAG antibody affinity resin, specific binding between PCD17 and MRG X in transfected cells was confirmed by im-munoblot with anti-Purkinje cell antibodies (anti-Yo)
1213	12006645_MI:0007	SpSld3-FLAG, SpMcm6, and SpCdc45 in the immunoprecipitates were analyzed by immunoblotting.
1214	12032852_MI:0007	In vitro labeled MYC-tagged DTrc8578 - 809 and HA-tagged DVhl proteins were mixed and immunoprecipitated (Figure 4b). The precipitation of HA-DVhl with anti-HA antibodies co-precipitated MYC-DTrc8
1215	12032852_MI:0007	When tested for possible physical interactions, we found JAB1 could be co-immunoprecipitated with HA-tagged wild type VHL from WT8 but not from PRC3 cells that lack HA-tagged VHL
1216	12039038_MI:0007	HA-ESC was immunoprecipitated from HA-esc extracts using the HA.11 MAb. An immunoblot of the precipitated proteins was probed with anti-dSAP18 antibodies, revealing co-immunoprecipitation of dSAP18
1217	12065423_MI:0007	Figure 6A shows that SMC was co-precipitated with ScpA-YFP and with ScpB-YFP,
1218	12080051_MI:0007	SKIP was co-imunoprecipitated with SPHK1
1219	12119386_MI:0007	It was found that Erg28p and Erg27p reciprocally coimmunoprecipitated (Fig. 5B);
1220	12150928_MI:0007	BAK1 Directly Interacts with BRI1 in Plants
1221	12150928_MI:0007	BRI1 Is Capable of Interacting with BAK1 in Plants
1222	12150928_MI:0007	This result indicates that the full-length BRI1 interacted with the full-length BAK1 in yeast.
1223	12165861_MI:0007	proteins from Cos-1 cells cotransfected by HA-tagged TACC1l with myc-tagged LSM7 or Myc-tagged SmG were immunoprecipitated with either anti-myc or anti-TACC1-C antibody and Western blotted. In both cases, blotting with the anti-HA antibody revealed TACC1l protein and blotting with the myc antibody revealed LSM7 or SmG.
1224	12165861_MI:0007	proteins from Cos-1 cells cotransfected by HA-tagged TACC1l with myc-tagged LSM7 or myc-tagged SmG were immunoprecipitated with either anti-myc or anti-TACC1l-C antibody and Western blotted. In both cases, blotting with the anti-HA antibody revealed LSM or SmG
1225	12167173_MI:0007	We had previously mapped the domain of Pop2p that interacts with Pop1p to an N-terminal fragment consisting of the first 241 amino acids and lacking the F-box ([20], Fig. 6B, lane 8). In co-immunoprecipitation experiments with overexpressed proteins, this fragment also bound to an N-terminal piece containing the first 402 residues of Pop1p (Fig. 6B, lane 12). Thus, the Pop1p-Pop2p interaction is mediated by their N-terminal domains. A further truncation mutant mapped the Pop2p binding domain to a region between residues 228 and 402 of Pop1p (Fig. 6B, lanes 9,10).
1226	12167173_MI:0007	We therefore tested the possibility that Pop2p can be tethered to the SCF core complex independently of its F-box via an interaction with Pop1p. Consistent with this hypothesis, co-immunoprecipitation experiments of overexpressed proteins revealed that the Pop1p-Pop2p interaction occurs independently of the F-boxes of both Pop1p and Pop2p (Fig. 6A).
1227	12196526_MI:0007	when p65PI3K and p85 regulatory subunits were immunopurified with anti-HA Ab, both subunits recruited similar amounts of SHP-1
1228	12223483_MI:0007	AMY-1-HA, on the other hand, was detected in the immunoprecipitate from FLAG-tagged AAT-1alpha -transfected cells with an anti-HA antibody
1229	12223483_MI:0007	First, binding of S-AKAP84 to either GST-AMY-1
1230	12223483_MI:0007	When the amount of GST-AMY-1 in a reaction mixture containing T7-AAT-1alpha , FLAG-S-AKAP84, and GST-AMY-1 was increased, it was observed that a constant amount of T7-AAT-1alpha  was precipitated (Fig. 5C, lanes 5-8), suggesting that AMY-1 and AAT-1alpha  do not competitively bind to S-AKAP84 but, rather, that they both make a ternary complex with S-AKAP84.
1231	12368503_MI:0007	Immunoblotting of the eluted matrix-bound proteins and samples of total protein extracts with anti-HA and anti-c-Myc antibodies showed that SPDS1-myc copurified with an equimolar amount of SPDS2-HA
1232	12368503_MI:0007	Similarly, SPDS2-myc immunoprecipitated an equimolar amount of SPMS-HA.
1233	12379796_MI:0007	The proteins encoded by AtCstF-64 and AtCstF-77 interact with each other. 35[S]-methionine-labelled in vitro translation products were immunoprecipitated as previously described
1234	12417715_MI:0007	hDcp1a and hDcp2 interact in an RNA-independent manner.
1235	12417715_MI:0007	hDcp1a and hDcp2 interact with the NMD protein hUpf1.hUpf1 interacts with the other hUpf proteins, hUpf2, hUpf3a, and hUpf3b.
1236	12417715_MI:0007	In contrast, anti-hUpf3b antibodies depleted both of the homologous hUpf3b and hUpf3a proteins as well as hUpf2 (Fig. 6C, lane 6, lower four panels).
1237	12417715_MI:0007	Passage of cell extracts over anti-hUpf1 or antihUpf2 antibody columns resulted in complete depletion of endogenous hUpf1 or hUpf2 proteins, respectively, whereas the other hUpf proteins were affected twofold or less (Fig. 6C, lanes 4 and 5, lower five panels).
1238	12417715_MI:0007	Western blot for Myc-tagged hDcp1a, hDcp2, or hnRNPA1, transiently expressed in HEK293 cells together with an empty vector (lanes 1 and 2) or a plasmid encoding FLAG-tagged hUpf1 (lane 3) and subjected to anti-FLAG immunoprecipitation after RNase treatment.
1239	12417715_MI:0007	Western blot for Myc-tagged hUpf1 or hnRNPA1, transiently expressed in HEK293 cells together with an empty vector (lanes 1, 2, 4, and 5) or a plasmid encoding FLAG-tagged hDcp1a (lane 3) or hDcp2 (lane 6) and subjected to anti-FLAG immunoprecipitation after RNase treatment. Immunoprecipitates (P; lanes 2, 3, 5, and 6) are compared to 5% of the total extract (T; lanes 1 and 4) in panels A and B.
1240	12441357_MI:0007	Western blot developed with a specific anti-TTF-1 polyclonal antibody showed the presence of TTF-1 co-immunoprecipitated protein only in the extract prepared from clone 3xFLAG-P8-8 (Fig. 2C).
1241	12456722_MI:0007	Mob2p and Orb6p were also found to interact by a binding assay using in vitro translated proteins (Fig. 5C), suggesting that their interaction is direct.
1242	12456722_MI:0007	Using a strain (YDM1151) expressing chromosomal Mob2p-13Myc and Orb6p-3HA, we found that the two proteins could be co-immunoprecipitated (Fig. 5B)
1243	12477395_MI:0007	Anti-HA immunoprecipitates from the APC4-HA MND2-myc and SWM1-HA APC4-myc strains contained both the HA-tagged proteins as well as Mnd2p-myc and Apc4p-myc (Figures 3B and 3C). Reciprocally, anti-myc immunoprecipitates contained the myc-tagged proteins and also Apc4p-HA and Swm1p-HA, respectively
1244	12477395_MI:0007	In an anti-myc immunoprecipitate from the lid1-myc apc13-HA strain (KGY3582), but not single-tagged strains (KGY1336 and KGY3398), both Lid1p-myc and Apc13p-HA were detected (Figure 1B), and, conversely, both Apc13p-HA and Lid1p-myc could be detected in an anti-HA immunoprecipitate
1245	12477395_MI:0007	In Cut9p-HA immunoprecipitates from cut9-HA apc14-myc (KGY3587) and cut9-HA apc15-myc(KGY3665) strains, Apc14p-myc and Apc15p-myc were each detected and were absent from the single cut9-HA strain
1246	12477395_MI:0007	In Cut9p-HA immunoprecipitates from cut9-HA apc14-myc (KGY3587) and cut9-HA apc15-myc(KGY3665) strains, Apc14p-myc and Apc15p-myc were each detected and were absent from the single cut9-HA strain. In reciprocal experiments, anti-myc immunoprecipitates from the double-tagged strains contained Cut9p-HA
1247	12477395_MI:0007	We also tested whether these proteins associate with one another. To this end, apc13-HA apc15-myc (KGY3735) and apc15-HA apc14-myc  (KGY1611) strains were constructed. Anti-HA immunoprecipitates from these strains contained Apc13p-HA and Apc15p-HA as expected and also contained Apc15p-myc and Apc14p-myc, respectively
1248	12482963_MI:0007	Anti-Myc antibodies were used to immunoprecipitate Ioc2p. As expected, Isw1p was coprecipitated; however, no detectable Ioc3p was precipitated (Fig. 2B, lanes 6 to 8).
1249	12482963_MI:0007	As shown in Fig. 2B (lanes 3 to 5), the IP of Isw1p coprecipitated Ioc2p and Ioc3p, as observed previously (Fig. 1A) (49).
1250	12482963_MI:0007	Conversely, the IP of Ioc3p with anti-HA antibodies pulled down Isw1p but not Ioc2p (Fig. 2B, lanes 9 to 11).
1251	12482963_MI:0007	To reveal interactions among Isw1 complex subunits, Isw1p was immunoprecipitated from strains from each of which the IOC2, IOC3, or IOC4 gene was deleted
1252	12493754_MI:0007	HA-tagged Chk2 and FLAG-tagged Plk1 coimmunoprecipitated when transiently expressed in 293T cells
1253	12525503_MI:0007	Reciprocally, truncated MAGE-A4 was detected in the anti-HA immunoprecipitates
1254	12525503_MI:0007	When cell lysates were immunoprecipitated with an anti-FLAG antibody, HA-gankyrin was detected in them but not in precipitates from cells co-transfected with parental FLAG vector and HA-gankyrin
1255	12525503_MI:0007	When U-2 OS cells were co-transfected with plasmids expressing FLAG-tagged gankyrin and EGFP-S6 fusion protein, EGFP-S6 was immunoprecipitated with anti-FLAG antibody as expected
1256	12525503_MI:0007	When U-2 OS cells were co-transfected with plasmids expressing FLAG-tagged gankyrin and HA-tagged Rb, HA-Rb was immunoprecipitated with anti-FLAG antibody as expected
1257	12529446_MI:0007	the band corresponding to HA-Gef1p was detected in the GST-Cdc42p immunoprecipitates and was stronger in GST-Cdc42T17N immunoprecipitates.
1258	12571277_MI:0007	Co-immunoprecipitation of AtKSS and prey proteins (left panel) using in vitro methionine 35S-labelled translated proteins (right panel). Proteins were incubated in the presence of either anti-HA or anti-c-Myc antibodies. Protein complexes were
1259	12646258_MI:0007	FLAG-ECRG2 was present in immunoprecipitates from HA-MT2A transfected cells
1260	12646258_MI:0007	This immunoblot again showed that the immunoprecipitate of FLAG-ECRG2 contained HA-MT2A
1261	12676088_MI:0007	Myc immunoblots (right panel) show that anti-GFP coprecipitates Trt1-myc in the presence (lane 2, right panel), but not in the absence (lane 4, right panel), of SpEst1-GFP (lane 4, right panel).
1262	12676088_MI:0007	Similarly, anti-myc precipitated SpEst1-GFP in the presence (lane 3, left panel), but not in the absence (lane 4, left panel), of Trt1-myc.
1263	12678503_MI:0007	However, both cyclin T and DAG-like proteins co-precipitated reproducibly with HA-tagged CDKC;1 and CDKC;2
1264	12679424_MI:0007	For WT IRS-1, the amount of associated p85 after insulin stimulation was significantly increased approximately 10-fold over the basal amount
1265	12679424_MI:0007	the amount of Grb-2 associated with IRS1- T608R in the insulin-stimulated state was similar to that observed for WT IRS-1.
1266	12711603_MI:0007	Here we show that histone H3 methylase Suv39h1 and the methyl lysine-binding protein HP1 directly interact with MBD of MBD1 in vitro and in cells.
1267	12711603_MI:0007	Immunoprecipitation analyses further showed that HDAC1/HDAC2 were present in both FLAG-tagged Suv39h1 and MBD1 immunoprecipitates
1268	12711603_MI:0007	MBD1 Interacts with Suv39h1-HP1{alpha} Complex via MBD
1269	12724534_MI:0007	As shown in Figure 5A, UFO-myc readily pulled down endogenous CUL1 as well as ASK1, a SKP1-like molecule in Arabidopsis, strongly supporting the existence of an SCFUFO ubiquitin ligase complex in vivo. Furthermore, all of the CSN subunits tested, but not the TATA Binding Protein (TBP), were coprecipitated with UFO-myc
1270	12724535_MI:0007	Coimmunoprecipitation Analysis of the Physical Association of CSN and SCFCOI1 in Vivo.
1271	12757932_MI:0007	The p80 coilin 266-576 protein was bound to the GST-ataxin-1 539-816 fusion protein
1272	12788081_MI:0007	To determine whether p250GAP interacts with Fyn in vivo, we carried out co-immunoprecipitation analysis in HEK293T cells transfected with the expression plasmids for Flag-tagged p250GAP and/or Fyn (FynY531F).
1273	12805220_MI:0007	A GST-LKB1 fusion protein, transfected into HEK-293T cells, associated with endogenous STRAD (Figure 2B).
1274	12805220_MI:0007	Flag-tagged STRAD and myc-tagged LKB1 could be co-immunoprecipitated following co-transfection of HEK- 293T cells (Figure 3A).
1275	12874027_MI:0007	menin may be involved in DNA damage repair in cooperation with FANCD2.
1276	12874027_MI:0007	protein fragment, F2, which includes amino acid residues 219-395 of menin, is capable of interacting with FANCD2 (Fig. 2
1277	12874027_MI:0007	The tagged menin and its associating proteins were separated by SDS-PAGE and stained with a sensitive silver staining method (Fig. 1B)Citation . A large preparation of the menin-interacting proteins from 100 x 150-mm dishes of 293 cells were separated by SDS-PAGE and stained with a Colloid Coomassie Blue staining kit. The stained protein band was excised from the gel and digested with trypsin for sequence analysis using mass spectrometry. A single peptide sequence, SEDKESLTEDASK, was identified and found to be identical to an internal peptide in a recently cloned gene, FANCD2 (28) .
1278	12874278_MI:0007	coimmunoprecipitation experiments were performed on lysates from 293 cells expressing Myc-tagged TIP-1 and HA-tagged 
-catenin. As shown in Fig. 1B, 
-catenin was readily observed in the anti-Myc immunocomplex.
1279	12881429_MI:0007	Although the C-terminal  both Upf1p and Upf2p immunoprecipitated Ski7p/C (Figure 5A and B, lanes 3 and 11).
1280	12881429_MI:0007	Upf1p interacts physically with the N domain of Ski7p in a manner dependent on Upf2p.                    We found that either of the two sequences of Ski7p, 1-96 or 80-184, was sufficient for the association with Upf1p (Figure 6A).      Immunoprecipitation analyses identified the amino acid sequence 80-100 of Ski7p as an important region for the interaction with Upf1p (Figure 6B, lanes 3-6).
1281	12972551_MI:0007	As shown in Figure 2D, Cdc42p-3HA could be coimmunoprecipitated by Gef1p-Flag.
1282	14506250_MI:0007	We confirmed the association of MRGX with HDAC1 by immunoprecipitation/ Western analysis and determined that MRGX complexes had HDAC activity.
1283	14519092_MI:0007	Analysis of the interaction of Bud32 with Grx4 by co-immunoprecipitation assay
1284	14565975_MI:0007	Spc105p could be detected in immunoblots of immunoprecipitates of Ndc80p-protein A using less stringent washing
1285	14597665_MI:0007	Intriguingly, Myr-SmoCT{Delta}625-818, which does not possess Hh signaling activity, appears to bind Cos2/Fu with affinity similar to that of Myr-SmoCT
1286	14597665_MI:0007	It appears that Myc-Smo binds Cos2 through at least two regions of Cos2: the microtubule-binding domain and the C-tail, as HA-Cos2MB, HA-Cos2CT1, and HA-Cos2CT2 were pulled down robustly by Myc-Smo
1287	14597665_MI:0007	Myc-Smo but not Myc-Smo{Delta}CT pulled down Cos2 and Fu
1288	14597665_MI:0007	Myc-Smo but not Myc-Smo{Delta}CT pulled down Cos2 and Fu.
1289	14597665_MI:0007	We also found that Myc-Smo expressed in S2 cells can pull down endogenous Cos2 and Fu
1290	14625560_MI:0007	We confirmed that Swi6 interacts with both Hsk1 and Dfp1 through co-immunoprecipitation experiments
1291	14625560_MI:0007	We therefore examined whether Dfp1 interacts with Psc3 and whether this interaction requires Swi6. Psc3 coprecipitated with Dfp1, demonstrating that these proteins interact
1292	14627543_MI:0007	Coimmunoprecipitation of VCY2 and VCY2IP-1 in vitro-transcribed/translated proteins
1293	14627983_MI:0007	HA-MAGI-1 was coimmunoprecipitated with Myc-Carom-1 and -6 (Figure 3Ab, arrows)
1294	14685242_MI:0007	The ankyrin domain of IkappaB-alpha was required for association with Murr1, as were amino acids 1-160 of Murr1
1295	14715275_MI:0007	Co-immunoprecipitation of dRpp20 with dSMN.
1296	14715275_MI:0007	direct interaction between dSMN and hSMN proteins by in vitro binding assays (Figs. 3A and B) and in vivo co-IP assays (Fig. 3C)
1297	14718544_MI:0007	MTCBP-1 expressed in cells formed a complex with MT1-MMP and co-localized at the membrane.
1298	14729613_MI:0007	in vitro translated RASSF1A-myc and E4F-HA were tested in a coimmunoprecipitation before resolving on a 10% SDS-PAGE gel and Western blotting. In agreement with the data obtained in the yeast two-hybrid system an interaction was observed generating specific bands close to the predicated sizes of Mr 41,000 and Mr 60,000.
1299	14729917_MI:0007	These results showed that MSG2 proteins could physically interact with NPH4 proteins in vitro.
1300	14739298_MI:0007	Interaction of MAGE-A4{Delta}N1 with endogenous Miz-1. HeLa cells were transfected with plasmids expressing FLAG-tagged MAGE-A4{Delta}N1 (+) or vector alone (-). Lysates (lower panel) and those immunoprecipitated with anti-FLAG antibody (upper panel) were analyzed by Western blotting using anti-Miz-1 antibody
1301	14739298_MI:0007	Reciprocally, MAGE-A4{Delta}N1 was detected in the anti-HA immunoprecipitates from cells co-transfected with plasmid expressing HA-Miz-1 and FLAG-MAGE-A4{Delta}N1
1302	14739298_MI:0007	To confirm that MAGE-A4{Delta}N1 interacts with Miz-1 in mammalian cells, COS-7 cells were co-transfected with plasmids expressing HA-tagged human full-length Miz-1 and FLAG-tagged MAGE-A4{Delta}N1. When cell lysates were immunoprecipitated with an anti-FLAG antibody, HA-Miz-1 was detected in the precipitates but not in those from cells co-transfected with the parental FLAG vector and HA-Miz-1
1303	14742702_MI:0007	It was found that Alp7-GFP specifically coprecipitated with Alp14-13myc (Figure 5A, lane 4).
1304	14742702_MI:0007	lp14 interacted with both the full-length and the C-terminal region of Alp7 (lanes 4 and 5), but not with the N-terminal region (lane 6).
1305	14742714_MI:0007	Immunoprecipitation of Tof1-3HA with anti-HA conjugated beads specifically coimmunoprecipitated Csm3-13Myc from extracts prepared from Tof1-3HA Csm3-13Myc cells (Figure 5B).
1306	14742714_MI:0007	Two specific proteins were evident in the Vik1-13Myc immunoprecipitate; one was Vik1-13Myc, whereas the other protein was identified as Kar3p using mass spectrometric analysis (Figure 5A).
1307	14742714_MI:0007	We identified two specific proteins in the Csm3-13Myc immunoprecipitate, one of which corresponded to Csm3-13Myc. Mass spectrometry was used to identify the other protein as Tof1p, one of the other gene products we found to be required for efficient sister chromatid cohesion (Figure 5A).
1308	14764652_MI:0007	The finding that TPR domains in PP5 are requisite sites for interaction with ERs was further confirmed by coimmunoprecipitation experiments, using 293T cells cotransfected with green fluorescent protein (GFP)-tagged ER along with Flag-tagged full-length PP5 or  a PP5 mutant with only its TPR domains
1309	14970237_MI:0007	As shown in Fig. 3A, Pop1-HA coimmunoprecipitated with Cig2 (lane 3). This interaction was specific, as Cig2 did not precipitate in the absence of primary anti-HA antibody (lanes 2 and 5), and in addition, Cdc13 was not pulled down in the precipitates under the same conditions (lanes 3 and 6). As Pop1 and Pop2 act in the same pathway by forming heterodimers as well as individual homodimers (26, 37), we then addressed whether Pop1 is still capable of interacting with Cig2 in the absence of Pop2. Pop1-HA was expressed in pop2 mutants, and immunoprecipitation was performed as described above. As shown in Fig. 3B, Pop1 coprecipitated with Cig2 in this mutant as efficiently as in wild type cells (lanes 4 and 7). Again, an interaction was specific, as Cig2 did not precipitate in the absence of primary antibody or with an excess amount of HA peptide competitors (lanes 3, 5, 6, and 8). These results show that Pop1 forms a complex with Cig2 in the cell, and for this interaction, its partner Pop2 is not required.
1310	14993272_MI:0007	As shown in Fig. 6, we found that Lub1 (full length) and Lub1 (1-279) were associated with Cdc48, whereas the binding between Cdc48 and Sts5 (33) could not be detected (Fig. 6, top).
1311	14998928_MI:0007	Upon immunoprecipitation of Myc-tagged Ttv from the cellular lysate of transfected cells, the Sotv protein could be detected by western blotting in the immunoprecipitate
1312	15024052_MI:0007	Coimmunoprecipitation assay of Dpb4p with both Pol2p and Isw2p.
1313	15024052_MI:0007	we next tested the extent to which Isw2p and Itc1p stably associate with Dls1p by a coimmunoprecipitation experiment
1314	15047801_MI:0007	Cells were lysed 6 h after infection and immunoprecipitated with a Flag-specific MAb, and then NPS3 was detected by immunoblotting with the NSP3-specific MAb ID3 (Fig. 3A).
1315	15047801_MI:0007	GFP-NSP3:150-313 also coimmunoprecipitated with RoXaN I:1-279, but not with RoXaN I:1-255 or RoXaN I:1-173 (Fig. 4, lanes 2, 3, and 4, respectively), suggesting that aa 256 to 279 of RoXaN I are important for the interaction with NSP3.
1316	15047801_MI:0007	Interaction of RoXaN I with eIF4G I is dependent on the two protein-binding domains of NSP3.
1317	15063184_MI:0007	Cell extracts were immunoprecipitated with an anti-HA antibody, followed by Western blot analysis with either anti-Su(fu) or anti-Flag antibody. As shown in Fig. 6C, Su(fu) was coimmunoprecipitated with Ci&#916;CORD in the absence of Flag-Cos2 (lane1); however, a diminishing amount of Su(fu) was coprecipitated with Ci&#916;CORD when Flag-Cos2 was coexpressed (lane 2), suggesting that binding of Cos2 to Ci&#916;CORD interferes with Su(fu)/Ci&#916;CORD interaction.
1318	15063184_MI:0007	Flag-Cos2 was coprecipitated with HA-Ci76 but not with HA-Ci76&#916;CDN whereas equal amounts of Flag-Su(fu) were coprecipitated with both HA-Ci76 and HA-Ci&#916;CDN. Hence, deletion of the Ci sequence from aa 346 to aa 440 compromises Cos2 binding to the N-terminal region of Ci, but does not significantly perturb Ci/Su(fu) interaction.
1319	15078334_MI:0007	In vitro coimmunoprecipitation amoung subunits of the G protein complexes.
1320	15078334_MI:0007	In vitro co-immunoprecipitation amoung the subunits of the G protein complexes.
1321	15105425_MI:0007	In the ATF2 immunoprecipitate the VRK1 protein is clearly detected (Fig. 1B,
1322	15107855_MI:0007	Transfection of epitope-tagged vectors into HEK 293 cells followed by immunoprecipitation showed that the HA-PCM1 fragment coprecipitated with Myc-BBS4 (Fig. 1c).
1323	15107855_MI:0007	we also observed seminative interaction between Myc-BBS4 and endogenous PCM1 using a polyclonal antibody to PCM1 (Fig. 1c).
1324	15133492_MI:0007	By immunoprecipitation followed by immunoblotting with either pair of antibodies, both HA- and -Flag-tagged E2F-7 were present in the immunocomplex (Figure 4a), arguing that E2F-7 molecules can interact.
1325	15138274_MI:0007	Elongator could, under those conditions, be specifically immunoprecipitated from wild type cell extracts carrying either Elp1 or Elp4 tagged with an HA epitope but not from control cells that did not express a tagged Elp protein
1326	15138274_MI:0007	Immunoprecipitation of a tagged subunit using 12CA5 monoclonal antibodies and Western blotting with antibodies directed against the six Elongator subunits were used to investigate the integrity of the Elongator complex in different mutant strains.
1327	15155892_MI:0007	As shown in Figure 2, GCR1 and GPA1 can be coimmunoprecipitated.
1328	15169888_MI:0007	binding of ABIN-2-FL to Myc-TPL-2 (Fig. 2D).
1329	15169888_MI:0007	the level of ABIN-2-FL which coimmunoprecipitated with HA-p105 (Fig. 2C).
1330	15197186_MI:0007	In this study, we show that hMOB1, the closest relative of yeast Mob1 and Mob2, stimulates NDR kinase activity and interacts with NDR both in vivo and in vitro.
1331	15197472_MI:0007	The yeast two-hybrid interaction of CYCP2;1, CYCP3;1, CYCP4;1, and CYCP4;2 with CDKA;1 was confirmed by co-immunoprecipitation.
1332	15208391_MI:0007	This observation demonstrates that CAND1 does not interact with the C-terminal TAP tag itself, and the association between CAND1 and CUL1-TAP is specific.
1333	15208391_MI:0007	Unmodified CUL1 was precipitated together with FLAG-CAND1.
1334	15272023_MI:0007	FLAG-Msx1 and FLAG-Msx2 were co-immunoprecipitated with endogenous MAGE-D1. Conversely, endogenous MAGE-D1 was co-immunoprecipitated with FLAG-Msx1 and FLAG-Msx2.
1335	15272023_MI:0007	Full-length MAGE-D1 and MAGE-D1{Delta}N was co-immunoprecipitated with necdin
1336	15280210_MI:0007	both OLIG1 and OLIG2 interact with the E2A proteins, E12 and E47
1337	15280210_MI:0007	OLIG1 and OLIG2 complexed with both ID2 and ID4
1338	15364927_MI:0007	Daxx constructs aa 1-574, 1-501, and a construct with deletion of aa 191-242 (a putative amphipathic helix (18)) bound to p53 less effectively than wild-type Daxx (lanes 4, 6, and 10). In addition, the Daxx construct with a deletion between aa 502 and 574 exhibited weak binding to p53 (Fig. 3B, lane 16). The Daxx NH2-terminal domain (aa 1-130) and the COOH-terminal constructs (aa 516-740 and 573-740) did not bind to p53. These results indicate that the acidic domain of Daxx is required for binding to p53, consistent with the results obtained from yeast two-hybrid assays (Fig. 1). To examine whether MDM2 was present in the same FLAGDaxx immunocomplexes, the same membrane shown in Fig. 3B was stripped and reprobed with anti-MDM2 antibody. MDM2 was coprecipitated with WT Daxx and its fragments (aa 1-574 and 1-502, Fig. 3C, lanes 2, 4, and 6).
1339	15364927_MI:0007	MDM2 appears to constitutively associate with Daxx
1340	15364927_MI:0007	WT p53 was very efficiently precipitated in the presence of MDM2 (Fig. 5C, lane 2). Small but detectable amounts of p53 was precipitated in the absence of MDM2 expression (lane 4, p53 band was visible upon longer exposure). p53 mutants K381A/K382A and L22Q/W23S were also coprecipitated with FLAG-Daxx, although to a much lesser extent than WT p53
1341	15377662_MI:0007	These results indicated that all of the FLAGp85 proteins (wild type, BH, R274A, and R151A mutants) can associate with the Myc-p110 protein and its encoded PI3K activity.
1342	15378002_MI:0007	In cells transfected with HA-c-Jun and VRK1-myc, the immunoprecipitation with anti-HA brings down VRK1 as detected in the immunoblot. The inverse situation, in the immunoprecipitate of VRK1, c-Jun is also detected with the anti-HA antibody
1343	15380617_MI:0007	To demonstrate the association of B' to Chk2 in cellulo, human HEK293 cells were transiently transfected to express Chk2 and B'g1, B'g2 or B'g3 proteins.
1344	15448699_MI:0007	Correspondingly, in vivo co-immunoprecipitation experiments showed that full-length Sic1 precipitated Hog1 (Fig. 3b).
1345	15467741_MI:0007	Magicin exhibits enhanced binding with S518A than "518D for both merlin isoforms 1 or 2
1346	15467741_MI:0007	Magicin exhibits enhanced binding with S518A than S518D for both merlin isoforms 1 or 2
1347	15469499_MI:0007	Co-immunoprecipitation experiments (Figure 4b) further demonstrated the interaction between FTA and FTB as well as FIE and MEA in the BiFC.
1348	15485916_MI:0007	The results showed that MmDph2 could be specifically coimmunoprecipitated with MmDph1 and vice versa
1349	15520167_MI:0007	To confirm additionally the interaction between MGC5306 and pol, we took advantage of GFP-tagged MGC5306 and analyzed by co-immunoprecipitation-Western blot analysis. A 39-kDa pol protein was identified in the immunoprecipitated product (Fig. 1B, bottom panel, Lane 1) when anti-GFP antibody was used to pull down the complex and Western blotting with anti-pol antibody, indicating the interaction of MGC5306 and endogenous WT-pol
1350	15534215_MI:0007	As illustrated in Fig. 4B, using the same approach described for the full-length proteins, we found that the SHDs of AtSCAR3 and AtSCAR1 (AtSCAR3-SHD and AtSCAR1-SHD) bound 5-fold more efficiently to T7-tagged AtBRK1 than to the T7-tagged NC proteins.
1351	15555586_MI:0007	myc-Skp1 co-purifies both with Mcs2-TAP (Fig. 3A) and Pmh1-TAP (Fig. 3B) thus extending the Skp1-Mcs2 and Skp1-Pmh1 two-hybrid interactions to fission yeast cells.
1352	15643072_MI:0007	Immunoprecipitation of Mcl1-GFP from fraction 9 coprecipitates Pol1p from all genetic backgrounds except nmt1GST-cds1, which contained no Mcl1-GFP in fraction 9 (Fig. 6B, top panels). Pol1p also precipitated with Mcl1-GFP from the trailing fractions of rad3 and cds1, indicating that the mobility differences observed in these mutants were not due to a loss of Pol1p interaction. In contrast, the slower-sedimenting material in hsk1-1312 and nmt1GST-cds1 fractions contained no detectable Pol1p (Fig. 6B, bottom panels), suggesting that in these backgrounds the association between Pol1p and Mcl1-GFP is weaker than in the other conditions.
1353	15652749_MI:0007	Coim-munoprecipitation (co-IP) analysis showed that p27wt interacted in vivo with stathmin and that this interaction derived cell clones, and of p27 wt and null cells. Expression of was severely imp27 had no effect on the adhesion of HT-1080 cells (Figure 2E) paired by the deletion of the last 27 amino acids of p27
1354	15660136_MI:0007	If Zip1 is a substrate for the SCFPof1, Pof1 is expected to bind Zip1. Immunoprecipitation was performed in a strain containing Pof1-GFP and Zip1-HA. To prevent degradation of Zip1, experiments were again carried out in an mts3-1 background. Under this condition, Zip1 was detected as a doublet, the lower band of which corresponded to the band seen in wild-type cells (band 1 in Figure 4C) and the upper of which appeared to correlate to the faster migrating form (band 2 in Figure 4C) of the phosphorylated Zip1 bands (Figure 4D, lanes 2 and 4). Immunoprecipitation using anti-GFP antibody showed that Pof1 co-immunoprecipitated with Zip1, specifi- cally the upper band of the doublet (Figure 4D, lane 5). Reciprocal immunoprecipitation with anti-HA antibody also co-precipitated Pof1-GFP, albeit very faintly (lane 4). This is probably due to the existence of an excess amount of free Zip1-HA dissociated from Pof1-GFP in the mts3-1 mutant. In order to examine which of Zip1 forms binds Pof1 in the pof1-6 background, immunoprecipitation was performed using samples prepared from the pof1-6 mutant used in Figure 4A (doubly tagged with Pof1-6-GFP and Zip1-HA). For comparison, parallel immunoprecipitation was also performed in extracts from mts3-1 cells and precipitates were run side-by-side. As shown in Figure 4E, it is evident that two phosphorylated Zip1 forms interacted with Pof1-6 (lane 7, marked as bands 2 and 3). Taken together, these findings indicate that Zip1 is phosphorylated and this phosphorylation leads to an interaction with Pof1 and subsequent degradation.
1355	15660136_MI:0007	Immunoblotting showed that Pof1-GST co-precipitated with Pcu1-13Myc (Figure 1A).
1356	15670823_MI:0007	As shown in Fig. 1C (upper panel), CNK1 was able to co-immunoprecipitate with RhoAV14, whereas the closely related members Rac or Cdc42 were unable to be co-immunoprecipitated.
1357	15670823_MI:0007	Consistent with these results, co-immunoprecipitation assays performed with an hCNK1 mutant lacking the PH domain were unable to interact with RhoAV14; on the other hand, the expression of the hCNK1 PH domain alone gave a potent signal of interaction in BRET assays (see Supplementary Fig. 3).
1358	15670823_MI:0007	Fig. 2A shows that only constitutive active RhoA is able to co-precipitate with CNK1.
1359	15674350_MI:0007	anti-FLAGIP of cells transfected with FLAG-BRCA1 mutant 1 brought down reduced anti-FLAGIP of cells transfected with FLAG-BRCA1 mutant 1 brought down reduced
1360	15674350_MI:0007	we performed immunoprecipitation (IP)-Western blotting assays to determine if ER-a binding BRCA1 protein fragments identified above associate with the endogenous ER-a protein in MCF-7 cells. MCF-7 cells were transfected with FLAG-tagged BRCA1 proteins encompassing aa 1-100, 101-200, and 201-300. Each of the FLAG-BRCA1 proteins was expressed well. Consistent with the GST capture assays, we found that IP of FLAG-BRCA1 1-100 and 101-200, but not 201-300, co-precipitated ER-a (Figure 3a) and vice versa
1361	15677333_MI:0007	LRRFIP2 can be coimmunoprecipated in a complex with Dvl3
1362	15677333_MI:0007	Myc-Dvl3 was detected in the immunoprecipitants of Flag-LRRFIP2-M4, Flag-LRRFIP2-M5, and Flag-LRRFIP2-M6.
1363	15684389_MI:0007	In the experiment shown in Fig. 2A, the cells were transiently transfected with HAKSR1, and KSR1 was immunoprecipitated from cytoplasmic lysates. Western blot analysis of the KSR1 immunoprecipitations was performed to ascertain relative binding levels of other KSR1 scaffold proteins. Increased binding of Hsp90 to KSR1 was again observed with the H1-177 cell line. In addition, a low level of increased Mek1-2 binding but equivalent 14-3-3 binding were observed with the H1-177 cells.
1364	15684389_MI:0007	In the experiment shown in Fig. 3B, comparable amounts of KSR1 were immunoprecipitated from cytoplasmic lysates of Nm23-H1-Flag/HA-KSR1- and control Flag/HA-KSR1-transfected cells. Coimmunoprecipitation of KSR1 and endogenous and Nm23-H1-Flag was observed and was more pronounced in the Nm23-H1-Flag/HA-KSR1 transfectants.
1365	15716105_MI:0007	eIF(iso)4E interacts with AtBTF3 in vitro. Co-immunoprecipitation of in vitro transcribed and translated T7 tagged-eIF(iso)4E and AtBTF3 products, with anti-T7 tag antibody.
1366	15721254_MI:0007	cells were transfected with V5-OS-9 ex-  pression vector and treated with desferrioxamine (DFO) to induce endogenous HIF-1alpha expression. Coimmuno-  precipitation was demonstrated only in cells expressing  both V5-OS-9 and endogenous HIF-1alpha
1367	15721254_MI:0007	endogenous PHD2 coimmunoprecipitated with V5-OS-9  and FLAG-HIF-1alpha
1368	15721254_MI:0007	PHD3 also interacted with V5-OS-9 in 293 cells
1369	15721254_MI:0007	V5-OS-9 coimmunoprecipitated HIF-1alpha-TM as efficiently as native HIF-1alpha
1370	15741320_MI:0007	Coimmunoprecipitation of HFR1 with COP1 protein.
1371	15798197_MI:0007	Figure 3A shows that Tim immunoprecipitates contain both ATRIP and ATR and that HU treatment significantly stimulates the Tim-ATRIP interaction.
1372	15798197_MI:0007	Tim was immunoprecipitated, and the immunoprecipitates were analyzed for endogenous Chk1.
1373	15798197_MI:0007	We tested for interaction between hTim and hChk1 kinase, which is the functional homolog of spCds1, by coimmunoprecipitation
1374	15798197_MI:0007	We transfected HEK293T cells with Flag-tagged Tim and Cry2 and observed a significant amount of Cry2 in the anti-Flag immunoprecipitates (Fig. 1A) from these cells
1375	15800064_MI:0007	In an anti-MYC immunoprecipitate from mto1-myc mto2-gfp strains but not from single-tagged strains, both Mto1p-MYC and Mto2p-GFP were detected (Figure 1A, IP:{alpha}-MYC).
1376	15800615_MI:0007	Preliminary studies showed that GST&#8722;TR2, but not the S3291E derivative, when expressed in vivo, interacted with RAD51 protein (Fig. 4d, lanes 2 and 4).
1377	15800615_MI:0007	Using cells stably expressing GST&#8722;B2-9, we found that decreased S3291 phosphorylation caused by ionizing radiation was associated with a doubling in ability to bind RAD51 (Fig. 4c).
1378	15805487_MI:0007	Furthermore, coimmunoprecipitation assays showed that TAPa-CRY1 bound endogenous CRY1, whereas a TAPa-green fluorescent protein (GFP) fusion did not (Figures 4D and 4E). Therefore, these data indicate that CRY1 homodimerizes in vivo in a light-independent manner.
1379	15809031_MI:0007	Furthermore, the interaction between tea1p and for3p in yeast extracts was not present in extracts from tea4
 cells (Figure 4C), showing that tea4p is required for for3p-tea1p interaction. Together, these results show that tea4p directly binds to for3p and tea1p and links these proteins together.
1380	15809031_MI:0007	In contrast, the association of tea1p with tip1p was tea4 independent (Figure 2G). Therefore, tea1p functions to link tip1p and tea4p in a common complex.
1381	15809031_MI:0007	tip1p coimmunoprecipitated with tea4p from tea1+ yeast extracts, but not from tea1
 yeast extracts (Figure 2F)
1382	15809031_MI:0007	We confirmed the interaction between tea1p and tea4p by using coimmunoprecipitation and two-hybrid approaches. Tea1p-HA and tea4p-GFP coimmunoprecipitated  in yeast extracts with either an anti-HA or an  anti-GFP antibody (Figure 1E).
1383	15809031_MI:0007	We tested whether tea4p interacts with for3p. In soluble yeast extracts, for3p-myc coimmunoprecipitated with tea4p-GFP (Figure 4A),
1384	15851471_MI:0007	Immunoblotting Myc-PEAR1 immunoprecipitates demonstrated that ShcA and B co-immunoprecipitate with Myc-PEAR1
1385	15879521_MI:0007	A greater amount of Mad2 coimmunoprecipitated with Cdc20-13Myc than with either Bub3-13Myc or Mad3-13Myc.
1386	15879521_MI:0007	and a small fraction of Mad2 copurified with Mad3-PrA (Fig. 2C, lanes 5 and 6), consistent with our previous observation.
1387	15879521_MI:0007	A small amount of Cdc20 copurified with Mad3-PrA (Fig. 2D, lanes 4 to 6) demonstrating that this complex contains Mad2, Mad3-PrA, and Cdc20-13Myc and therefore is MCC (37).
1388	15886098_MI:0007	Anti-Flag (ABL2)-immunoprecipitated material was immunobloted with anti-RIN1 (left), and anti-RIN1-immunoprecipitated material was immunobloted with anti-Flag (right).
1389	15886098_MI:0007	Expression of HRASG12V (activated RAS), RIN1, and ABL2 resulted in the formation of a complex including all three proteins, as detected by immunoprecipitation of either ABL2 or HRAS (Figure 6A).
1390	15886098_MI:0007	RIN1 tyrosine phosphorylation is required for ABL2 binding. RIN1-ABD and an SH2 mutant (RIN1-ABDR94N), but not a triple-tyrosine mutant (RIN1-ABDTM)
1391	15896299_MI:0007	Fig. 9B shows that PTP1B and PLD2 were reciprocally co-immunoprecipitable.
1392	15896299_MI:0007	Grb2 was pulled down with myc-specific antibodies
1393	15899842_MI:0007	The direct association of Trm11p and Trm112p was then tested by coimmunoprecipitation analysis.
1394	15915339_MI:0007	The physical interaction between Mcl1p and Pola was also examined in cell extracts using HA-tagged Mcl1p and 6xHis-Myc-tagged Pola. The eptitope-tagged proteins were co-expressed from two different plasmids in wild-type cells with no adverse effect on cell viability or growth. Crude cell extracts were prepared and immunoprecipitated with antibody to the HA or Myc epitope tag (Fig. 5c). Anti-HA antibody co-precipitated Mcl1p and Pola (Fig. 5c, lane 11) and similar results were observed with anti-Myc antibody (lane 12), suggesting that Mcl1p and Pola interact physically in vivo. However, only a small fraction of Mcl1pD in the extract co-precipitated with PolaD (and vice versa), suggesting that the complex between them may not be very stable or may be transient.
1395	15935327_MI:0007	These experiments revealed association between Raf-1 and DSCR1.4.
1396	15935775_MI:0007	BRI1 interacted with itself in plants, both in the presence and absence of ligand, and BL treatment appeared to increase the extent of coimmunoprecipitation,
1397	15960622_MI:0007	The coiled-coil domain itself (SPA1-CC) also interacted with HFR1
1398	15976448_MI:0007	Co-immunoprecipitation of PHR1 and the myosin 1c tail.
1399	15976448_MI:0007	Myosin VIIa binds to PHR1.
1400	15983381_MI:0007	DJ-1 interacts with Daxx.
1401	16043432_MI:0007	As expected, we found that BRK1 bound to the SHD of ITB1/SCAR2 (Figure 7, lanes 7 and 8; note presence of ITB SHD band in lane 8). However, BRK1 did not bind to an 1106-amino acid fragment that did not contain the SHD (Figure 7, lanes 5 and 6; note absence of ITBDSHD band in lane 4). This result shows that the SHD of ITB1/SCAR2 is both necessary and sufficient for binding to BRK1.
1402	16043509_MI:0007	As shown in Figure 2AGo, Ski2-myc was specifically associated with Ski3-HA, while no signal was observed when immunoprecipitations were performed with untagged Ski2p or with the N-terminal deletion of Ski2p (deleted of amino acids 1-279).
1403	16043509_MI:0007	Both full-length Ski3-HA and Ski3deltaC-HA associated with Flag-Ski7 with or without Ski2p and Ski8p (Fig. 5C, right and left panels), indicating that Ski3p and Ski7p can interact with each other directly.
1404	16043509_MI:0007	Full-length Ski2-myc coimmunoprecipitated with Flag-Ski7 in the ski2delta-ski7delta double-mutant strain (expressing Ski3p and Ski8p), while the N-terminal deletion of Ski2p (which has lost the ability to interact with Ski3p and thus Ski8p) could not (Fig. 5A, right panel).
1405	16053918_MI:0007	pCMV-Myc- A2.8 and pCMV-HA-K2.1 were co-transfected or pCMV-HA-K2.1 was alone transfected into COS-7 cells. As shown in Fig. 2B, transfected Myc-A2.8 was able to be immunoprecipitated from the co-transfected cell lysate by an anti-HA antibody
1406	16100110_MI:0007	Alg13 and Alg14 physically interact and under normal conditions, are associated with the ER membrane.
1407	16107882_MI:0007	Importantly, specific point mutations in the Glc7p-interaction motif of Bud14p (V377A and F379A; Figure 4A) strongly diminished its ability to interact with Glc7p both by two-hybrid (Table I) and coimmunoprecipitation assays (Figure 4B), implying that Glc7p indeed interacts with Bud14p through this conserved domain.
1408	16132846_MI:0007	pcDNA4/His- Max-DAPk1 was co-immunoprecipitated with pEGFPC1-PDCD6
1409	16142218_MI:0007	Dicer,TRBP interaction studied with a HEK293 cell line expressing haemagglutinin (HA)-tagged TRBP2.
1410	16177806_MI:0007	Here we describe Cardif, a new CARD-containing adaptor protein that interacts with RIG-I and recruits IKKalpha, IKKbeta and IKKvarepsilon kinases by means of its C-terminal region, leading to the activation of NF-kappaB and IRF3.
1411	16214168_MI:0007	HA-tagged Nmi could be precipitated with an anti-myc-tag antibody if myc-tagged Sox10 was present in the extract
1412	16214168_MI:0007	Sox10 was immunoprecipitated selectively from the extracts that contained the Nmi protein
1413	16221674_MI:0007	The association of FLN29 and FLAG-tagged TRAF6 transfected to 293T cells was observed by immunoprecipitation experiment (Fig. 5B).
1414	16229834_MI:0007	Immunoprecipitation of GFP-Amida with an anti-GFP antibody specifically coprecipitated a protein of about 48 kDa representing the FLAG-Par-4 fusion protein
1415	16229834_MI:0007	when employing anti-FLAG specific antibodies, a protein of about 68 kDa corresponding to the GFP-Amida fusion protein (Fig. 2B, lane 4) was only present in the precipitate from FLAGPar-4-expressing cells but not from mock-transfected cells
1416	16230351_MI:0007	The C-terminal 52 amino acids of SIAH1 are required for dimerization and auto-destabilization (5, 29). We found that, despite its greatly enhanced stability and consequent elevated expression, SIAH1 with these residues deleted (SIAH1 {Delta}C2) was severely compromised for interaction with POSH
1417	16230351_MI:0007	used co-immunoprecipitation to confirm that SIAH1 and POSH interact in mammalian cells
1418	16234233_MI:0007	PDZ-dependent interaction of NHERF-1 and NHERF-2 with ASIC3 in COS-7 cells.
1419	16253990_MI:0007	Introduction of the Grb2 mutations also abrogated ligand-induced Shc binding to Gab2 (Fig. 4C), indicating that Gab2-bound Grb2 normally acts to bind tyrosine-phosphorylated Shc via the Grb2 SH2 domain.
1420	16254079_MI:0007	COS-7 cells were transfected with a myc-tagged Sin3A expression construct and a FLAG-tagged ebp1 expression construct. Cell lysates were immunoprecipitated with a polyclonal antibody to the myc-epitope tag and probed with a mouse monoclonal antibody to the FLAG-tag. Results indicated that Ebp1 was found in myc, but not isotype control, immunoprecipitates
1421	16254079_MI:0007	Endogenous Sin3A was found in FLAG immunoprecipitates from the FLAG-Ebp1
1422	16257957_MI:0007	EBNA-3 interacts with an immunophilin-like protein XAP2/ARA9/AIP
1423	16257957_MI:0007	In this study, we show that EBNA-3 interacts specifically with AhR
1424	16257958_MI:0007	Immunoprecipitation with anti-GFP antibody and immunoblotting with anti-HA confirmed that the HA-kif17 coimmunoprecipitates with GFP-Kv4.2C
1425	16257970_MI:0007	Binding to Pex1pandPex6p of patient-derived Pex26p mutants.
1426	16260785_MI:0007	In the inverse experiment we were able to specifically coimmunoprecipitate a tagged form of Arr4p (Arr4p-4PC) with Gef1p (Fig. 1C). We conclude that Arr4p interacts with Gef1p.
1427	16263721_MI:0007	Here we describe physical and genetic interactions involving Swi1 and Hsk1-Dfp1/Him1. Dfp1/Him1 was identified in a yeast two-hybrid screen with Swi1. Hsk1 and Dfp1/Him1 both co-immunoprecipitate with Swi1.
1428	16275645_MI:0007	Fbx4 forms stable complexes with endogenous Pin2/TRF1 in cells
1429	16275645_MI:0007	Fbx4 was detected in anti-Pin2 immunoprecipitates
1430	16275660_MI:0007	The interaction between VCP and AMFR was also detected by co-immunoprecipitation experiments using transiently transfected COS-1 cells co-expressing full-length VCP and an amino-terminally truncated HA-tagged AMFR fragment.
1431	16278047_MI:0007	As positive controls, we overexpressed hFBX4 and hFBX7 which have been shown to bind Cul1 and Skp1
1432	16278047_MI:0007	hFBX25 interacts with Skp1 and Cul1. A serine at position 244 in its F-box is important for these interactions.
1433	16278218_MI:0007	It is known that only a small fraction of transfected HSF1 is able to bind HSE and activate hsp transcription and this fraction appears to be the fraction that is not phosphorylated at serine 121 or bound to HSP90
1434	16278681_MI:0007	As shown in Figure 2c, the association of CRIPak with PAK1 in COS7 cells was demonstrated by co-immunoprecipitation.
1435	16278681_MI:0007	We found that CRIPak binds to ER in a ligand-sensitive manner, as these effects were blocked by anti-estrogen ICI-182780 (Figure 7f).
1436	16280322_MI:0007	35S-HA2-Pex19p and 35S-FLAG-Pex16p were detected specifically in the immunocomplexes of 35S-FLAG-Pex3p- EGFP (Fig. 4A, lanes 1-4 and 6), indicating that these three peroxins formed a ternary complex.
1437	16280322_MI:0007	Furthermore, Pex19p complexes with PMPs such as Pex16p and Pex26p bound to Pex3p in vitro, indicating that the ternary complexes were formed.
1438	16282325_MI:0007	For these experiments, wild-type cIAP1 and mutants of cIAP1 were expressed with FLAG tags in HEK293T cells, and their ability to bind mature SMAC protein present within detergent lysates was analyzed by SDS-PAGE/immunoblotting.
1439	16282325_MI:0007	However, SMAC did co-immunoprecipitate with full-length XIAP and with all fragments of XIAP containing BIR3.
1440	16282325_MI:0007	In contrast, SMAC co-immunoprecipitated with all cIAP1 fragments that contained BIR3 while failing to associate with all cIAP1 fragments lacking BIR3 (Fig. 2A)
1441	16282325_MI:0007	the BIR1 domain of cIAP1 is necessary and sufficient for interaction with TRAF2.
1442	16282325_MI:0007	These mutant BIR1 proteins were then expressed as Myctagged proteins in HEK293T cells and assessed for their ability to bind endogenous TRAF2 present in the cell lysates by co-immunoprecipitation assay.
1443	16284401_MI:0007	To confirm the specificity of the phosphotyrosine antibody, we transfected HEK293 cells with wild type ARMS and ARMSY1096F together with TrkA.
1444	16286473_MI:0007	DGK Binds pRB, p107, and p130 in Cells
1445	16291752_MI:0007	wild type survivin and survivin-2beta but not survivin-deltaEx3, could immunoprecipitate aurora-B, borealin, and wild type survivin
1446	16291752_MI:0007	wild type survivin and survivin-2beta but not survivin-deltaEx3, could immunoprecipitate aurora-B, borealin, and wild type survivin.
1447	16291752_MI:0007	wild type survivin and survivin-2beta but not survivin-deltaEx3, could immunoprecipitate aurora-B, borealin,and wild type survivin.
1448	16293632_MI:0007	From all the combinations tested with the TRPV4-A-FLAG-tagged protein coexpressed with TRPV4-YFP isoforms in HEK-293 cells, we were able to coimmunoprecipitate only the TRPV4-D variant (Fig. 6C, top panel).
1449	16299379_MI:0007	Runx2 was immunoprecipitated by an anti-Myc antibody, and Smurf1 and Smad6, which interacted with Runx2, were detected by Western blot using an anti-FLAG antibody
1450	16299379_MI:0007	Smad6 interacts with Runx2 in 293 cells
1451	16301316_MI:0007	Immunoprecipitation of Dop1-ZZ gives a second prominent band, identified by mass spectrometry as Mon2.
1452	16301319_MI:0007	Erbin bound to Sur-8 and inhibited the interaction of Sur-8 with Ras and Raf
1453	16316992_MI:0007	Cellular association of full-length MAGI-3 and full-length beta1AR.
1454	16316996_MI:0007	Following coexpression of HA-tagged Ras mutants with Epac2, Ras proteins were immunoprecipitated with HA antibody, and Epac2 was found to co-precipitate with oncogenic Ras mutants, but not with the closely related M-RasLeu-71 that has an activating mutation equivalent to H-RasLeu-61 (Fig. 2C). Interestingly, Kand N-Ras bound more effectively to Epac2 than did H-Ras.Binding to activated H-Ras proteins containing Ser35, Gly37, or Cys40 mutations in their effector-binding loop was diminished (Fig. 2D).
1455	16316999_MI:0007	SLK underwent dimerization via the C-terminal domain, and dimerization enhanced SLK activity.
1456	16319058_MI:0007	Despite the lack of IKK homodimer (Fig. 5C), formation of stable IKK/IKK heterodimer was also observed in cotransfection experiments with the two IKK constructs (Fig. 6C), consistent with their selective capacities to react with manumycin A.
1457	16319058_MI:0007	Ectopic expression of murine IKK but not human IKK elicited formation of the complex in manumycin A-treated cells (data not shown and Fig. 5C).
1458	16319058_MI:0007	Manumycin A Impairs IKK Interaction with IKK
1459	16319058_MI:0007	We found that manumycin A caused covalent IKK dimerization in intact cells (Fig. 6C).
1460	16319069_MI:0007	Under basal conditions an alanine substitution of Pro-9 led to a 4-fold decrease in the amount of beta-arrestin2-GFP co-immunoprecipitated by the 5HT2cR
1461	16326701_MI:0007	Purification of stable complexes f fUDG-A20 and fUDG-A20-Pol.
1462	16326701_MI:0007	The fUDG-A20 interaction is preserved in vitro and does not require catalytically active UDG.
1463	16326701_MI:0007	Vaccinia virus UDG protein is an early protein that interacts with A20 in vivo.
1464	16331268_MI:0007	As shown in Figure 3a, STAT3 interacted with Daxx in transient transfected 293T cells.
1465	16332682_MI:0007	Only PSD95 constructs including the PDZ2 domain immunoprecipitated with NR2A
1466	16332682_MI:0007	only PSD95 constructs including the PDZ2 domain were immunoprecipitated with NR2B
1467	16332682_MI:0007	PSD95 co-precipitated with the intracellular domain of ApoEr2
1468	16332688_MI:0007	After eukaryotic expression plasmid encoding FLAG-tagged Parkin was transfected into the SH-SY5Y cells (Fig. 1B), the immunoprecipitation was performed with either anti-RanBP2 or anti-FLAG antibodies. As shown in Fig. 1B, Parkin selectively binds to endogenous RanBP2.
1469	16332688_MI:0007	plasmids encoding for FLAG-tagged Parkin were co-transfected into HEK293 cells with a construct designed for the expression of GFP-tagged RanBP2 deletion mutant (IR1 + 2), spanning amino acids 2633-2761 of RanBP2, followed by immunoprecipitation with either anti-FLAG or anti-GFP antibodies, respectively.
1470	16332688_MI:0007	When co-immunoprecipitation was performed in reverse with anti-FLAG antibodies, followed by immunoblot analysis with anti-RanBP2 IgGs, the results was the same.
1471	16332960_MI:0007	TAZ, but not YAP, could also form a homodimer and the coiled-coil domain was important for homodimer formation
1472	16332960_MI:0007	TAZ physically associated with HAT proteins, such as p300 and PCAF
1473	16332960_MI:0007	TAZ showed physical association with TBX5 in coimmunoprecipitation assays
1474	16332960_MI:0007	YAP forms a stable heterodimer with TAZ
1475	16338934_MI:0007	myosin Vb constructs co-immunoprecipitated BERP
1476	16364915_MI:0007	At low tetracycline concentrations, FLAGhDcp1a and FLAG-hDcp1b primarily colocalize with endogenous hDcp1a in cytoplasmic PBs (Figure S1 available in the Supplemental Data online, and data not shown) and coprecipitate with endogenous hDcp1a, hDcp1b, and hDcp2 proteins (Figure S2).
1477	16364915_MI:0007	At low tetracycline concentrations, FLAG-hDcp1a and FLAG-hDcp1b primarily colocalize with endogenous hDcp1a in cytoplasmic PBs (Figure S1 available in the Supplemental Data online, and data not shown) and coprecipitate with endogenous hDcp1a, hDcp1b, and hDcp2 proteins (Figure S2). These cell lines were therefore useful for purification of hDcp complexes.
1478	16364915_MI:0007	both hDcp2 and Hedls copurify with hDcp1a when all three are coexpressed
1479	16364915_MI:0007	By contrast, hUpf1 interacts with hDcp2, but not with hEdc3 (lanes 6 and 12).
1480	16364915_MI:0007	hDcp2, which readily copurifies with Hedls (Figure 2A, lane 4)
1481	16364915_MI:0007	Neither TTP nor hUpf1 associate with Rck/p54 (lanes 7-9) or Hedls (lanes 13-15), whereas weak association was observed with hDcp1a (lanes 1-3).
1482	16364915_MI:0007	Proteins that consistently copurified specifically with FLAG-hDcp proteins were subjected to analysis by mass spectrometry, which identified three hDcp-associated proteins: Rck/p54, hEdc3, and Hedls (Figures 1A and 1B)
1483	16364915_MI:0007	Schematic depicting observed interactions between proteins in decapping
1484	16364915_MI:0007	This suggests that the FLAG-hEdc3 complex purified in Figure 6C, lane 5, consists of an hDcp2-containing complex that contains at least four subunits, hEdc3, hDcp1a, Hedls, and hDcp2 (corresponding to lanes 4 and 5), as well as smaller complexes of hEdc3 with hDcp1a and/or Rck/p54, in the absence of hDcp2 and Hedls (corresponding to lanes 1-3).
1485	16364915_MI:0007	TTP displays strong association with both hDcp2 and hEdc3 (lanes 5 and 11).
1486	16364915_MI:0007	we tested the ability of coexpressed hDcp and hDcp-associated proteins to coimmunopurify with TTP and hUpf1. As seen in Figure 6B, when coexpressed, each decapping subunit copurifies with hUpf1 and TTP, with the possible exception of Rck/p54, which we were unable to detect due to its comigration with IgGs (lanes 2 and 3).
1487	16364915_MI:0007	whereas hDcp2 and Hedls do not individually associate with hDcp1a (Figure 2, lanes 1, 3, and 6), both hDcp2 and Hedls copurify with hDcp1a when all three are coexpressed
1488	16365431_MI:0007	a deletion mutant of the SH2-like domain of STAP-2 failed to interact with IKK-, while full-length and deletion mutants of the PH or C-terminal domains of STAP-2 retained strong binding to IKK-. Therefore, the SH2-like domain of STAP-2 can bind to both MyD88 and IKK-.
1489	16365431_MI:0007	The Jurkat/STAP-2 cells were lysed, immunoprecipitated with an anti-Myc Ab and immunoblotted with an anti-IKK- Ab. As shown in Fig. 3D, the immunoprecipitates contained endogenous IKK- proteins.
1490	16365431_MI:0007	the precipitate for GST-STAP-2 SH2 contained both MyD88 and IKK-
1491	16365431_MI:0007	we assessed the association of MyD88 with IKK- in the absence or presence of STAP-2. Expression vectors for FLAG-tagged MyD88 and Histagged IKK- together with or without Myc-tagged STAP-2 were transfected into 293T cells. The cells were lysed, immunoprecipitated with an anti-His Ab, and immunoblotted with an anti-FLAG or anti-His Ab. As shown in Fig. 3F, the association between MyD88 and IKK- was only detected in the presence of STAP-2. Therefore, STAP-2 associates with MyD88 and IKK-, and plays a role in forming a complex of these three molecules.
1492	16365431_MI:0007	When expression vectors for FLAG-tagged MyD88 or His-tagged IKK- together with Myc-tagged STAP-2 were transfected into 293T cells and the cells were lysed, immunoprecipitated with an anti-Myc Ab, and immunoblotted with an anti-FLAG or anti-His Ab, the immunoprecipitates contained MyD88 and IKK- (Fig. 3, B and C), indicating that STAP-2 associated with MyD88 and IKK- in 293T cells.
1493	16369483_MI:0007	Selective interactions of chromogranins with mutant SOD1 species but not with wild-type SOD1.
1494	16407827_MI:0007	As shown in Figures 7a and b, mycPLD2 WT interacts with Sos in vivo.
1495	16415207_MI:0007	The immunoprecipitates were examined for the presence of CDKA;1 by protein gel blot analysis with an antibody specific to the peptide sequence PSTAIR, which CDKA;1 only contains in Arabidopsis. A signal band was detected at a position corresponding to the 34-kD band (Figure 8A), indicating that mDB-CYCA2;3-GFP binds to CDKA;1 in planta
1496	16415858_MI:0007	Western blot analysis (right panel) showing co-immunoprecipitation and interaction of Arf6-HA with c-HSV in HEK cells.
1497	16415858_MI:0007	Western blot analysis using anti-Arf6 antibody shows the specific co-immunoprecipitation of endogenous Arf6 (upper panel) but not Arf1 (lower panel) with the c-subunit from MTC, HeLa and HEK vesicular fractions. (i, j)
1498	16449187_MI:0007	or the ability of Bub2-myc9 to pull down Bfa1-HA6 and vice versa (Fig. 5 G).
1499	16449236_MI:0007	HA-PITX2A was recovered by {alpha}-Xpress in an Xp-FOXC1-dependent manner
1500	16449236_MI:0007	Xp-FOXC1 was recovered in {alpha}-HA IP isolates in an HA-PITX2A-dependent fashion
1501	16461343_MI:0007	However, only the DACS mutant of PTPN22 co-immunoprecipitated significant amounts of phosphorylated TCR{zeta} (seen as multiple bands on the immunoblot; Fig. 5A, lanes 1 and 2), indicating that the substrate-trapping mutant of full-length PTPN22 interacts with TCR{zeta} in transfected cells.
1502	16472779_MI:0007	AtCRK3 was specifically co-immunoprecipitated with AtGLN1;1 and vice versa. These results suggest that AtCRK3 and AtGLN1;1 associate in Arabidopsis cells.
1503	16472779_MI:0007	In vitro binding assays for AtGLN1;1 and AtCRK3.
1504	16473966_MI:0007	CFP-tagged SERK1 was immunoprecipitated with anti-GFP antibodies, and the precipitated proteins were detected using anti-BRI1 antibodies. A band with the expected mobility of BRI1 was visualized (Figure 3A, lane 1) that was absent in an immunoprecipitation of wild-type plants with the GFP antibody
1505	16476580_MI:0007	When Myc-Nek6 was immunoprecipitated, Flag-Pin1 was co-precipitated with Nek6 (Fig. 2B, lane 6 ) blotted with anti-Flag mAb.
1506	16497658_MI:0007	Clearly, AtCyp59-GFP coprecipitated significant amounts of RNA pol II
1507	1651502_MI:0007	We also show that UBC2 is physically associated with UBR1, the recognition component of the N-end rule pathway.
1508	16525419_MI:0007	Nck recruitment to phosphorylated nephrin facilitates localised actin reorganisation.
1509	16533805_MI:0007	The resulting mutant protein was expressed in human kidney epithelial (HEK293) cells and compared with wild-type, FLAG-tagged MKK7 for its ability to bind to co-overexpressed JNK1, as assessed by co-immunoprecipitation (Fig. 5A).
1510	16537536_MI:0007	Deletion mutational analyses revealed that the minimum binding domain of Asf1 for p60, histones H3/H4, and HIRA was confined to 1-155 aa, which lacks a Ser- and Thr-rich region of the C-terminal tail.
1511	16537536_MI:0007	Deletion mutational analyses revealed that the minimum binding domain of Asf1 for p60, histones H3/H4, and HIRA was confined to 1-155 aa, which lacks a Ser- and Thr-rich region of the C-terminal tail. This N-terminal domain, containing 10 beta-sheets, has been well defined to be structurally conserved
1512	16537536_MI:0007	mutant protein Asf also abolished binding ability as to p60 but retained binding ability to histones H3/H4 (Fig. 5B). These findings were also confirmed in COS-7 cells, in which those were transiently expressed
1513	16537908_MI:0007	This ESCL-E(Z) complex appears identical in subunit composition to an ESC-E(Z) complex purified in parallel (lanes 1 and 2) except for the replacement of ESC with ESCL.
1514	16537909_MI:0007	We generated strains coexpressing endogenous COOH-terminal fusions of Glc7-HA3 with Pex31-myc13, Sol1-myc13, and Fun21-myc13 and found that all three proteins immunoprecipitated Glc7 (Fig. 4B).
1515	16541025_MI:0007	Meiotic shugoshin of fission yeast also associates with PP2A, with both proteins collaboratively protecting Rec8-containing cohesin at centromeres.
1516	16555005_MI:0007	In cells co-synthesising epitope-tagged Tre-GAP and Myl2 or LOC91526, we detected the expected interactions by immunoblotting (Figure 3), thus confirming their occurrence in vivo.
1517	16567647_MI:0007	Co-IP assays with hNkd1 show that both PR72 and PR130 interact with Nkd, and the PP2A holoenzyme complex components PR65 and PP2Ac are also coimmunoprecipitated (Fig. 1C).
1518	16567647_MI:0007	We generated a hemagglutinin (HA)-tagged expression construct for PR130 and found that, when coexpressed with flag-tagged human Naked cuticle (hNkd1) in human embryonic kidney (HEK) 293 cells, HA-PR130 was detected in an anti-flag-IP
1519	16581772_MI:0007	HA-tagged AGO1 immunoprecipitated very inefficiently (Fig. 5A). Nonetheless, miR-13b and bantam coimmunoprecipitated with HA-tagged AGO1 (Fig. 5B). HA-tagged AGO2 also immunoprecipitated these miRNAs above background levels, indicating that a small fraction of endogenous miRNAs can be found in association with AGO2 (Fig. 5B).
1520	16603654_MI:0007	These results support in vivo interactions of WRKY18 protein with itself and with WRKY40 and WRKY60.
1521	16612387_MI:0007	In 293T cells, IKK-a co-immunoprecipitated with IRF-7
1522	16636664_MI:0007	Flag-TRAF2 but not Flag-TRAF6 specifically associated with GSTP1-1
1523	16636664_MI:0007	GSTP1 inhibits TRAF2-induced ASK1 catalytic activity.
1524	16636664_MI:0007	interaction between TRAF2 and MEKK1
1525	16636664_MI:0007	Mapping of TRAF2 domains required for GSTP1-1 binding
1526	16643855_MI:0007	Co-immunoprecipitation between ZCCHC11L and TIFA was clearly observed only after LPS treatment.
1527	16672379_MI:0007	As seen in Figure 1C, coimmunoprecipitations of GFP-SNAP-25 revealed interaction with myc-tagged 5'LCR.
1528	16672379_MI:0007	To test whether Rab11a is contained within the same 5'LSD/GFP-SNAP-25 complex, whole protein lysates from cotransfected COS-7 cells were collected and analyzed. Lysates containing transfected 5'LSD and GFP-SNAP-25 proteins were probed for Rab11a and were subsequently found to contain endogenous Rab11a in the 5'LSD/GFP-SNAP-25 complex (Figure 5). Myosin Vb, a key regulator of Rab11a-containing recycling vesicles (Lapierre et al., 2001), was also found in the complex (Figure 5). We coimmunoprecipitated the same lysates and identified VAMP2 to be associated in the complex (Figure 5).
1529	16682412_MI:0007	DNMT3s (DNMT3A and DNMT3B2) instead of DNMT1 associate with SETDB1.
1530	16740636_MI:0007	CatSper1 was detected in the proteins immunoprecipitated by anti-Cav3.3 antibody only when Cav3.3 and CatSper1 co-expressed in the cells.
1531	16760425_MI:0007	Furthermore, we generated a U2OS cell line stably expressing a GFP-CaM fusion protein to examine whether immunoprecipitates of the epitope-tagged protein contain endogenous CP110. We observed that endogenous CP110 specifically coimmunoprecipitates with recombinant GFP-CaM (Figure 1C).
1532	16762630_MI:0007	we made DP1-Myc fusion protein and incubated the fusion protein with protein extracts from HEK 293 cells transfected with HCCR-1 fused to a V5 (Invitrogen). HCCR-1 protein specifically coprecipitated with DP1
1533	16766265_MI:0007	HEK293 cells were transiently cotransfected with hemagglutinin (HA)-tagged-HMGA2 and pRB expression vectors. Protein lysates were immunoprecipitated with antipRB or anti-HA antibodies and immunoblotted with anti-HA or anti-pRB, respectively (Figure 2A, right panels). Coexpression of pRB and HMGA2 resulted in coimmunoprecipitation of the two proteins.
1534	16775625_MI:0007	Interaction of hPFTAIRE1 with 14-3-3 proteins in HeLa cells
1535	16775625_MI:0007	The physical interactions between the hPFTAIRE1 and the four 14-3-3 isoforms were confirmed by coimmnoprecipitation in yeast cells.
1536	16777605_MI:0007	Thus, DAF-16 can physically interact with 14-3-3 proteins in C. elegans.
1537	16777956_MI:0007	Interestingly, PKS1 coimmunoprecipitated with phot1-GFP and phot1 coimmunoprecipitated with PKS1-GFP, whereasneither of those proteins were present in the Col-O andLTI6b-GFP controls, showing that phot1 and PKS1 interact invivo
1538	16815998_MI:0007	We observed that Drosophila AGO1 coimmunoprecipitated with HA-GW182 from S2 cell lysates, but not with the negative control, an HA fusion of maltose-binding protein (MBP) (Fig. 3A, lanes 9,10).
1539	16828757_MI:0007	As shown in Fig. 1C, pcDNA4/HisMax- CCS-3 was co-immunoprecipitated with pEGFPC1-PLZF
1540	16845383_MI:0007	Mutations of Mdm2 at Ser395 do not affect the interactions of Mdm2 with Daxx and Hausp. p53-/-Mdm2-/- MEF cells were co-transfected with HA-Daxx, HA-Hausp, together with Flag- Mdm2, -Mdm2(S395A), or -Mdm2(S395D) as indicated. Cells were treated with 20 &#956;M MG-132 for 4h. Lysates and anti-Flag immunoprecipitates were analyzed by Western blot.
1541	16854975_MI:0007	SPA proteins interact with CO in vitro.
1542	16854975_MI:0007	The CCT domain of CO is necessary for the in vitro interaction with SPA1.
1543	16857903_MI:0007	BKI1-FLAG interacts with endogenous BRI1 in planta.
1544	16862148_MI:0007	Endogenous FLNa associates with recombinant FilGAP in cells.
1545	16868027_MI:0007	ADAM22 interacts with all 14-3-3 protein family members expressed in the brain. HEK 293T cells co-expressing FLAG-tagged full length ADAM22v4 and Myc-tagged full length 14-3-3 proteins , , , , or HA-tagged 14-3-3 were lysed and proteins were immunoprecipitated (IP) with anti-Myc or anti-HA antibodies and probed with anti-FLAG antibody. Immunoblots were then re-probed with anti-Myc or anti-HA antibodies.
1546	16885985_MI:0007	The Coomassie-stained gel also revealed a band at a molecular mass of about 130 kDa, which by immunoblot was identified as MYPT-1
1547	16887178_MI:0007	physical binding occurs between endogenous DmIKK3 and endogenous DIAP1 in S2 cells
1548	16888242_MI:0007	FHL2 interacted only with SK1 C-terminal portion consisting of C4 and C5 domains
1549	16888242_MI:0007	Immunoprecipitation of FLAG-tagged SK1 led to coimmunoprecipitation of Myc-tagged FHL2 when both proteins were cotransfected
1550	16888242_MI:0007	immunoprecipitation of Myc-tagged FHL2 resulted in coimmunoprecipitation of FLAG-tagged SK1
1551	16888242_MI:0007	SK2, which shares approximately 80% similarity with SK1 in the C-terminal portion,11 also interacted with FHL2
1552	16892067_MI:0007	MST1 and RAPL could be immunoprecipitated together using antibody to V5 (anti-V5) or anti-Myc. Deletion of the C-terminal region of RAPL abolished its association with MST1 but deletion of the N-terminal region of RAPL did not (Fig. 1a)
1553	16901789_MI:0007	RMA1 and CFTRDF508 can be coprecipitated with each other.
1554	16905657_MI:0007	In addition to to HA:VSTI11, ESPIN1:GFP was detected in the immunoprecipitaes.
1555	16905657_MI:0007	In addition to VSR1:HA, EPSIN1:GFP was detected in the immunoprecipitates.
1556	16919153_MI:0007	Cdc48p and Npl4p coprecipitate with Sel1p-HA.
1557	16919237_MI:0007	BRMS1 and FLAG-epitope tagged HDAC-cDNAs were co-transfected in COS7. The immunoprecipitations by anti- FLAG antibodies showed BRMS1 co-immunoprecipitation (Fig. 5A). The reverse co-immunoprecipitation further confirmed these interactions
1558	16923726_MI:0007	In vitro translated AtPEX19 interacts with PEX10.
1559	16930133_MI:0007	As seen in Fig. 1B, both Mst1 and Mst2 were efficiently coimmunoprecipitated with flag-Sav.
1560	16930133_MI:0007	hSalvador can homo-multimerize independently of its C-terminal coiled-coil domain
1561	16930133_MI:0007	Moreover, endogenous Mst1 was easily detected in antiflag immune complexes in cells that expressed flag-Sav.
1562	16963448_MI:0007	When insect cells were infected with baculoviruses expressing GST-Chk1 and FLAG-Claspin, we observed an interaction between Chk1 and Claspin by either pulldown with glutathione beads (Fig. 2A) or immunoprecipitation using anti-FLAG beads (Fig. 2B).
1563	16963744_MI:0007	From the results shown in Fig. 4(b), BHRF1 could be precipitated from HA-tagged VRK2-transfected N27-2 cells by using anti-HA antibody.
1564	16963744_MI:0007	From the results shown in Fig. 4(b), BHRF1 could be precipitated from HA-tagged VRK2-transfected N27-2 cells by using anti-HA antibody. The interaction was also observed in a reciprocal experiment
1565	16966434_MI:0007	HA-ZNF652 was clearly detected in complexes immunoprecipitated with anti-myc antibody that binds to myc- CBFA2T3
1566	16966434_MI:0007	This interaction was specific to CBFA2T3 as coimmunoprecipitation of the related proteins CBFA2T2 and CBFA2T1 showed only a weak interaction with ZNF652
1567	16982639_MI:0007	Interaction of XE7 with ZNF265
1568	16982639_MI:0007	Interaction of XE7 with ZNF265F
1569	16990252_MI:0007	In co-immunoprecipitation assays, FLAP1 associated strongly with the C-terminal fragment of GRIP1 and weakly with the N-terminus of GRIP1 and with catenin (Figure 3B, upper panel, lanes 3, 5 and 6).
1570	16997270_MI:0007	A substantial amount of Skp1 also copurified with Pof3-13myc (Fig. 1B), again serving as an internal control.
1571	16997270_MI:0007	To confirm this interaction in Schizosaccharomyces pombe cells we performed immunoprecipitation experiments (Fig. 1B and C). Strains carrying either Pof3-13myc or GFP-Mcl1, the latter under the control of the thiamine-repressible nmt1 promoter, or both were grown in YE5S medium, harvested, and immunoprecipitation was performed from cell extracts using either anti-myc (Fig. 1B) or anti-GFP antibody (Fig. 1C). Western blot analysis of the precipitates showed that the band corresponding to GFP-Mcl1 could only be detected in the samples containing Pof3-13myc, demonstrating that purification of GFPMcl1 is dependent on its interaction with the F-box protein. The same was true for the immunoprecipitation of GFPMcl1 (Fig. 1C), in which Pof3-13myc could only be precipitated with GFP antibodies in the presence of GFP-Mcl1 but not in its absence. We therefore concluded that Mcl1 is indeed a binding partner of Pof3.
1572	17007873_MI:0007	Physical and functional interactions between PP1c isoforms and a novel PP1c-binding protein, CG1553.
1573	17008405_MI:0007	The analysis, done in duplicate for each sample, revealed numerous FLAG-CPSF100-specific peptides corresponding to ESP5 CPSF100, CPSF160, CPSF73, ESP4, and FY. FY is a homologue of yeast Pfs2p, which is part of the CPF complex in Saccharomyces cerevisiae
1574	17012248_MI:0007	Immunoprecipitates by an anti-FLAG Ab contained Siglec-14, and Siglec-14 R362A mutant showed negligible association with DAP12 (Fig. 5 )
1575	17016471_MI:0007	However, it is not likely to be the case because when immunoprecipitating Skp1 in the presence or absence of stress (40 min, 0.2mM H2O2), a similar amount of Pof14 was co-precipitated (Figure 3D), although the total Pof14 concentration was elevated as shown above (Figure 3B). This rather suggests that the SCF might be saturated when Pof14 is induced, therefore leading to a stabilisation of the Pof14 pool present in the cell. Pof14 could then only reach its normal level after transcriptional induction has been turned off.
1576	17016471_MI:0007	Pof14 and Erg9 could be co-immunoprecipitated from fission yeast extracts (Figure 2C), supporting the fact that the two-hybrid interaction is physiologically relevant. However, neither Skp1 (Figure 2C) nor Pcu1 (data not shown) could be co-immunoprecipitated with Erg9, raising the possibility that two Pof14-containing complexes might coexist in vivo, one of them being a canonical SCF and the other one containing Erg9.
1577	17016471_MI:0007	The induction of pof14 transcription by hydrogen peroxide prompted us to analyse the Pof14-Erg9 interaction under oxidative stress conditions (H2O2 0.2mM for 40 min). An increased amount of Pof14, proportional to its elevated level in total cell extract, was co-precipitated by Erg9, suggesting that after induction, the newly synthesised Pof14 proteins bind to Erg9 (Supplementary Figure 1).
1578	17016471_MI:0007	We checked the ability of Pof14 to form an SCF complex in vivo. Co-immunoprecipitations from fission yeast extract revealed that Pof14 forms a complex with the SCF core components Skp1 and Pcu1 (Figure 1D).
1579	17041588_MI:0007	To confirm these interactions, these WDR proteins were tagged with a Flag-epitope tag and expressed in human cells by transfection (Fig. 2). Our studies confirmed that these WDR proteins interact with the CUL4-DDB1 complexes in vivo
1580	17095503_MI:0007	FLAG-Nix was detected only in immunoprecipitates from cells expressing Myc-ZnPOSH
1581	17095503_MI:0007	we also performed reciprocal immunoprecipitations using anti-FLAG. Fig. 1B shows that Nix and ZnPOSH again specifically co-immunoprecipitated under these conditions.
1582	17098746_MI:0007	Flag-FBXO11 transfected into HEK 293 cells co-immunoprecipitates endogenous Cullin1, Skp1 and Roc1
1583	17113272_MI:0007	antibodies against Parafibromin co-precipitate BCL9-2
1584	17113272_MI:0007	If BCL9-2 is a functional homolog of Lgs, it should also, like Lgs, bind Pygo in vivo (Thompson, 2004). This assumption was confirmed by co-immunoprecipitation experiments in HEK293T cells
1585	17138694_MI:0007	By contrast, SUF4:MYC was detected in the anti-HIS or anti-HA immunoprecipitates repeatedly, demonstrating the direct physical interactions of SUF4 with FRI, FRL1, and LD in plant cells.
1586	17157259_MI:0007	We confirmed the interaction between c-Myc and SNIP1 in HEK293 cells using transiently overexpressed c-Myc and HA-tagged SNIP1
1587	17157788_MI:0007	A strong interaction between Che-1 and Chk2 was detected after DNA damage (Figure 3C) and confirmed in U2OS cells transfected with Myc-Che-1 and Flag-Chk2 and treated with Dox or IR
1588	17157788_MI:0007	Myc-Che-1 strongly interacted with p65 whereas Myc-Che-1S4A did not bind this protein,
1589	17158449_MI:0007	The GFP fusion protein containing TAK1-C100 and TAK1-(479-553) interacted with both TAB2 and TAB3 by co-immunoprecipitation
1590	17159996_MI:0007	Our results indicated the presence of a series of slowly migrating bands (because sumoylation increases the relative molecular mass (Mr) of the target protein by 15,000-20,000) in cells that were coexpressing PTP1B and SUMO-1, indicating that PTP1B was sumoylated at multiple sites (Fig. 1b).
1591	17183697_MI:0007	Cno and N proteins directly interacted in vitro
1592	17183697_MI:0007	We found that addition of increasing amounts of Dsh led to reduced amounts of RasV12 (RasAct) co-immunoprecipitated with Cno
1593	17189269_MI:0007	After HA-5-HT6R and Fyn were transfected into CHO/K-1 cells, the immunoprecipitation was performed with either anti-HA or anti-Fyn antibodies.
1594	17189269_MI:0007	As shown in Fig. 2C, the transfected HA-5-HT6R was able to bind to endogenous Fyn (lane 2) in the HEK293 cells while no signal was detected from non-transfected cells (lane 1)..
1595	17189269_MI:0007	As shown in Fig. 2D, HA-5-HT6R was co-immunoprecipitated with both exogenous (lane 2 & 3) and endogenous Fyn (lane 4) while no signal was detected in immunoprecipitates from non-transfected cells (lane 1).
1596	17196367_MI:0007	As shown in Fig. 4b (lower right panels), PKD3 was detected in VAMP2 immunoprecipitates
1597	17196367_MI:0007	In contrast, VAMP2 was only minimally detected in the PKD3 immunoprecipitates
1598	17196367_MI:0007	the association  of PKD3 and VAMP2 was confirmed in vivo in mammalian cells by Immunoprecipitation (IP).
1599	17210579_MI:0007	HA-ASK1-CT but not HA-ASK1-
 was found to be co-precipitated  with FLAG-ASK2, indicating that ASK1-CT was necessary and sufficient for the binding of ASK1 to ASK2 (Fig. 3B).
1600	17210579_MI:0007	We also detected the interaction between Myc-tagged ASK1 (Myc-ASK1) and FLAG-tagged ASK2 (FLAG-ASK2) by co-immunoprecipitation analysis in HEK293 cells (Fig. 1D).
1601	17210637_MI:0007	HA-tagged NF2 and Flag-tagged NGB were cotransfected into HEK293 cells. After 48 h of the transfection, the cells were lysed and immunoprecipitated with anti-HA (NF2) or anti-Flag (NGB) antibody. The immunoprecipitates were subjected to Western blot analysis. As shown in Fig. 2A and B, Flag-NGB and HA-NF2 were readily detected in anti-HA and anti-Flag immunoprecipitates, respectively.
1602	17210637_MI:0007	Immunoprecipitation experiments showed that mutation of lysine-395/arginine-394 to alanine (NGB-K395/R394A) significantly reduced the ability of NGB to bind to merlin
1603	17213653_MI:0007	By both co-immunoprecipitation and yeast two-hybrid experiments, specific interaction between Rcr1 and the ubiquitin ligase Rsp5 was found.
1604	17216128_MI:0007	Interestingly, immunoprecipitation with an anti-Myc antibody for LKB1 was able to co-purify the Flag-tagged WDR6 (Fig. 1A).
1605	17220200_MI:0007	We next examined whether the full-length PIP5K9 protein was able to interact with CINV1. The entire coding regions of PIP5K9 and CINV1 were fused with those of binding domain (BD) and activating domain (AD), respectively, and the resulting constructs harboring fused MYC-PIP5K9 and HA-CINV1 were cotransformed into yeast cells. Detection of the relevant proteins with antibodies showed that anti-MYC antibody not only immunoprecipitated MYC-PIP5K9 but also coimmunoprecipitated HA-CINV1 from the protein extracts, whereas no HA-CINV1 signals were detected from the immunoprecipitates of yeast cells expressing MYC-PIP5K9 and HA or HA-CINV1 and MYC (two negative controls). These results confirm the interaction of PIP5K9 and CINV1 in yeast cells
1606	17237231_MI:0007	hSR-A clearly interacted with the N-terminal truncated form of hHK3
1607	17237231_MI:0007	in HEK293 cells and immunoprecipitated by anti-V5-agarose, endogenous hHK3 was cosedimented with full-length hSR-A
1608	17237231_MI:0007	the amount of hHK3 co-sedimented with hSR-A was apparently increased after fucoidan was added to the cells.
1609	17237354_MI:0007	indicating that PGP1-cmyc and PIN1 coimmunoprecipitated.
1610	17237354_MI:0007	Reciprocal coimmunoprecipitations of microsomal proteins from PGP19-HA overexpression lines were performed using anti- HA, and protein gel blots probed with PIN1 antiserum showed a signal at ;67 kD
1611	17237354_MI:0007	This finding indicates that PIN1-GFP coimmunoprecipitated with PGP19.
1612	17255092_MI:0007	The co-immunoprecipitations between SRG3 and other components (SNF5, BAF60a, and BAF57) of the SWI/SNF complex are also carried out to result in the same conclusions
1613	17255092_MI:0007	wild-type SRG3 and the N-terminal region of SRG3 were co-immunoprecipitated with SNF5, but the C-terminal region of SRG3 was not.
1614	17272281_MI:0007	Rad4TopBP1 Associates with Srr2 Protein in Response to Environmental Stress, and the Association Is Compromised by the Mutation in rad4-c17TopBP1
1615	17276458_MI:0007	Moreover, Grb2 association with PLD2 appeared to be independent of EGFR stimulation of COS7shGrb2 cells
1616	17276458_MI:0007	PLD2 WT interacts with Grb2/Sos
1617	17280616_MI:0007	Immunoblotting of the precipitates using anti-HA antibodies indicated that Flag-Bcl-GL was co-precipitated with HA-WT-MELK
1618	17283121_MI:0007	Ku70 seems to suppress the transcriptional activity of TCF-4 by inhibiting the participation of beta-catenin in the transcriptional complex containing TCF-4.
1619	17283121_MI:0007	Ku70 was coimmunoprecipitated with FLAG-TCF-4 even in the absence of PARP-1 (Fig. 4A), revealing that PARP-1 is not necessary for the interaction between TCF-4 and Ku. Restoration of PARP-1 did not affect the total amount of Ku70 in the nucleus (Fig. 4B, Total), but the amount of Ku70 coimmunoprecipitated with FLAG-TCF-4 was reduced (Fig. 4B, IP: FLAG), suggesting that PARP-1 competes with Ku70 for binding to TCF-4.
1620	17283121_MI:0007	Only the full-length Ku70 protein (WT) and the Ku70 protein lacking the SAP domain (DC560) interacted with TCF-4
1621	17283121_MI:0007	The protein identification was confirmed by Western blotting with anti-Ku70 and anti-Ku80 antibodies. Ku70, Ku80, and PARP-1 proteins were detected in the immunoprecipitate with anti-FLAG antibody
1622	17283121_MI:0007	To identify the region of TCF-4 that is essential for its interaction with Ku70, we expressed serially truncated forms of FLAG-TCF-4 and evaluated their binding activity to Ku70 (Fig. 2A). Only constructs carrying the high-mobility group (HMG) box [wild-type (WT), DC439, and DN316] were found to bind to Ku70
1623	17283121_MI:0007	We previously identified one of these proteins as PARP-1 (Fig. 1A). Proteins of f70 kDa (Fig. 1A, b) and 86 kDa (Fig. 1A, a) were also constantly coimmunoprecipitated with FLAG-tagged TCF-4 and were subjected to protein identification by mass spectrometry. Peptide mass fingerprinting and tandem mass spectrometry (data not shown) revealed that these proteins were Ku70 (70-kDa thyroid autoantigen/thyroid-lupus autoantigen/G22P1) and Ku80 (X-ray repair, complementing defective, in Chinese hamster, 5/XRCC5).
1624	17289571_MI:0007	the Ste5-16E mutant showed normal protein levels (Figure 3C), and it still bound Ste4
1625	17292829_MI:0007	We confirmed that Gstm2 can also interact with ASK1
1626	17292860_MI:0007	To determine whether PSMA1 and Notch3 could interact in mammalian cells, we performed immunoprecipitations in transfected 293 cells. Notch3 specifically immunoprecipitated with PSMA1, suggesting that the two proteins bind in mammalian cel
1627	17297443_MI:0007	we co-transfected expression vectors that can produce the flag(f)-epitopetagged FL and ND133 HtrA2 proteins, and a myc epitope- tagged GRIM-19 protein into MCF-7 cells. Cell lysates were immunoprecipitated (IPed) using mycepitope tag-specific antibodies and then subjected to a Western blot (WB) analysis with f-tag-specific antibodies
1628	17297443_MI:0007	we transfected GRIM-19 into MCF-7 cells and stimulated with IFN/RA for various time points. Cell lysates were IPed with myc-tag specific antibodies and the products were subjected to WB analysis with HtrA2-specific antibodies (Figure 3k and m). IFN/RA stimulated GRIM-19s interaction with endogenous HtrA2
1629	17304241_MI:0007	We observed that ZYG-11 co-purified with CUL-2-Flag, by using both western blot and mass spectrometry, indicating physical association in vivo
1630	17308091_MI:0007	Experiments introducing Fl-HOXB7 into CHO cells (Fig. 4A) showed that coexpression of human Ku70 and human Ku80 was required for the association of either Ku subunit with HOXB7.
1631	17308091_MI:0007	Immunoprecipitation with GFP antibodies (which also recognize the YFP variant) showed that Ku70 and Ku80 associated with HOXB7 in vivo
1632	17308091_MI:0007	The results showed that deletion of helix 3 from the homeodomain in HOXB7 (lane 3) completely abolished the interaction between HOXB7 and Ku70/80 proteins.
1633	17310983_MI:0007	HA-p53 was detected in GFPS7 immunoprecipitates of lysates from cells transfected with GFP-S7, T7-MDM2 and HA-p53, but not in cells overexpressed with one or two of these. This indicates the formation of a ternary complex among MDM2, S7 and p53.
1634	17310983_MI:0007	When full-length S7 and different mutants of MDM2 were co-transfected into COS7 cells, sequential immunoprecipitation and immunoblotting assays showed that the binding region in MDM2 is between aa 180-298
1635	17310983_MI:0007	When full-length S7 and different mutants of MDM2 were co-transfected into COS7 cells, sequential immunoprecipitation and immunoblotting assays showed that the binding region in MDM2 is between aa 180-298 (Figure 1g1). Similarly, S7 aa 59-134 are responsible for the S7-MDM2 binding in COS7 cells (Figure 1g2).
1636	17310983_MI:0007	when pCGT-T7-MDM2 and pCMV-Myc-S7 were co-transfected into COS7 cells, sequential immunoprecipitation (IP) using a Myc antibody (Figure 1c1) or T7 antibody (Figure 1c2) and immunoblotting assay with a T7 antibody or Myc antibody demonstrated binding between MDM2 and S7
1637	17310990_MI:0007	Precipitation of INT6 using the antibody to FLAG was found to bring down MCM7 and conversely INT6 was coprecipitated when MCM7 was pulled down with the antibody to the MYC epitope
1638	17314099_MI:0007	To map the domain(s) within STRAP required for its association with NM23-H1, we generated a set of eight STRAP deletion mutants (Fig. 3A) and examined their ability to interact with NM23-H1 in an in vivo binding assay.
1639	17314511_MI:0007	Coimmunoprecipitation of exogenous c&#8209;MYC with endogenous proteins. HEK293T cells transfected with an expression construct for c&#8209;MYC&#8209;HA or untransfected control cells were subjected to immunoprecipitation with mouse anti&#8209;HA antibody and precipitates were analyzed by Western blot.
1640	17314511_MI:0007	The conserved MYC&#8209;box II was indispensable for the interaction with MCM7
1641	17314511_MI:0007	The conserved MYC-box II and the C-terminal BR-HLH-LZ domain of c-MYC were also necessary for the interaction with FBX29.
1642	17324924_MI:0007	Lysates from cells cotransfected with pcDNA3-Myc-HIF-2; and pcDNA3-HA-Int6-wt (lane 1), pcDNA3-HA-Int6-;C (lane 2, amino acids 1-326), pcDNA3-HA-Int6-N (lane 3, amino acids 1-150) or pcDNA3-HA-Bax (lane 4) were immunoprecipitated (IP) with anti-HA-conjugated agarose (middle panel, input), and detected by anti-HA antibody on western blots. Coimmunoprecipitated (Co-IP) Myc-HIF-2; was detected by western blotting with anti-Myc polyclonal antibody
1643	17347412_MI:0007	ABA disrupts the GCR2-GPA1 interaction in yeast.
1644	17347412_MI:0007	We also confirmed their in vivo interaction by a coimmunoprecipitation assay. GCR2 and GPA1 can be coimmunoprecipitated; and we could detect GPA1 in the immunocomplex precipitated with an antibody to FLAG from GCR2-FLAG transgenic plants (Fig. 1C). Thus, results from four distinct assays all supported the interaction between GCR2 and GPA1.
1645	17347654_MI:0007	293T cells were transfected with Myc-PRB and HA-CUEDC2 and cultured in the absence or presence of 100 nM progesterone (Figure 1B). HA-CUEDC2 was immunoprecipitated from cell lysates by anti-HA and analyzed for Myc-PRB binding by immunoblotting. As indicated in Figure 1B, Myc-PRB could be co-immunoprecipitated in a ligand-independent manner in the presence of HA-CUEDC2.
1646	17347654_MI:0007	As shown in Supplementary Figure S2A, we found that CUEDC2 also interacted with ERa.
1647	17349584_MI:0007	hCdc25C and hLzts1 coprecipitated
1648	17349584_MI:0007	hCdc25C and hLzts1 coprecipitated (Figure 6C), and the increased expression of hLzts1 resulted in increased interaction between hCdc25C and endogenous Cdk1
1649	17350576_MI:0007	SSH1L-GFP coimmunoprecipitated both Coronin 1B and Arp2/3 complex from a mock depleted lysate
1650	17350576_MI:0007	SSH1L-myc interacted with endogenous Coronin 1B using reciprocal coimmunoprecipitations (Figure 4H). Arp2/3 complex (as reported by the p34 subunit) was detected in both the Coronin 1B and SSH1L immunoprecipitates.
1651	17353262_MI:0007	In addition, endogenous XRCC1 was immunoprecipitated from Myc-APLF-transfected HeLa cell extracts by anti-Myc antibodies but was not immunoprecipitated by control anti-FLAG antibodies (Fig. 2B, upper panel) or by anti-Myc antibodies from untransfected cells (Fig. 2B, lower panel).
1652	17369373_MI:0007	Anti-glutathione S-transferase (GST) antibodies were able to pull down not only the recombinant GST-tagged version of ESR with the size of &#8764;64 kD but also the recombinant His-tagged version of WRKY53 with the size of &#8764;40 kD
1653	17374643_MI:0007	The reverse experiment, precipitation with an anti-HA antibody, again confirmed the interaction of PR65alpha5 with the HREV1dCHA
1654	17374643_MI:0007	Using the anti-V5 antibody for immunoprecipitation, we observed the HREV1dCHA protein only in the presence of PR65alphaV5
1655	17395368_MI:0007	a co-IP experiment was performed with Flag-FB1 and Myc-ELL. The cell lysates were immunoprecipitated with Myc-antibody- conjugated agarose and then immunoblotted with Flag antibody. Fig. 5a shows that FB1 interacts with ELL.
1656	17395368_MI:0007	Fig. 1a shows that Myc-FB1 co-precipitated GFP-U19/EAF2, but not GFP.
1657	17395368_MI:0007	Fig. 3 shows that Myc-FB1 co-precipitated GFP-EAF1, but not GFP, confirming the interaction of FB1 with EAF1.
1658	17395368_MI:0007	Flag-U19/EAF2 also co-precipitated Myc-FB1, further demonstrating the interaction between FB1 and U19/EAF2
1659	17403664_MI:0007	Both Def-6 and Swap-70 Bind Specifically to the Cytoplasmic Part of the Integrin 7A Subunit
1660	17403664_MI:0007	Def-6 coprecipitated only with GST-{alpha}7A,
1661	17416892_MI:0007	Though in the absence of mycSP65 the beads nonspecifically pulled down a small amount of &#916;SP85, the amount was greatly increased if mycSP65 was present.
1662	17418796_MI:0007	Immunoprecipitation of CRY from fly head extracts with anti-MYC antibody followed by western blot with anti-SGG antibody validated the CRY-SGG interaction
1663	17418796_MI:0007	We then determined that the CRY-SGG interaction was direct both in transgenic flies and in S2 cells. First, SGGV5, CRY-His6, or both were overexpressed in S2 cells, immunoprecipitated with anti-V5 antibody, Nickel beads, or both, and probed for CRY, SGG, or both, respectively
1664	17446396_MI:0007	SCR is coimmunoprecipitated with SHR-GFP.
1665	17470967_MI:0007	Protein gel blots showing interaction between AtSWC6 and SUF3.
1666	17470967_MI:0007	The interactions of AtSWC6-SUF3, AtSWC6- AtSWC2, AtSWC2-HTA11, PIE1-SUF3, and PIE1-AtSWC6 were confirmed by the in planta coimmunoprecipitation assay.
1667	17474147_MI:0007	HA-tagged HPK1 was coexpressed with FLAG-tagged PLCg1 or an SH3-defective mutant in HEK293Tcells and their interactions probed by co-IP using an anti-FLAG antibody followed by Western blotting using an anti-HA antibody.
1668	17510388_MI:0007	The reciprocal immunoprecipitation was done in LAPC4cells expressing a NH2-terminally HA-tagged DJ-1. Immunoprecipitation with anti-HA antibody coimmunoprecipitated HA-tagged DJ-1, endogenous DJ-1, and AR. DJ-1 exists as an obligatory dimer
1669	17511879_MI:0007	Protein was immunoprecipitated using antibodies against BRCA1, or an antibody against the Flag epitope to immunoprecipitate Flag epitope tagged PP1, , or. BRCA1 coimmunoprecipitated all three PP1 isoforms, and conversely, PP1 , and coimmunoprecipitated BRCA1
1670	17513757_MI:0007	Only HA-PRP4-transfected COS7 lysates immunoprecipitated with an anti-HA Ab against tagged PRP4 pulled down KLF13 (Fig. 1A),
1671	17517622_MI:0007	As shown in Fig. 2C, p21 cCip1 was coimmunoprecipitated with full-length PFTK1 and its D1 derivative
1672	17517622_MI:0007	As shown in Fig. 2d, PFTK1 interacted with D, D2 and N fragments of p21Cip1
1673	17517622_MI:0007	On the other hand, another CDK inhibitor p16Ink4a failed to interact with PFTK1 although it associated with its known binding partner CDK4 readily,
1674	17517622_MI:0007	PFTK1 forms a ternary complex with p21Cip1 and CCND3
1675	17517622_MI:0007	The association between CCND3 and PFTK1 was relatively weak (Fig. 2f)
1676	17517622_MI:0007	To examine the in vivo interaction and physiological relevance between PFTK1 and p21Cip1 identified in the yeast two-hybrid screening, we first conducted semiendogenous coimmunoprecipitation experiments.
1677	17525340_MI:0007	Binding of ABRA1 to BRCA1 requires phosphorylation
1678	17525340_MI:0007	CtIP was detected in RAP80 immunoprecipitates
1679	17535814_MI:0007	we used rabbit anti-GFP antibody to immunoprecipitate wild-type GFP-HsNUF2 proteins and potential partner proteins from lysates of mitotically arrested HeLa cells transiently transfected to express wild-type HsNUF2 and deletion mutants
1680	17540172_MI:0007	H1b coprecipitated with L3MBTL1-F but not with L3MBTL2-F using anti-FLAG antibodies (Figure 3A).
1681	17540172_MI:0007	H1b coprecipitated with L3MBTL1-F but not with L3MBTL2-F using anti-FLAG antibodies (Figure 3A). A similar result was obtained in reciprocal immunoprecipitation assays (Figure S5).
1682	17540172_MI:0007	HP1gamma was detected in the L3MBTL1 and L3MBTL2 affinity-purified fractions (Figure 2C), a result consistent with previous findings (Ogawa et al., 2002). This interaction is specific, as the L3MBTL3-F affinity-purified fraction was devoid of HP1gamma. Using two antibodies from different sources, we also detected the human Rb protein within the affinity-purified L3MBTL1 and L3MBTL2 samples
1683	17540172_MI:0007	L3MBTL1 Associates with Core Histones, Histone H1 and HP1gamma
1684	17540172_MI:0007	the observed interaction of HP1&#947; with L3MBTL1-F (Figure 1A) could be mediated through its interaction with H1. However, the amount of endogenous HP1&#947; in the anti-FLAG immunoprecipitates was relatively similar regardless of whether H1b was coprecipitated or not (Figure 3C).
1685	17540176_MI:0007	FLAG-tagged wild type Abeta and Abeta mutants were overexpressed HEK TER cells and immune complexes were isolated using anti-Flag (M2) agarose.  Immunoprecipitation was followed by immunoblotting with antibodies specific for B55alpha, B56gamma, B56delta, B56epsilon, Calpha or FLAG.
1686	17540176_MI:0007	FLAG-tagged WT Abeta and Abeta mutants were overexpressed HEK TER cells, FLAG immune complexes were isolated, and immunoblotting was performed using antibodies against FLAG or PP2A Calpha subunits (lower panel).
1687	17540176_MI:0007	We also found that endogenous RalA interacts with FLAG-tagged Abeta in 293T cells (Figure 3D)
1688	17540176_MI:0007	When we attempted to verify these putative A&#946; interacting proteins, we found that the small GTPase protein RalA was the only protein that specifically formed complexes with A&#946; subunit (Figures 3D and S6B).
1689	17540176_MI:0007	When we overexpressed HA-tagged-RalA and FLAG-tagged Abeta in 293T cells, we found that immune complexes isolated using either HA- or FLAG-specific antibodies contained both RalA and Abeta (Figure 3E).
1690	17553790_MI:0007	Autoradiographs revealed the interaction of ILK and kAE1 in HEK 293 cells was detected immediately after the 1-h pulse (Fig. 7B).
1691	17553790_MI:0007	Co-immunoprecipitation was carried out using the lysate from HEK 293 cells co-expressing the kAE1 CH domain, with ILK or alone. Anti-His antibody brought down the CH domain when co-expressed with His-tagged ILK (Fig. 4, lane 2)
1692	17553790_MI:0007	{Delta}NtILK bound kAE1 efficiently (Fig. 2B, lane 2), indicating that the C-terminal catalytic domain of ILK is sufficient for kAE1 binding.
1693	17565979_MI:0007	A specific interaction of 3XFLAG-P-Rex1 full length with HA-mTOR prey is shown.
1694	17575050_MI:0007	AtCDC5 coimmunoprecipitates with MOS4-GFP in nuclear extracts from mos4-1 complemented by gMOS4-GFP transgenic plants
1695	17575050_MI:0007	Using an IP-Western procedure similar to what was done with MOS4, it was demonstrated that AtCDC5 coimmunoprecipitated with PRL1-GFP
1696	17577629_MI:0007	Co-IP assays showed that SETDB1 interaction with both Akt1 and Akt2
1697	17577629_MI:0007	Co-IP assays showed that SETDB1 interaction with both Akt1 and Akt2 (Fig. 4). Interestingly, it seems that the affinity of SETDB1 with Akt2 was higher than SETDB1 with Akt1, due to the fact that more SETDB1 proteins were co-immunoprecipitated by Akt2 (Fig. 4, top panel, lane 8) when equal amounts of Akt1 and Akt2 proteins were immunoprecipitated by Flag antibodies
1698	17577629_MI:0007	wild type (wt) Akt1 proteins could be co-immunoprecipitated by SETDB1
1699	17592114_MI:0007	Diversin (Div), which is involved in JNK activation (27), is found to interact with Csrp1, as revealed by coprecipitation of these two proteins from HEK293 cells
1700	17592114_MI:0007	we analyzed molecules coprecipitated with Csrp1. Interestingly, Dishevelled 2 (Dvl2) was found in the precipitate (Fig. 3G).
1701	17612295_MI:0007	Confirmation of the interaction between Uri1p and the preys Ssb1p, Fpr1p, Tef1p, or Tef4p by co-immunoprecipitation.
1702	17620405_MI:0007	an in vitro coimmunoprecipitation assay was applied in which full-length HA-p65 and FLAG-UXT proteins were generated and labeled, respectively, with [35S]methionine by in vitro translation. The products were mixed and immunoprecipitated with either control IgG or anti-HA antibody. As shown in Fig. 1 C, UXT could be coprecipitated by antibody against the HA epitope but not by control IgG, which suggests that UXT indeed interacts directly with full-length p65.
1703	17620405_MI:0007	p65 fragments spanning amino acids 1-286, 1-312, or 1-372 fully retained their binding capability and interacted with UXT as well as the wild type
1704	17620405_MI:0007	there exhibited a strong interaction between nuclear p65 and UXT upon TNF- stimulation.
1705	17626179_MI:0007	Using &#945;GFP antibodies, AtFLS2 coimmunoprecipitated with BAK1-GFP only after flg22 elicitation but not after a water control treatment (Fig. 1E), confirming the stimulus-specific interaction of the two proteins
1706	17635584_MI:0007	Immunoprecipitation of cell extracts and western blot analysis with a-myc reveals EVI1myc in cells transfected with pcDNA3EVI1myc, as expected (Fig. 3; IP a-9E10). In addition, western blot analysis of a-myc-immunoprecipitated cell extracts with a-HA shows HAUXT only in those extracts that also contain EVI1myc, confirming that these two proteins form a complex.
1707	17657516_MI:0007	IB analysis with anti-Flag antibody (&#945;-Flag) revealed that CCM1 (lane 2, asterisk) and CCM3 coprecipitated with CCM2
1708	17657516_MI:0007	Interaction of Flag-CCM2 with Myc-CCM1 was used as positive control
1709	17657516_MI:0007	Myc-CCM2 did coprecipitate with Flag-CCM3
1710	17657516_MI:0007	Reproducibly, an increase in CCM3 band intensity could be visualized after triple transfections (Fig. 4d) indicating that CCM1 supports coprecipitation of CCM2 with CCM3 and that simultaneous interaction of CCM1 and CCM3 with CCM2 is possible.
1711	17657516_MI:0007	STK25 coprecipitates with CCM2.
1712	17657516_MI:0007	Western blot analyses showed that the interactors STK25 and FAP-1 specifically coprecipitated with HA-CCM3 but not with the controls (Fig. 2b).
1713	17667950_MI:0007	TP0974 interacts with the sigma-factor TP0709, which was confirmed by co-immunoprecipitation (Figure 5B)
1714	17690294_MI:0007	Epitope-tagged forms of Wnt1, Wnt4 and Wnt5A all appear capable of co-immunoprecipitation with klotho when coexpressed in HEK-293 cells. The reciprocal immunoprecipitation of the various Wnts also co-precipitates klotho.
1715	17690294_MI:0007	Klotho associated with immu-noprecipitated Wnt3, and the reciprocal immunoprecipitation of klotho contained Wnt3
1716	17690294_MI:0007	The Wnt binding domain was contained within the amino-terminal portion of klotho-s KL1 domain (amino acids 1 to 285)
1717	17693260_MI:0007	Our results showed that myc-syntaxin 3 was specifically coprecipitated with FLAG-SARA by anti-FLAG Ab (Figure 6D).
1718	17699755_MI:0007	Coimmunoprecipitation of endogenous HFR1 with LAF1 protein.
1719	17699755_MI:0007	Coimmunoprecipitation of HFR1 with LAF1 protein.
1720	17702749_MI:0007	We demonstrated in vitro binding of recombinant Myc-L-UT and HA-snapin by co-immunoprecipitation using Myc or HA antibody (Fig. 2A) respectively.
1721	17704763_MI:0007	Expression constructs of ZTL were co-infiltrated with full-length green fluorescent protein (GFP)-tagged GI into N. benthamiana. ZTL interacts strongly with GI in vivo (Fig. 2d; compare lanes 1 and 9), as do FKF1 and LKP2
1722	17704763_MI:0007	We extended these trials to test discrete domains of ZTL (LOVF, Fkelch) and found that only the LOVF polypeptide interacts with GI
1723	17709393_MI:0007	The endogenous VRK2A stably interacts with the transfected HA-TAK1a protein under normoxic conditions (Fig. 6C, second lane), and this association was not affected by the DFO exposure of VRK2 protein
1724	17728244_MI:0007	T7-tagged MM-1 co-precipitated with transfected vIRF-3 protein
1725	17728244_MI:0007	vIRF-3 competes with MM-1 for binding to c-Myc
1726	17803915_MI:0007	Consistent with a function as a ubiquitin ligase, ubiquitinated proteins coimmunoprecipitated (co-IPed) with FLAG-tagged SCRAPPER (FLAG-SCR) from lysates of MG132-treated (a proteasome inhibitor) cells (Figure 2B).
1727	17855368_MI:0007	After immunoprecipitation with anti-FLAG M2 affinity resin, Cav-1-HA was detected in the precipitates derived from the cells co-transfected with both Id-1-FLAG and Cav-1-HA (Fig. 1A, lane 4), indicating co-immunoprecipitation of Cav-1 with Id-1.
1728	17855368_MI:0007	Reciprocally, after immunoprecipitation with anti-HA-agarose affinity resin (Fig. 1A, lower panel), Id-1-FLAG was detected in the cells co-transfected with the two proteins (lane 8), confirming the interaction between Cav-1 and Id-1.
1729	17872410_MI:0007	A minimal amount of HA-FKF1 was coimmunoprecipitated with GI-TAP protein in the dark
1730	17872410_MI:0007	In long days, the peak expression of FKF1 and GI proteins coincided (Fig. 2A). The HA-FKF1 and GI-TAP interaction was observed in the late afternoon (Fig. 2A), when daytime CO expression occurs (Fig. 2E) (4, 13). In short days, HA-FKF1 peaked about 3 hours later than the GI-TAP peak expression, and the FKF1 and GI interaction occurred only at the beginning of the FKF1 expression period (Fig. 2B).
1731	17872410_MI:0007	In plant materials harvested in the morning, HA-CDF1 was coimmunoprecipitated with GI-TAP (Fig. 3A).
1732	17872410_MI:0007	In the 35S::HA-FKF1 35S::GI-TAP #18 / fkf1 line, a similar amount of GI-TAP protein was precipitated at every time point in both long-day (16 hours light/8 hours dark) and short-day (8 hours light/16hours dark) conditions
1733	17872410_MI:0007	Similar amounts of FKF1 and GI interacted in blue-light irradiated samples (Fig. 1E) compared to whitelight grown samples, but little interaction was observed in red-light irradiated samples (Fig. 1E), indicating that blue light induces this interaction.
1734	17872410_MI:0007	Similar amounts of FKF1 and GI interacted in blue-light irradiated samples (Fig. 1E) compared to whitelight grown samples, but little interaction was observed in red-light irradiated samples (Fig. 1E), indicating that blue light induces this interaction. Further analysis revealed that the FKF1 and GI interaction is fluence rate-dependent
1735	17875722_MI:0007	FLAG-DI expression disrupted MDM2-p53 and MDMX-p53 coprecipitations
1736	17889654_MI:0007	we found that Yki associates with 14-3-3 in the presence, but not in the absence, of activated Hippo signaling (Figure 1C)
1737	17891176_MI:0007	Coexpression of hemagglutinin (HA)-tagged full-length S5A and FLAG-tagged wild-type (wt) ID1 and ID1- mutants in U2OS confirmed the interaction of wt-ID1 with S5A
1738	17893151_MI:0007	Figure 2A reveals that recombinant PKC was present in immunoprecipitates of FLAGRINCK1
1739	17893151_MI:0007	TsA201 cells were transfected with the cDNAs encoding a PKC from each class: PKC &#946;II (another conventional isozyme), PKC (novel), or PKC (atypical). The Western blot in Figure 3 shows that all three isoforms were present in immunoprecipitates of FLAG-RINCK1
1740	17911168_MI:0007	POT1A interacts with TERT-V(I8) in vitro.
1741	17922164_MI:0007	Coimmunoprecipitation of SEPT9 and SEPT14
1742	17936559_MI:0007	Ubiquitination of Mdm2 is inhibited by Wip1.
1743	17936559_MI:0007	Wip1 diminishes Mdm2 self-interaction.
1744	17937504_MI:0007	AtMND1 also interacted with itself, but the coimmunoprecipitation of an AtMND1-AtMND1 complex was only possible with one of the two epitope tags used
1745	17937504_MI:0007	Both AtMND1 and AHP2 interacted with AtDMC1 (Figure 9, lanes 3 and 4).
1746	17937504_MI:0007	In addition, both AHP2 and AtMND1 interacted with AtRAD51 (Figure 9, lanes 5 and 6). While the AHP2-AtRAD51 interaction was detected with only one of the two epitope tags used (Figure 9, lane 5), the interaction of AtMND1 with AtRAD51 was detected with both of the two epitope tags
1747	17937504_MI:0007	Interactions of AtMND1 with itself have also been reported in a yeast two-hybrid assay (unpublished data). Both AtMND1 and AHP2 interacted with AtDMC1 (Figure 9, lanes 3 and 4). In addition, both AHP2 and AtMND1 interacted with AtRAD51 (Figure 9, lanes 5 and 6). While the AHP2-AtRAD51 interaction was detected with only one of the two epitope tags used (Figure 9, lane 5), the interaction of AtMND1 with AtRAD51 was detected with bothof the two epitope tags
1748	17937504_MI:0007	We demonstrated binding of AtMND1 and AHP2
1749	17944809_MI:0007	Conversely, we detected APC2 protein in HA immunoprecipitates from protein extracts of pHBT::HA-HBT-expressing plants (Figure 4c), confirming the association between APC2 and HA-HBT.
1750	17951446_MI:0007	we found that HA-RHL2 protein was immunoprecipitated with anti-GFP beads and RHL1-CFP with anti-HA beads from the plants harboring the 35S:RHL1-CFP and 35S:HA-RHL2 constructs
1751	17965176_MI:0007	Interaction assays between HXK1 and mitochondrial porin proteins and between HXK1 and actin proteins after their transient expression in maize leaf protoplasts.
1752	17965176_MI:0007	Interaction assays between HXK1 and mitochondrial porin proteins and between HXK1 and actin proteins after their transient expression in maize leaf protoplasts. A, Protoplasts were transfected with HXK1-FLAG and/or porin-HA, labeled with [35S]Met, then pulldown assays were done using anti-FLAG antibody (F) or anti-HA antibody (H). HK, HXK1; Hsr, VDAC (At5g515090); por, porin (At3g01280). B, Protoplasts were transfected with HXK1-FLAG, ACT2-HA, and/or truncated calcium-dependent protein kinase (Ck)- HA. Comparable pull-down assays were done as in A.
1753	17981125_MI:0007	Coimmmunoprecipitation of IP3R3 with endogenous immunoreactive Sig-1R or Sig-1R EYFP.
1754	17981125_MI:0007	Effect of ATP on BiP association with Sig-1R-EYFP
1755	17986458_MI:0007	293T cells were transiently transfected with expression plasmids for fulllength DGKi and the long and short isoforms of pVHL, respectively. DGKi was efficiently co-immunoprecipitated with both pVHL isoforms
1756	18001824_MI:0007	binding between ectopic RNF8 and endogenous MDC1 was monitored by immunoprecipitation with anti-FLAG antibody
1757	18001824_MI:0007	HEK293T cells were cotransfected with the HA-tagged N-terminal fragment of MDC1 (amino acids 1-1100) and the indicated versions of FLAG-RNF8. Interactions between MDC1 and RNF8 were assessed by immunoprecipitation (IP) of HA-tagged proteins followed by immunoblotting with anti-FLAG antibody.
1758	18001824_MI:0007	The indicated fragments of HA-tagged human MDC1 were co-expressed with FLAG-RNF8 in 293T cells, and their interaction was measured by immunoprecipitation with anti-HA-antibody followed by immunoblotting with anti-FLAG antibody (the same conditions as in Fig. 2B).
1759	18001824_MI:0007	the same MDC1-3A mutant remained fully proficient to interact with NBS1 (Figure S3B)
1760	18022368_MI:0007	Myc-p31comet WT, but not Myc-p31comet Q83A/F191A, efficiently bound to the endogenous Mad2 protein (Figure 5B).
1761	18024891_MI:0007	HA-XPC (aa 509-835) was precipitated specifically from BGLF4 (K102I) and HA-XPC (aa509-835)-cotransfected 293T cells by using anti-BGLF4 antibody (Fig. 1b, lane 1). This interaction also was detected in a reciprocal co-immunoprecipitation assay performed with anti-HA antibody
1762	18029035_MI:0007	Immunoprecipitation and immunoblot analysis revealed that HA-tagged A20 interacted with FLAG-tagged Ymer
1763	18029035_MI:0007	The immunoprecipitates with antibodies to Ymer contained RIP1
1764	18045535_MI:0007	A similar analysis of RPS3 revealed that the N-terminal region (aa 1-111), particularly the KH domain (aa 41-111), was needed for p65 binding (Figure 4G).
1765	18055606_MI:0007	The interaction between TOC1 and PRR3 was also verified in vivo by transient expression of PRR3 and TOC1 in tobacco (Nicotiana bethamiana) leaves.
1766	18056989_MI:0007	This interaction appears to occur in mammalian cells because BCRP was co-immunoprecipitated with Pim-1L
1767	18056989_MI:0007	This interaction appears to occur in mammalian cells because BCRP was coimmunoprecipitated with Pim-1L but not Pim-1S which lacks the N-terminal proline-rich region
1768	18086875_MI:0007	FAK also bound to Wrch1
1769	18086875_MI:0007	it was found that Pyk2 bound to wild-type Wrch1 and to the constitutively active mutants of Wrch1.
1770	18086875_MI:0007	Nck2, which requires the Wrch1 N-terminal domain for binding, bound with equal affinity to all three mutants
1771	18086875_MI:0007	we could see that Pak1 bound to Wrch1(F83G) and only weakly to Wrch1(P80G) and Wrch1(F86C)
1772	18093972_MI:0007	both N-terminal WSB-1 (aa 1-279, 1-5th WD40 repeats) and C-terminal WSB-1 (aa 200-421, 4-7th WD40 repeats and SOCS box) were associated with full-length HIPK2 in cultured cells
1773	18093972_MI:0007	The bindings of WSB-1 to both wild-type HIPK2 and catalytically inactive HIPK2 K221R mutant were obviously diminished following Adriamycin administration.
1774	18093972_MI:0007	The specific interactions between WSB-1 and HIPK2 were verified in the yeast two-hybrid and co-immunoprecipitation assays in cultured cells
1775	18160036_MI:0007	Endogenous mouse mTOR and ATM could be coimmunoprecipitated with myc-tagged Tel2 expressed in MEFs
1776	18188704_MI:0007	the pDED of HIPPI retained the capacity to bind BLOC1S2
1777	18188704_MI:0007	we performed co-immunoprecipitation (co-IP) experiments, wherein BLOC1S2 and HIPPI were expressed in HEK293T cells with various epitope tags. In accordance with the yeast two-hybrid assays, these studies indicated that BLOC1S2 binds to HIPPI
1778	18191224_MI:0007	Chemical crosslinking was performed using microsomes containing Ste6p*HA and Doa10p13myc.
1779	18191224_MI:0007	In addition, we found that a TAP-tagged version of Cdc48p coprecipitated with ubiquitinated substrate (Figure 6C
1780	18191224_MI:0007	In vitro polyubiquitination of CFTR.
1781	18191224_MI:0007	in vitro polyubiquitination of Sec61-2p
1782	18191224_MI:0007	In vivo ubiquitination of Ste6p* in UFD2 and ufd2&#916; cells.
1783	18191224_MI:0007	Moreover, Ssa1p was a component of a putative multichaperone complex, which may include Ydj1p and Hsp82p, and Ste6p* (Figure 4E).
1784	18191224_MI:0007	Ste6p* Is Ubiquitinated In Vitro
1785	18191226_MI:0007	Following Flag immunoprecipitation in the same buffer, coimmunoprecipitation of the known &#946;Arr2 interaction partners, clathrin, MDM2, Raf1, ERK1, and ERK2, was determined.
1786	18191611_MI:0007	Co-affinity purification of Oct-4 with PKM2 from transfected cells.
1787	18223036_MI:0007	Coimmunoprecipitation of DDB1b and CUL4 in FLAG-DDB1b/ddb1a transgenic plants.
1788	18223036_MI:0007	DWD proteins PRL1 (At4g15900), TRIP-1 (At2g46280), and FY (At5g13480) were efficiently retrieved from the DDB1b immunocomplex together with CUL4, a positive control for DDB1 binding, whereas the negative control RPN6, 26S proteasome regulatory subunit 6 (At1g29150, subunit 9 of the 19S proteasome) was not.
1789	18223036_MI:0007	Moreover, PRL1 was efficiently retrieved from the CUL4 immunocomplex in FLAG-CUL4 transgenic lines, whereas RPN6 was not, showing that PRL1 associates with CUL4 in vivo
1790	18223036_MI:0007	Since antibodies were not available for the otherDWDproteins tested in Figure 3, we generated MYC-tagged constructs for the DWD proteins At3g45620, At4g35050, At1g65030, At2g19430, and At4g29830 and transformed them into FLAG-DDB1b/ddb1a lines. As shown in Figure 5, all of these proteins were coimmunoprecipitated with FLAG-DDB1b, with the exception of At1g04140,
1791	18242510_MI:0007	We confirmed that CDK10 binds to ETS2 using coimmunoprecipitation
1792	18245485_MI:0007	caspase-8 was readily seen along with ARC in the precipitates obtained from cells treated with thapsigargin or tunicamycin.
1793	18250306_MI:0007	Immunoprecipitation of GFP-Bcl-xL with anti-GFP antibody coprecipitated endogenous Drp1
1794	18250314_MI:0007	TPD1-FLAG was detected when proteins from EMS1::EMS1-cMyc TPD1::TPD1-FLAG double-transgenic plants were immunoprecipitated with an anti-cMyc antibody
1795	18250314_MI:0007	TPD1 interacts with EMS1 in planta in coimmunoprecipitation assay. (B) EMS1-cMyc (Upper) and TPD1-FLAG (Lower) were detected in EMS1::EMS1-cMyc TPD1::TPD1-FLAG double-transgenic plants, respectively, by Western blot.
1796	18267075_MI:0007	NRIP1-Cerulean coimmunoprecipitated with p50-TAP but did not with TAP alone
1797	18267075_MI:0007	We also confirmed the association of N's TIR domain and NRIP1-Cerulean. NRIP1-Cerulean coimmunoprecipitated with N(TIR)-TAP in the absence and presence of p50, but not with TAP alone
1798	18287201_MI:0007	Co-immunoprecipitation of UFO-Myc with LFY-FLAG in planta. Protein from wild-type, 35S::LFY-FLAG, 35S::UFO-Myc; ufo-2 (LF; UM) or 35S::UFO-Myc (UM) floral buds were used to precipitate the LFY immune complex using -FLAG. For control immunoprecipitations, normal mouse IgG serum conjugated to agarose beads was used. Myctagged UFO specifically co-precipitated with LFY-FLAG from 35S::LFYFLAG, 35S::UFO-Myc tissue only. DEVELOPMENT
1799	18303029_MI:0007	we co-transfected mammalian expression plasmids of HA-BAF60a and FLAG-p53 in COS-1 cell line and performed reciprocal immunoprecipitation assays with both anti-FLAG and anti-HA antibodies. As shown in Fig. 2A, the interaction between exogenous p53 and BAF60a was confirmed by reciprocal coimmunoprecipitation in mammalian cells.
1800	18313049_MI:0007	RNF43(M) was also ubiquitylated in vivo
1801	18313049_MI:0007	we expressed RNF43-V5 along with HA-ubiquitin in 293 cells and the immunoprecipitates recovered with anti-V5 antibody were immunoblotted with anti-HA antibody.
1802	18313049_MI:0007	Westernblot analysis of the immunoprecipitate withanti- HA antibody revealed that RNF43 co-immunoprecipitated HAtagged HAP95 (HAP95-HA),
1803	18319262_MI:0007	A549 cells were co-transfected with FDXRV5 and FHIT plasmids, and proteins precipitated with monoclonal anti-V5; co-precipitated Fhit was detectable only after DSP cross-linking
1804	18329368_MI:0007	Caspase-1 Binds to proIL-1&#945;
1805	18329368_MI:0007	ProIL-1&#945; bound to the p20 subunit of caspase-1
1806	18329369_MI:0007	Both BRUCE and MKLP1 interact with UBPY.
1807	18329369_MI:0007	BRUCE associates with mitotic kinases Plk-1, MEK1,
1808	18329369_MI:0007	BRUCE can co-precipitate survivin.
1809	18329369_MI:0007	HEK293T cells transfected with GFP-FLAG-BRUCE-C were lysed and proteins immunoprecipitated with rabbit IgG (control) or anti-MKLP1
1810	18329369_MI:0007	Importantly, Rab8 and Rab11, as well as the exocyst subunits Sec6 and Sec8, physically associate with BRUCE, as demonstrated by immunoprecipitations
1811	18329369_MI:0007	Rab8 co-purifies with endogenous BRUCE.
1812	18329369_MI:0007	The midbody ring-targeting domain of BRUCE interacts with MKLP1.
1813	18329369_MI:0007	The N-terminus of BRUCE mediates interaction with Sec8
1814	18329370_MI:0007	Crtam interacts with Scrib PDZ3
1815	18332111_MI:0007	Although -actin did not  directly associate with JRAB/MICAL-L2-F in BHK cells expressing HA-JRAB/MICAL-L2-F alone, the interaction between actin and JRAB/MICAL-L2 was clearly detected when Myc-actinin-4-F was coexpressed in these cells
1816	18332111_MI:0007	Myc-actinin-4-F was specifically precipitated with HA-JRAB/MICAL-L2-F
1817	18332111_MI:0007	Myc-actinin-4 was specifically coimmunoprecipitated with HA-Rab13 in the presence of Myc-JRAB/MICAL-L2
1818	18332111_MI:0007	The specific interaction between JRAB/MICAL-L2 and actinin-4 was also detected by reverse coimmunoprecipitation experiments
1819	18332111_MI:0007	When Myc-actinin-4-F and HA-JRAB/MICAL-L2-F were coexpressed with Myc-Rab13 T22N orMyc-Rab13 Q67L in BHK cells, the amount of Myc-actinin-4-F coimmunoprecipitated with HA-JRAB/MICAL-L2 was increased in the presence of Myc-Rab13 Q67L compared to that of Myc-Rab13 T22N
1820	18332111_MI:0007	When Myc-actinin-4-F and HA-JRAB/MICAL-L2-F were coexpressed with Myc-Rab13 T22N orMyc-Rab13 Q67L in BHK cells, the amount of Myc-actinin-4-F coimmunoprecipitated with HA-JRAB/MICAL-L2 was increased in the presence of Myc-Rab13 Q67L compared to that of Myc-Rab13 T22N (Fig. 4B). The effect of Rab13 activation on the actinin-4-JRAB/MICAL-L2 interaction was also detected by reverse coimmunoprecipitation experiments (Fig. 4C).
1821	18339839_MI:0007	HEK293 cells stably overexpressing FLAG-tag or FLAG-tagged ILK were immunoprecipitated and analyzed by GeLC-MS/MS. Together with proteins already known to bind ILK (eg. PINCH, parvin; ref. 16), novel interactors were identified, including rictor
1822	18339839_MI:0007	Rictor copurified specifically with FLAGtagged ILK
1823	18344519_MI:0007	pcDNA4/HisMax-AGTR2 was co-immunoprecipitated with pEGFPC1-TIMP-3
1824	18347058_MI:0007	we isolated the zinc finger domain of EWS as a specific RASSF1A binding partner that could be recapitulated by overexpression and coimmunoprecipitation
1825	18358808_MI:0007	Anti-Flag immunoprecipitation in Flag-pontin+shRNA and Flag-reptin+shRNA cells readily recovers endogenous dyskerin and TERT.
1826	18358808_MI:0007	Co-expression of V5-pontin enabled HA-TERT to interact with Flagreptin.
1827	18358808_MI:0007	endogenous pontin and reptin were stably associated with Flag-TERT (Figure 1E).
1828	18358808_MI:0007	Endogenous TERT is detected in pontin and reptin complexes purified from Flag-pontin+shRNA and Flag-reptin+shRNA cells.
1829	18358808_MI:0007	Expression of a subset of the deletion mutants of TERT in RRL showed the same requirement for the RT domain in binding pontin seen in transfected cells (Figures 5B and 5C).
1830	18358808_MI:0007	Expression of Flag-tagged pontin fragments (Figure 5F) with HA-dyskerin in 293T cells revealed that pontin-C and pontin-D fragments bound HA-dyskerin like full-length pontin.
1831	18358808_MI:0007	Flag-dyskerin coimmunoprecipitates endogenous pontin and reptin in transfected 293T cells. HA-TERT interacts weakly with Flag-dyskerin, but shows enhanced binding by coexpression of TERC.
1832	18358808_MI:0007	Flag-dyskerin expressed in RRL coimmunoprecipitated rabbit pontin intrinsic to the lysate,
1833	18358808_MI:0007	Flag-pontin, but not Flag-reptin, brought down co-expressed HA-TERT
1834	18358808_MI:0007	HA-dyskerin associates with either Flag-pontin or Flag-reptin by anti-Flag immunoprecipitation from cotransfected cells.
1835	18358808_MI:0007	Immunoprecipitation of Flag-reptin showed that neither the total reptin pool nor the amount of pontin or dyskerin bound to reptin varied through the cell cycle. In marked contrast, the amount of TERT associated with reptin peaked in S phase. The amount of TERT bound to reptin was 3-fold higher in S phase than in G2, M, or G1 (Figure 6B).
1836	18358808_MI:0007	Interaction and co-depletion of pontin and reptin by immunoprecipitation.
1837	18358808_MI:0007	Mass spectrometric analysis of the 50 kDa band, one of the most prominent TERT-associated proteins by SDS-PAGE, revealed that it comprised two independent proteins, the related ATPases pontin and reptin.
1838	18358808_MI:0007	The point mutations, which abolish ATP hydrolysis activity, did not alter the binding potential of pontin or reptin for TERT.
1839	18358808_MI:0007	Transfection assays in 293T show that Flag-tagged fragments of TERT incorporating the central reverse transcriptase domains efficiently coimmunoprecipitate endogenous pontin and reptin
1840	18358808_MI:0007	we measured the amount of TERC bound by TERT
1841	18387811_MI:0007	Focusing initially on Homer3, we found that immunoprecipitation of APP751 with the R1(57) antibody (Fig. 1B, panel 1, lane 4) resulted in co-precipitation of Homer3 (Fig. 1B, panel 2, lane 4)
1842	18387811_MI:0007	Immunoprecipitation of Homer2 (Fig. 2, panel 1, lane 5) but not of Homer1 (Fig. 2, panel 1, lane 3) resulted in the co-precipitation of APP
1843	18387811_MI:0007	In this case, immunoprecipitation of Homer3 (Fig. 3, panel 1, lanes 3 and 5), using the anti-myc antibody 9B11, resulted in the co-precipitation of wild type and deletion mutant APP (Fig. 3, panel 2, lanes 3 and 5).
1844	18408009_MI:0007	HPV-16E7 associates with USP11
1845	18408009_MI:0007	the Flag antibody coprecipitated HA-USP11 from extracts of cells transiently transfected with both Flag-HPV-16E7 and HA-USP11
1846	18408765_MI:0007	V5-tagged CDK1 was detected in the protein complex immunoprecipitated by the anti-FLAG antibody. Reciprocally, FLAG-tagged FOXO1 was detected in the protein complex immunoprecipitated by the anti-V5 antibody
1847	18420585_MI:0007	between RACK1 and DLC1
1848	18420585_MI:0007	Co-immunoprecipitation assay was carried out in HEK293T cells transiently transfected with Flag-DLC1 to confirm the yeast two-hybrid result. The interaction between RACK1 and DLC1 was detected upon treatment of the cells with UV-irradiation, paclitaxel, or staurosporine
1849	18420585_MI:0007	The interaction between RACK1 and BimEL was also through N-terminal portion of RACK1
1850	18430226_MI:0007	Both PER2 (Fig. 1B) and the CRY proteins (Fig. 1D, E) could be co-immunoprecipitated from extracts of HER911 cells co-transfected with Bmal1-GFP and the respective interaction partner using an anti-GFP antibody.
1851	18430226_MI:0007	Using an anti-HA antibody, were we able to co-immunoprecipitate PER2 from extracts of cells co-transfected with Per2 and HA-tagged Clock (Fig. 2B). Our results hint at a binding of PER2, but not CRY1 or CRY2, to CLOCK.
1852	18455983_MI:0007	Interaction of TIPE2 with caspase-8.
1853	18485870_MI:0007	Moreover, both forms of p53 also bound equally to the transcriptional coactivators/acetylases CBP and Tip60 (Figures S3A and S3B),
1854	18505803_MI:0007	Co-immuno-precipitation of MTA-HA and FIP37.
1855	18505803_MI:0007	We tested whether the interaction between MTA and FIP37 occurs in vivo by carrying out coimmunoprecipitation experiments. The MTA coding sequence was fused at its C-terminus to four copies of the c-Myc epitope tag. This construct was used to transform hemizygous SALK_074069 plants, and complementing lines were isolated. Coimmunoprecipitation was carried out using an anti-c-Myc antibody (Invitrogen), and protein gel blot analysis of the precipitated proteins was performed using a polyclonal antibody previously raised against FIP37 (Vespa et al., 2004). A band corresponding to FIP37 was only detectable in extracts from the MTA-c-Myc-tagged Arabidopsis plants and was not present in the wild type (Figure 7B).
1856	18510931_MI:0007	Immunoprecipitation analysis using HEK293 lysates (Figure 5A) showed that XFDL efficiently coprecipitated with p53 (lane 4; human).
1857	18510931_MI:0007	immunoprecipitation of endogenous XFDL protein with HA-tagged Xenopus p53 was seen from animal cap extracts
1858	18510931_MI:0007	The p53 deletion analysis (Figure S4A) showed that the aminoterminal transactivation domain (TAD) was dispensable for the binding to XFDL
1859	18555774_MI:0007	After incubation, we retrieved mEphrinB2-Fc and EphA4 proteins complexes and immunoblotted with the anti-FLAG antibody.
1860	18555774_MI:0007	Purified FLAG-tagged VPR-1 MSP (VPR-1MSP-FLAG) and V5-tagged VAB-1 ECT domain (VAB-1 Ex-V5) were coimmunoprecipitated using FLAG antibody (C) and V5 antibody (D)
1861	18555774_MI:0007	We incubated mEphA4Ex-V5His together with hVAPMSP-His proteins and performed coIP assays with the V5 antibody.
1862	18555782_MI:0007	The KD value for complex formation between Sse1p and the NBD of Ssa1p, Ssa1N, was estimated from the distribution of Ssa1N between supernatant and Ni2+ resin-bound His-tagged Sse1p at different concentrations.
1863	18557765_MI:0007	Lysates of C2C12 cells transfected with plasmid expression cDNAs encoding Xpress-tagged necdin (Xpress-Ndn) and HA-tagged EID-1 (HA-EID-1) were immunoprecipitated with an anti-Xpress monoclonal antibody. HA-EID-1 was then detected by anti-HA immunoblot analysis of the immunoprecipitated protein. In reciprocal experiments, immunoprecipitation of identically co-transfected C2C12 cell lysates with a monoclonal anti-HA antibody revealed the presence of Xpress-Ndn upon immunodetection with an anti-Xpress antibody.
1864	18557765_MI:0007	These results suggest that endogenous necdin interacts with EID-1.
1865	18585352_MI:0007	Immune precipitation of Mps3p-FLAG coprecipitates Csm4p and Ndj1p-HA
1866	18585352_MI:0007	In immune co-IP experiments, Mps3p pulls down Ndj1p even in the absence of Csm4p
1867	18585352_MI:0007	In immune co-IP experiments, Mps3p pulls down Ndj1p even in the absence of Csm4p and pulls down Csm4p even in the absence of Ndj1p
1868	18585357_MI:0007	an in vitro-translated dominant-negative (DN) form of DSCAM (lacking the cytoplasmic domain) was capable of precipitating netrin-1 but not HGF (Figure 3C
1869	18585357_MI:0007	As a control, the DN form of Met precipitated HGF but not netrin-1 (Figure 3C).
1870	18585357_MI:0007	As shown in Figure 5C, DSCAM coprecipitated with DCC
1871	18585357_MI:0007	DCC oligomerization in vitro.
1872	18585357_MI:0007	Netrin-1 triggers the dissociation of DSCAM and DCC
1873	18591351_MI:0007	Co-IP from Arabidopsis confirmed the interaction between GFP-WIT1 and endogenous RanGAP1 and WIP1 (Figure 2E).
1874	18591351_MI:0007	Co-IP from N. benthamiana showed that WIT1 interacted with both RanGAP1 and RanGAP2 as well as with WIP protein family members and with itself
1875	18591351_MI:0007	While capable of interacting with WIT1, WIP1 did not show homodimerization ability in the same assay (Figure 2D).
1876	18612383_MI:0007	p300 C/H3 domain directly binds to transactivation domain of p53.
1877	18614018_MI:0007	Arp3 coprecipitated with LAP-WHAMM,
1878	18624398_MI:0007	Coimmunoprecipitated PRKAB1 with Grb2 was detected by immunoprecipitation with Flag antibody (Figure 5a, upper panel lane 6)
1879	18624398_MI:0007	RBBP6 can bind to SFRS7 according to co-IP assay (Figure 5e).
1880	18624398_MI:0007	While wild type AKT1 and constitutively active AKT1 (ca) can effectively bind with ASXL1
1881	18632581_MI:0007	After immunoprecipitation of HA-SNIP1with an anti-HAantibody, we were able to detect the presence of Drosha-Flag in the SNIP1 immunoprecipitate, but not in the control immunoprecipitate, with an anti-Flag antibody
1882	18632581_MI:0007	As shown in Fig. 5B, an anti-HA antibody detected the enrichment of HA-DDL in the DCL1-YFP immunoprecipitate relative to the control immunoprecipitate, suggesting the association between DDL and DCL1.
1883	18649364_MI:0007	Co-immunoprecipitation assay for the interaction between TSPY and FLAG-eEF1A1.
1884	18649364_MI:0007	The dimerization of TSPY was analyzed by co-immunoprecipitation assay, using FLAG-TSPY[76-150].
1885	18653891_MI:0007	BSK1-myc protein was immunoprecipitated by anti-GFP antibodies only in transgenic Arabidopsis plants expressing both BRI1-GFP and BSK1-myc
1886	18674533_MI:0007	Interaction of atSC35 with SCL30 (lanes 1), SCL30a (lanes 2), SCL33 (lanes 3), and atSC35
1887	18674533_MI:0007	Interaction of SCL33 with SCL28 (lanes 1), SCL30 (lanes 2), SCL30a (lanes 3), and SCL33 (lanes 4). SCL33-GFP was co-expressed in tobacco protoplasts with the indicated HA-tagged proteins. Protein extracts were immunoprecipitated with anti-GFP antibody
1888	18674809_MI:0007	in AD293 cells cotransfected with Flag-PPAR&#948; and with either catalytic AMPK &#945;1 or &#945;2 subunits, we discovered that each of the AMPK subunits coimmunoprecipitated as a complex with Flag-PPAR&#948; (Figure 5G).
1889	18692471_MI:0007	IKK2 and SNAP-23 coimmunoprecipitated in the raft fractions following Fcvar epsilonRI stimulation (Figure 4C).
1890	18692471_MI:0007	IKK2 associates with GFP-SNAP-23 when coexpressed in 293T cells by immunoprecipitation (IP) assay.
1891	18775313_MI:0007	HIF1&#945; peptides identified by mass spectrometry in Flag-UBXD7 immunoprecipitates from cells treated with MG132 for 2 hr
1892	18775317_MI:0007	Immunoprecipitation assays of dnBMP1 (using a Flag antibody) showed that the association of dnBMP1 and Chordin substantially increased when a small amount of ONT1 was present
1893	18775317_MI:0007	ONT1 binds to the Chordin-BMP4 complex.
1894	18776063_MI:0007	The protein complexes immunoprecipitated by the anti-MYC antibody from protein extracts of leaves coexpressing MYC-HDA19 and FLAG-WRKY38 or MYC-HDA19 and FLAG-WRKY62 generated positive interactions to the anti-FLAG antisera
1895	18805088_MI:0007	Coimmunoprecipitation assays show that PopZ forms a complex with ParB in vivo.
1896	18805089_MI:0007	Coimmunoprecipitation (Co-IP) experiments using anti-GFP antibody (which recognizes YFP) and cell lysates of CB15N popZ::popZ-yfp revealed that ParB is specifically pulled down with PopZ-YFP (Figure 3I).
1897	18805089_MI:0007	Consistent with this idea, both CckA and DivJ coimmunoprecipitated with PopZ-YFP (Figure 5B).
1898	18805096_MI:0007	. Figure 4D (lanes 2 and 3) shows that Map1b mRNA (Bagni and Greenough, 2005) was detected in the CYFIP1 immunoprecipitate.
1899	18830673_MI:0007	CoIP and BiFC experiments for protein interactions between BIM1 and DRN or DRNL. Full-length BIM1 protein can specifically co-precipitate either full-length DRN or DRNL
1900	18830673_MI:0007	His-tagged full-length DRN protein, HA-tagged full-length BIM1 protein and full-length myc-tagged PHV were co-transcripted/translated in vitro, and CoIP was performed via the myc and HA tags. BIM1 could be co-precipitated by PHV and reciprocally, PHV by BIM1 (Fig. 3a, b). In the same experiment, DRN could be co-precipitated by both PHV and BIM1
1901	18835031_MI:0007	GFP-BH4 or Bcl-2/&#916;BH4 was transfected alone or together into HEK293T cells, and their interaction was analyzed by CoIP.
1902	18835031_MI:0007	Interaction of NuBCP with antiapoptotic Bcl-2 family members, Bcl-B, Bfl-1, and Bcl-2.
1903	18835031_MI:0007	. Similarly, addition of NuBCP-9 and its enantiomer induced the binding of the BH4 domain to Bcl-2 (Figure 7C).
1904	18836139_MI:0007	Co-immunoprecipitation of in vitro transcription/translation products to the GAL4(TA)-ACBP4 fusion protein, immobilized to protein A/agarose beads, using monoclonal antibody against GAL4(TA), showed that the GAL4(TA)-ACBP4 fusion protein significantly binds AtEBP
1905	18948957_MI:0007	Co-immunoprecipitation of FBL17, Cullin1 and ASK1 with monoclonal anti-GFP antibody in total protein extracts from Arabidopsis protoplasts transfected with Cullin1-HA, FBL17-HA and ASK1-GFP.
1906	18948957_MI:0007	In addition, in co-immunoprecipitation assays haemagglutinin (HA)-tagged FBL17 was pulled down in extracts of transfected protoplasts by GFP-tagged KRP6 and KRP7,
1907	18984158_MI:0007	The apparent association was confirmed by overexpression of RG9MTD1 with a FLAG- instead of a 6x His-tag and subsequent anti-FLAG immunoprecipitation instead of immobilized metal affinity chromatography (IMAC) (Figures 2C and 2D). Mass spectrometry revealed the 26 kDa protein to be hydroxysteroid (17-&#946;) dehydrogenase 10 (HSD17B10)
1908	18984162_MI:0007	anti-HA immunoprecipitates from A375M2 cells transfected with HA-DOCK3 immunoblotted for NEDD9.
1909	18984162_MI:0007	anti-NEDD9 immunoprecipitates immunoblotted for DOCK3.
1910	19103756_MI:0007	lysates were used for immunoprecipitation with either an anti-HA (Fig. 3A, bottom left) or anti-Flag antibody (Fig. 3A, bottom right), and the immunoprecipitates were used for immunoblotting with the reciprocal antibody. In both cases the VRK1-Plk3 interaction was detected
1911	19135891_MI:0007	Expression of the MukE and MukF proteins were confirmed by partial purification of MukB-GFP containing complexes, coimmunoprecipition with agarose-conjugated anti-GFP antibody (&#945;-GFP), followed by mass spectrometric analysis of the major bands on a denaturing gel (bottom, right).
1912	19135895_MI:0007	Coimmunoprecipitation of GPA1 and the GTGs
1913	19135897_MI:0007	Ca2+ dependence of the binding of Miro-Myc to KIF5C(1-335)-YFP, by precipitation from lysates of transfected HEK cells with anti-Myc and probing with anti-GFP (KIF5C(1-335)-YFP).
1914	19135897_MI:0007	Immunoprecipitations with anti-Myc from cells expressing Myc-tagged full length (FL, left two panels) or truncated KHC 1-682 (682, right two panels), and T7-tagged DMiro&#916;TM, but not milton.
1915	19135897_MI:0007	The co-immunoprecipitation of Miro-Myc and KHC-ECFP from HEK cells requires milton.
1916	19135897_MI:0007	We investigated the possibility that Ca2+ induced a direct interaction of Miro and KHC, and found that Miro and KHC would indeed co-precipitate in elevated Ca2+
1917	7505116_MI:0007	Coinfection of SF9 cells with baculovirus vectors encoding these EPO receptor forms and the p85 subunit of PI3-K resulted in the association of p85 with HER-E374, HERAB X 2, and the wild-type HER as shown by coimmunoprecipitation with MoAb 12CA5 and Western blotting of precipitates with p85 antiserum
1918	7664335_MI:0007	Thus, the N-terminal 146 amino acid residues of the CSA protein are apparently sufficient for its interactions with both the p44 subunit of the TFIIH complex and the CSB protein.
1919	8521818_MI:0007	In contrast, a ternary complex consisting of CDK7, cyclin H and p36 could be readily precipitated from the lysate containing all three proteins (lane 7).
1920	8668140_MI:0007	Rsp5 coimmunoprecipitates with Bul1.
1921	9125210_MI:0007	In vivo association of EF1a and rL3 with CAP
1922	9144171_MI:0007	The interaction of RAS with RIN1 was confirmed by copurification of activated RAS with an epitope tagged form of the carboxyl terminus of RIN1 (RIN1C) from cells expressing these proteins (Fig. 2B).
1923	9173976_MI:0007	Co-purification of the hSUG1 protein with TFIIH by affinity chromatography.
1924	9203581_MI:0007	To define the biochemical function of teh Pop1 protein more precisely, the possibility of physical interaction between Pop1 and Cdc18 was examined. Cell extracts were prepared from cells that expressed HA-tagged Pop1 (Pop1-HA) and myc-tagged Cdc18 (myc-Cdc18) (Fig. 8, lane 1), and immunoprecipitation was performed with anti-HA antibody in the presence or absence of competitors.
1925	9235916_MI:0007	When either epitope-tagged human (Fig. 3, panel B) or mouse (Fig. 4, lane 4) p110d was expressed in COS or 293T cells and recovered by immunoprecipiation, a 85-kDa protein was detected with p85-specific antiserum in the immunoprecipitates. Thus, both human and murine p110d associate with endogenous p85 after transfection into COS or 293T cells, respectively.
1926	9242378_MI:0007	HA-Rho1p and HA-Cdc42p were co-immunoprecipitated with myc-Rho GDI.
1927	9418871_MI:0007	A monoclonal antibody against the T7 epitope coimmunoprecipitated 35Slabeled p125DDB from a mixture of T7-p48DDB and 35Slabeled p125DDB
1928	9418871_MI:0007	It is also noteworthy that cells expressing the T7 epitope-tagged p125DDB subunit alone exhibited detectable coprecipitation of E2F1 with the T7 antibody
1929	9418871_MI:0007	Western blot assay of the HA immunoprecipitate with T7 antibody detected the presence of p48DDB only when the extracts from cells expressing both subunits were used
1930	9428767_MI:0007	association of Ste4 with Ste20 in the absence of pheromone
1931	9428767_MI:0007	Ste5 also formed a complex with Ste4
1932	9477315_MI:0007	The translated proteins were incubated together prior to immunoprecipitation. Under these conditions it was found that R only immunoprecipitated in the presence of full-length GL1
1933	9504914_MI:0007	Coprecipitation of Spt4p and Hir1p from yeast cell extracts.
1934	9504914_MI:0007	In contrast, only the LexA-Hir1(Cterm) fusion protein was coprecipitated with HA-Hir2p (Figure 2B, lane 6),
1935	9504914_MI:0007	The results showed that both the Hir1p WD repeats and C terminus could be coprecipitated with fulllength HA-Hir1p
1936	9614176_MI:0007	In a reciprocal experiment, rum1HAp immunoprecipitation was found to coprecipitate 2 pmol of cig2p and 6 pmol of cdc13p (Figure 3C). Similar results were obtained by immunoprecipitations of rum1p from a cig2-HAcyr1Dsxa2D strain (our unpublished results). The different amounts of cig2p and cdc13p in rum1p precipitations are similar to the different cyclin B concentrations in the cell, because the level of cdc13p is about three times that of cig2p (Figure 3C and our unpublished results).
1937	9614176_MI:0007	In a reciprocal experiment, rum1HAp immunoprecipitation was found to coprecipitate 2 pmol of cig2p and 6 pmol of cdc13p (Figure 3C). Similar results were obtained by immunoprecipitations of rum1p from a cig2-HAcyr1Dsxa2D strain (our unpublished results). The different amounts of cig2p and cdc13p in rum1p precipitations are similar to the different cyclin B concentrations in the cell, because the level of cdc13p is about three times that of cig2p (Figure 3C and our unpublished results). The increased amount of cdc13p associated with rum1p is consistent with rum1p having an effect on the cdc13passociated cdc2p protein kinase.
1938	9653157_MI:0007	To test for associations with specific target proteins, we examined the ability of Sud1 to interact physically with Cdc18. Through coprecipitation studies, we found that Sud1 and Cdc18 bind one another in vivo (Fig. 5A).
1939	9653157_MI:0007	To test for associations with specific target proteins, we examined the ability of Sud1 to interact physically with Cdc18. Through coprecipitation studies, we found that Sud1 and Cdc18 bind one another in vivo (Fig. 5A). To determine the functional significance of this interaction, we examined the role of Cdc18 phosphorylation in the process. As we reported previously, mutation of the six CDK consensus sites in Cdc18 abolishes its in vivo phosphorylation pattern and renders it immune to rapid degradation (6). Interestingly, the Cdc18DCDK1-6 mutant protein is incapable of binding to Sud1, unlike wild-type Cdc18 (Fig. 5B). These data indicate that Sud1 binding requires phosphorylation of Cdc18 by fission yeast CDKs and is required for rapid proteolysis of Cdc18.
1940	9735357_MI:0007	SNR1 coimmunoprecipitates with BRM
1941	9756887_MI:0007	co-immunoprecipitation of FAK with Hic-5
1942	9756887_MI:0007	Paxillin binds to the C-terminal domain of FAK by its N-terminal half.
1943	9763420_MI:0007	To eliminate the possibility that CENP-E binding resulted from an artifact created by the proA:hBUBR1 fusion, we demonstrate that endogenous CENP-E can also associate with gfp:hBUBR11-1051 but not gfp alone (Fig. 8 b, lanes 3 and 4).
1944	9891039_MI:0007	tagged Pcn1 and Rfc1 coprecipitated with Cdc24
1945	9989503_MI:0007	a deletion mutant lacking this region, Stat5b del(232 to 321), associated with Nmi much less efficiently than did full-length Stat5b
1946	9989503_MI:0007	FLAG-tagged Stat5b(232 to 321) coprecipitated similar amounts of HA-tagged Nmi
1947	9989503_MI:0007	Stat5b was found in anti-HA immunoprecipitates when HA-tagged Nmi was coexpressed
1948	9990507_MI:0007	To address the sugeestion as to how Pop1 and Pop2 interact in the cell, a series of combinations of tagged pop1þ and pop2þ genes were constructed (they were all functional, see Experimental procedures), expressed in the fission yeast, and a physical interaction between Pop1 and Pop2 was examined. As shown in Fig. 4, the myc-Pop1 protein was specifically co-immunoprecipitated with anti-HA (haemagglutinin) antibody (lanes 3) but not upon mock treatment (lane 2). Likewise Pop1- HA and GST (glutathione S-transferase)-Pop2 were co-immunoprecipitated with anti-HA antibody (lane 5). Conversely pull-down experiments using GSH (glutathione)-coupled beads also precipitated both myc-Pop1 and GST-Pop2 (lane 6). These results strongly suggest that Pop1 and Pop2 act as heterodimers or hetero-multimers in the cell.
1949	9990507_MI:0007	To analyse a functional relationship between cullin and the SCF complex in the fission yeast, a physical interaction between Pcu1, Pop1 and Pop2 was examined. For this purpose, a tagged version of pcu1þ (myc-pcu1þ) was constructed (Experimental procedures). As a control for the specificity of an interaction, the tagged pcu3þ gene (GST-pcu3þ) was also constructed. pop1þ-HA or pop2þ-HA was co-expressed with either myc-pcu1þ or GST-pcu3þ and immunoprecipitation was performed using anti-HA antibody. As shown in Fig. 6, myc-Pcu1 was co-immunoprecipitated with Pop2-HA (lane 2) also with Pop1-HA (data not shown). This binding was specific to anti-HA antibody, as neither of the two proteins was precipitated upon mock treatment (lane 1). Remarkably myc-Pcu1 was still capable of forming a complex with Pop2-HA in Dpop1 cells (lanes 3 and 4). These results indicate that Pcu1 is a component of SCFPop2, and that complex formation is not abrogated in the absence of Pop1. In sharp contrast to the result for Pcu1, GST-Pcu3 was not co-precipitated with Pop1-HA (lanes 6 and 7) although the protein was expressed (lane 5).
1950	imex:IM-11822_MI:0007	To establish that these interactions between Prop1 and &#946;-catenin holoproteins occur in a cellular context, we performed coimmunoprecipitation in GHFT-1 cells,
1951	imex:IM-11846_MI:0007	ectopic PTEN189 interacts with endogenous wild-type PTEN
1952	imex:IM-11847_MI:0007	GFP::RSA-1 coprecipitated with the PP2A catalytic and structural subunits LET-92 and PAA-1, indicating that RSA-1 functions as part of a PP2A heterotrimeric complex. In addition to the PP2A core heterodimer, we consistently coimmunoprecipitated the core centrosomal protein SPD-5 and an uncharacterized protein, Y48A6B.11
1953	imex:IM-11864_MI:0007	Anti-Myc precipitates, prepared from 293T cells cotransfected with IFNalphaR2 and STAT2 or IRF9, were probed with anti-HA (IFNalphaR2) or anti-Myc (IRF9 and STAT2).
1954	imex:IM-11864_MI:0007	IH1D (339-393) of IRF9 interacts with STAT2.
1955	imex:IM-11864_MI:0007	In 293T cells, the Myc-IFNalphaR2 C-terminal truncation mutants were cotransfected with HA-CBP for an association analysis.
1956	imex:IM-11867_MI:0007	Immunoprecipitation experiments detected HIF-1a in an extract where RSUME was immunoprecipitated (Figure 6F), indicating an interaction between RSUME and HIF-1a during hypoxia that could account for the observed effects
1957	imex:IM-11877_MI:0007	NALP1 was found to associate with Bcl-2 and Bcl-XL by coimmunoprecipitation (coIP) experiments using lysates prepared from transfected HEK293T cells expressing epitopetagged proteins.
1958	imex:IM-11877_MI:0007	Removal of the loop from Bcl-2 or Bcl-XL abolished interaction with NALP1 (Figures 4A and S7A). In contrast, deleting BH3 or BH4 domains from Bcl-XL did not impair binding to NALP1, as determined by coIP experiments
1959	imex:IM-11877_MI:0007	we attempted to map the region of NALP1 required for binding Bcl-XL. These experiments demonstrated that the LRRs (but not the CARD or FIIND domains)of NALP1 are necessary, but insufficient, for binding Bcl-XL
1960	imex:IM-11877_MI:0007	When active MDP-LD (but not MDP-DD) was added to extracts derived from HEK293T cells transfected with plasmids encoding GFP-tagged ASC and epitope-tagged NALP1, we observed that GFP-ASC inducibly associated with NALP1 (Figures 3C and 3D). Addition of Bcl-XL or Bcl-2 to the extracts prevented GFP-ASC from binding to NALP1.
1961	imex:IM-11882_MI:0007	Please note that the signals for tagged TAF3 are similar in the TBP and FLAG precipitates, while the signals for TAF1, TAF5 and TBP are weaker in the FLAG precipitates.
1962	imex:IM-11883_MI:0007	293T cells were transiently cotransfected with Myc-tagged NIK plasmid and indicated Flag-tagged c-IAP1 constructs.
1963	imex:IM-11883_MI:0007	IAP antagonists block XIAP-BIR3 binding to processed caspase-9.
1964	imex:IM-11888_MI:0007	Coimmunoprecipitation confirmed the association of LIMP-2 and &#946;GC as well as the association of the LIMP-2 ER retention mutant with &#946;GC (Figures 4G and S5A).
1965	imex:IM-11888_MI:0007	Co-immunoprecipitation of over-expressed LIMP-2 and &#946;GC
1966	imex:IM-11891_MI:0007	Next, we performed the reciprocal experiment to determinethe regions of Cep97 involved in binding CP110. We constructed and transfected a set of Flag-tagged Cep97 amino- and carboxy-terminal truncation mutants and performed anti-Flag immunoprecipitation and Western blotting to detect endogenous CP110. We found that a region of Cep97 containing residues 300-750 was required for stable binding to CP110 (Figures 6C and 6D). In total, our data indicate that an amino-terminal region of CP110 directly interacts with residues in the middle and carboxy-terminal portion of Cep97.
1967	imex:IM-11891_MI:0007	We confirmed the interaction between Cep97 and CP110 by ectopically expressing Flag-tagged Cep97 and immunoprecipitating this protein using antibodies against CP110 (Figure S1B). Similarly, anti-Flag antibodies coprecipitated both Cep97 and CP110. In addition, Cep97 associates with CaM, an observation anticipated by the presence of an IQ domain.
1968	imex:IM-11891_MI:0007	We cotransfected human cells with Cep97-GFP and a series of Flag-tagged CP110 truncation mutants, and performed immunoprecipitations with anti-Flag antibodies. Cep97-GFP was readily detected on Western blots after immunoprecipitation of Flag-CP110, as expected (Figures 6A and 6B). We found that a fragment containing 223 amino-terminal residues was necessary and sufficient to bind Cep97 (Figure 6B).
1969	imex:IM-11905_MI:0007	HEK293T cells were co-transfected with HA-tagged Cdh1 and the indicated FLAGtagged deletion mutants of Claspin. Whole cell extracts (WCE, bottom panel) were immunoprecipitated
1970	imex:IM-11905_MI:0007	Next, to test whether Cdc14B and Cdh1 physically interact in response to DNA damage in G2, we performed coimmunoprecipitation experiments in G2 U2OS cells.
1971	imex:IM-11905_MI:0007	only Cdh1 was able to coimmunoprecipitate endogenous Claspin
1972	imex:IM-11909_MI:0007	BMAL1 Acetylation at Lys537 Is Regulated by SIRT1
1973	imex:IM-11909_MI:0007	In coimmunoprecipitation experiments we reveal that SIRT1 interacts with CLOCK
1974	imex:IM-11918_MI:0007	Overexpressed NDUFS3 and K56A-NDUFS3 were incorporated into complex I since they coimmunoprecipitated with NDUFA9, MTND6, and NDUFB6 using an HA antibody
1975	imex:IM-11923_MI:0007	Associations between BAP31 and either Sec61&#946; (Figure 1C, left) or TRAM (Figure 1C, right) were likewise demonstrated by transient cotransfection of vectors expressing the epitope-tagged proteins in Cos1 cells, followed by immunoprecipitation of either the BAP31 protein or the Sec61&#946; and TRAM proteins.
1976	imex:IM-11923_MI:0007	The ability of BAP31 to associate with Derlin1 and RMA1 was monitored by immunoblotting of anti-Flag immunoprecipitates with antibodies against HA or anti-BAP31.
1977	imex:IM-11924_MI:0007	Fmi coimmunoprecipitates Fz from pupae.
1978	imex:IM-11924_MI:0007	FmideltaNYFP coimmunoprecipitates Fz.
1979	imex:IM-11925_MI:0007	We found that immunoprecipitation of Myc-tagged CALHM1 coprecipitated V5-tagged CALHM1 (Figure 4B),
1980	imex:IM-11930_MI:0007	Both FBXL3 and OVTM interacted strongly with native CRY1 and CRY2 proteins.
1981	imex:IM-11930_MI:0007	Very weak or no interaction of FBXL3 was seen with PER1 and PER2, especially in comparison to that seen between the PERs and betaTrCP1, an F-box protein known to interact with the PERs
1982	imex:IM-11930_MI:0007	We also used tagged proteins in coimmunoprecipitation assays in 293A cells, which are easily transfected and express relatively low levels of clock proteins. Both FBXL3 and OVTM interacted strongly with CRY1 and CRY2 (Figure 5B).
1983	imex:IM-11934_MI:0007	we transiently transfected 293T cells with expression vectors for Flag-tagged PML-RARa and the trimeric PRC2 complex (EED/EZH2/SUZ12) (Cao and Zhang, 2004a; Pasini et al., 2004). We found that all PRC2 components could be specifically immunoprecipitated with PML-RARa, using the anti-Flag antibody
1984	imex:IM-11936_MI:0007	Cell lysates from HeLa cells infected with WT/IpaBFLAG were immunoprecipitated with anti-FLAG antibody or mouse IgG, and then immunoblotted with anti-Mad2L2 or -FLAG antibodies (left)
1985	imex:IM-11936_MI:0007	Mad2L2 bound Cdh1.
1986	imex:IM-11943_MI:0007	Mass spectrometry analysis revealed the presence of VPS35 and VPS26 isoforms associated with VPS29-GFP in the immunocomplex
1987	imex:IM-11953_MI:0007	As shown in Figure 4E, Topo IIalpha indeed coimmunoprecipitated with HA-RanBP2(2553-2838) from these extracts.
1988	imex:IM-11955_MI:0007	The association of SKAR and Flag-Upf3b with CBP80-bound mRNPs was determined by immunoblotting.
1989	imex:IM-11956_MI:0007	Evidence that Upf1 interacts directly with eIF3
1990	imex:IM-11956_MI:0007	Upf1 Phosphorylation Promotes Upf1 Binding to eIF3 Subunits
1991	imex:IM-11956_MI:0007	where HA-eIF2&#945;(WT) and eIF3 did co-immunoprecipitate with FLAG-Upf1
1992	imex:IM-11971_MI:0007	The interaction between the luminal domain of Hrd3p and Yos9p is probably direct
1993	imex:IM-11979_MI:0007	To verify the interaction between LC3 and p62 in vivo, we first carried out immunoprecipitation assay with cultured hepatocytes isolated from green fluorescent protein (GFP)-LC3 transgenic (Tg) mice (GFP-LC3 tg) (Mizushima et al., 2004) and confirmed the coimmunoprecipitation of p62 with GFP-LC3 under both nutrient-rich and -poor conditions (Figure 1A).
1994	imex:IM-11982_MI:0007	we transfected HEK293 cells with Flag-tagged Jmjd3 or Utx and analyzed their incorporation in endogenous complexes by coimmunoprecipitation (Figure 6A). Anti-Flag immunoprecipitates were immunoblotted with antibodies against Wdr5, RbBP5, and Ash2L. Utx and Jmjd3 coimmunoprecipitated comparable amounts of all these proteins,
1995	imex:IM-11988_MI:0007	Immunoblot analysis showed that eIF3f-HA was specifically coisolated with hGle1-GFP.
1996	imex:IM-11991_MI:0007	We found that soluble e-H3.1 readily associates with CAF-1 outside S phase, as efficiently as in S phase
1997	imex:IM-11993_MI:0007	we could immunoprecipitate Sgs1 and its SUMO-modified forms from strains having the endogenous Sgs1 tagged at its C terminus with 3HA or 3FLAG (Figure 6D). The Sgs1 sumoylation is dependent on Ubc9, as no SUMO-modified forms of Sgs1 were visible in ubc9-1 mutants (Figure 6D).
1998	imex:IM-11993_MI:0007	we could immunoprecipitate Sgs1 and its SUMO-modified forms from strains having the endogenous Sgs1 tagged at its C terminus with 3HA or 3FLAG (Figure 6D). The Sgs1 sumoylation is dependent on Ubc9, as no SUMO-modified forms of Sgs1 were visible in ubc9-1 mutants (Figure 6D). Sgs1 sumoylation is increased upon exposure to MMS, but it is not diminished in the mms21 mutation context, under either normal or DNA-damaging conditions
1999	imex:IM-12002_MI:0007	Human Cdc25C also coprecipitated with HA-tagged B56 (&#948; isoform) from transfected HEK 293 cells (Figure 3E).
2000	imex:IM-12004_MI:0007	In coimmunoprecipitation experiments using 293T cells, Trib2 association with C/EBPap42 was detected only in the presence of MG132, whereas C/EBPap30 coimmunoprecipitated in the presence and absence of MG132
2001	imex:IM-12018_MI:0007	Borealin10-109 (but not Borealin10-57) interacts with INCENP, Aurora B, and Survivin
2002	imex:IM-12018_MI:0007	Borealin R35E,L46Y binds Survivin but not INCENP/Aurora B
2003	imex:IM-12018_MI:0007	Borealin W70E,F74E mutant binds INCENP and Aurora B but not Survivin.
2004	imex:IM-12018_MI:0007	INCENP F22R,L34R failed to bind Borealin and Survivin but retained binding to Aurora B.
2005	imex:IM-12059_MI:0007	preliminary experiments suggest that the ability of Twist proteins to prevent the Ras-mediated activation of p16INK4A might be associated with their ability to interact with the Ras effector Ets2
2006	imex:IM-12065_MI:0007	293 cells transiently cotransfected for 48 hr with V5/His-c-Myc, and Flag-CIP2A expression constructs were subjected to immunoprecipitation by anti-V5 antibody.
2007	imex:IM-12065_MI:0007	To strengthen the interaction data between CIP2A and the PP2A complex, a series of Flag-tagged CIP2A deletion constructs (Figure S1) were transiently transfected into HeLa cells for 48 hr, followed by immunoprecipitation with anti-Flag antibody.
2008	imex:IM-12128_MI:0007	NML interacts with SUV39H1.
2009	imex:IM-12128_MI:0007	NML/SIRT1/SUV39H1 complex was eluted using FLAG peptides then immunoprecipitated with anti-myc antibody.
2010	imex:IM-12128_MI:0007	We next tested the interaction between NML and SIRT1 by coimmunoprecipitation and found that SIRT1 interacts with NML (Figure 3D)
2011	imex:IM-12133_MI:0007	As determined by coimmunoprecipitation (Figure 5E), LRAP35a&#916;IE showed impaired interaction with MRCK and not with MYO18A
2012	imex:IM-12133_MI:0007	As LRAP35a was a predicted adaptor, we sought to identify interacting proteins other than MRCK. FLAG-tagged LRAP35a from COS7 and HeLa lysates was immunoprecipitated using FLAG antibodies.
2013	imex:IM-12133_MI:0007	HA-tagged LRAP35a was found to coimmunoprecipitate with both FLAG-tagged MRCK&#945;
2014	imex:IM-12133_MI:0007	HA-tagged LRAP35a was found to coimmunoprecipitate with both FLAG-tagged MRCK&#945; and MRCK&#946; but not with FLAG-ROK&#945; (Figure 2A
2015	imex:IM-12133_MI:0007	Since the LRAP35a interacting sites for MRCK and MYO18A were separate, we next investigated whether the three proteins could associate to form a tripartite complex.
2016	imex:IM-12133_MI:0007	the MRCK/LRAP35a&#916;TFL complex (Figure 3E).
2017	imex:IM-12135_MI:0007	Pull-down assays showed that both full-length ACF7 and ACF7-NC (81 kDa) associated with F-actin, MTs, and +tip proteins (Figures 5B and 5C).
2018	imex:IM-12136_MI:0007	Although the immunoprecipitates contained comparable amounts of aPKC, only the Baz complex
2019	imex:IM-12137_MI:0007	Coimmunoprecipitation (Co-IP) showed that Myc-Clr8 coprecipitated with Lid2 (Figure 1D).
2020	imex:IM-12137_MI:0007	Co-IP showed that point mutation at the iron-binding site (H512A) of Lid2 did not disrupt its interaction with Set1 (upper panel) or Cul4 (lower panel).
2021	imex:IM-12137_MI:0007	Lid2 interacts with Rik1 as shown by a Co-IP
2022	imex:IM-12137_MI:0007	Lid2-TAP and Lsd1-Myc coprecipitated (Figure 6E),
2023	imex:IM-12138_MI:0007	Lrp4 and MuSK interact in cis, as they coimmunoprecipitate when expressed together in the same cell.
2024	imex:IM-12142_MI:0007	Co-IP was performed on lysates of 293T cells expressing V5-tagged MyoVb and GFP-tagged Rab11-FIP2 in different concentrations of free Ca2+. ms, control mouse serum.
2025	imex:IM-12143_MI:0007	Analysis of the Spo13-Cdc5 interaction in anti-Myc IPs from PCLB2-CDC20 cells with Myc9-SPO13 (Z11436) or Myc9-spo13-m2 (Z11437).
2026	imex:IM-12143_MI:0007	Binding of Lrs4 to Csm1 in anti-Myc IPs from LRS4-ha3
2027	imex:IM-12143_MI:0007	Binding of Mam1 to Csm1 in anti-Myc IPs
2028	imex:IM-12143_MI:0007	Binding of Mam1 to Hrr25 in anti-Ha IPs
2029	imex:IM-12143_MI:0007	Cdc5 binds to DDK (Figure 1A) and both kinases copurify with Lrs4
2030	imex:IM-12143_MI:0007	Cdc5 binds to kinase-dead DDK
2031	imex:IM-12143_MI:0007	Cdc7 associates with kinase-dead Cdc5
2032	imex:IM-12143_MI:0007	Spo13 binds to Cdc5-s polo-box domain
2033	imex:IM-12143_MI:0007	the association of Cdc5 with Lrs4.
2034	imex:IM-12143_MI:0007	Upon induction of meiosis, Cdc7 associates first with Dbf4 (to form DDK) and then with Cdc5 (Figure 1A)
2035	imex:IM-12146_MI:0007	Exogenously expressed &#946;-catenin, TCF4, and RUNX3 coimmunoprecipitate.
2036	imex:IM-12146_MI:0007	HCT116 cells were transfected with Flag-tagged RUNX3 derivatives and Myc-tagged full-length TCF4.
2037	imex:IM-12146_MI:0007	Interaction between RUNX3 and TCFs (TCF1, Lef1, and TCF3).
2038	imex:IM-12146_MI:0007	Interaction of RUNX3(R178Q) with &#946;-catenin/TCF4
2039	imex:IM-12146_MI:0007	Mapping of the TCF4 domain that interacts with RUNX3.
2040	imex:IM-12146_MI:0007	Oncogenic &#946;-catenins have a higher affinity for RUNX3 than wild-type &#946;-catenin.
2041	imex:IM-12146_MI:0007	Ternary complex of exogenously expressed &#946;-catenin/TCF4/RUNX3 detected by two-step coimmunoprecipitation.
2042	imex:IM-12149_MI:0007	Caco2 cells were transiently transfected with PLEKHA7-Flag and Nezha-GFP or control GFP vector (left), and their lysates were subjected to immunoprecipitation with anti-GFP antibodies.
2043	imex:IM-12149_MI:0007	PLEKHA7 associates with p120 and E-cadherin
2044	imex:IM-12152_MI:0007	However, CENP-T and CENP-C coprecipitated with CENP-A when the partially digested chromatin was used.
2045	imex:IM-12152_MI:0007	Indeed, SDS-PAGE and mass-spectrometry analysis indicated that CENP-H IPs primarily contained CENP-H, -I, -K, -L, -M, and -N, but not CENP-T.
2046	imex:IM-12152_MI:0007	Silver staining and western blot analysis with antibodies against CENP- T confirmed clear coprecipitation of CENP-T with CUG2
2047	imex:IM-12155_MI:0007	Cdc13-T308A still interacts with Est1 and Stn1 when Est1 and Stn1 are overexpressed.
2048	imex:IM-12155_MI:0007	Reduced telomerase recruitment efficiency by Cdc13-T308A as indicated by reduced association of Cdc13-T308A and TLC1 (p values < 0.01), quantified by real-time QRT-PCR.
2049	imex:IM-12156_MI:0007	Western blot (WB) analysis reveals RELA protein in immunoprecipitates (IP) of FLAG-tagged SIRT6
2050	imex:IM-12166_MI:0007	Consistent with this possibility, Cdc20 and Id1 formed a physical complex in a D-box-dependent manner in cells (Figure S11A, bottom)
2051	imex:IM-12166_MI:0007	Lysates of 293T cells transfected with HDAC6-FLAG together with the myc-Cdc20 expression plasmid or control vector were immunoprecipitated with the myc antibody and immunoblotted with the indicated antibodies.
2052	12907755_MI:0008	PTPH1 only bound Tyr534
2053	12907755_MI:0008	we found that TC-PTP, PTP-, PTP1B, SAP1, Pyst-2, megakaryocyte phosphatase (Meg-2), and PTP-H1 reproducibly bind phosphorylated, but not native GHR
2054	14550308_MI:0010	The strength of the interaction between the KD and C1 domain with MT 2A was tested using the liquid b-galactosidase assay. MT 2A showed strong interaction with KD and a relatively weak interaction with the C1 domain
2055	17347654_MI:0010	As indicated in Figure 1F, the IF domain was found to be essential for the interaction of PRB with CUEDC2 in yeast.
2056	15670823_MI:0012	As shown in Fig. 1A (left panel), we were able to detect a significant signal of interaction (90-100% over the controls) in cells expressing both Luciferase Raf-BXB and GFP-CNK1.
2057	15670823_MI:0012	None of the wild type forms of Rho proteins was able to give a positive signal of interaction with the exception of RhoH that is known to be locked in a constitutively active form [26] and the active form of Rho C that gives a moderate interaction signal with hCNK1 (see also Fig. 1B).
2058	15670823_MI:0012	The results shown in Fig. 1B demonstrate that hCNK1 interacts specifically with GTP bound Rho A proteins and in less extent with Rho C.
2059	16326715_MI:0013	In contrast, the P(r) for the complex showed a peak at 20Å and a skirt extending up to 60Å (Fig. 2b). From these findings, we concluded that p47phox-(151-286) has a compact globular structure when complexed with p22phox-(149-168), whereas the peptide-free form has an extended structure.
2060	12372836_MI:0014	dimeric state of both MobB and MoeA.
2061	12372836_MI:0014	Interestingly, MoeA interacts with both MogA and MobA to result in significant complementation
2062	12372836_MI:0014	MobB interacts with MoeA, MogA, and MobA to varying extents
2063	12372836_MI:0014	MoeA interactswith both MogA and MobA
2064	14674886_MI:0014	any interaction between two tagged NapH proteins was fairly weak.
2065	14674886_MI:0014	A strong interaction was shown between NapC and NapH, provided that the NapC tag was located on the N-terminus, which is consistent with the predicted localization of the C-terminus of NapC in the periplasm.
2066	14674886_MI:0014	There are strong indications that NapC, and possibly also NapH, forms a multimeric complex.
2067	18854156_MI:0014	Bacterial two-hybrid analysis of Soj variants and DnaA
2068	10716984_MI:0016	The CD spectra of the H6Rnr2p, Rnr4p, and coexpressed H6Rnr2p/Rnr4p showed characteristics of an alpha-helical structure with minima at 208 and 222 nm (Fig. 3).
2069	15358149_MI:0016	showed that Ca2+-KChIP1 interaction
2070	15358149_MI:0016	The negative peaks in the CD spectra of KChIP2.1 and KChIP2.2 became more pronounced upon the addition of Ca2
2071	18835031_MI:0016	CD spectra for the binding of NuBCPs (30 &#956;M) to GST-Bcl-2/29-90 (2 &#956;M).
2072	18835031_MI:0016	We next determined whether NuBCPs can induce a conformational change of purified GST-Bcl-2 protein using circular dichroism (CD) analysis.
2073	16230340_MI:0017	titrations of 50-285 nM labeled ProT indicated that SC-(1-325) bound ProT with a 0.84-1.00 stoichiometry for those that could be determined (ACR, AF350, BD, 4'F, 5F, OG, and TMR)
2074	16288713_MI:0017	Interaction between eIF2a and PERK by fluorescence spectroscopy.
2075	16317001_MI:0017	Binding of Sfi1 peptide to CRC-N.
2076	16326715_MI:0017	The Kd values for complex formation between p47phox-(151-286) and the two p22phox peptides were subsequently determined by fluorescence titration method. The fluorescence data gave Kd values of 8.67 
M for p22phox-(149-162) and 0.64 
M for p22phox-(149-168), respectively (Fig. 1, c and d), indicating that residues 163-168 of p22phox enhance the binding affinity of p22phox for p47phox by more than 10-fold.
2077	16368681_MI:0017	We found that at 3 
M, the N-terminal active site (ACxxCA
AxxA) has over a 4-fold defect in the initial rate of oxidation when compared with wild-type PDI (Fig. 3A). In contrast, as we saw previously AAxxAA
CxxC has a rate of oxidation that is close to that of wild-type PDI, and when the Ero1p concentration is increased modestly (1.3-fold), the initial rates of oxidation can be matched (Fig. 3A)
2078	16368681_MI:0017	We found, using the ThioGlo1 assay, that ERp57 and the individual ERp57 thioredoxin domains, A and A
, are all oxidized by Ero1p in vitro (Fig. 6B).
2079	16368681_MI:0017	We used the ThioGlo1 fluorescence assay to establish conditions in which the initial rate of oxidation of PDI is linearly dependent on its concentration and the relative rate of oxidation of the PDI active sites can be compared (Fig. 4A).
2080	16474402_MI:0017	Interactions of these peptides with the USP7 NTD were determined by monitoring the change in intrinsic fluorescence of USP7 at peptide concentrations up to 100 muM. Whereas no binding was detected with peptides 1 (85-LFGVPSFSVK-94), 2 (109-VVVNQQESSDS-118) and 3 (126-RCHLEGGSDQ-135), titratable binding was seen with peptides 4 (141-ELQEEKPSSS-150), 5 (152-LVSRPSTSSR-161) and 6 (143-QEEKPSSSHL-152)
2081	16474402_MI:0017	More quantitative analyses were then conducted for Asp164 and Asn169 mutants by following the change in fluorescence of the USP7 NTD upon titration with EBNA1, p53 and MDM2 peptides (Table 1). This analysis could not include the Trp165 mutant, as this residue is responsible for the fluorescence signal that is altered by peptide binding. These assays confirmed that there was little effect of the Asn169 mutation on binding to any of the peptides, although EBNA1 binding was reduced approximately two-fold.
2082	16474402_MI:0017	More quantitative analyses were then conducted for Asp164 and Asn169 mutants by following the change in fluorescence of the USP7 NTD upon titration with EBNA1, p53 and MDM2 peptides (Table 1). This analysis could not include the Trp165 mutant, as this residue is responsible for the fluorescence signal that is altered by peptide binding. These assays confirmed that there was little effect of the Asn169 mutation on binding to any of the peptides, although EBNA1 binding was reduced approximately two-fold. The Asp164 mutation decreased binding two- to three-fold for all target peptides.
2083	16474402_MI:0017	we generated two 10-residue fragments of p53 containing residues 358-EPGGSRAHSS-367 and 356-GKEPGGSRAH-365 and quantified binding by following the change in intrinsic fluorescence of the USP7 NTD (Table 1). The 358-367 fragment bound the USP7 NTD with a similar affinity to that of the 355-393 fragment (Kd = 11 muM).
2084	16474402_MI:0017	we generated two 10-residue fragments of p53 containing residues 358-EPGGSRAHSS-367 and 356-GKEPGGSRAH-365 and quantified binding by following the change in intrinsic fluorescence of the USP7 NTD (Table 1). The 358-367 fragment bound the USP7 NTD with a similar affinity to that of the 355-393 fragment (Kd = 11 muM). Peptide 356-365 also bound USP7, although with a slightly reduced affinity
2085	17951432_MI:0017	By using this real-time assay, the kobs value for GTPS binding by AtGPA1 was 14.4 min1, a value 22-fold faster than the most rapidly exchanging G
 subunits previously described
2086	18384742_MI:0017	Fluorescence polarization studies of ETR1-AHP1 interaction
2087	18585358_MI:0017	Fluorescence Emission Spectra of cVA Binding to wild type and LUSHF121A
2088	imex:IM-11882_MI:0017	Dissociation constants of TAF3-PHD binding to H3 peptides (residues 1-17) carrying the indicated modifications as determined by tryptophan fluorescence.
2089	imex:IM-11954_MI:0017	Denatured DM-MBP bound efficiently to DnaK/DnaJ in the presence of ATP, resulting in inhibition of folding (Figure S4)
2090	imex:IM-11961_MI:0017	We first tested whether the CASK CaM-kinase domain interacts with the ATP analog TNP-ATP that becomes fluorescent when inserted into the hydrophobic ATP-binding pocket
2091	10079358_MI:0018	we tested the ability of this D.hydei Hairless domain for the binding of the D. melanogaster Su(H) protein in a yeast two-hybrid assay. As shown in Fig. 5, a very strong binding is observed which is in the range of the corresponding D. melanogaster Su(H)-binding domain.
2092	10092179_MI:0018	The conserved N-terminal region of the large subunit is involved in the interaction with the small subunit in yeast 2-hybrid system
2093	10094392_MI:0018	Assessed by growth on -His-medium, the N-terminal fragments b(1-55), (1-149) and (1-145) were in all combinations able to interact with the C-terminal fragments b(132- 215), (132-200), (152-215) and (152-200), whereas, the neighbouring deletions b(1-165) and (1-132) did not show this behaviour.
2094	10094392_MI:0018	To map the domain of CK2b involved in binding to CK2a, C-terminal CK2b deletion mutants were tested for interaction with CK2a by using the two-hybrid system.
2095	10094392_MI:0018	Under the most sensitive conditions, i.e. yeast strain CBY14 and the growth on -His medium we detected an interaction between CK2b (1-145) and wildtype b (Fig. 2).
2096	10209756_MI:0018	As seen in Table 1, a fusion containing the full-length ZipA interacted with FtsZ, as did a fusion containing only the C-terminal domain (residues 176 328). Thus, only the C-terminal domain of ZipA is sufficient for interaction with FtsZ.
2097	10209756_MI:0018	In contrast, SulA, which was used as a control, interacts with both the full-length FtsZ and FtsZ320.
2098	10220404_MI:0018	An interaction was detected when chickadee was cotransformed with Ena amino acids 440-490 and not Ena amino acids 490-684, suggesting that this interaction is mediated by proline-rich sequences in Ena
2099	10220404_MI:0018	The region of the Ena protein used as bait in the yeast two-hybrid screen contains several matches to a putative profilin binding site (4, 9, 26, 27). To test whether these sequences were important for mediating the interaction with chickadee
2100	10220464_MI:0018	Interactions of AKIN10 and AKIN11 with SNF4p and PRL1 in the yeast two-hybrid system
2101	10220464_MI:0018	The GBD-fusion protein carrying the AKIN10 catalytic domain between positions 1 and 381 did not interact either with GAD-PRL11-195, carrying 195 N-terminal amino acids from PRL1, or GAD-SNF4p
2102	10220464_MI:0018	The yeast strain expressing GBD-SNF1 and GADPRL1 grew in the presence of 50 mM 3-aminotriazole HIS3 inhibitor, as well as the control, and displayed LacZ1 phenotype in filter lift assays (16, 17), indicating that an interaction between SNF1p and PRL1 led to the activation of the GAL4- controlled HIS3 and LacZ reporter genes. A similar assay with pACT2prl11-620 and pAS1snf1 showed that PRL1 sequences located between the N terminus and amino acid position 195 were involved in the binding of SNF1p
2103	10330469_MI:0018	FUS5 Interacts with Both COP9 and FUS6 in the Yeast Two-Hybrid Assay.
2104	10383400_MI:0018	Co-immunoprecipitation from T-cells of theta PKC and p59fyn.
2105	10383400_MI:0018	Likewise, screening a human cDNA library yielded several p59fyn clones but no p56lck clones.
2106	10420643_MI:0018	One of the isolated clones (LDV59) contained a gene encoding a protein showing similarity to the previously identifed D-type cyclins of A. thaliana. This new cyclin gene (GenBank accession number AJ131636) was denoted CYCD4;1
2107	10420643_MI:0018	Specific interaction of CDC2aAt with LDV59.
2108	10488108_MI:0018	The RING finger domain of COP1 interacts with CIP8 in the yeast two-hybrid system
2109	10488108_MI:0018	Three of the four cDNAs displayed specific interaction to the LexA-N282 protein (data not shown). Sequencing analysis of the three classes of cDNAs revealed that one of them codes for a partial 92-amino acid fragment largely consisting of a RING-H2 motif, a variant type of the RING finger (Fig. 1A). This clone was designated CIP8. Because it exhibited strong and specific interaction to the COP1 RING finger, it was further characterized.
2110	10488241_MI:0018	Only the positivecontrol pair and the combination of pBD-HHMFP1 and pAD21-1 gave rise to colonies growing on Leu 2 , Trp 2 , and His 2 plates,
2111	10488241_MI:0018	Sequencing of the inserts showed that the three cDNAs encoded an identical protein sequence in frame with the GAL4 DNA binding domain. The deduced protein was named MAF1 (for MFP1 associated factor 1).
2112	10498867_MI:0018	53BP2 (477  1005) interacted more strongly with p65 (176  405)
2113	10498867_MI:0018	co-transfection with pM-53BP2 (477  1005) and pVP16- p65 (176  405) activated transcription (49-fold)
2114	10498867_MI:0018	co-transfection with pM-53BP2 (full) and pVP16-p65 (full) activated transcription from the reporter gene about 14-fold
2115	10498867_MI:0018	The interaction between p65 (176  405) and p65 (176  405)
2116	10512628_MI:0018	Results of two-hybrid experiments (Figure 2 and Table 1) indicated that the N-tube but not the tube C-terminal fusion protein was capable of interacting with N-pelle.
2117	10515947_MI:0018	Results of the liquid beta -galactosidase assay with ONPG as substrate to demonstrate NifL-NifA interactions
2118	10542152_MI:0018	significant interactions were only observed between coiled-coil-containing NPH3 polypeptide fragments and the NH2-terminal two-thirds of NPH1
2119	10590166_MI:0018	Figure 4 shows an interaction between CIPK1 and AtCBL1, AtCBL3, or AtCBL4/SOS3.
2120	10590166_MI:0018	In this study, the shortest polypeptide fragment sufficient for interacting with AtCBL1 was identified as a 123-amino acid stretch located between amino acid residues 276 and 398.
2121	10593939_MI:0018	A, in vivo interaction of SR33 with itself and three other SR proteins (SR45, SRZ21, and SRZ22).
2122	10593939_MI:0018	As shown in Fig. 1A, both SR proteins interacted with the full-length U1-70K but not with the truncated proteins from the N-terminal construct or the alternative transcript. In control experiments, neither U1-70K proteins nor SR proteins alone showed beta -galactosidase activity (Fig. 1A). These results demonstrate that interaction of SR33 and SR45 proteins with U1-70K takes place via C-terminal arginine-rich region.
2123	10593939_MI:0018	As shown in Fig. 7A, SR33 interacted with itself and SR45 but not with SRZ21 or SRZ22.
2124	10593939_MI:0018	Five cDNA clones showed beta -galactosidase activity only in the presence of C-terminal U1-70K. Sequence analysis revealed that these five clones fall into two groups. Three identical clones form one group of cDNAs (SR33) and the second group (SR45) of two clones differs only in their length by 31 bases at the 5' end.
2125	10593939_MI:0018	the highest level of beta -galactosidase activity was observed in the U1-70K/SRZ22 interaction whereas U1-70K/SR33 and U1-70K/SR45 interactions showed the same level of beta -galactosidase activity".
2126	10594004_MI:0018	Sla1p interacts with Pan1p through binding of its C-terminal repeats to LR1 of Pan1p.
2127	10602478_MI:0018	We tested the ability of human PRUNE protein to interact with human nm23-H1 in interaction-mating experiments
2128	10633111_MI:0018	A weak interaction of VirB7 with itself was observed.
2129	10633111_MI:0018	Studies on interactions of the VirB proteins indicated that VirB7 interacts with VirB9
2130	10633111_MI:0018	The N-terminal fusion (residues 17 to 122) interacted with all three proteins, indicating that this region contains the VirB8, VirB9, and VirB10 interaction domains (Fig. 3C).
2131	10633111_MI:0018	Two VirB10 fusions that contained residues 47 to 277 or 167 to 377 fused to the LexA DNA binding domain were analyzed to identify the VirB10 interaction domains. The N-terminal domain fusion interacted with VirB8, VirB9, and VirB10, indicating that this fragment contains all three interaction domains (Fig. 3D).
2132	10633111_MI:0018	VirB10 interacts with VirB8, VirB9, and itself
2133	10633111_MI:0018	VirB8 interacts with VirB9, VirB10, anditself (row 2).
2134	10633111_MI:0018	VirB9 interacts with VirB8, VirB10, and itself
2135	10656681_MI:0018	Coimmunoprecipitations performed with Fyn, Lck or anti-magicin (Tim3) antibodies revealed anin vivo association of magicin with both Fyn and Lck at the endogenous levels in Jurkat cells (Fig. 4B).
2136	10656681_MI:0018	Ten highly conserved amino acids within TRX SET (Tripoulas et al., 1996; Jenuwein et al., 1998) were mutated. These alterations resulted in loss of all or most of all the capacity of the modified polypeptides to self-associate in yeast
2137	10656681_MI:0018	This clone contained a TRX segment encompassing residues 3389-3759 and spanning the SET domain
2138	10659709_MI:0018	he truncated forms of these six factors also exhibited differential interaction with NPR1, with the following order of apparent affinity: DTGA2 > DTGA3, DTGA5, DTGA6 > DTGA1 > DTGA4
2139	10659709_MI:0018	Therefore, we conclude that all four npr1 point mutations known to disrupt SA signaling in planta also prevent NPR1 from interacting with several TGA family members in yeast. Furthermore, since all four mutations are in the ankyrin repeat region, these results provide further evidence that this region is critical for binding the TGA factors.
2140	10659709_MI:0018	Therefore, we suggest that these five TGAs differentially interact with NPR1, with the following order of apparent affinity: TGA3 > TGA2 > TGA5 > TGA6 > TGA1.
2141	10659709_MI:0018	Thus, coexpression of NPR1 with either truncated TGA1 or truncated TGA5 was required for His and Ade prototrophy.
2142	10659709_MI:0018	Yeast two-hybrid assay of the interaction between NPR1 and truncated forms of TGA1 or TGA5.
2143	10662555_MI:0018	The interaction between MAGOH and RBM8 was demonstrated by both yeast two-hybrid and GST fusion protein pull-down assays
2144	10662555_MI:0018	The interaction between MAGOH and RBM8 was demonstrated by both yeast two-hybrid and GST fusion protein pull-down assays.
2145	10704439_MI:0018	Fig 4 a shows that full-length Mad3p interacts with both Bub3p and Cdc20p in the two-hybrid assay, but not significantly with Mad1p, Mad2p, Bub1p, or Bub2p.
2146	10704852_MI:0018	in yeast two-hybrid assays, EXD can interact with full-length HTH and &#916;HD but not with &#916;MH
2147	10717484_MI:0018	Two-hybrid mapping of the Bicoid-interacting domain of Bin3.
2148	10717484_MI:0018	Using a 0-12 h Drosophila embryonic cDNA library, four clones were identified; Bin1-Bin4
2149	10717484_MI:0018	Using a 0-12 h Drosophila embryonic cDNA library, four clones were identified; Bin1-Bin4 for (Bicoid-Interacting protein 1-4).
2150	10727209_MI:0018	we identified 12 independent clones in which the LexA-driven reporters were active only in galactose, indicating that they contained cDNA-encoded proteins that interacted with LexA-12-LOX. We isolated the library plasmids from these clones and determined that they represented four different cDNAs. Six identical clones encoded the carboxy-terminal 330 amino acid residues of type II keratin K5
2151	10727209_MI:0018	we identified 12 independent clones in which the LexA-driven reporters were active only in galactose, indicating that they contained cDNA-encoded proteins that interacted with LexA-12-LOX. We isolated the library plasmids from these clones and determined that they represented four different cDNAs. Six identical clones encoded the carboxy-terminal 330 amino acid residues of type II keratin K5. Two clones encoded the carboxy-terminal 202 residues of the nuclear envelope protein lamin A.
2152	10727209_MI:0018	we identified 12 independent clones in which the LexA-driven reporters were active only in galactose, indicating that they contained cDNA-encoded proteins that interacted with LexA-12-LOX. We isolated the library plasmids from these clones and determined that they represented four different cDNAs. Six identical clones encoded the carboxy-terminal 330 amino acid residues of type II keratin K5. Two clones encoded the carboxy-terminal 202 residues of the nuclear envelope protein lamin A. Another two clones encoded the cytoplasmic domain of integrin 4.
2153	10727209_MI:0018	we identified 12 independent clones in which the LexA-driven reporters were active only in galactose, indicating that they contained cDNA-encoded proteins that interacted with LexA-12-LOX. We isolated the library plasmids from these clones and determined that they represented four different cDNAs. Six identical clones encoded the carboxy-terminal 330 amino acid residues of type II keratin K5. Two clones encoded the carboxy-terminal 202 residues of the nuclear envelope protein lamin A. Another two clones encoded the cytoplasmic domain of integrin 4. The final two clones encoded a phosphoprotein, C8FW
2154	10747865_MI:0018	We found a single positive clone, CCTe, that could interact with the THEG protein
2155	10758489_MI:0018	These results indicate that ICK1 and ICK2 specifically interact with Cdc2aAT, while ICK3 interacts with Cdc2aAt as well as Cdc2bAt
2156	10798620_MI:0018	We observed specific interaction of AtRhoGDI1 with wild-type AtROP4 and AtROP6, but not with control AtRAB11c
2157	10814541_MI:0018	Binding of the proteins encoded by the three candidate clones containing the VDUP1 sequence with hTrx was confirmed by performing the secondary yeast two-hybrid assay on each clone
2158	10814541_MI:0018	In the present study, a possible interaction between hTrx and VDUP1 in HeLa cells was suggested using a yeast two-hybrid system.
2159	10869553_MI:0018	Forty out of 41 clones were identified as the S100A4 cDNA fused in-frame with GAL4-AD, indicating the homodimerization of S100A4 in vivo.
2160	10869553_MI:0018	Forty out of 41 clones were identified as the S100A4 cDNA fused in-frame with GAL4-AD, indicating the homodimerization of S100A4 in vivo. Besides the S100A4 dimers, one of the clones was identified as a cDNA encoding the S100A1 protein.
2161	10899120_MI:0018	For Mpc54p, self-interactions of the full-length proteins as well as the N-terminal and the coiled-coil domains were observed.
2162	10899120_MI:0018	Mpc54p interacts with the C-terminal domain of Nud1p.
2163	10899120_MI:0018	Mpc54p interacts with the C-terminal domain of Nud1p and with Spc42p.
2164	10899120_MI:0018	Mpc70p also showed interactions with Spc42p and the C-terminal domain of Cnm67p. These interactions, however, were observed only for one direction in the two-hybrid assay.
2165	10899120_MI:0018	Mpc70p also showed interactions with the C-terminal domain of Cnm67p (aa386-580). These interactions, however, were observed only for one direction in the two-hybrid assay.
2166	10899120_MI:0018	Mpc70p interacts strongly with full-length Mpc54p. These interactions were independent of which domain was fused to the lexA DNA-binding domain and to the Gal4 activation domain.
2167	10899120_MI:0018	Mpc70p interacts strongly with itself. These interactions were independent of which domain was fused to the lexA DNA-binding domain and to the Gal4 activation domain.
2168	10899120_MI:0018	Mpc70p interacts strongly with the C-terminal half of Nud1p (aa405-852). These interactions were independent of which domain was fused to the lexA DNA-binding domain and to the Gal4 activation domain.
2169	10903443_MI:0018	This result demonstrates that Dazl1 is able to interact with itself in yeast cells in the presence of an excess of unrelated proteins
2170	10915743_MI:0018	A plasmid library representing the fetal human liver was screened with LexA-E12 bait in a yeast reporter strain. Of 1 3 106 independent clones screened, 92 clones with a Leu1 LacZ1 phenotype were obtained. The rep-resentative plasmids from each group of positives were retransformed back into yeast to confirm their correct phenotype. Finally, of 14 true positive clones, 5 independent clones were identified as follows: Id1 (5 clones), Id2 (4 clones), Id3 (3 clones), alpha-1-antitrypsin, and 1 clone encoding the unknown sequence.
2171	10915743_MI:0018	In an attempt to identify partners for the E12 protein that may exert control during liver development, we performed the yeast 2-hybrid screen using an expression complementary DNA library from human fetal liver. A novel dominant inhibitory HLH factor, designated HHM (human homologue of maid), was isolated and characterized.
2172	10930412_MI:0018	Constructs containing the GAL4 activation domain and either the C-terminal HBO1 or ARA70 (23), an AR coactivator, showed a strong induction with the AR-DBD-LBD in the presence of DHT. An AR-LBD construct also showed an increase in b-gal in the presence of DHT
2173	10930412_MI:0018	To identify AR interacting proteins, we screened a human prostate library with a GAL4 DBD fusion encoding the DBD and LBD of AR. Of 2 3 106 transformants, 75 positive clones were identified by both adenine and b-galactosidase production in the presence of DHT. Sequence analysis revealed that one of these clones (PG159) is identical to the C terminus of a recently identified novel protein (GenBankTM accession number AF074606), named HBO1 (histone acetyltransferase binding to the origin recognition complex 1)
2174	10930573_MI:0018	As shown in Fig. 2, we detected direct interactions between ETR1 and all ATHPs,
2175	10930573_MI:0018	between CKI1 and ATHP1 or ATHP2.
2176	10930573_MI:0018	Therefore, the receiver domain of ATHK1 (ATHK1-RD) and the fulllength coding regions of ATHP1-3 were expressed as fusion proteins to a LexA DNA-binding domain (pLexA) and to a VP16 activation domain (pVP16), and were tested for both growth on His-lacking medium and L-galactosidase activity in yeast. Reciprocal combinations of the pLexA and pVP16 plasmids were also tested to confirm the positive interactions. ATHK1 interacted with ATHP1
2177	10930573_MI:0018	We also detected interactions between yeast SLN1 and ATHP1 or ATHP3
2178	10930573_MI:0018	We detected interactions between ATHP2 and ATRR4,
2179	10930573_MI:0018	We detected interactions between ATHP2 And ATRR4,
2180	10930573_MI:0018	We detected interactions between ATHP2 and ATRR4, and between ATHP3 and ATRR1 or ATRR4
2181	10954706_MI:0018	D, identification of the coil II region of K18 that is sufficient for binding to Mrj.
2182	10954706_MI:0018	To further examine the function of Mrj, we determined which region of Mrj interacts with Hsp/c70 and K18 using the two-hybrid system. As shown in Fig. 5 (A and B), Mrj-F interacted with both K18 and Hsc70, but not with K8. Mrj-C (aa 99-242) strongly interacted with K18, but Mrj-N1 (aa 1-100) and Mrj-N2 (aa 1-146) did not bind to K18. In contrast, Mrj-N1 and Mrj-N2 bound to Hsc70, but Mrj-C did not interact with Hsc70.
2183	10954706_MI:0018	To investigate the function of K8/18, we screened a human liver cDNA library using the yeast two-hybrid technique and full-length K18.
2184	10984058_MI:0018	and the tail of Myo2 interacts with Smy1
2185	10984058_MI:0018	As expected, Kar9 also interacts with the microtubule-binding protein Bim1
2186	10984058_MI:0018	Kar9 interacts with the tail domain of wild-type Myo2, but not with the motor or central domains.
2187	11003656_MI:0018	Among the positive clones obtained, four identical clones typified by clone 55.1 specifically interacted in a two-hybrid assay with HaHSP27 and HuHSP27, but not with ras (val 12) and lamin C (data not shown). Sequence analysis revealed that clone 55.1 corresponded to the carboxy terminus of the human Daxx protein from amino acid 472 to 740
2188	11003656_MI:0018	Transient expression in yeast and immunoprecipitation indicated that the FBD domain of Daxx was sufficient to mediate the interaction of Daxx with HSP27.
2189	11006339_MI:0018	To determine whether the sos3-1 mutation affects SOS3 interaction with SOS2, we conducted a yeast two-hybrid assay, using the mutant SOS3&#916;EF as the bait and pACT-SOS2 as the prey. Figure 7 shows that unlike the wild-type SOS3, SOS3&#916;EF was not capable of interacting with SOS2.
2190	11018023_MI:0018	CLIF interacts with EPAS1 and CLOCK.
2191	11018516_MI:0018	Next, we carried out the deletion analysis of the CEO1-coding sequence. The two-hybrid assay was also used to identify domains of interaction of CEO1 with its preys. For this purpose, five deletions in the coding region of CEO1 were generated by PCR (see Section 2) and cloned into the pGBT9 vector as carboxyl-terminal fusions with the DNA-binding domain of GAL4. Yeast HF7c was transformed with all combinations of the CEO1 deletions and the isolated preys. The protein-protein interactions were assessed by growth of the transformants in SD His&#8722; medium with or without 20 mM AT and by subsequent &#946;-galactosidase staining. As summarized in Fig. 5, the interacting domain of CEO1 was located in its carboxyl-terminal part, between the amino acids 345 and 589.
2192	11018516_MI:0018	One of the cDNAs encoded the protein STO (X95572) from A. thaliana, a protein that confers salt tolerance to yeast [20]. STO is highly similar to putative zinc finger-containing proteins, such as CO (Gi 2695703).
2193	11022036_MI:0018	full-length CR6 interacted with PCNA
2194	11022036_MI:0018	full-length PCNA interacted with CR6. PCNA C-terminal (PCNA/224-261), N-terminal (PCNA/1-46), and middle (PCNA/87-127) peptides also interacted with CR6.
2195	11022036_MI:0018	It can be seen that CR6/76-159 interacted with PCNA as well as full-length CR6, whereas CR6/1-135 failed to interact
2196	11027267_MI:0018	Using a two-hybrid screening with TOM1, a putative ubiquitin-ligase gene of Saccharomyces cerevisiae, we isolated KRR1
2197	11029466_MI:0018	Despite this, the results clearly show a direct interaction between eIF3b and eIF3c.
2198	11029466_MI:0018	eIF3e also interacted with eIF3c, suggesting that the immunoprecipitation of eIF3c and eIF3e is a result of direct interaction between these proteins.
2199	11029466_MI:0018	The interaction of eIF3e with CSN7 clearly activated b-galactosidase activity indicating a direct interaction between eIF3e and CSN7 and further supporting the immunoprecipitation data.
2200	11029584_MI:0018	deletion of the POU-homeodomain in GAL4 Brn-2 1±355 (POU-S/L) increased the interaction with the VP16 Brn-2 1±443 fulllength fusion protein relative to that initially found with GAL4 Brn-2 1±443 itself (Fig. 2B). This suggests that the POUhomeodomain may offer some steric hindrance to dimerization in this arrangement. Further C-terminal deletion of the POUhomeodomain and linker region in GAL4 Brn-2 1±336 (POU-S) resulted in loss of interaction with the VP16 Brn-2 1±443 full-length target.
2201	11029584_MI:0018	Full-length Brn-2 was able to interact with TBP in this assay system, however, in contrast to the Oct-1 and Oct-2 interaction it was not able to show that the Brn-2 187-443 POU domain alone was sufficient for this interaction.
2202	11029584_MI:0018	It was notable that this level of interaction, although much less than the 70-200-fold seen between Brn-2 itself (Fig. 2), is similar to that seen between Sox10 itself (Gal4 Sox10: VP16 Sox10
2203	11029584_MI:0018	Only the results of interaction with GAL4 p300 1±149 are shown (Fig. 3) as this is the only portion of the p300 protein that demonstrated significant interaction with Brn-2.
2204	11029584_MI:0018	the interaction of Pax3 with Sox10 was also examined and shown to be of the same order of magnitude as Pax3 with Brn-2
2205	11029584_MI:0018	there was a 10-fold activation of reporter activity between full-length Pax3 and the VP16 Brn-2 fusion proteins compared with VP16 alone, and again this level of interaction was lost in the each of the C-terminal truncated Brn-2 proteins indicating that an intact POU domain was required for interaction.
2206	11029584_MI:0018	There was a sevenfold activation of reporter activity between full-length Sox10 and Brn-2 fusion proteins compared with VP16 alone and this level of interaction was lost with each of the C-terminal truncated Brn-2 proteins, indicating that an intact POU domain was required for interaction
2207	11030144_MI:0018	Figure 1a shows that co-expression of BUBR1 and p55CDC greatly activated the expression of beta-Gal, suggesting that BUBR1 interacted with p55CDC.
2208	11042178_MI:0018	We therefore investigated the possibility of interactions between the C-terminal domains of KAT1 and KAT2 using the two-hybrid system in yeast (38) and obtained positive results
2209	11042198_MI:0018	With this assay, as shown in Table I, beta -galactosidase activity is observed for four of the eight pairs of constructs tested for interaction between IDH1 and IDH2.
2210	11046044_MI:0018	The interaction between RACK-1 and IFN-RßL detected in the two-hybrid system was shown to be specific, because both the pACT-C1-L and pACT-C2-N1 clones failed to produce ß-galactosidase-positive colonies when either was reintroduced with one of two different control plasmids (pLAM 5'-1 or pVA3-1) in CG1945 cells (Fig. 1). Cotransformation of the control (pLAM 5'-1 or pVA3-1) and bait plasmids (pACT-C1-L or pACT-C2-N1) was confirmed by the observed growth of transformed yeast in tryptophan- and leucine-deficient media (Fig. 1).
2211	11046044_MI:0018	Yeast two-hybrid interaction of RACK-1 with the cytoplasmic domain the IFN-RßL chain.
2212	11058119_MI:0018	These results indicate that XAB1 interacts with the N-terminal region of XPA and that the five basic amino acid residues (residues 30-34) of XPA are important for the binding to XAB1.
2213	11058119_MI:0018	Two of them encoded known proteins that bind to XPA; 145 clones were ERCC1 and 45 clones were RPA34.
2214	11058119_MI:0018	Using the yeast two-hybrid system, we elucidated that XAB1 binds to the N-terminal region of XPA.
2215	11058127_MI:0018	Two-hybrid analysis to detect interactions of AtWRNexo with AtRecQl1 to 3. AtWRNexo and AtRecQl2 showed a strong interaction after 4 h X-gal staining (left)
2216	11073942_MI:0018	We employed the two-hybrid method using Rag A as the bait to identify proteins binding to Rag A, and we isolated two novel human G proteins, Rag C and Rag D.
2217	11084035_MI:0018	The shortest clone (clone 16) isolated in the two-hybrid screening encodes 18 out of the 25 repeats, and the sequence was included in all of the overlapping clones, suggesting that the WQXPXX repeat region represents the binding site of the N-terminal domain of Dlx5 (Fig. 2A). No significant homology to any protein sequences was found in the N-terminal part of Dlxin-1 by searching data bases.
2218	11090136_MI:0018	Thus, the C-terminal region of Ci from aa 941 to aa 1065 defines a Cos2 binding domain
2219	11108847_MI:0018	The conserved dimerization domain of the AtE2Fs seemed to be important for the interaction with the AtDPs, because mutational analysis showed that deletion neither of the N-terminal extension nor the C-terminal part of AtE2Fa and AtE2Fb impaired the interaction with the DPs (Fig. 2B,C, lower). Similar results were obtained by two-hybrid analysis (Table 1).
2220	11108847_MI:0018	The pGBTE2FaBD screen yielded a clone containing an approximately 1.1 kb cDNA insert showing considerable homology with animal DP sequences. The full-length cDNA of AtDPa isolated by rapid amplication of 5P cDNA ends encoded a protein of 292 amino acids with predicted molecular mass of approximately 33 kDa.
2221	11108847_MI:0018	The screening with pGBTE2Fb-Rb resulted in the identication of a positive clone that turned out to be the AtE2Fb itself.
2222	11112409_MI:0018	Cotransformation of pLexA/sentrin and pJG4-5/Daxx resulted in the expression of the reporters LacZ.
2223	11112409_MI:0018	pJG4-5/Daxx also interacted with the pLexA/Ubc9.
2224	11112409_MI:0018	We also tested whether sentrin could form homo-oligomers by protein-protein interaction. As shown in Fig. 1, pLexA/sentrin and pJG4-5/sentrin interacted in yeast two-hybrid system.
2225	11115898_MI:0018	As shown in Figure 4A, both 35 and 20 amino acid fragments interacted with AtCBL4 but not with AtCBL1 and AtCBL3. Compared with the interaction strength between AtCBL4 and the entire C-terminal region of CIPK5 (CIPK5C), the two fragments interacted with AtCBL4 at significantly reduced levels (Fig. 4B). These results suggest that the conserved domain in the C-terminal region of CIPKs may be sufficient for interacting with certain AtCBL member(s) but may need surrounding sequences to have an optimum interaction.
2226	11117257_MI:0018	An Arabidopsis cDNA library in the plasmid pACT (Durfee et al., 1993), where the inserts are fused to the GAL4 activation domain, was introduced into the yeast strain L40 by co-transformationwith the pLex-4E2 plasmid. About 106 leucine and tryptophan autotrophs were screened for histidine autotrophy. A total of 75 HIS C clones were further tested for LacZ activity, and 45 clones showed a strong blue color formation. Plasmids were rescued from yeast, sequenced and the sequences compared to databases. Plasmids were also tested for reproducibility and specificity by retransformation of L40 in combination with pLex-4E2 or pLex-Lamin, a negative interaction control. Four clones with a confirmed interaction were obtained. One of the interacting clones was homologous to the cDNA sequence of the A. thaliana lipoxygenase 2 (AtLOX2). The AtLOX2 clone gave reproducible and high levels of LacZ activity with the pLex-4E2 plasmid.
2227	11117257_MI:0018	Localization of the eIF(iso)4E interaction domain in LOX2.
2228	11117257_MI:0018	The cells containing both pLex-4E2 and pGAD-Wp86 were histidine autotrophs and lacZ-positive, showing that the Arabidopsis eIF(iso)4E expressed in yeast was interacting with wheat eIF(iso)4G
2229	11117257_MI:0018	To test this possibility in the yeast two-hybrid assay, pACT-LOX2 was co-transformed with plasmids pGBT-wp26 and pGBT-wp28 encoding the wheat eIF4E and eIF(iso)4E fusion proteins respectively, and also with pGBT-nCBP containing a novel cap-bindingprotein identified in Arabidopsis (Ruud et al., 1998). LacZ activity tests showed that LOX2 interacts with both wheat cap-binding proteins and with nCBP (Figure 5), suggesting that AtLOX2 contains a sequence motif that interacts with a common surface on eIF4E factors.
2230	11121078_MI:0018	Both AGB1 and TGB1 interacted very strongly with AGG1
2231	11121078_MI:0018	The remaining 10 positive clones included the 26S ribosomal RNA gene, sedoheptulose-1,7-bisphosphatase, and several genes of unknown function that were not investigated any furthe
2232	11121078_MI:0018	The tobacco &#946;-subunit TGB1 was used as bait to screen 4.2 million transformants from an Arabidopsis seedling yeast two-hybrid library (CD4-22; ref. 13). After both primary and secondary screenings, 14 positive clones were obtained. These clones were sequenced and analyzed for the following structural features conserved in all known G protein &#947;-subunits (20): (i) coding for a small 6- to 13-kDa peptide (21); (ii) coiled-coil domain at the N terminus (9); and (iii) a C terminus CAAX motif (A, aliphatic amino acid; X, any amino acid; ref. 7). Four clones contained an identical coding region meeting these criteria. The longest (595 bp) of these four clones was designated AGG1
2233	11148284_MI:0018	Although MEA was shown to bind weakly to itself
2234	11148284_MI:0018	In the reciprocal two-hybrid experiment, expression of GAL4BD-MEA and GAL4AD-FIE activated HIS3 reporter expression (Figure 1E), but no b-GAL reporter expression was detected (Figure 1F).
2235	11148284_MI:0018	Our results show that the N-terminal 168 amino acids of MEA are sufficient to interact with FIE in the yeast two-hybrid system.
2236	11156409_MI:0018	In a yeast 2-hybrid assay, caspase-2L-Pro interacted with both procaspase-2L and RAIDD/CRADD,
2237	11168407_MI:0018	Intensities of proteinn protein interactions of wild-type and mutant SAT-A as quantified with the yeast two-hybrid system.
2238	11169732_MI:0018	Table 1 summarizes the levels of beta-galactosidase activity obtained from four different experiments. The coiled-coil fragment of M282 interacted with both hPrt1(129-873) and K7(325-468), generating beta-galactosidase activity of 19 muller units for hPrt1(129-873), and 47 muller units for K7(325-468).
2239	11178989_MI:0018	coexpression of VP-MDM2 with GAL-ER remarkably increased luciferase activity only in the presence of E2;
2240	11256608_MI:0018	For this screen, the first 245 amino acids of GAGA, which include the POZ domain (Figure 2A), were used. One of the 20 different clones isolated in this screen showed high homology to SAP18
2241	11256608_MI:0018	However, the dSAP18, POZ245 interaction is weaker than the very strong homomeric POZ245, POZ245 interaction
2242	11259404_MI:0018	Pex19p, either full-length or carboxyl- but not amino-terminal, strongly activated the beta -galactosidase reporter, indicating that it is the carboxyl terminus of p19ARF that interacts with Pex1p (Fig. 1A).
2243	11259404_MI:0018	We isolated a 33-kDa protein, Pex19p/HK33/HsPXF, as a p19ARF-binding protein in a yeast two-hybrid screen
2244	11274188_MI:0018	The COOH-terminal tail of PMCA2b isolated the membrane-associated guanylate kinase (MAGUK) protein SAP97/hDlg as a binding partner in a yeast two-hybrid screen.
2245	11274204_MI:0018	A two-hybrid assay confirmed that a fragment of Net1 containing residues 1-601 could interact with Cdc14
2246	11274204_MI:0018	In addition to a genetic screen described by Shou et al. (18), we and others (19) also identified Net1 in a yeast two-hybrid screen for regulators or substrates of Cdc14
2247	11275986_MI:0018	When both LexA-fused p73 and VP16-fused E6, derived from either HPV-16 or HPV-11, were introduced, a 4- to 7-fold increase in b-galactosidase activity was observed,
2248	11278694_MI:0018	To study the mechanisms of STRA13 regulation on protein level we searched for STRA13-binding partners using a yeast two-hybrid system. Out of 186 confirmed positive clones, five represented the entire cDNA (1.1 kilobase pair) of the UBC9 (human ubiquitin-conjugating enzyme) gene.
2249	11278976_MI:0018	Tat1/MgcRacGAP interaction was analyzed in two-hybrid experiments and in vitro binding assays using recombinant proteins and anti-Tat1C-ter antibodies. In the yeast two-hybrid assay, Tat1 COOH-terminal region strongly interacts with the Mgc-N region (aa 1-180) but not with the GAP domain (Fig. 8A).
2250	11283334_MI:0018	Protein-Protein Interaction of CalS1 with Phragmoplastin and UGT1 in a Yeast Two-Hybrid System.
2251	11283335_MI:0018	Both controls were negative in the 5-bromo-4-chloro-3-indolylb-D-galactopyranoside (X-Gal) assay (Figure 1A), suggesting that the presence of both phragmoplastin and the UGT1 proteins encoded by pPIL33 is required for the observed interactions.
2252	11302744_MI:0018	In the two-hybrid screening of the rat fetal forebrain cDNA library using the full-length MEN1 cDNA as bait, several cDNA clones were obtained. A comparison of the amino acid sequence with known protein sequences revealed that one of them was identical to the nonmetastatic 23b (nm23b; its counterpart in human is called nm23-H1), also known as c-myc regulatory factor PuF and nucleoside diphosphate (NDP) kinase.
2253	11302744_MI:0018	Only the constructs lacking the C-terminal region (Men del 1; 1-486 amino acids) showed transcriptional activation of b-gal at low level.
2254	11306572_MI:0018	these binding data indicate that cpSRP54 binds cpSRP43 via the chromodomains
2255	11306572_MI:0018	When the third ankyrin repeat is also removed (cpSRP43-(61-193)), dimerization is essentially abolished. No binding was detected between cpSRP43 and cpSRP43-(61-159) containing the first ankyrin repeat only. These data together with the results from Table II indicate that the third and fourth ankyrin repeats each are capable of mediating the dimerization of cpSRP43.
2256	11328817_MI:0018	pKGIRp produces a GAL4 DNA-binding domain (DBD)Rp protein which interacts with mCtBP2 in yeast AH109 cells
2257	11353774_MI:0018	In the yeast two-hybrid assay (Fig. 2A), in the presence of E2, coexpression of two chimeric proteins (GAL4 AD-FKHR (amino acids 402-629) and GAL4 DBD-hERa) resulted in good cell growth on selection medium, and the colonies turned blue within 1 h in the b-gal filter lift assay (Fig. 2A, E2), whereas a minimal growth was seen either in the absence of ligand (Fig. 2A, No ligand) or the presence of anti-estrogen
2258	11356864_MI:0018	Both J/Jn and P/Pn fragments of neurofibromin were able to interact with syndecans 1-4
2259	11356864_MI:0018	By yeast two-hybrid assays either Jn (aa 1357-1473) or Pn (aa 2619-2719) regions of neurofibromin were sufficient to interact with syndecan-2
2260	11377421_MI:0018	By a yeast two-hybrid approach, we identified an interaction between the GUK domain of CASK and the C2B domain of rabphilin3a, a presynaptic protein involved in synaptic vesicle exocytosis.
2261	11388671_MI:0018	The diploid colonies generated in the mating between the murine p53 bait yeast and one candidate p53-binding yeast clone (AD107) grew in the absence of histidine and adenine and also produced blue-staining in the X-gal filter-lift assay, confirming an interaction between p53 and the AD107-produced protein (Figure 1). Sequencing revealed that the AD107 cDNA contained a potential open-reading frame encoding a protein 500 amino acids in length (See Genbank accession # AF164437) that showed almost complete homology to the PIASy member of the PIAS inhibitor family
2262	11388671_MI:0018	When yeast expressing the 93 carboxyl amino acids of p53 were mated with yeast expressing PIASy, the diploid colonies grew in the absence of histidine (Figure 3B). These colonies also turned blue in the presence of X-Gal, indicating that PIASy bound to the carboxyl terminus of p53.
2263	11397012_MI:0018	A 0- to 12-h embryonic cDNA library was screened, and out of approximately 105 clones, 11 unique interacting constructs were recovered (data not shown). One of these, which we have subsequently named tantalus (tan), is described here.
2264	11397085_MI:0018	There was no interaction between the two intracellular kinase domains of AtSERK1 (AtSERK1(266-625) in Figure 6) whereas the AtSERK1 extracellular domains do interact with each other (AtSERK1(26-234) in Figure 6) as indicated by the b-galactosidase activity and the growth without leucine.
2265	11402167_MI:0018	Like PKS6, PKS7 also had the strongest interaction with SCaBP5
2266	11402167_MI:0018	PKS2 interacted relatively strongly with SCaBP4 and SOS3
2267	11402167_MI:0018	PKS3 interacted strongly with SCaBP5 and weakly with SOS3
2268	11402167_MI:0018	PKS4 showed interaction with SCaBP5 and SCaBP6
2269	11402167_MI:0018	PKS5 interacted weakly with SCaBP1 but showed no substantial interaction with SOS3 or any of the other SCaBPs (Figure 6).
2270	11402167_MI:0018	PKS6 showed preferential interaction with SCaBP1, SCaBP5, and SCaBP6
2271	11402167_MI:0018	PKS6 showed preferential interaction with SCaBP1, SCaBP5, and SCaBP6. This protein kinase also interacted weakly with SOS3
2272	11402167_MI:0018	PKS7 showed some weak interaction with SCaBP6 as well as with SOS3.
2273	11402167_MI:0018	PKS8 exhibited a strong interaction with SCaBP6 (Figure 6). In fact, the interaction between SCaBP6 and PKS8 was stronger than that between SCaBP6 and any of the other protein kinases tested (Figure 6).
2274	11402167_MI:0018	The N-terminal 267-amino acid residues of SOS2 were cloned into the bait vector pAS2 and then introduced into yeast strains containing the various truncated SOS2 preys. Figure 7 shows that the SOS2 N-terminal bait interacted strongly with the SOS2 C-terminal prey, SOS2T1 (i.e., amino acid residues 304 to -446). The N-terminal bait also interacted strongly with a C-terminal region covering amino acid residues 257 to -368 but not with the full-length SOS2 or other SOS2 truncations
2275	11402167_MI:0018	The results show that residues between Asp304 and Tyr321 are required for SOS2 interaction with SOS3 (Figure 1). SOS2T4, which spans from Gly257 to Arg368, was found to be sufficient to interact with SOS3. We further delimited the region sufficient for SOS3 interaction to a stretch of 21 amino acids between Met309 and Arg330 of SOS2 (Figure 1). SOS2D1, in which this 21 amino acid motif was deleted, failed to interact with SOS3 at all (Figure 1).
2276	11402167_MI:0018	When the SCaBP baits were introduced into yeast harboring the prey pACT-SOS2, {beta}-galactosidase assays for LacZ reporter expression showed that SOS2 was able to interact very strongly with SOS3
2277	11402167_MI:0018	When the SCaBP baits were introduced into yeast harboring the prey pACT-SOS2, {beta}-galactosidase assays for LacZ reporter expression showed that SOS2 was able to interact very strongly with SOS3 and to a lesser extent with SCaBP1, SCaBP3, SCaBP5, and SCaBP6 as well
2278	11404324_MI:0018	HIR1 interacts with ASF1 in the yeast two-hybrid sys-tem
2279	11410368_MI:0018	we were able to demonstrate that AtTop6B is interacting strongly with AtSpo11-2
2280	11410368_MI:0018	we were able to demonstrate that AtTop6B is interacting strongly with AtSpo11-2 (Fig. 4, left upper panel) and also significantly with the AtSpo11-3 protein
2281	11410595_MI:0018	evidence for direct binding interactions between the human Atp11p and beta  subunit proteins.
2282	11410595_MI:0018	human Atp12p interacts with the F1 alpha  subunit in a two-hybrid screen
2283	11410595_MI:0018	The truncated human Atp11p also interacts with the beta  subunit of S. cerevisiae in the two-hybrid assay
2284	11431700_MI:0018	Using the yeast two-hybrid system with Nkx2-5 as the 'bait', we isolated the T-box-containing transcription factor Tbx5
2285	11432958_MI:0018	In order to identify whether other proteins interact with CKS1At, a two-hybrid screen was performed as described earlier (De Veylder et al., 1999Go) using as bait a fusion protein between the GAL4 DNA-binding domain and CKS1At. After sequential selection rounds, four different CKS1At-specific interacting clones were identified. Two clones encoded Arath;CDKA;1 and Arath;CDKB1;1, whereas the two others coded for novel CDK-related proteins and were designated Arath;CDKB1;2 and Arath;CDKB2;1
2286	11438682_MI:0018	In addition, library screening revealed a specific interaction between SNX2 and FBP17 (blue-colored colonies).
2287	11449057_MI:0018	Among the positive clones, three different p27Kip1-like genes were identified: KRP1, KRP2, and KRP3.
2288	11449057_MI:0018	To investigate the presence and function of plant CKIs, a two-hybrid screen was performed with the Arabidopsis CDKA;1. Among the interacting clones, three putative CKIs were identified, two of which were identical to the ICK1 and ICK2 genes described previously
2289	11455422_MI:0018	(Fig. 2A) show that interaction with Bin1 does not require the Bicoid acidic activation domain (AD), or the polyglutamine (Q) or polyalanine (A) domains.
2290	11461834_MI:0018	The interaction of 52 kDa SSA/Ro and UnpEL gave a 20-fold higher signal than the negative control
2291	11477570_MI:0018	we employed a 2-hybrid screening in yeast for proteins interacting with SART3, and this method yielded a pre-mRNA splicing factor (RNA-binding protein prevalent during the S phase or RNA-binding protein with a serine-rich domain [RNPS1])
2292	11489176_MI:0018	both ABI3 and ABI5 strongly interacted with ABI5.
2293	11513956_MI:0018	As expected, removal of the relatively short N-terminus (coiled-coil domain) from both L-subunits abolished the interaction with the fulllength AGG2 (Fig. 5, AGG2 (C) and (F)), its coiled-coil domain (Fig. 5, AGG2N (C) and (F)) and its C-terminus (Fig. 5, AGG2C (C) and (F)). This result is in agreement with several studies that found the L-subunit's coiled-coil domain to be essential for association with GQ [8,42,43].
2294	11513956_MI:0018	Screening of the Arabidopsis seedling yeast two-hybrid library (CD4-22) [30] using the tobacco heterotrimeric G-protein L-subunit (TGB1) as bait yielded the ¢rst plant G-protein Q-subunit (AGG1)
2295	11513956_MI:0018	Screening of the Arabidopsis seedling yeast two-hybrid library (CD4-22) [30] using the tobacco heterotrimeric G-protein L-subunit (TGB1) as bait yielded the ¢rst plant G-protein Q-subunit (AGG1) and several genes that displayed no signi¢cant homology to any gene in the Gen- Bank database [8]. One of these clones (AGG2) contained an open reading frame (ORF) encoding 69 amino acids that displays approx. 50% amino acid identity to the predicted AGG1 peptide sequence.
2296	11543633_MI:0018	Of the 43 clones, 41 passed the mating test for interaction specificity. GenBank database searches showed that 14 of the 41 clones encoded seven proteins of known function. All were membrane-associated receptors or transporters. Among them, four were confirmed to physically interact with LASS2 in the GST pull-down assay as described below: the high-affinity asialoglycoprotein receptors type 1 (AGPRH1; GenBank acc. no. M10058) and type 2 (AGPRH2; GenBank acc. no. U97179), the organic cation transporter-1 (OCT1; GenBank acc. no. U77086), and the proteolipid subunit of vacuolar H+ATPase (VPL; GenBank acc. no. M62762)
2297	11545742_MI:0018	We used the yeast two-hybrid system to test for Pol&#951; interaction with PCNA in vivo
2298	11560889_MI:0018	Figure 1A shows that the AD-Rhp55 construct activated transcription of the lacZ reporter 24-fold when present in the cell together with DBD-Rhp57. Reciprocally, an even higher increase in beta-galactosidase activity (147-fold) was observed when the AD-Rhp57 fusion was combined with the DBD-Rhp55 construct.
2299	11560889_MI:0018	Finally, we found that Rad11p (Rpa1p) bait could interact strongly with Rti1p (73-fold increase) and less strongly with Rad22p (12-fold increase).
2300	11560889_MI:0018	Indeed, strong interaction between Rti1p and Rhp51deltaNp was detected with both bait and prey Rti1p constructs (49-fold and 539-fold, respectively), which implicates the region of Rhp51 protein between amino acids 114 and 365 in binding with Rti1p (Table 3).
2301	11560889_MI:0018	Moreover, moderate but significant self-interactions of Rad22p-Rad22p (38-fold increase) and Rti1p-Rti1p (10-fold increase) were observed, suggesting that in vivo these proteins may exist as oligomers.
2302	11560889_MI:0018	The N-terminal fusions of the full-length Rad22, Rhp51, Rhp54, Rhp55, and Rhp57 proteins with DBD (bait) and AD (prey) of yeast two-hybrid vectors were constructed and pairwise interactions were tested. As shown in Table 1,
2303	11560889_MI:0018	Therefore, we extended our analysis of interactions involving Rhp51p by using truncated versions of the protein. The N-terminal domain of Rhp51p (aa 1-117) was fused with DBD and AD to generate Rhp51deltaC bait and prey plasmids (Figure 4). Likewise, the core and C-terminal domains of Rhp51p (114-365) were used to construct Rhp51deltaN bait and prey. The results of two-hybrid analysis with these constructs are shown in Table 2. Both Rhp51deltaN and Rhp51deltaC were found to interact strongly with the full-length Rhp51p (763-fold and 2300-fold increases, respectively), which is consistent with the ability of RecA/Rad51-family members to polymerize on DNA via monomer-monomer interaction.
2304	11560889_MI:0018	When Rad22p was used as the DBD and Rti1p as the AD fusion, their interaction was manifested by a 111-fold increase in beta-galactosidase activity compared to the control (Table 3).
2305	11564868_MI:0018	The growth arrest and DNA damage-inducible protein, GADD34, was identified by its interaction with human inhibitor 1 (I-1), a protein kinase A (PKA)-activated inhibitor of type 1 protein serine/threonine phosphatase (PP1), in a yeast two-hybrid screen of a human brain cDNA library.
2306	11564868_MI:0018	we rescreened all I-1 interactors for their binding to yeast PP1 (GLC7).
2307	11574472_MI:0018	fter transformation of the two-hybrid library in yeast strain EGY191(p8op- LacZ/pLex-EDS1), 6 000 000 primary transformants were obtained and 60 000 000 yeast clones were screened for potential EDS1 interactors. The dominant class of interactor (in 11 isolates) was identified as PAD4. Only full-length PAD4 inserts were recovered from the screen. EDS1-PAD4 interaction was also tested in the reciprocal combination with PAD4 fused to the LexA domain and was found to be stronger than the original interaction (data not shown). EDS1
2308	11574472_MI:0018	The C-terminus of EDS1 was sufficient for interaction with full-length EDS1 (Figure 2B), suggesting that EDS1 dimerization occurs through the C-terminal end.
2309	11574472_MI:0018	We found that PAD4 interacted with full-length EDS1 but not with any EDS1 subdomain tested, as shown in Figure 2B. PAD4 association with EDS1 was through its N-terminal region, comprising the predicted lipase domain.
2310	11591686_MI:0018	Figure 6B shows that the &#955;cI-AsiA chimera activated transcription from the modified test promoter in the presence of the &#945;-&#962;70 chimera derived from &#962;70 of either E. coli or P. aeruginosa (similar findings with the &#945;-&#962;70 chimera from E. coli have been obtained by S. Pande and D.
2311	11591686_MI:0018	Rsd can interact with region 4 of 70 from P. aeruginosa, and AlgQ can interact with region 4 of 70 from E. coli.
2312	11592991_MI:0018	These results indicate that a relatively intact LBD is essential for target recognition by FTZ.
2313	11606059_MI:0018	ALG-2 interacted with Fas in yeast
2314	11683500_MI:0018	The full-length Bob1 protein was tested for two-hybrid interactions with Byr1 and other components of the Ras1-dependent mating response pathway in fission yeast. Representative two-hybrid assays are shown in Figure 2A. The full-length Bob1 protein retained interaction with Byr1 in the two-hybrid assay, but did not interact detectably with Ras1, Gpa1, Byr2, or Spk1.
2315	11684708_MI:0018	To confirm that full-length TRADD (TRADD-F) interacts with K18 and to determine if TRADD can bind to other IF proteins, we examined the interaction of TRADD-F and TRADD-C with K5, K8, K14, K18, and type III IF proteins in the two-hybrid system (Fig. 1 B).
2316	11684708_MI:0018	To identify proteins interacting with K8/18, we screened a human liver cDNA library, using the yeast two-hybrid procedure with full-length K8 or K18 as a bait.
2317	11684708_MI:0018	We next analyzed the region of K18 that contained the TRADD interaction site. For this, the binding between a series of truncations of K18 and TRADD-F or TRADD-C was determined using the two-hybrid system (Fig. 1 C).
2318	11690648_MI:0018	Independently, the Schizosaccharomyces pombe cDNA library was screened with the SnwA ortholog Snw1 and the ortholog of CypE (named Cyp2) was found.
2319	11690648_MI:0018	We screened the Dictyostelium discoideum two-hybrid cDNA library with the SNW/SKIP transcription coregulator SnwA and identified a novel cyclophilin CypE.
2320	11701877_MI:0018	CSN6 interacted strongly with CSN5 and CSN7
2321	11701877_MI:0018	CSN6 interacted strongly with CSN5 and CSN7 and interacted weakly with CSN3 and CSN4 in a yeast two-hybrid assay.
2322	11722727_MI:0018	both CheC and CheD are capable of interacting with McpB directly.
2323	11722727_MI:0018	CheC interacts with CheA in the yeast two-hybrid assay
2324	11731480_MI:0018	In a two-hybrid screen with Sas2, we also identified Cac1 as an interacting partner (amino acids 80-517).
2325	11731480_MI:0018	To identify proteins that interact with Sas2, we performed a two-hybrid screen (Chien et al. 1991). One interacting clone specific for Sas2 contained a fragment of the SAS4 gene (amino acids 4-329; Table 1).
2326	11731480_MI:0018	Two-hybrid interactions between SAS-I components and chromatin assembly factors
2327	11751918_MI:0018	The Ish1-Ish1 interaction is largely unaffected by the N-terminal deletion.
2328	11786550_MI:0018	Isolation of NHERF2 in a Yeast Two-hybrid Screen Using PMCA2b as Bait
2329	11807141_MI:0018	However, the interaction between full-length HSF and HSP70/HSC70 resulted in much higher levels of ß-galactosidase activity
2330	11820777_MI:0018	To determine the region required for Pof10/Skp1 complexing, the abilities of Pof10 mutants (diagramed in Fig. 2A) to interact with S. pombe Skp1 were tested by yeast two-hybrid assay (Fig. 2B). Full-length Pof10 and a mutant Pof10 lacking the NH2-terminal domain (DN) were associated with Skp1.
2331	11820777_MI:0018	To isolate proteins that interact with S. pombe Skp1, we performed a yeast two-hybrid screening of a S. pombe cDNA library with using S. pombe Skp1 as the bait.
2332	11820777_MI:0018	To isolate proteins that interact with S. pombe Skp1, we performed a yeast two-hybrid screening of a S. pombe cDNA library with using S. pombe Skp1 as the bait. The most frequently isolated clones, Sbp1 (8 out of 18 clones, 605 amino acids) and Sbp2 (6 out of 18clones, 662 amino acids), turned out to be novel F-box proteins that had been deposited in the database as Pof1 and Pof10.
2333	11826307_MI:0018	To determine whether OsDr1 and OsDrAp1 interact with each other, we first used the yeast two-hybrid system
2334	11854419_MI:0018	Point mutation in fus6-T236 disrupts CSN1 interactions with CSN2 and CSN4 in a yeast-two-hybrid assay.
2335	11877381_MI:0018	Using the yeast two-hybrid system, we found that the full-length GEX-2 could interact with the full-length GEX-3 (Fig. 6A).
2336	11889033_MI:0018	Self-association of AN in a yeast two-hybrid system.
2337	11903063_MI:0018	a series of smaller TACC constructs were constructed and expressed as GAL4 DNA-binding domain constructs in yeast strain Y187. TACIP38 (in yeast strain CG1945) was mated to each construct and assayed for speci®c interaction with each region of TACC1. Interaction was only obtained with constructs containing amino acids 206±427
2338	11903063_MI:0018	Subsequent isolation and sequence analysis revealed that four of these clones corresponded to the C-terminal 529 amino acids of a previously identi®ed TACC binding protein, the human ch-TOG protein
2339	11903063_MI:0018	Subsequent isolation and sequence analysis revealed that four of these clones corresponded to the C-terminal 529 amino acids of a previously identi®ed TACC binding protein, the human ch-TOG protein (Figure 1A), and that ®ve corresponded to the C-terminal region of the putative oncogenic transcription factor GAS41}NuBI1
2340	11903063_MI:0018	To determine whether the TACC1 binding site on GAS41}NuBI1 overlapped with that for NuMA, we generated an additional smaller construct containing the C-terminal amino acids 168±227. This construct activated the His3 and LacZ reporter genes in the diploid strain only in the presence of the pASTACC1 construct
2341	11909642_MI:0018	To eliminate a false positive, we moved the A-Raf from the PB42AD to the pLexA vector and handled MEK2 vice versa.
2342	11909642_MI:0018	Using MEK2 as bait in yeast two-hybrid screening, besides c-Raf and KSR, A-Raf was identified as a novel partner that interacts with MEK2.
2343	11909951_MI:0018	Gal4DBD-Hbs1p and Gal4ACT-Dom34p fusion proteins were assayed for interaction in two-hybrid reporter strain pJ69-4A on C-Leu-Trp-His + 1 mM 3-AT and on C-Leu-Trp-Ade plates.
2344	11909951_MI:0018	Gal4DBD-Snf1p and Gal4ACT-Snf4p serve as positive control for an interaction
2345	11914126_MI:0018	Indeed, Ci340-445 is sufficient to interact in yeast with Cos348-546
2346	11914126_MI:0018	In the yeast two-hybrid assay, Fureg (Fu306-805) interacts specifically with the C-terminal part of Cos2 (Cos538-1201)
2347	11919189_MI:0018	Forty-two positive clones were obtained and sequenced. BLAST searches in cDNA data bases revealed that four inserts overlap with the cytoplasmic domain of beta 1 integrin, confirming the reported ICAP-1alpha /beta 1 integrin interaction already described
2348	11919189_MI:0018	To search for potential ICAP-1alpha -binding proteins, we used a yeast two-hybrid screen and identified the human metastatic suppressor protein nm23-H2 as a new partner of ICAP-1alpha .
2349	11932251_MI:0018	We now report that RanBP3 associates with the Ran-specific guanine nucleotide exchange factor, regulator of chromosome condensation 1 (RCC1).
2350	11943170_MI:0018	The binding specificity of SibI to Sig1R4 among plastid sigma factors in A. thaliana was examined by yeast two-hybrid assays (Table 1). Yeast cells co-transformed with pAS-sig1R4 and pACT-sibI (expressing AD-SibI hybrid) were histidine-autotrophic and lacZ positive. In contrast, none of baits containing R4 of Sig2, Sig4, or Sig5 activated the His and lacZ reporter gene expressions in the presence of pACT-sibI, indicating that the interaction between SibI and Sig1R4 is specific among the examined R4s of plastid sigma factors.
2351	11943170_MI:0018	We have searched proteins interacting with the R4 of Sig1 by yeast two-hybrid screening. Two positive clones were obtained, which encoded the same protein, but were heterogeneous in the length of their 3&#8242;-UTR ( Fig. 1A). To identify the corresponding full-length cDNA, we screened the A. thaliana cDNA library by using the obtained cDNA fragment as a probe. The largest open reading frame in the longest cDNA encoded 151 aa residues. This protein was named SibI (Image gma factor Image inding protein Image ).
2352	11959851_MI:0018	we performed yeast two-hybrid screening using a fragment including NHD as bait. Screening of 3 million transformants resulted in isolation of three independent clones encoding Praja1 and another clone encoding the mouse orthologue of rat Neurodap1
2353	11973299_MI:0018	In addition to Mpc70p, Ady3p interacted specifically with fusions con-taining sequences from Cnm67p and Nud1p, compo-nents of the outer plaque during both mitotic and meiotic growth, and the central plaque protein Spc42p
2354	11983923_MI:0018	Yeast two-hybrid assay showing that the AtTOR FRB domain is able to form a complex with rapamycin and ScFKBP
2355	11988016_MI:0018	As shown in Fig. 2, deletion of amino acids 120 to 141 of PCD17 corresponding to the leucine zipper domain resulted in loss of LacZ reporter activities, indicating that this region is required for binding to MRG X.
2356	11988016_MI:0018	deletion of amino acids 249 to 270 of MRG X containing the leucine zipper domain failed to induce LacZ reporter activities in interaction with PCD17. These results suggest that the leucine zipper domain is necessary for interaction with MRG X.
2357	11988016_MI:0018	Seven of the other fifteen clones turned out to be ADH1, Eif-2, NADUF7, pI esterase, folate binding protein, arginosuccinate synthetase, and isocitrate dehydrogenase.
2358	11988016_MI:0018	This suggests that PCD17 physically interacts with MRG X in the two-hybrid system.
2359	12007189_MI:0018	These results suggest that putative SSX2-interacting domains are either interrupted or absent in all three deletion constructs or, alternatively, that both N-terminal (from position 79) and C-terminal (up to position 304) sequences are required for interaction with SSX2.
2360	12007189_MI:0018	The SSX2IP cDNA fragment initially identified by yeast two-hybrid screening corresponded to the C-terminal end of the protein, encompassing amino acids 384 to 614
2361	12007189_MI:0018	Thus, both RAB3IP and SSX2IP interact with an N-terminal domain of SSX2, with RAB3IP requiring amino acids 25 to 80 and SSX2IP requiring amino acids 1 to 80.
2362	12007405_MI:0018	Strong reporter gene activation was detected when BIN2 and BES1 were coexpressed in yeast in two hybrid vectors, demonstrating a specific interaction between BIN2 and BES1 proteins
2363	12008900_MI:0018	We therefore proceeded to test if GRR1 and At- GRH1 can interact with AtSKP1a and AtSKP1b in the two-hybrid system. We could detect significant interactions of each of the two AtSKP1 proteins with both GRR1 and AtGRH1
2364	12008900_MI:0018	yeast SKP1 interacted more weakly, and only with yeast GRR1.
2365	12015115_MI:0018	In addition, using UNC-97/PINCH as the bait protein in a yeast two-hybrid screen of a C. elegans library, we identified positive clones containing PAT-4/ILK.
2366	12015115_MI:0018	Residues 213-474 of PAT-4/ILK, corresponding to the carboxy-terminal kinase domain, were found to be required for PAT-4/ILK to bind full-length UNC-112 (Figure 7B).
2367	12015115_MI:0018	To map the regions of UNC-112 and PAT-4/ILK that are required for this interaction, we made a series of in-frame deletions and found that the amino half of UNC-112, corresponding to amino acid residues 1-396, is critical for its ability to bind PAT-4/ILK,
2368	12015115_MI:0018	Using UNC-112 as the bait protein in a yeast two-hybrid screen of a C. elegans cDNA library, we identified several positive clones encoding PAT-4/ILK.
2369	12032852_MI:0018	we performed a yeast 2-hybrid screen of a Drosophila embryo library (Clontech) using the Gal4 DNA binding domain fused to DTrc8 amino acids 277 - 744 containing the Patched-like loop and RING-H2 finger but lacking the C-terminal PEST sequences (Figure 4a). Two independent isolates of Drosophila CSN-5/ JAB1 (Claret et al., 1996) were identified
2370	12039038_MI:0018	Additional yeast two-hybrid tests revealed that this truncated version of dSAP18 interacts not only with E(Z)512-760, but also with another E(Z) region located within E(Z)1-511
2371	12039038_MI:0018	Identification of E(Z)-dSAP18 interaction in a yeast two-hybrid system screen
2372	12039038_MI:0018	Unlike the truncated dSAP18, full-length dSAP18 was found to self-interact
2373	12056412_MI:0018	As shown in Fig. 5, the AtmybL2 protein directly binds the GL3 proteinat least in yeast,
2374	12080051_MI:0018	In this study, we used the yeast two-hybrid screening system to identify proteins that interact with SPHK1 and potentially regulate its function. We cloned a SPHK-interacting protein (SKIP) that interacts with SPHK1
2375	12082530_MI:0018	Another clone with a 2.5 kb insert was identical to RanBPM
2376	12082530_MI:0018	The fourth clone had a 1.05 kb insert identical to a human Jun activation domain- binding protein that was initially called p38JAB1
2377	12082530_MI:0018	two of the clones had an identical 1.4-kb insert with 100% homology to the human ubiquitin-conjugating enzyme UBC9
2378	12140326_MI:0018	AtSWI3B is also capable of forming homodimers as indicated by the activation of &#946;-galactosidase activity in yeast expressing both AtSWI3B fused to GAL4 DNA-binding domain and AtSWI3B fused to GAL4 activation domain (Fig. 5A).
2379	12150928_MI:0018	Based on previous genetic evidence that the cytoplasmic kinase domain of BRI1 (BRI1CK) is crucial for BR signaling (Li and Chory 1997; Noguchi et al. 1999 and Friedrichsen, D.M., Joazeiro, C.A., Li, J., Hunter, T. and Chory, J., 2000. Brassinosteroid-insensitive-1 is a ubiquitously expressed leucine-rich repeat receptor serine/threonine kinase. Plant Physiol. 123, pp. 1247-1256. Full Text via CrossRefFriedrichsen et al. 2000), we used this domain as bait and conducted a yeast two-hybrid screen for potential BRI1-interacting proteins. Among the 96 BRI1-interacting clones, there are six overlapping cDNAs encoding an LRR-containing receptor-like kinase of 615 amino acids, with their 5&#8242;-ends near the activation loop (A loop) of its catalytic domain. We named this interactor as BAK1 for BRI1 Associated receptor Kinase 1.
2380	12165861_MI:0018	we used the two-hybrid system in yeast to isolate potential TACC1 partners. We screened a human mammary gland cDNA expression library with the 805 amino-acid residues of human TACC1l fused to the Gal4-binding domain. We isolated 10 cDNA clones. Eight encoded the 103 amino-acids of the LSM7 protein and two encoded the 76 amino-acids of the snRNP Sm protein G
2381	12223483_MI:0018	To determine the AAT-1alpha -binding region of AMY-1, three deletion constructs fused to the GALAD were used for the two-hybrid assay with AMY-1alpha  as a bait (Fig. 4A).
2382	12223483_MI:0018	To determine the molecular function of AMY-1, a two-hybrid screening of cDNAs encoding AMY-1-binding proteins was carried out with AMY-1 as a bait using a human testis cDNA library, and a clone encoding a novel protein, AAT-1, was obtained.
2383	12354775_MI:0018	In Nkd, the EFX domain, a 66-amino acid region conserved between fly and vertebrate Nkd is sufficient to bind Dsh in the yeast two-hybrid assay
2384	12368503_MI:0018	Characterization of the pACT2 cDNA clones by DNA sequencing identified two cDNA classes that code for SPDS2- interacting proteins. Both identified sequences were already annotated in the databases. The first class included fulllength SPDS1 cDNAs (gene At1g70310), whereas the other class involved full-length cDNAs (gene At5g53120) coding for a gene product that had homology with aminopropyl transferases,
2385	12368503_MI:0018	To confirm the results of primary two-hybrid screens, the coding regions of SPDS, SPDS1 , and SPMS cDNAs were inserted into the bait (pAS2.1) and prey (pACT2) vectors (Durfee et al., 1993; Harper et al., 1993), and the interaction of each bait was tested with each prey in the yeast twohybrid system using LacZ filter-lift assays (Figure 3). The results showed that none of the proteins was capable of interacting with itself to form a homodimer, but all combinations of different baits and preys activated the LacZ reporter gene, indicating heterodimerization capabilities for all tested proteins.
2386	12383081_MI:0018	Follow-up experiments showed that activation of the two reporter genes required the simultaneous presence of both the NIM1/NPR1 bait plasmid and either of the two isolated prey plasmids (Figure 1). Isolation and sequencing of the cDNA inserts from the two NIM1/NPR1-interacting clones revealed that they encoded partial length members of a subclass of bZIP transcription factors previously identified as AtHBP-1b and OBF-5 (Kawata et al., 1992; Lam and Lam, 1995; Zhang et al., 1993). Because both bind TGA elements within the promoters of target genes, they have also been called TGA2 and TGA5
2387	12393858_MI:0018	Both bait-vector (PP1Calpha  or Inh2) and prey-vector (KPI-2-wt or AA-mut) were cotransformed into HF7c yeast strain, and protein-protein interaction was determined by growth of clones on the medium lacking histidine.
2388	12421467_MI:0018	Psoriasin was demonstrated to specifically interact with RanBPM in the yeast system
2389	12421467_MI:0018	We pursued the interaction of RanBPM (clone 6-3) with psoriasin as it presented the strongest interaction
2390	12434308_MI:0018	bovine PP1alpha1 produced a strong two-hybrid signal when tested with pRb
2391	12434308_MI:0018	bovine PP1alpha1 produced a strong two-hybrid signal when tested with pRb, but surprisingly, only a weak signal was observed with p107
2392	12434308_MI:0018	pRb, p107 and p130 all produced a dark blue beta-galactosidase signal when tested with BRG1
2393	12434308_MI:0018	The screen resulted in recovery of a cDNA clone encoding bovine protein phosphatase 1 alpha1
2394	12456722_MI:0018	Beta-galactosidase assays to test for interaction between Mob2p and Orb6p
2395	12456722_MI:0018	In fact, Mob2p was identified independently in a two-hybrid screen for Orb6p-binding partners (see Materials and Methods).
2396	12482983_MI:0018	dADA2a interacts with dGCN5 but not with dADA3 whereas dADA2b interacts with both dGCN5 and dADA3.
2397	12482983_MI:0018	Tested whether interaction would exist between dRPB4, encoded by the alternatively spliced mRNA, and its putative partner dRPB7 (36). For this purpose, the dRPB7 cDNA was inserted in frame in the GAL4 expression vector. In the two-hybrid assay, these two Pol II subunits interacted as expected (Table 2).
2398	12482983_MI:0018	The interactions between dADA2a and hGCN5-S or dADA2b and hGCN5-S were comparable to that observed between hADA2a and hGCN5 or yADA2 and yGCN5
2399	12493774_MI:0018	we screened for partner proteins for Jem1p by the yeast two-hybrid system and identified Nep98p.
2400	12511573_MI:0018	Pof6 was identified through a twohybrid interaction with Skp1 (Fig. 3A).
2401	12518317_MI:0018	A slightly weaker induction was found with full-length Sec72p and Ylr301wp
2402	12518317_MI:0018	Firstly, we found that a construct (pBY20) expressing the last 51 residues of Sec63p (residues 612-663 fused to the Gal4p activation domain) interacted strongly with the N-terminal Sec62 fusion (Figure 3A).
2403	12518317_MI:0018	We found only two combinations that gave rise to his+ cells, viz. the N-terminal 158 residues of Sec62p fused to the Gal4p activation domain (pBY6) interacts with the C-terminal 424 residues of Sec63p fused to the Gal4p binding domain (pBY3)
2404	12525503_MI:0018	By contrast, a truncation of 10 amino acids from the C terminus of MAGE-A4 abolished its binding to gankyrin (Fig. 4B). The interaction was specific to MAGE-A4, because the corresponding regions of other MAGE proteins, although structurally quite similar to MAGE-A4, did not interact with gankyrin (Fig. 4, C and D). These results indicate that the C-terminal region of MAGE-A4 containing the HLA-A2-presented peptides (11, 12) (GVYDGREHTV and YLEYRQVPV) specifically interacts with gankyrin.
2405	12525503_MI:0018	MAGE-A4 did not interact with the GAL4 DNA binding domain alone (Fig. 1A), indicating that it interacted with gankyrin.
2406	12529446_MI:0018	Gef1p specifically interacted with the GDP-bound form of Cdc42p (Cdc42D118A or Cdc42T17N)
2407	12553664_MI:0018	After a thorough analysis of the obtained two-hybrid system candidate clones, the gene YDR229w (named IVY1 for: Interacting with Vps33p and Ypt7p) was singled out as the only new protein faithfully interacting with the GTP-binding protein Ypt7p.
2408	12569402_MI:0018	The yeast two-hybrid assay results indicate that ICK1 protein interacted with Arabidopsis Cdc2a, but not with Cdc2b.
2409	12571277_MI:0018	A katanin p80 subunit ortholog (Chromosome 1, BAC F11P17) was abundantly represented in the clones obtained from the library screen.
2410	12571277_MI:0018	Another putative AtKSS-interacting protein (accession number, CAB89396; referred to here as KSN1) was isolated as two independent yeast clones from the library screen.
2411	12571277_MI:0018	rotein-protein interactions in yeast were confirmed by transforming the PJ69-4A strain (auxotrophic for TRP, LEU, HIS and ADE) with plasmids containing GAL4-BD-AtKSS (pGBT7-AtKSS; TRP marker) and GAL4-activation domain (pGAD10-prey; LEU marker). All transformants grew on SD medium lacking TRP, LEU, ADE and HIS (Fig. 6B, right). Additionally, they exhibited strong ß-galactosidase activities (Fig. 6B, center)
2412	12602868_MI:0018	Yeast cells that carried both an AD-CPSF100CC gene and a BD-PAP gene (see Figure 4A for a depiction of these constructs) were capable of growing on media lacking histidine or adenine (not shown), as well as on media lacking both supplements
2413	12612082_MI:0018	the two-hybrid system was used to identify potential HEI10 interactive partners by using a bait representing the amino-terminal 143 aa of HEI10. Clones encoding cyclin B1 (aa 315 to end [5]) and the E2 ubiquitin-conjugating enzyme UbcH7 (aa 29 to end [41]) were isolated as candidate interacting partners of HEI10.
2414	12620624_MI:0018	FliS bound the C terminal sequence of FliC 1 309, but not the C terminally deleted 410 494
2415	12646039_MI:0018	Both RHA2a(1+/-155)+/-BD, representing full-length RHA2a fused to the BD of the GAL4 protein, and RHA2a (3+/-155)+/-BD, lacking the putative RHA2a N-terminal transmembrane region, were used as baits. The screened cDNA library was from Arabidopsis leaf and root mRNAs. Of approx. 4-10' transformants, 15 colonies were able to grow on selective medium and expressed b-galactosidase activity. Sequencing revealed that four clones encoded the NAC protein At1g52890, here named ANAC.
2416	12646039_MI:0018	Control experiments using RHA2a (1+/-155)+/-BD and AD showed no growth on selective medium. The truncated RHA2a versions, RHA2a(38+/-155)+/-BD, lacking the N-terminal hydrophobic region, and RHA2a(77+/-155)+/-BD, containing only the RING-H2 domain, were also able to interact with ANAC(1+/-317)+/-AD
2417	12646039_MI:0018	Surprisingly, signi®cant interaction was measured between RHG1a(584±691)±BD and ANAC (1±317)±AD
2418	12646039_MI:0018	The RING-H2 domains from RHG1a, RHA2a, and RHA2b showed marked interaction with ANAC and contain an acidic amino acid at this position.
2419	12646258_MI:0018	The genes identified by the yeast two-hybrid approach were metallothionein 2A (MT2A), metallothionein 1H,
2420	12646258_MI:0018	The genes identified by the yeast two-hybrid approach were metallothionein 2A (MT2A), metallothionein 1H, metallothionein 1G,
2421	12646258_MI:0018	The genes identified by the yeast two-hybrid approach were metallothionein 2A (MT2A), metallothionein 1H, metallothionein 1G, ferritin, erythrocyte membrane protein band 4.2,
2422	12646258_MI:0018	The genes identified by the yeast two-hybrid approach were metallothionein 2A (MT2A), metallothionein 1H, metallothionein 1G, ferritin, erythrocyte membrane protein band 4.2, hemoglobin, mitochondrial ribosomal protein S12,
2423	12646258_MI:0018	The genes identified by the yeast two-hybrid approach were metallothionein 2A (MT2A), metallothionein 1H, metallothionein 1G, ferritin, erythrocyte membrane protein band 4.2, hemoglobin, mitochondrial ribosomal protein S12, hypothetical protein FLJ10101,
2424	12646258_MI:0018	The genes identified by the yeast two-hybrid approach were metallothionein 2A (MT2A), metallothionein 1H, metallothionein 1G, ferritin, erythrocyte membrane protein band 4.2, hemoglobin, mitochondrial ribosomal protein S12, hypothetical protein FLJ10101, and a novel gene whose cDNA was found to have no strong homology to any other previously characterized protein and Gen- Bank Accession No. is AF422192.
2425	12646258_MI:0018	Using the fulllength ECRG2 cDNA as bait to screen a human fetal liver cDNA library, we found that nine positive clones could bind to the ECRG2 protein. Here we report one candidate clone, which encoded human metallothionein2A (MT2A).
2426	12649160_MI:0018	AD-FANCE also interacted with BD-FANCD2.
2427	12649160_MI:0018	Interactions were also observed between AD-FANCG and both BD-FANCA and BD-FANCF.
2428	12649160_MI:0018	Interaction was observed between the AD-FANCC and BD-FANCE combination, as well as the reciprocal pairing of AD-FANCE and BD-FANCC.
2429	12651155_MI:0018	a series of ezrin constructs in the pGBT9 vector were generated and tested for their interaction with pGAD10-clone 33 in the yeast 2-hybrid assay (Fig. 1B). No interaction was observed with two N-terminal ezrin constructs (1-247 and 11-247), whereas a full-length ezrin (1-585), a construct deleted in the first 10 amino acids(11-585), and a C-terminal construct (243-585) gave positive reactivity
2430	12651155_MI:0018	a yeast 2-hybrid screen was undertaken using ezrin as a bait. We describe here the identification and cloning of a novel protein, PACE-1
2431	12657652_MI:0018	Likewise, an interaction between the ABI3 N and AtbZIP25 C-terminal region was also detected.
2432	12657652_MI:0018	The results of such analyses are displayed in Fig. 5B, showing that AtbZIP10 and ABI3 are able to interact through the Nterminal regions of both proteins.
2433	12674497_MI:0018	Co-transformation experiments of the yeast strain L40 with pBTM116-AUF1- p37, -p40, -p42 and -p45 and pACT2-NSEP-1, pACT2-NSAP-1 and pACT2-IMP-2 (Figure 1C) demonstrated that the three RNA binding proteins NSEP-1, NSAP-1 and IMP-2 all interact only with AUF1p37 and p40 but not with p42 or p45. In contrast, protein UBCE2I interacted with all four isoforms.
2434	12674497_MI:0018	Our analysis revealed that AUF1p37 only interacts with the AUF1 isoforms p37 and p40 but not with p42 or p45 (Figure 1B).
2435	12674497_MI:0018	Our results show that the construct that encompasses the RRM domains 3 and 4, as well as that which contains domains 2 and 3, both interact with AUF1p37, whereas a construct containing domains 1 and 2 did not interact.
2436	12674497_MI:0018	These results suggest that more than two of the B/A islands are required for the interaction with AUF1. Two constructs that encompass three B/A islands (1-2-3 and 2-3-4) were both able to interact with AUF1p37.
2437	12674497_MI:0018	the two constructs containing the KH domains 2 and 3 or 3 and 4 were able to interact with AUF1.
2438	12678503_MI:0018	AAD46000 (Arabidopsis cyclin T, AtCycT), G71404 [ribonucleoprotein (RNP)]; AAG09542 [DNA-binding protein (GT-1)], BAA97063 (DAG homologue protein), BAB08556 (unknown protein) for the two-hybrid CDKC;2 interacting proteins.
2439	12678503_MI:0018	The two-hybrid analysis showed that Arath;CDKC;2 interacts with other proteins, such as a ribonucleoprotein (RNP), a DNA-binding protein (GT-1), and a DAG-homologous protein.
2440	12678503_MI:0018	To understand the possible function of the Arath;CDKC;2 protein, a yeast two-hybrid screen was undertaken to search for its protein partners. One of the interacting clones identified encodes a protein (designated Arabidopsis cyclin T, or AtCycT) with sequence similarity to animal cyclins from the T and K group
2441	12678503_MI:0018	Yeast two-hybrid interaction of CDK proteins (CDKA;1, CDKB1;1, and CDKC;2) with the cyclin T (CYCT) from Arabidopsis. HF7c transformant cells of yeast were streaked on plates with (His+) and without (His-) histidine. Reconstitution of the GAL4 activity in the positive transformants restored the ability of yeast to grow in histidine-deficient medium. This shows that the plant cyclin T homologous protein can interact with Arath;CDKC;2 but not with Arath;CDKA;1 or Arath;CDKB1;1.
2442	12740913_MI:0018	Only coexpression of EBNA-5 and p14ARF resulted in significant activation of the reporter lacZ gene. The strength of interaction was 6% of the strong SV40 LT-p53 or 8.3% of SV40LT-Rb interactions as measured by -galactosidase units in 4 independent cotransfection experiments. This interaction was not dependent on the configuration of the constructs. It was also detected when EBNA-5 and p14ARF were swapped in the AD/BD vectors.
2443	12757932_MI:0018	a specific interaction exists between p80 coilin and ataxin-1.
2444	12757932_MI:0018	Using the yeast two-hybrid system and co-immunoprecipitation experiments, we have found that p80 coilin, coiled body-specific protein, binds to ataxin-1.
2445	12787365_MI:0018	These data demonstrated that Sfh, StpA and H NS each had that capacity to engage in three way protein protein interactions in vivo, forming dimers with itself and with each of the other H NS like proteins.
2446	12788081_MI:0018	To identify molecules that interact with Fyn, we performed yeast two-hybrid screening using full-length Fyn as a bait.
2447	12805220_MI:0018	We screened a fetal brain library using kinase-dead (KD) LKB1 (D176Y) as bait, and identified a single clone that interacted specifically with LKB1 and not with control baits.
2448	12826617_MI:0018	However, only the N-terminal 85-aa fragment,which terminates at the end of the F-box, interacts with ASK1 with similar apparent affinity as full length UFO. All other engineered deletions show dramatically reduced affinity for ASK1 despite containing an intact F-box. These results suggest that, whereas the F-box is apparently sufficient for high-affinity interaction with ASK1, the overall structure of the protein may be important for allowing ASK1 access to the motif.
2449	12837948_MI:0018	Reconstitution of the yeast two-hybrid interaction between AtPirin1 and GPA1.
2450	12837948_MI:0018	The interaction between the Arabidopsis proteins ETR1 and CTR1 (Clark et al., 1998) served as a positive control for the assay (Figure 1A).
2451	12837948_MI:0018	Therefore, we named this GPA1-interacting protein AtPirin1
2452	12838411_MI:0018	AspA91 312/NtrB pair of fusion proteins gave strong signals in strain Y190. Similar signals were obtained for AspA91 312/NtrBHNG, while weak but significant signals were obtained when AspA91 312 was paired with NtrBSHN, NtrBSH, NtrBHN or NtrBH
2453	12838411_MI:0018	constructs containing only N and NG regions are not sufficient to generate Y2H signals with GlnK, suggesting that part of the H domain is also required for contacts with PII proteins
2454	12857813_MI:0018	Interaction between CDKB2;1 and CYCD4;1 in yeast.
2455	12857813_MI:0018	The full-length coding region of the CDKB2;1 cDNA was fused in-frame with the GAL4 DNA-binding domain and used as bait. Screening was performed with an Arabidopsis cDNA library derived from mRNA of suspension cultured cells. About 2.1 x 105 clones were screened on a medium lacking His, and, finally, 98 clones turned out to be His+ and LacZ+. Among them, 81 clones encoded a homolog of yeast p13Suc1, named Csk1At
2456	12857813_MI:0018	The full-length coding region of the CDKB2;1 cDNA was fused in-frame with the GAL4 DNA-binding domain and used as bait. Screening was performed with an Arabidopsis cDNA library derived from mRNA of suspension cultured cells. About 2.1 x 105 clones were screened on a medium lacking His, and, finally, 98 clones turned out to be His+ and LacZ+. Among them, 81 clones encoded a homolog of yeast p13Suc1, named Csk1At (De Veylder et al., 1997), and eight clones contained the full-length cDNA of CYCD4;1
2457	12857841_MI:0018	One of the CBP genes, TCH3 (At2g41100), was identified previously by Braam and Davis (1990) in a screen for genes that are up-regulated in response to mechanical stimuli such as wind and touch.
2458	12857841_MI:0018	PID interacts with PBP1 and TCH3 in yeast.
2459	12857841_MI:0018	The second gene we identified, PINOID BINDING PROTEIN 1 (PBP1, At5g54490), encodes a previously uncharacterized protein of 127 amino acids with three possible EF-hand calcium-binding motifs.
2460	12874278_MI:0018	these results clearly demonstrate a direct physical association between the extreme C terminus of 
-catenin and the PDZ domain of TIP-1 and reveal an alternative mechanism for complex formation in vivo.
2461	12874278_MI:0018	Various deletion mutants of TIP-1 were tested in an in vivo interaction assay with coexpressed 
-catenin, and the obtained results clearly demonstrated the requirement of the intact PDZ domain for complex formation (Fig. 2A). Interestingly, although the removal of the first 12 amino acids of TIP-1 had no significant effect on the interaction with 
-catenin, deletion of the last eight residues resulted in a 3-fold reduction of binding efficiency, suggesting a possible role for this protein region in the formation or stability of the complex.
2462	12874278_MI:0018	we screened out the murine homologue of the PDZ domain protein, TIP-1, as a novel binding partner of 
-catenin
2463	12917293_MI:0018	The first 100 amino acids were required for interactions with myb proteins GL1, PAP1 and PAP2, CPC and TRY (the latter fourpresented here; Table 2), (2) approximately amino acids 200-400 mediated interaction with TTG1,
2464	12917293_MI:0018	Two-hybrid studies (Table 2) showed that the EGL3 amino fragment interacted with full-length TTG1 and the myb domains of GL1, PAP1 and PAP2, CPC and TRY. The EGL3 carboxy fragment interacted with itself and the full-length and bHLH end of GL3. All EGL3 interactions observed were consistent with a model where EGL3 and GL3 are able to form essentially the same protein-protein interactions.
2465	12917293_MI:0018	We previously found that GL3 had three distinct proteinprotein interaction domains (Payne et al., 2000). (1) The first 100 amino acids were required for interactions with myb proteins GL1, PAP1 and PAP2, CPC and TRY
2466	12917293_MI:0018	We previously found that GL3 had three distinct proteinprotein interaction domains (Payne et al., 2000). (1) The first 100 amino acids were required for interactions with myb proteins GL1, PAP1 and PAP2, CPC and TRY. presented here; Table 2), (2) approximately amino acids 200-400 mediated interaction with TTG1, and (3) a carboxy end fragment including the bHLH domain was able to interact with itself (homodimerize).
2467	12923097_MI:0018	GlnB-NtrB interaction in a yeast two-hybrid assay
2468	12923097_MI:0018	Screening of an R. capsulatus genomic library identified NtrB, NifA2, DraT, and PcrA as proteins that interact with GlnB and Era as a protein that interacts with GlnK.
2469	12972551_MI:0018	To test for physical interaction of Gef1p with Cdc42p, we carried out a yeast two-hybrid assay.
2470	14519092_MI:0018	The first was by a reciprocal two-hybrid assay, which showed that reconstitution of the Gal4 activator occurs also when the Grx4 protein is fused to Gal4 BD and the Bud32 protein to Gal4 AD.
2471	14521924_MI:0018	From these studies, it was found that deletion of only the C-terminal 16 amino acids from p35 resulted in complete loss of hAATYKs-p35BP binding activity.
2472	14521924_MI:0018	Screening of a splice variant of the human homologue of AATYK as a p35 binding protein by the yeast two-hybrid system
2473	14521924_MI:0018	These results indicate that the region of hAATYKs-p35BP critical for binding to p35 is located in the 17 N-terminal amino acids between amino acid residues 40 and 56 (indicated by black in p35BPN169) and that the C-terminal region may assist in the binding.
2474	14550308_MI:0018	MT 2A interacted strongly with KD, relatively weakly with C1 domain, and failed to interact with C2, PH or KM domain
2475	14550308_MI:0018	we report the results of our YHS screening experiment, which identified metallothionein 2A (MT 2A) as an interactor with the kinase domain of PKCl.
2476	14551247_MI:0018	On plates lacking histidine, and thus requiring activation of the least stringent reporter for cell growth, we saw that Rdh54 interacted with both Dmc1 and Rhp51. On selection for ade
 or for -galactasidase activity, however, Rdh54 only interacted with Dmc1 (Figure 3). These data suggest that Rdh54 can interact with both Dmc1 and Rhp51 but that the interaction is stronger between Rdh54 and Dmc1.
2477	14551247_MI:0018	Rhp51 also gave a positive signal with itself, with Rti1, and with Rad22 (Figure 3).
2478	14551247_MI:0018	Rhp54 interacted only with Rhp51 and not Dmc1 (Figure 3)
2479	14557665_MI:0018	Full-length Daxx (Fig. 1C and D, sector 2), aa 1 to 574 (sector 3), and aa 516 to 574 (sector 6), as well as aa 621 to 740 (see Fig. 1A) bind to both the Ad2 and Ad12 E1B 55-kDa proteins.
2480	14557665_MI:0018	this Daxx fragment bound to Ad2 E1B aa 155 to 495 (sector 2) and the full-length Ad12 E1B protein (sector 6), as well as the Ad2 C-terminal aa 437 to 495 fragment
2481	14557665_MI:0018	With Ad2 E1B aa 155 to 495 as bait, we have screened approximately 106 yeast transformants. Among 11 positive clones, two identical clones encoding Daxx C-terminal aa 621 to 740 were isolated.
2482	14561633_MI:0018	yeast containing either sst-AD or GL3-AD and GL1-BD, TRY-BD or TTG1-BD exhibited b-gal activity (Fig. 6A-C). However, there was a significant difference in activity level between the strains containing either sst-AD or GL3-AD. Yeast isolates containing GL1-BD and GL3-AD exhibited
2483	14627543_MI:0018	A bait vector encoding full-length VCY2 was used in yeast two-hybrid screens of a human testis cDNA library. Twenty-six positive-interacting clones were isolated and characterized, 16 of which encoded the same 948-bp cDNA insert. This VCY2-interacting clone (MHC1) was named VCY2IP-1 (VCY2-interacting protein-1).
2484	14627983_MI:0018	We obtained the KIAA0769 gene product through the yeast two-hybrid screening using MAGI-1 as a bait and named it Carom.
2485	14645241_MI:0018	As demonstrated with the mammalian two hybrid tests (Fig. 2B), AR interacted with ASC2-2b that consists of the ASC-2 residues 622-849 (13) in a testosterone independent manner
2486	14645241_MI:0018	We further localized the Rb-interacting region of ASC-2 to ASC2-2b in the mammalian two hybrid tests
2487	14675532_MI:0018	Both F box proteins were able to interact with ASK1 in yeast two-hybrid assays
2488	14675532_MI:0018	The two F box proteins and their corresponding LRR domains interact with EIN3 in yeast two-hybrid assays.
2489	14701856_MI:0018	To isolate new PPAR{gamma} coregulators we performed a yeast two-hybrid screen of a human adipose tissue cDNA library with the DE domain of PPAR{gamma}2
2490	14718544_MI:0018	Thus, these two cDNAs are presumably derived from transcripts of a single gene that has multiple transcriptional termination sites. Both transcripts have one open reading frame that potentially encodes a 179-amino acid polypeptide. Because the product of the gene is expected to bind to the cytoplasmic tail of MT1-MMP, it was
2491	14729613_MI:0018	The bait RASSF1A-BD was then used to screen a pretransformed MATCHMAKER human adult brain cDNA library 103 p120E4F AS AN INTERACTING PARTNER OF RASSF1A (BD-Clontech). Approximately 6 106 independent transformations were screened, of which 103 clones were positive for -galactosidase expression. Nucleotide sequence analysis revealed that two separate clones (designated E4F)contained a 1-Kb insert with an open reading frame of 1113 bp encoding a protein fragment of 324 amino acids, which corresponds to the COOH-terminus half of the E1A regulated transcription factor p120E4F (NP 004415).
2492	14729613_MI:0018	We also identified a number of other interesting targets including the proapoptotic protein kinases MST1 and MST2 (10 clones) already known to interact with RASSF1A
2493	14729917_MI:0018	Although the GAL4 DBD-ARF7 CTD fusion proteins alone did not stimulate reporter gene expression (Figure 9B, bar 2), cotransformation of S. cerevisiae cells with GAL4 DBD-ARF7 CTD and GAL4 activation domain (AD)-ARF7 CTD constructs increased LacZ activity significantly (Figure 9B, bar 3), indicating homotypic interaction between ARF7 CTD.
2494	14729917_MI:0018	Because transformation of GAL4 AD-IAA19 alone did not induce expression of the reporter genes (Figure 9B, bar 8), this result demonstrates heterodimer formation between ARF7 CTD and IAA19
2495	14730064_MI:0018	AtCBL1 exhibited a significant interaction only with a subset of six CIPKs (AtCIPK1, 7, 8, 17, 18, and 24).
2496	14739298_MI:0018	We identified 10 clones of 3.5 x 106 yeast clones transformed with a human U-2 OS cell cDNA library. Each clone proliferated on media containing the histidine inhibitor 3AT and was positive for {beta}-galactosidase staining (Fig. 5A and data not shown). DNA sequencing of the rescued plasmids revealed that two clones encoded the C-terminal 391 amino acids of Miz-1
2497	14742702_MI:0018	Two-hybrid analyses between full-length Alp14 and subclones of Alp7 indicate that the C-terminal coiled-coil region of Alp7 plays a major role in binding to Alp14 (Figure 6C).
2498	14756317_MI:0018	Full-length human hnRNP A1 and Nab2p[159-348] strongly interacted with AtTRN1
2499	14756317_MI:0018	In case of AtGRP7, deletion of 24 amino acid residues from the C-terminus had little effect on the interaction with AtTRN1 (not shown), whereas further deletion (AtGRP7[1-116]; Figure 2A, C) considerably diminished it.
2500	14756317_MI:0018	To delineate the transportin-interacting domain of AtRNP1, we assayed the glycine-rich C-terminus without the RRMs (AtRNP1[183-411]; Figure 2A, C), which still interacted strongly with AtTRN1. In contrast,  deletion of 75 (AtRNP1[1-336]; Figure 2A, C) or 156 (AtRNP1[1-255]; not shown) amino acid residues from the C-terminus abolished the interaction.
2501	14764652_MI:0018	A yeast two-hybrid screening identified a serine/threonine protein phosphatase (PP5) as an interactant of ER (1-481), a dominant negative ER mutant.
2502	14764652_MI:0018	The interactions of the PP5 clones between ER (1-481) were confirmed by the galactose-dependent growth of yeast strain EGY48, which was cotransformed with pSH18-34 LacZ reporter plasmid, pEG202NLS-ER (1-481), and the PP5 clones in galactose-inducible pJG4-5
2503	14764652_MI:0018	The most significant luciferase activity was observed when PP5 interacted with E domains of ERs without containing the activation domain (AD) core regions within AF-2
2504	14970209_MI:0018	Co-transfection of VP16-TAZ and M-TTF-1 markedly enhanced reporter gene expression, demonstrating a direct protein-protein interaction between TAZ and TTF-1 proteins in MLE-15 cells (Fig. 4B).
2505	14978263_MI:0018	Fig. 4A shows that mCCA1 can interact physically with CKB3; the domain responsible for the interaction with CKB3 is in both CCA1 and mCCA1 comprised between amino acids 317 and 608.
2506	14978263_MI:0018	To address the importance of a CCA1
 CCA1 homodimer in the regulation of the circadian clock, we performed yeast two-hybrid assays between the full-length CCA1 protein, and full-length or deletions of CCA1 and mCCA1 proteins. Fig. 4B shows that CCA1 can interact physically with itself. A very strong 
-galactosidase activity was monitored with two copies of the full-length CCA1 protein. The domain responsible for this interaction is between amino acids 100 and 317. When these experiments were performed with mCCA1, the interaction strength was reduced dramatically; it was 7.7-fold weaker with full-length mCCA1 than with full-length CCA1.
2507	15047801_MI:0018	Discovery of RoXaN by interaction with NSP3 in a yeast two-hybrid assay.
2508	15047801_MI:0018	Localization of NSP3 and RoXaN I interaction domains by yeast two-hybrid assay.
2509	15063184_MI:0018	Ci fragment from aa 1 to aa 440 interacts with Cos2 in yeast, albeit with an affinity much lower than that of CORD/Cos2 interaction (Fig. 3B). Deletion from either end (Ci 212 440 or Ci 1 346) greatly reduces but not completely abolishes Cos2 binding, suggesting that the N-terminal Ci sequence required for Cos2 binding is dispersed.
2510	15063184_MI:0018	Cos2 fragment containing sequence from aa 547 to aa 750 (Cos2 547-750) is sufficient to bind Fu.
2511	15063184_MI:0018	Cos2 sequence involved in CDN binding is dispersed. By contrast, the Cos2 sequence that mediates CORD interaction can be narrowed down to two small discrete regions as Cos2 fragments both from aa 143 to aa 343 and from aa 343 to aa 447 interact with CiC
2512	15063184_MI:0018	we tested whether LexA-CiN or LexA-CiC interacts with the Fu-GAD fusion protein in yeast. As shown in Fig. 5C, CiC but not CiN binds Fu
2513	15078334_MI:0018	Two hybrid assay of the subunits of the rice G protein complexes
2514	15107855_MI:0018	A second yeast two-hybrid screen of a human kidney cDNA library with BBS4 as bait also identified independent clones containing coding regions of PCM1
2515	15107855_MI:0018	BBS4 interacts with PCM1 in yeast two-hybrid analysis.
2516	15138274_MI:0018	Elp4 and Elp6 interaction shown by two-hybrid interaction.
2517	15141306_MI:0018	The two additional plasmids validated in the initial screen with the larger tricalbin 2 bait construct were both found to encode 207 C-terminal residues of Pdr1p.
2518	15141306_MI:0018	This suggested that tricalbins 1 and 2 may interact through their C-terminal domains.
2519	15147888_MI:0018	(B) Dimerization of CGI-99.
2520	15147888_MI:0018	One novel gene, CGI-99, was demonstrated to associate with hNinein in the yeast two-hybrid method and in vitro GST pull-down assay.
2521	15147888_MI:0018	, we then tested the interaction between hNinein and CGI-99 using the yeast two-hybrid system. The data show that C-terminal of the CGI-99 coiled-coil structure (151-244 aa) specifically interacts with hNinein in a very C-terminal coiled-coil domain (1931-2090 aa),
2522	15159385_MI:0018	Interaction of HAX-1 with BSEP in yeast.
2523	15165234_MI:0018	As the GlnB subunits interact with each other to form the trimeric PII structure, interaction of a GlnB-GAL4AD fusion with a GlnB-GAL4BD fusion confirmed that the screening procedure revealed interactions of physiological relevance.
2524	15165234_MI:0018	Identification of PII interaction with NAG kinase by yeast two-hybrid screening
2525	15171681_MI:0018	A mutation, which resulted in the conversion of F15 of S100A1 into an alanine residue (termed F15A) (Figure 6), and multiple mutations, S100A1L11H+F15A+F71L (named 3M),which disrupted the interaction between the mutant and wildtype S100A1 in the yeast two-hybrid system, also disrupted the interaction between S100A1 and wtS100P
2526	15171681_MI:0018	Prey plasmidDNAwas isolated from these four transformants and the nucleotide sequences of two target plasmids were identical with that of human S100A1 cDNA and the other two were identical with that of human S100P cDNA.
2527	15171681_MI:0018	S100P mutants, I11A+I12A, F15A, F71A, F74G, F74V, I75G, abolished almost completely the interaction of S100P with wtS100P, and also almost completely abolished the interaction with wtS100A1 (Figure 6). These results broadly suggest that the same amino acid residues associated with homodimerization of S100A1 or S100P are involved in the S100P/S100A1 interaction and further suggest that this interaction is heterodimerization. However, the S100P mutant V76G abolished its interaction almost completely with wtS100P molecules,
2528	15171681_MI:0018	the S100P mutant V76G abolished its interaction almost completely with wtS100P molecules, but did not interrupt its interaction with S100A1, an effect that was evident even when combined with the I75G mutant that on its own almost completely abolished interaction with S100A1
2529	15182174_MI:0018	the yeast two-hybrid assay demonstrated a protein-protein interaction between SCP-2 and caveolin-1 in vivo
2530	15197472_MI:0018	To test the ability of CYCPs to interact with CDK proteins of Arabidopsis, the full-length cDNA of each CYCP gene was isolated and cloned into an appropriate yeast two-hybrid vector, resulting in a transcriptional fusion between the CYCPs and the GAL4 transcriptional activation domain (pGADCYCP1;1-CYCP4;3). In a yeast reporter strain, the pGADCYCP1;1-CYCP4;3 plasmids were co-transformed with vectors encoding a fusion between the CDKA;1, CDKB1;1, CDKC;1 and the GAL4 DNA-binding domain (pGBTCDKA;1; pGBTCDKB1;1 and pGBTCDKC;1), and with the empty pGBT9 vector as a control. Transformed strains were plated on medium without histidine, which allows growth of yeast only when the two proteins interact. All P-type cyclins interacted with CDKA;1, except for CYCP3;1
2531	15197472_MI:0018	To test the ability of CYCPs to interact with CDK proteins of Arabidopsis, the full-length cDNA of each CYCP gene was isolated and cloned into an appropriate yeast two-hybrid vector, resulting in a transcriptional fusion between the CYCPs and the GAL4 transcriptional activation domain (pGADCYCP1;1-CYCP4;3). In a yeast reporter strain, the pGADCYCP1;1-CYCP4;3 plasmids were co-transformed with vectors encoding a fusion between the CDKA;1, CDKB1;1, CDKC;1 and the GAL4 DNA-binding domain (pGBTCDKA;1; pGBTCDKB1;1 and pGBTCDKC;1), and with the empty pGBT9 vector as a control. Transformed strains were plated on medium without histidine, which allows growth of yeast only when the two proteins interact. All P-type cyclins interacted with CDKA;1, except for CYCP3;1 (fig. 4A). Only CYCP1;1 bound to CDKB1;1, and none associated with CDKC;1
2532	15208391_MI:0018	To further characterize the interaction between Arabidopsis CAND1 and CUL1, we tested their interaction in a yeast twohybrid assay. Wild-type CUL1 interacts with CAND1 in yeast, as shown by an eightfold increase in b-galactosidase (b-gal) activity over the vector control (Figure 3D). When the RUB modification site on CUL1 (del Pozo and Estelle, 1999) is mutated from Lys to Arg (K682R), the b-gal activity is further increased by 10-fold (Figure 3D). It is shown in Figure 3E that Arabidopsis CUL1 is indeed modified by RUB in yeast, whereas the mutant CUL1 protein is not.
2533	15225636_MI:0018	Furthermore, we have identified interactions between the &#945;7 subunit (HC8) of the 20S &#945;-ring, and the &#945;1, &#945;2, &#945;3, &#945;4, &#945;6 and &#945;7 subunits
2534	15225636_MI:0018	The &#945;4 subunit also interacts with &#945;2
2535	15256549_MI:0018	Bracketing the C-terminal region that resulted in the loss of yeast two-hybrid-galactosidase reporter activity with the nearest positives indicates that the essential SseD binding region is within amino acids 138 194.
2536	15256549_MI:0018	Bracketing the region that resulted in loss of binding with the nearest positives allows the SseB binding region to be narrowed to a 46 aa region spanning amino acids 137 182.
2537	15256549_MI:0018	using the yeast-two hybrid system. SseA1 31 still binds SseB, as represented in Fig. 4a, indicating that the N-terminus of SseA is dispensable for interaction with SseB. However, loss of the region containing the SseA C-terminal amphipathic helix (68 98) renders SseA67 108 unable to bind its partner.
2538	15277686_MI:0018	The LUG protein can be divided into three domains: the N-terminal LUFS domain, the central Q-rich domain, and the C-terminal 7-WD repeat domain. Full-length LUG, LUFS, LUFS+Q, and Q+WD were each fused to the DNA-binding domain of GAL4 (GAL4BD) and were tested for interaction with full-length SEU which was fused to the activation domain of GAL4 (GAL4AD). Whereas full-length LUG, LUFS, and LUFS+Q interacted with full-length SEU, Q+WD failed to interact with SEU (Fig. 1A). This finding suggested that the LUFS domain is both necessary and sufficient for interacting with SEU. Interestingly, the strongest interaction was observed between the LUFS and SEU
2539	15280210_MI:0018	Bacterial two-hybrid and co-immunoprecipitation studies demonstrated that ID4, and to a lesser extent ID2, complexed with the basic-helix-loop-helix transcription (bHLH) factors OLIG1 and OLIG2
2540	15294869_MI:0018	However, when ATROP2 was co-expressed with PIR a strong interaction was detected
2541	15294869_MI:0018	In another set of inter-kingdom two-hybrid assays, PIR displayed a strong interaction with RAC1 and human SRA1 interacted with ATROP2
2542	15294869_MI:0018	interaction between the human SRA1 and NAP125
2543	15294869_MI:0018	We also detected a direct interaction between Arabidopsis PIR and ATNAP125.
2544	15296760_MI:0018	by using the two-hybrid assay and also confirmed the direct interaction between GRL and ATSRA1
2545	15296760_MI:0018	Despite GRLa nd human NAP125 sharing only 22% identity, we detected a robust two-hybrid interaction between human NAP125 and ATSRA1
2546	15296760_MI:0018	We also detected a direct interaction between human NAP125 and SRA1 by using the two-hybrid assay
2547	15299139_MI:0018	NZZ interacts with FIL in yeast
2548	15299139_MI:0018	NZZ interacts with FIL in yeast and in vitro.
2549	15310821_MI:0018	a strong interaction of LKP2 and TOC1 was detected, and a weak interaction of LKP1 and TOC1 was detected
2550	15310821_MI:0018	a strong interaction was detected between LKP2 and APRR5, and a weak interaction was detected between LKP1 and APRR5.
2551	15310821_MI:0018	Interactions were observed between LKP2 and LKP1, LKP2 and LKP2, and LKP2 and FKF1, but none were detected between LKP1 and LKP1, or LKP1 and FKF1 by yeast growth tests on restricted medium
2552	15310821_MI:0018	The F-box regions of LKP1, LKP2, and FKF1 are sufficient to bind to ASK proteins (Fig. 3B-D).
2553	15316289_MI:0018	and a very weak interaction between AtBT4 and AtBET10/GTE11 was also observed (Figure 8D).
2554	15316289_MI:0018	AtBT1 protein interacts with two Arabidopsis BET proteins which are members of fsh/Ring3 class transcriptional regulator family
2555	15316289_MI:0018	Growth of transformants on the synthetic dropout medium without His Leu and Trp (SD/-HLW) indicated that AtBT2 and AtBET10/GTE11 exhibit an interaction comparable
2556	15316289_MI:0018	The protein- protein interaction confirmation results between AtBT1 and AtBET10/GTE11 in yeast cell are shown in Figure 8A.
2557	15319482_MI:0018	The N Terminus of TTL Is Crucial for TTL-BRI1 Interaction
2558	15319482_MI:0018	To identify potential targets of the activated BRI1 receptor kinase in response to BR signal, we conducted a yeast two-hybrid screening using the kinase domain of BRI1 (BRI1CK) as the bait. Out of 96 positive BRI1-interacting clones, 60 were found to be derived from the same Arabidopsis gene (At5g58220) that encodes a hypothetical protein of 324 amino acids.
2559	15326298_MI:0018	Thus, of the 193 interacting proteins, 178 were encoded by GIF1 and 5 by GIF2, which is strong evidence that GIF1 and GIF2 are partner proteins of GRF1.
2560	15326298_MI:0018	Yeast cells expressing both GRF1 and GIF1 grew on His-deficient medium and gave the color reaction for 
-galactosidase activity, but none of the other combinations of GRF1 or GIF1 gave a positive response, thereby confirming the screening result
2561	15361138_MI:0018	Additionally, CPC and AtMYBL2 were detected with TT8 as bait.
2562	15361138_MI:0018	Deletion of the entire C-terminal region (AtMYB4_1-118) resulted in strong interaction with BHLH012 and weaker but significant interaction with TT8.
2563	15361138_MI:0018	EGL3, AtBHLH012 and TT8 consistently activated both reporters when cotransformed with AtMYB5, with the MYB proteins of subgroup 5 (PAP1, PAP2, AtMYB113 and AtMYB114) and with TT2 (subgroup 6), respectively. In contrast, MYB proteins from subgroup 15 (GL1, WER, AtMYB23) interacted with EGL3 and AtBHLH012 but not with TT8 (Figure 1a,b).
2564	15361138_MI:0018	four 1R MYB proteins (AtMYBL2, CPC, At1g01380 and At2g30420) were identified in screenings using AtBHLH012 as bait protein.
2565	15361138_MI:0018	Furthermore, AtMYBL2 and the CPC-homologue At1g01380 were isolated in screenings using EGL3 as bait.
2566	15361138_MI:0018	In addition to mutations D12N, L20V and L29I obtained by the randommutagenesis approach, the single-site mutants L13I, R16E, R16K, R19S, L20A, R33D and R33A were analysed. With the exception of R19S, all of these exchanges led to temperature- sensitive interaction with EGL3, revealed by reduced growth of yeast cells at non-permissive temperatures.
2567	15361138_MI:0018	Protein fragments were fused to the GAL4-AD and tested for interaction with the set of AtBHLH transcription factors. The minimal domain necessary for interaction was confined to amino acids 53 to 114 comprising accurately the complete R3-repeat of the MYB domain of PAP1.
2568	15361138_MI:0018	Protein fragments were fused to the GAL4-AD and tested for interaction with the set of AtBHLH transcription factors. The minimal domain necessary for interaction was confined to amino acids 53 to 114 comprising accurately the complete R3-repeat of the MYB domain of PAP1. These findings were supported by the fact that, from the library screenings, several N-terminally truncated MYB proteins have been isolated. The shortest 1R MYB proteins identified were CPC consisting of amino acids 37-94 and the CPC-homologue At1g01380 comprising amino acids 33-83, respectively (Figure 3).
2569	15361138_MI:0018	The shortest 1R MYB proteins identified were CPC consisting of amino acids 37-94
2570	15364927_MI:0018	Deletion of the acidic domain (aa 434-496) from Daxx abolished its interaction with p53
2571	15364927_MI:0018	p53 constructs with progressive deletions from the NH2 terminus up to residue 253 were able to bind to Daxx
2572	15371304_MI:0018	In these experiments the DNA binding partner contained AtBRM residues 16 to 952 fused to the GAL4 DNAbinding domain (GBD-AtBRM16-952) while the full length CHB4 protein was fused to the GAL4 activation domain (GAD-CHB4). As shown in Table 1, the co-expression of both proteins in yeast activated the expression of a chromosomal GAL1::lacZ reporter gene, indicating that the amino terminus of AtBRM interacts with CHB4.
2573	15380617_MI:0018	Interactions of human Chk2 with the B' regulatory subunits of PP2A in yeast cells
2574	15448699_MI:0018	Two-hybrid analysis of Cdc4 fused to the GAL4 activator domain with wild-type Sic1DeltaCDK (SIC1) or Sic1 T173EDeltaCDK (Sic1-TE) fused to the LexA-DNA binding domain were evaluated by the filter and liquid beta-galactosidase assay (U, Miller units from three independent assays).
2575	15448699_MI:0018	Two-hybrid experiments using a Sic1 form that does not contain the CDK inhibitory domain to prevent cell-cycle arrest (Sic1DeltaCDK), showed that Hog1 interacted with Sic1 as efficiently as the Hog1 downstream target Smp1 (ref. 16) (Fig. 3a).
2576	15451437_MI:0018	using IEX-1 as the bait protein, and examined interactions between IEX-1 and proteins expressed by a human kidney cDNA expression library. We found that IEX-1 interacts with several proteins of which at least four are known to play a role in the regulation of apoptosis: (1) calcium-modulating cyclophilin ligand
2577	15451437_MI:0018	we performed yeast two-hybrid studies using IEX-1 as the bait protein, and examined interactions between IEX-1 and proteins expressed by a human kidney cDNA expression library. We found that IEX-1 interacts with several proteins of which at least four are known to play a role in the regulation of apoptosis: (1) calcium-modulating cyclophilin ligand; (2) tumor necrosis factor-related apoptosis-inducing ligand (tumor necrosis factor superfamily, member 10
2578	15451437_MI:0018	we performed yeast two-hybrid studies using IEX-1 as the bait protein, and examined interactions between IEX-1 and proteins expressed by a human kidney cDNA expression library. We found that IEX-1 interacts with several proteins of which at least four are known to play a role in the regulation of apoptosis: (1) calcium-modulating cyclophilin ligand; (2) tumor necrosis factor-related apoptosis-inducing ligand (tumor necrosis factor superfamily, member 10); (3) ML-1 myeloid cell leukemia gene encoded protein;
2579	15451437_MI:0018	we performed yeast two-hybrid studies using IEX-1 as the bait protein, and examined interactions between IEX-1 and proteins expressed by a human kidney cDNA expression library. We found that IEX-1 interacts with several proteins of which at least four are known to play a role in the regulation of apoptosis: (1) calcium-modulating cyclophilin ligand; (2) tumor necrosis factor-related apoptosis-inducing ligand (tumor necrosis factor superfamily, member 10); (3) ML-1 myeloid cell leukemia gene encoded protein; and (4) BAT3
2580	15456723_MI:0018	All prey fusions that contained an intact C5 domain were able to interact with the EMF2-VEFS domain (427-631). The shortest region of CLF sufficient for interaction comprised residues 257-331.
2581	15456723_MI:0018	In addition, we found that both CLF and SWN can interact with FIE through a 110 amino acid motif at their N-termini
2582	15456723_MI:0018	Interaction of CLF C5 domain (257-331) with the VEFS domains of EMF2, VRN2 and FIS2
2583	15456723_MI:0018	Interaction of SWN C5 domain (252-331) with the VEFS domains of EMF2 (510-631),
2584	15456723_MI:0018	Interaction of SWN C5 domain (252-331) with the VEFS domains of EMF2 (510-631), VRN2 (275-440)
2585	15456723_MI:0018	Interaction of SWN C5 domain (252-331) with the VEFS domains of EMF2 (510-631), VRN2 (275-440)and FIS2 (394-692).
2586	15456723_MI:0018	Interaction of the VEFS domain of FIS2 (residues 466-692) with full-length MEA protein.
2587	15456783_MI:0018	Complementation studies in diploid cells plated on selective media (Fig. 2C) demonstrated that Vangl1 and Vangl2 proteins were indeed able to interact with the N-terminal half of each of the three Dvl proteins tested.
2588	15467741_MI:0018	Isolation of merlin binding proteins using the yeast two-hybrid system
2589	15483055_MI:0018	Yeast two-hybrid analysis of interactions of the PAKc CRIB/AI domain with RacB
2590	15503857_MI:0018	TCTEL1 (t-complex testis expressed protein 1) was found as HSPB9-interacting protein in both libraries
2591	15503857_MI:0018	TCTEL1 (t-complex testis expressed protein 1) was found as HSPB9-interacting protein in both libraries, while CTCF (CCCTC-binding factor; zinc finger protein), NUDT5 (nudix hydrolase) and an unknown protein (not similar to a known protein using BLAST search) were only found in the HeLa library.
2592	15503857_MI:0018	We therefore tested whether mouse HSPB9 could bind human TCTEL1, and found indeed interaction, but not as strong as for human HSPB9
2593	15503857_MI:0018	When tested for interaction with TCTEL1, the C-terminus was positive, while the N-terminus was negative
2594	15509655_MI:0018	In this assay, the PakB PBD interacted strongly with activated human Rac1 and Cdc42, used as positive controls, and with Dictyostelium Rac1a, b, and c; the GTPase domain of RacA (a member of the RhoBTB protein family); and RacB, RacC, and RacF1 (Table 1)
2595	15520167_MI:0018	A novel protein MGC5306 has been identified in yeast-two-hybrid analysis by screening a HeLa cDNA library with a truncated DNA polymerase(pol) as bait.
2596	15520167_MI:0018	galactosidase activity was detected in the colony with XRCC1 shown in Fig. 1A, Lane 2. XRCC1, a known nuclear repair protein interacts with pol
2597	15555586_MI:0018	Subsequently we performed a second yeast two-hybrid screen using Skp1 as bait. Interestingly, we also identified a full-length cDNA predicted to encode a fission yeast protein with significant similarity to mammalian Mat1 (mouse; gi19860537, 35%) and budding yeast Tfb3p (gi1778061, 41%). Therefore, we designated the gene pmh1 (for pombe mat1 homolog; GenBank Accession No. AF191500).
2598	15555586_MI:0018	The original identification of Skp1 was made in a yeast two-hybrid screen using the Mcs2 (LexA-Mcs2) cyclin as bait (Fig. 1). The isolated partial cDNA (clone c57) encodes the C-terminal 118 amino acids of Skp1 and activates both LEU2 and lacZ reporters in a yeast two-hybrid assay (Fig. 1A).
2599	15555586_MI:0018	To further characterize this interaction, we compared the strength of the interaction between Mcs2 and full length Skp1 to the interaction between Mcs2 and its cognate CDK, Mcs6, using a quantitative b-galactosidase assay (Fig. 1B). Measurement of b-galactosidase activity demonstrated an interaction of similar strength between Mcs2 and Skp1 when compared to the interaction between Mcs2 and Mcs6. Most importantly, the interaction between Mcs2 and Skp1 was almost completely abolished when a Skp1 mutant (skp1-3) [40] with a single amino acid change (I172R) was used (Fig. 1B).
2600	15584952_MI:0018	. In the absence of methionine, where At1g01380-free expression would be at maximum levels, the GL1-GL3 interaction was inhibited as indicated by the lack of beta-galactosidase activity (Figure 8b).
2601	15584952_MI:0018	To determine whether the At1g01380 protein behaves in a similar fashion, the ability of At1g01380 to interact with GL3 was tested first. As shown in Figure 8(a), these proteins are able to interact.
2602	15592873_MI:0018	As summarised in Table 1, AtCDC48549-809 appears to interact not only with AtSERK1 but also with itself, with GF14 and with KAPP.
2603	15592873_MI:0018	AtCDC48549-809 appears to interact not only with AtSERK1 but also with itself, with GF14 and with KAPP.
2604	15592873_MI:0018	The AtSERK1 kinase domain interacts with AtCDC48 and GF14 in yeast
2605	15592873_MI:0018	While AtSERK1 interacts with the kinase interaction domain of KAPP, AtCDC48549-809 only interacts with the complete KAPP protein.
2606	15604664_MI:0018	However, when both the MADS and I domains are deleted from AP1 (AP1-KC), both SEP1 and SEP3 interact strongly with AP1-KC
2607	15604664_MI:0018	In summary, these results demonstrate that SEP1, SEP2, and SEP3 are capable of interacting in yeast two-hybrid assays with several MADS proteins including AP3, PI, AP1 and AG.
2608	15604664_MI:0018	PI mutants in different regions of the K domain exhibit differential effects on the strength of PI/AP3 and PI/SEP3 (or PI/SEP1) interaction
2609	15604664_MI:0018	SEP1, SEP2, and SEP3 proteins interact with MADS-deleted versions of AP3 (AP3-IKC)
2610	15604664_MI:0018	SEP1, SEP2, and SEP3 proteins interact with MADS-deleted versions of AP3 (AP3-IKC) and PI (PI-IKC). Note that the interaction strength is only between 5-30% of the AP3-IKC/PI-IKC interaction.
2611	15632444_MI:0018	ShcS1 and ShcO1 both interact with two different effectors, HopS1' and HopO1-1
2612	15632444_MI:0018	ShcS1 interacts with HopS1' in yeast
2613	15632444_MI:0018	These experiments revealed that, as expected, ShcS1 and ShcO1 can homodimerize. In addition, ShcS1 and ShcO1 also interact with each other, suggesting that they are able to form heterodimers.
2614	15634206_MI:0018	However, unlike NPR4, NPR1 also interacts with NIMIN3.
2615	15634206_MI:0018	NPR4 interacts with these TGA factors. Cells harboring NPR4:DB along with TA fusions of either TGA1, TGA4, or NIMIN3 produced a white color indicating that NPR4 does not interact with these proteins in yeast. NPR1:DB interacts with the same spectrum of TGA factors as does NPR4 (Figure 2a). However, unlike NPR4, NPR1 also interacts with NIMIN3.
2616	15634206_MI:0018	The entire coding region of NPR4 was inserted into the GAL4 DNA binding domain (DB) fusion expression vector pBI880 (Kohalmi et al., 1997) and co-transformed into yeast cells along with the GAL4 transactivation domain (TA) fusion expression vector pBI881 containing the coding region from one of the TGA factors or NIMIN3. XGAL filter assays of colonies harboring NPR4:DB along with TA fusions of TGA2, TGA3, TGA5, TGA6, or TGA7 yielded a blue color (Figure 2a), indicating that NPR4 interacts with these TGA factors.
2617	15659634_MI:0018	ABIL1 interacted with both human NAP1 and GRL (NAP1) in the yeast two-hybrid assay.
2618	15659634_MI:0018	DIS3/SCAR2 and human WAVE1 interact with ARPC3 in a yeast twohybrid assay.
2619	15659634_MI:0018	The SHD domain of DIS3/SCAR2 interacts with ABIL1 in the yeast two-hybrid assay.
2620	15694377_MI:0018	The constructed fusion proteins in mammalian two-hybrid protein-protein interaction system were used for analysis of the binding activities between the full length of CASK and two isoforms of Id1 and Id1prime.
2621	15694377_MI:0018	To explore the molecular mechanism, we identified a novel CASK-interacting protein, inhibitor of differentiation 1 (Id1) with a yeast two-hybrid screening.
2622	15714319_MI:0018	ARR3 was found to interact with a DNA J-like protein (At5G21510).
2623	15714319_MI:0018	IGPS interacted with a member of the hydroxyproline-rich glycoprotein family
2624	15714319_MI:0018	Of the proteins with unknown interacting partners APRT was found to form homodimers,
2625	15714319_MI:0018	The function of At5G09540, the interaction partner of ARR9, is unknown.
2626	15714319_MI:0018	Using the prey library derived from the hormone-treated seedling, we were able to detect interactions with several different clones of AHPs, namely AHP1 and AHP3, when ARR1 was used as bait.
2627	15716105_MI:0018	One of the cDNA clones with similarity to the mammalian BTF3 factor encodes the full-length predicted polypeptide AtBTF3 (accession number AJ242970). The two other clones are identical and encode a polypeptide with only the first 101 amino acids.
2628	15720729_MI:0018	AML1 interacts with AtRaptor1B in a yeast two-hybrid assay
2629	15721254_MI:0018	The prey  vectors started at nucleotides 484 and 1106 of the full  length OS-9 mRNA sequence (GenBank accession number AB002806) and encoded fusion proteins containing aa 49-667 and 357-667, respectively, of OS-9
2630	15741320_MI:0018	HFR1 and COP1 interact in vitro and in vivo.
2631	15743878_MI:0018	This indicates that the BAR domain is required and is sufficient for the formation of the VAN3 homodimer.
2632	15774864_MI:0018	Among all the tested proteins, the dimerization of only FtsA and FtsAFtsZ association has been experimentally documented by several independent approaches (protein overlay and yeast and bacterial two-hybrid systems). These interactions were clearly confirmed by the BACTH system
2633	15774864_MI:0018	FtsA was also found to interact with several of the Fts membraneassociated proteins, in particular FtsI, FtsN, and FtsQ.
2634	15774864_MI:0018	FtsB and FtsL formed heterodimers
2635	15774864_MI:0018	FtsB and FtsL formed heterodimers,
2636	15774864_MI:0018	in DHM1 cells overexpressing FtsL, a weak complementation between T18-FtsB and T25-FtsI could be detected.
2637	15774864_MI:0018	Interactions of FtsQ with FtsA and FtsI were clearly confirmed here by BACTH assays
2638	15774864_MI:0018	Interactions of FtsQ with FtsA and FtsI were clearly confirmed here by BACTH assays.
2639	15774864_MI:0018	Our present BACTH data indicate that FtsN can indeed associate with FtsQ and FtsI
2640	15774864_MI:0018	our results indicate that FtsQ could associate with nearly all the tested Fts proteins
2641	15774864_MI:0018	our results indicate that FtsQ could associate with nearly all the tested Fts proteins, although with quite different efficiencies.
2642	15774864_MI:0018	The BACTH analysis also showed that, in addition to FtsA, two other Fts proteins, FtsN and FtsQ, were able to dimerize or multimerize
2643	15774864_MI:0018	the dimerization of only FtsA and FtsAFtsZ association has been experimentally documented by several independent approaches (protein overlay and yeast and bacterial two-hybrid systems). These interactions were clearly confirmed by the BACTH system
2644	15774864_MI:0018	the FtsW binding site encompasses an extended transmembrane region of FtsI (aa 1 to 70)
2645	15774864_MI:0018	The integral membrane protein FtsX was found to associate specifically with FtsA and FtsQ, thus suggesting that FtsX may contribute to the cytokinetic process.
2646	15774864_MI:0018	upon overexpression of FtsL, T18-FtsB was shown to complement efficiently T25-FtsW whereas no complementation was detected between these two hybrid proteins in cells expressing normal levels of FtsL.
2647	15774864_MI:0018	we found that overexpression of FtsL strongly enhanced association between T18-FtsB and T25-FtsQ
2648	15774864_MI:0018	YmgF was able to associate with three other Fts proteins: FtsI, FtsN, and FtsQ.
2649	15805487_MI:0018	Interaction of CNT with Full-Length CRY and CNT Itself in Yeast Cells.
2650	15805487_MI:0018	Yeast two-hybrid assays showed that all of these point mutations abolished CNT1-CRY1 interaction
2651	15809031_MI:0018	An interaction between tea1p and the CLIP170 tip1p has been shown to concentrate tea1p at the MT plus end (Feierbach et al., 2004). The kelch repeats at the N terminus of tea1p were necessary and sufficient for this interaction (Figure 2E).
2652	15809031_MI:0018	No specific domain of tea4p could be defined in for3p binding. Neither the tea4p C-terminal region, which mediates the interaction with tea1p, nor the N-terminal half interacted with for3p reproducibly (Figure 4E), suggesting that multiple parts of the protein may be required for strong interaction. What is clear though is that the SH3 domain of tea4p was dispensable for binding, as shown by deletion or specific point mutation in the SH3 domain.
2653	15809031_MI:0018	Tea1p and tea4p also showed a strong interaction in the two-hybrid system (Figures 1C and 1D), which allowed us to map the regions of the proteins important for these interactions.
2654	15809031_MI:0018	We mapped the interaction domains between for3p and tea4p. Deletion analysis defined amino acids 137-515 in for3p as the minimal sufficient region for interaction with tea4p (Figure 4D). This region overlaps with the predicted FH3 domain of for3p (aa 306-507, as defined by SMART) and the rho binding region (Nakano et al., 2002). This N-terminal region is necessary and sufficient for localization of for3p at cell tips (Nakano et al., 2002), suggesting that tea4p binding to this for3p region may regulate for3p localization.
2655	15827353_MI:0018	We created two different constructs, one encoding the N terminus of the 97-kDa PF6 protein and the other encoding its C terminus, and tested them for the ability to interact with SPAG6 in a yeast two-hybrid system.
2656	15870463_MI:0018	DifA interacted with DifC, and DifC interacted with DifA and DifE. DifD interacted with two proteins, DifE and DifF, and DifE also interacted with two proteins, DifC and DifD. DifF interacted with DifD only.
2657	15870463_MI:0018	Furthermore, the DifE bait was able to pull out Nla19
2658	15870463_MI:0018	These data further validate the interactions between DifC and DifE, DifD and DifE, and DifF and DifD
2659	15870463_MI:0018	We further mapped the region of TAF-4 necessary and sufficient for OMA-1/2 interaction to amino acids 333-382, which overlaps the HFD (Figure 4A and Figure S1B).
2660	15887118_MI:0018	A yeast 2-hybrid screen identified Jun activation domain-binding protein 1 (Jab1) as a binding partner for HHM.
2661	15899844_MI:0018	Interestingly, S. pombe Rad51 was found to interact with human Rad51,
2662	15899844_MI:0018	Using two-hybrid analysis, the homotypic interactions of Rad51 and Dmc1 were characterized further.
2663	15901727_MI:0018	A600 values obtained after overnight growth of either the CsdA-LexA/CsdE-B42 pair or the CsdA-B42/CsdE-LexA pair were consistent with CsdA interacting with CsdE
2664	15901727_MI:0018	CsdA was found to interact with itself, indicating that it forms homodimers.
2665	15915339_MI:0018	The possibility that Mcl1p interacts physically with Pola was examined using a yeast two-hybrid assay. The results shown in Fig. 5b indicate that Mcl1p interacts with Pola and the interaction is mediated by the C-terminal region of Mcl1p (amino acids 420-815) and the Nterminal region of Pola (amino acids 1-866), indicating that WD repeats in Mcl1p are not involved in this interaction.
2666	15917470_MI:0018	we found that only the expression of both pBT-Oct-4 and pTRG-EWS in bacterial reporter cell line allowed growth on +Kan/+Chl/+Tet LB plates containing 0.47 or 0.59 mM carbenicillin, indicating a physical interaction between Oct-4 and EWS
2667	15917470_MI:0018	we identified five interesting clones as the Oct-4-binding partners. In addition, through nucleotide sequence determination and comparison with GenBank and SwissProt databases, we found that one clone contained the cDNA sequence of EWS
2668	15936270_MI:0018	we searched for proteins interacting with the non-catalytic domain of Win1 MAPKKK by yeast two-hybrid screens. These screens repeatedly isolated cDNA clones containing an open reading frame SPBC1706.01; we named this gene wsh3+
2669	15937161_MI:0018	Moreover, protein fusions carrying only the cytoplasmic (Cd, the C terminal 20 amino acids) domain of NarC, rendered even higher galactosidase signals with NarI.
2670	15960617_MI:0018	As expected, AN3 interacted strongly with AtGRF5 and AtGRF9, but only weakly with AtGRF4 (Figure 5c).
2671	15960622_MI:0018	Thus, the coiled-coil region of SPA1 appears to be required, and sufficient, for mediating the interaction between SPA1 and HFR1,
2672	15964553_MI:0018	The yeast two hybrid assay and GST fusion protein pull down experiment demonstrated that TSSK5 physically interacts with CREB in vitro.
2673	15983381_MI:0018	Another notable DJ-1-interacting clone was a protein corresponding to the carboxyl terminus (amino acids 638-739) of human Daxx,
2674	15983381_MI:0018	One of these isolated clones encode DJ-1 itself, a finding consistent with reports that DJ-1 may act as a homodimer
2675	15983381_MI:0018	Other positive clones that were found to interact with DJ-1 are small ubiquitin-like modifier (SUMO) 1, SUMO-activating enzyme Uba2, and SUMO-conjugating enzyme Ubc9, which are components of the sumoylation system.
2676	15990873_MI:0018	MPK4 interacts in yeast and in vitro with MKS1
2677	15990873_MI:0018	To further investigate MKS1 function, we conducted a second Y2H library screen to identify additional MKS1 interacting proteins. Of 6107 clones screened, four encoding WRKY25 (W25) and 11 encoding WRKY33 (W33) were identified and confirmed by b-galactosidase assays.
2678	16002617_MI:0018	Approximately 1.2 x 107 transformants with Arabidopsis yeast two-hybrid cDNA library (Clontech) were screened using the LKP2 kelch domain bait for growth selection in the absence of His and in the presence of 5 mM 3-AT, and for &#946;-gal activity selection (we originally obtained clones containing the partial sequences of CDF2, and CDF3 genes as LKP2 kelch domain interactors).
2679	16002617_MI:0018	Interaction between the FKF1, LKP2, and ZTL kelch domains and the CDF1, CDF2, and CDF3 proteins in yeast.
2680	16002996_MI:0018	From a genomic prey library, we obtained several clones carrying either slr1694 itself or slr1693 (data not shown).
2681	16002996_MI:0018	The interaction of the Slr1694 and Slr1693 proteins, which was confirmed in both directions, strongly suggests a possible signal transduction pathway as discussed below.
2682	16002996_MI:0018	To confirm the specificity of the screening, we introduced the coding region of slr1694 into the prey vector and then assayed it with bait clones carrying the full-length coding regions of the six patA-like genes and the slr1694 gene. Again, slr1693 as well as slr1694 gave positive results (Fig. 8).
2683	16003391_MI:0018	Interactions between AtBAG6 and AtCaM2 in yeast.
2684	16003391_MI:0018	interactions between tumor suppressor p53 (pTD1-1) and simian virus 40 large T-antigen (pVA3-1);
2685	16003391_MI:0018	we employed the yeast two-hybrid screening system using full-length AtBAG6 as bait. We identified 33 yeast colonies that expressed both reporter genes (Adeþ/lacZþ) in an AtBAG6-dependent manner. Sequence analyses revealed that all the AtBAG6-associated proteins are AtCaM isoforms, specifically, five AtCaM1s (accession no. At5g37780), 14 AtCaM2s (accession no. At2g41110), seven AtCaM3s (accession no. At3g56800), two AtCaM4s (accession no. At1g66410), three AtCaM6s (accession no. At5g21274) and two AtCaM7s (accession no. At3g43810).
2686	16014621_MI:0018	AtMinD1(K72A) Is Unable to Interact with AtMinE1
2687	16043509_MI:0018	Domain interactions within ski2/3/8 identified by directed two hybrid
2688	16053918_MI:0018	We identified a 1A6/DRIM (down-regulated in metastasis) interacting protein, KIAA0649 during the yeast two-hybrid screen.
2689	16055636_MI:0018	ATSWI3D recognized only ATSWI3B as a binding partner
2690	16055636_MI:0018	BSH only by forming a heterodimer with either ATSWI3A or ATSWI3B.
2691	16055636_MI:0018	In addition to binding ATSWI3B, ATSWI3A also showed interaction with BSH/SNF5 and with the C-terminal region of FCA, which also mediates the interaction with ATSWI3B
2692	16055636_MI:0018	we observed that ATSWI3A can also form homodimers
2693	16055636_MI:0018	we observed that ATSWI3A can also form homodimers as well as heterodimers with ATSWI3C.
2694	16091426_MI:0018	Again, an interaction with Sec24Dp was also detectable (Fig. 1C).
2695	16091426_MI:0018	A specific interaction was seen between Sec23Ap and the region of PCTAIRE-1 corresponding to that of PCTAIRE-3 identified in the initial screen (exons 4-8).
2696	16091426_MI:0018	A weaker interaction was also detectable with Sec24Dp
2697	16091426_MI:0018	Thus, the central regions of both PCTAIRE-3a and -3b (Herskovits and Davies, 2004Go) interact with Sec23Ap
2698	16091426_MI:0018	We screened a human brain cDNA library using the two-hybrid method to identify proteins that interact with Sec23Ap
2699	16094715_MI:0018	HCV p7 protein also interacts with Homo sapiens signal sequence receptor
2700	16094715_MI:0018	HCV p7 protein also interacts with Homo sapiens signal sequence receptor, Homo sapiens H19, imprinted maternallyexpressed untranslated mRNA, Homo sapiens spermatid perinuclear RNA binding protein
2701	16094715_MI:0018	HCV p7 protein also interacts with Homo sapiens signal sequence receptor, Homo sapiens H19, imprinted maternally expressed untranslated mRNA, Homo sapiens spermatid perinuclear RNA binding protein, Homo sapiens colon cancer associated antigen and Homo sapiens CLL-associated antigen KW-13.
2702	16107882_MI:0018	As shown in Table I, Bud14p fused to the activation domain (AD) strongly interacted with Glc7p fused to the DNA-binding domain (DBD).
2703	16109709_MI:0018	Yeast two-hybrid screening of 3.8x106 independent clones of a Synechocystis genomic library with Synechocystis PII as bait yielded four positive clones. One of these four clones contained the PII gene (glnB) itself, consistent with the trimeric nature of PII, and the other three clones were found to harbor the 3' terminal region of a predicted gene sll0985.
2704	16132846_MI:0018	the b-galactosidase activity between PDCD6 and DAPk1 was fully observed,
2705	16132846_MI:0018	we searched a human ovary cDNA library for a novel PDCD6 binding protein using a yeast two-hybrid system. The selected protein was the human death-associated protein kinase 1 (DAPk1)
2706	16142218_MI:0018	Dicer and TRBP interact in a yeast two-hybrid (2H) assay through the carboxy-terminal domain of TRBP.
2707	16183855_MI:0018	indicating that caspase-8 is capable of interacting with Bcl-2 via its small subunit.
2708	16204054_MI:0018	A two-hybrid assay revealed that the NH2-terminal amino acids 1 to 161 of actinin-4 and the NH2-terminal amino acids 1 to 249 of h-catenin were responsible for the interaction
2709	16214168_MI:0018	Interaction of Nmi and Sox10 in yeast and mammalian cells
2710	16229834_MI:0018	The interaction between Par-4 and Amida was first confirmed by retransformation of yeast cells with plasmids coding for pAD-Amida and pBD-Par-4 including the appropriate controls
2711	16229834_MI:0018	Using Par-4 as bait in a yeast two-hybrid screen, we identified Amida as a novel interaction partner
2712	16229834_MI:0018	we used Par-4 as bait to screen a cDNA library from SV52 rat fibroblasts. Seven positive clones were identified from histidine negative plates which were also positive for h-galactosidase expression. Sequence analysis revealed one clone coding for Par-4, showing the ability of the protein to self-associate,
2713	16230351_MI:0018	Full-length POSH was cloned into a bait vector, and a total of ~2 x 106 independent transformants from a mouse brain library were analyzed. Fifty-two strong to very strong positive clones were observed, and their identities were established by sequencing. Fourteen clones corresponded to Siah1a, two to Siah1b, and three to Siah2
2714	16234233_MI:0018	The yeast two-hybrid system was used to identify putative ASIC3-interacting proteins. A rat DRG cDNA library (18) was screened with the last 68 amino acids of rat ASIC3 as a bait. Among the isolated clones, one clone encoded a full-length NHERF-1 protein, also named EBP50 (ezrin-radixin- moesin-binding phosphoprotein of 50 kDa), and another encoded a partial NHERF-2 protein, also identified as E3KARP (Na
/H
 exchanger 3 kinase A-regulatory protein), TKA-1 (tyrosine kinase activator- 1), or SIP-1 (SRY-interacting protein-1).
2715	16236155_MI:0018	Only the combination of GAL4BD- AtGRIP or GAL4BD-GRIP2 with GAL4AD-ARL1-Q71L produced colonies
2716	16260785_MI:0018	although Snf4p did interact with its partner subunit Snf1p (Fig. 1A).
2717	16260785_MI:0018	FIGURE 1. Arr4p interacts with the CT of Gef1p.
2718	16260785_MI:0018	homotypic Arr4p interaction assayed by the two-hybrid system. Bait and prey fusions contained the indicated double mutation.
2719	16260785_MI:0018	In search for proteins that would bind to the C terminus (CT) of Gef1p, we screened 6 million co-transformants of the bait plasmid and a yeast genomic two-hybrid library constructed in the prey plasmid.
2720	16275660_MI:0018	Overlay experiments with the SH3 domain of amphiphysin II allowed the identification of the known interaction partner dynamin (Table I). In addition, the proteins Discs large-associated protein 4 (DLP4), XRCC4 (DNA repair protein), and fructose-1,6-bisphosphatase (FBP) (Table I) were identified as novel amphiphysin II interaction partners and verified by in vitro pull-down and two-hybrid assays (Fig. 4, A and B)
2721	16275660_MI:0018	Overlay experiments with the SH3 domain of amphiphysin II allowed the identification of the known interaction partner dynamin (Table I). In addition, the proteins Discs large-associated protein 4 (DLP4), XRCC4 (DNA repair protein), and fructose-1,6-bisphosphatase (FBP) (Table I) were identified as novel amphiphysin II interaction partners and verified by in vitro pull-down and two-hybrid assays (Fig. 4, A and B).
2722	16278681_MI:0018	By performing a yeast two-hybrid screen of a mammary gland library, we identified cysteine-rich inhibitor of Pak1 (CRIPak) as a novel Pak1-interacting protein.
2723	16278681_MI:0018	GBD-PAK1 interacts with GAD-CRIPak in yeast cells as shown bytheir growth on media lacking histidine (Figure 2a).
2724	16282318_MI:0018	However, these assays also suggested that the first 137 amino acids of AtFip1(V) interact with the Arabidopsis homologs of PAP, CPSF30,CstF77, CFIm-25, and PabN1 (summarized in Table 2).
2725	16284419_MI:0018	These results suggest that OSH15 and OsBEL form homodimers and/or heterodimers together.
2726	16284419_MI:0018	These results suggest that OsWUS and OsPRS form homodimers and/or heterodimers together.
2727	16293618_MI:0018	the PDZ domain of Shank2 showed a potent induction of both HIS3 and -galactosidase reporter genes in yeast, indicating a direct protein-protein interaction between the carboxyl terminus of NHE3 and the PDZdomain of Shank2.
2728	16299177_MI:0018	First, ABF4 interacts also with AtCPK10 and AtCPK30,
2729	16299177_MI:0018	In summary, our results indicated that full-length AtCPK32 is necessary for the normal interaction with the C2-C3 region of ABF4. Although necessary, the kinase domain was not sufficient for the interaction, and both the N-terminal variable region and the C-terminal EF hand region were required.
2730	16299177_MI:0018	Interaction between ABF family members and CDPKs. Interaction between AtCPK32 and ABF family members (ABF1, ABF2, or ABF3)
2731	16299177_MI:0018	Specificity of interaction.Interaction of AtCPK32 with an unrelated protein, nuclear lamin (lamin), or with the C2-C3 region of ABF4 was investigated by two-hybrid assay.
2732	16301118_MI:0018	After mating of the prostate cancer cDNA library transformed AH109 and transglutaminase transformed Y187 yeast strains, 65 colonies of interactors were identified. We analyzed all the colonies and identified partial cDNA sequences encoding A kinase anchor protein 13 variant 3 (AKAP13) in 3 independent colonies.
2733	16301118_MI:0018	AKAP13 interacted with transglutaminase and failed to interact with GTPase
2734	16332538_MI:0018	Light-Regulated Interaction of FHY1 and phyA In Vitro and In Yeast
2735	16332688_MI:0018	After screening human fetal brain cDNA library, several previously known and novel proteins were identified to interact with Parkin, including cyclin E, -tubulin, and RanBP2 (data not shown).
2736	16339310_MI:0018	we used a yeast two-hybrid assay to examine whether RHL1 interacts with topo VI in vivo. Hartung and Puchta (24) previously reported that AtSPO11-3/RHL2 can interact with AtTOP6B/HYP6/RHL3 in a yeast interaction assay. In addition, we found that both proteins also self-interact
2737	16339760_MI:0018	The coiled-coil domains of HAP1 do not appear to mediate the binding of HAP1 to KLC, as HAP1 fragments that contained coiled-coil domains but lacked C-terminal amino acids failed to yield a positive interaction
2738	16339760_MI:0018	Yeast two-hybrid analysis revealed that a C-terminal fragment of HAP1 present in both rodent isoforms binds kinesin light chain-2 (KLC-2, Fig. 1), a subtype of KLC that is highly homologous to kinesin light chain-1 (KLC-1) with 71.1% amino acid identity
2739	16339850_MI:0018	COL3 Interacts with COP1 in Yeast, and a VP Pair in the C Terminus Is Critical for the Interaction.
2740	16339850_MI:0018	The Zn2+-ligating B-box has been proposed to be a protein interaction domain, but it does not appear to be required for the interaction with COP1 in yeast because all three cDNAs identified in the screen encode a truncated COL3 protein lacking the 75 N-terminal amino acids
2741	16369483_MI:0018	Interaction of CgA and CgB with mutant SOD in cultured cell lines.
2742	16415858_MI:0018	Mammalian two-hybrid (M2H) assay demonstrating direct interaction of a2N(pMa2N) with ARNO(pVARNO) in HEK cells.
2743	16438971_MI:0018	The interaction of AtCPK4-F305A with AtDi19 is not surprising, as AtCPK11 and AtCPK4 are two of the most closely related CDPKs in Arabidopsis.
2744	16438971_MI:0018	The weak interaction detected between AtCPK12-F302A and AtDi19 is consistent with the above observations as this kinase is the next most closely related member of the CDPK superfamily.
2745	16438971_MI:0018	We identified five clonesvcorresponding to the AtDi19 gene (Dehydration-induced 19,b At1g56280) [9]. Moreover, AtDi19 was detected in the screens performed using the three different forms of AtCPK11 baits
2746	16461579_MI:0018	A similar result was obtained when WSIP1 was tested in the yeast two-hybrid screen for interaction with Antirrhinum ROA; once again, a strong interaction was obtained, but the interaction was dependent on the presence of the C-terminal conserved domains of ROA
2747	16461579_MI:0018	Both isolated prey clones and full-length WSIP1 were tested in the yeast two-hybrid system for interaction with a variety of full-length and truncated WUS proteins. Interaction was observed in all cases, but only when the expressed WUS protein contained the conserved C-terminal domains
2748	16461579_MI:0018	Therefore, WUS is capable of interacting with at least two related Arabidopsis proteins, and yeast two-hybrid and pulldown evidence suggests that the conserved C-terminal domains of WUS are important for this interaction.
2749	16461579_MI:0018	The two isolated prey cDNAs (At1g15750 and At3g15880; renamed WSIP1 and WSIP2 here) represent different members of a small gene family in Arabidopsis and other plant species (Figure 7C). Both WUS-interacting proteins are predicted to contain N-terminal LisH (for Lis1-homologous) and CTLH (for C-terminal to LisH) domains, a Pro-rich region, and two domains containing multiple tandem WD repeat motifs (Figures 6C and 7A).
2750	16472779_MI:0018	Both full length and partial form (AtCRK3P1) of AtCRK3 could interact with AtGLN1;1 (full length) and AtGLNP2 (catalytic domain of AtGLN1;1) in yeast, but not with AtGLNP1 (the N-terminal beta-grasp domain of AtGLN1;1).
2751	16472779_MI:0018	suggesting AtCRKP1 could interact with almost full length AtGLN1;1 protein in yeast.
2752	16480949_MI:0018	AH109 cotransformed with pGBKT7-53/pGADT7-T was used as a positive control since p53 is known to interact with SV40 large T-antigen,
2753	16480949_MI:0018	Yeast two-hybrid analysis of the interaction of AICD with flotillin-1
2754	16489121_MI:0018	These data indicated that the Gln-rich domain of GRP23 is essential for the interaction with RNA polymerase II subunit III
2755	16489121_MI:0018	To further investigate the biochemical function of GRP23, a two-hybrid screen was performed using the full-length GRP23 coding sequence fused to the GAL4 DNA binding domain as bait (pBD-GRP23). Of 1.2 x 106 transformants screened, four clones were identified, all of which contained the same gene, encoding the 36-kD subunit III (RBP36B) of the DNA-directed RNA polymerase II
2756	16497658_MI:0018	A partial cDNA clone encoding the C-terminal half of the Arabidopsis AtCyp59 (Fig. 1A) was isolated in a two-hybrid screen with the SR protein SCL33/SR33 as the bait.
2757	16497658_MI:0018	AtCyp59 interacts with the RNA polymerase II CTD.
2758	16522632_MI:0018	An in vivo interaction between Fet5p and Fth1p in the yeast vacuolar membrane has been documented by co-immunoprecipitation assay (13). This pair of proteins was used as a positive control in a yeast two-hybrid analysis
2759	16522632_MI:0018	a specific interaction between Fet5p and Fth1p was localized also to the cytoplasmic, CT domains of these two proteins
2760	16522632_MI:0018	identification of Fet3p, Fetr1p interaction motifs.
2761	16522632_MI:0018	Yeast two-hybrid analysis of the carboxyl-terminal ferroxidase-permease interaction.
2762	16541025_MI:0018	Here we find a specific subtype of serine/threonine protein phosphatase 2A (PP2A) associating with human shugoshin.
2763	16555005_MI:0018	The Tre-GAP-binding proteins identified in this experiment are Myl2 (muscle library) and LOC91526 (placental library).
2764	16600381_MI:0018	In addition to the co-immunoprecipitation, we demonstrated CIITA-ZXDC association by mammalian two-hybrid.
2765	16600381_MI:0018	Thus, the region to which CIITA binds is the final 170 amino acids of ZXDC, from amino acid position 689 to 858, just C-terminal of the transcriptional activation domain of ZXDC.
2766	16600381_MI:0018	To better understand the function of CIITA, we performed yeast two-hybrid with the C-terminal 807 amino acids of CIITA, and cloned a novel human cDNA named zinc finger, X-linked, duplicated family member C (ZXDC).
2767	16603654_MI:0018	In addition, these three WRKY proteins interacted with each other: WRKY18 interacted with WRKY40 and WRKY60,
2768	16603654_MI:0018	Indeed, both WRKY40 and WRKY60 self-interacted based on yeast two-hybrid assays
2769	16603654_MI:0018	Since WRKY18 interacts with itself
2770	16603654_MI:0018	Since WRKY18 interacts with itself and with WRKY40,
2771	16603654_MI:0018	The yeast strain transformed with the bait construct failed to grow in the selective medium (data not shown), indicating that WRKY18 did not confer transcriptional activation activity to the fusion protein in yeast. We screened >2 x 107 independent transformants of a cDNA library generated from SA-treated Arabidopsis plants at a complexity of 2 x 106. The screens yielded two groups of cDNA fragments. The first group, which was isolated twice, encodes WRKY18, suggesting that this DNA binding protein can self-interact.
2772	16603654_MI:0018	The yeast strain transformed with the bait construct failed to grow in the selective medium (data not shown), indicating that WRKY18 did not confer transcriptional activation activity to the fusion protein in yeast. We screened >2 x 107 independent transformants of a cDNA library generated from SA-treated Arabidopsis plants at a complexity of 2 x 106. The screens yielded two groups of cDNA fragments. The first group, which was isolated twice, encodes WRKY18, suggesting that this DNA binding protein can self-interact. The second group, which was isolated six times, encodes WRKY40.
2773	16603654_MI:0018	WRKY40 interacted with both WRKY18
2774	16603654_MI:0018	WRKY40 interacted with both WRKY18 and WRKY60
2775	16619302_MI:0018	Transcriptional interaction between GR and MVP.
2776	16622416_MI:0018	Identification of APPL1 as an AdpioR1 interacting protein
2777	16622416_MI:0018	Sequence analysis revealed 7 of the 17 positive clones contained a cDNA encoding the C-terminus of an adapter protein previously named APPL or DIP13
2778	16672379_MI:0018	A Y2H screen was used to identify novel cytLEK1 binding partners and further characterize cytLEK1 function. The region chosen as bait to screen an embryonic whole mouse cDNA library consisted of the N-terminal most 689 aa of cytLEK1 beginning at the translation start site (base pairs 1-2067; termed 5' LCR for cytLEK Coil Region; Figure 1).
2779	16672379_MI:0018	Next, we analyzed the region within SNAP-25 that was responsible for cytLEK1 interaction. SNAP-25 deletion studies revealed that the N-terminal 75 aa of the protein, termed SNAP-25 Lek1 binding Domain (SNLD), were sufficient and required for the interaction of the 5'LSD domain of cytLEK1 (Figure 1, A and B).
2780	16675552_MI:0018	DdVASP interacts with dDia2 in a yeast two-hybrid assay through its FH2 domain.
2781	16678774_MI:0018	We also confirmed a known interaction between Inp2p and Pex19p
2782	16678774_MI:0018	We performed yeast two-hybrid analysis to test the ability of Inp2p to interact with the carboxy-terminal globular domain of Myo2p (amino acids 1113-1574).
2783	16760425_MI:0018	To understand how CP110 functions at the centrosome and to identify potential upstream and downstream regulators, we performed a stringent yeast two-hybrid screen using full-length CP110 as bait. From ~380,000 transformants, 98 positive clones were identified, and their inserts were sequenced. Remarkably, 82 clones carried cDNAs that encoded CaM (Figure 1A). Several other well- or partially characterized proteins were also identified, but each was isolated once or in some cases a few times (Figure 1A). We focused on CaM because this protein has been previously implicated in centrosome function.
2784	16762630_MI:0018	we performed a yeast 2-hybrid screen and identified the DP1 protein,6-8 encoded by the gene C5orf18 (GenBank accession number NM_005669), was interacted with HCCR-1.
2785	16763194_MI:0018	Whereas all plasmid combinations enabled yeast strain AH109 to grow on synthetic dropout (SD) medium selecting for the presence of the plasmids (SD -Leu/-Trp), only simultaneous transformation of plasmids encoding AtMND1 and AHP2 fusion proteins led to growth on selective plates (SD -Leu/-Trp/-His). We therefore conclude that AtMND1 interacts with AHP2.
2786	16766674_MI:0018	While the full-length protein did not interact, we could detect a weak but significant interaction for ICK1/KRP1109-191 with XPO1
2787	16766694_MI:0018	No online version of this paper was available; therefore source text annotations are not entered.
2788	16775625_MI:0018	In this study, we screened hPFTAIRE1 interacting proteins in two hybrid system and identified four 14-3-3 isoforms (beta, epsilon, eta, tau).
2789	16775625_MI:0018	The interactions between hPFTAIRE1 and the four 14-3-3 isoforms were verified by two hybrid analysis.
2790	16777849_MI:0018	To identify proteins that interact with Fyn in the brain, we carried out yeast two-hybrid screening with full-length Fyn as bait.
2791	16792691_MI:0018	By contrast, deletion of the first 304 amino acids of the cullin (CUL4304&#8722;793) completely abolished interaction with DDB1a. This loss of interaction was not based on protein misexpression since RBX1 was still able to assemble with the C-terminal of the partial CUL4 protein
2792	16792691_MI:0018	DDB1a protein fragment containing only amino acids 300-666 (DDB1a300&#8722;666) was sufficient for interaction with full-length CUL4
2793	16792691_MI:0018	Likewise, DDB2 interacts in Y2H assays with DDB1a.
2794	16792691_MI:0018	To map the domains required for CUL4-DDB1a interaction, different Y2H expression constructs for partial CUL4 and DDB1a proteins were generated (Figure 2a,b). As shown in Figure 2(a) the first 453 amino acids of CUL4 were sufficient to allow CUL4-DDB1a assembly. By contrast, deletion of the first 304 amino acids of the cullin (CUL4304-793) completely abolished interaction with DDB1a.
2795	16792691_MI:0018	Yeast two-hybrid analysis shows assembly of Arabidopsis DET1 with full-length DDB1a
2796	16792696_MI:0018	Interactions of XERICO with AtUBC8 and AtTLP9 were confirmed by His and Ade auxotrophic growth of yeast.
2797	16810321_MI:0018	Combinatorial control of Arabidopsis proline dehydrogenase transcription by specific heterodimerisation of bZIP transcription factors
2798	16814720_MI:0018	CIPK23 interacted with six members of the CBL family, including CBL1, CBL2, CBL3, CBL5, CBL8, and CBL9
2799	16814720_MI:0018	CIPK23 Interacts with AKT1
2800	16828757_MI:0018	A homology search in GenBank using the BLAST program revealed that all six plasmids encoded CCS-3 (GenBank Accession No. AF322220).
2801	16828757_MI:0018	Cells containing only full-length PLZF cDNA construct and BTB-PLZF grew on the Ura, His, Trp and Leu deficient plates, whereas yeast cells transformed with both deletion mutant colonies (RD2, and ZF) failed to grow
2802	16844784_MI:0018	we used the Y2H system and in vivo pull-down assays to: (i) independently verify the Cfp-10/ClpC1, Cfp-10/Pks13, Cfp-10/FtsQ Cfp-10/Rv2240c, and Cfp-10/Rv0686 interactions
2803	16849595_MI:0018	The Nkd proteins lacking Dsh-binding regions had reduced associations with Dsh or DshbPDZ by quantitative Y2H
2804	16854969_MI:0018	Interactions between SEU and AP1/SEP3 in yeast and in vitro.
2805	16854969_MI:0018	SEU interacted strongly with AP1
2806	16857903_MI:0018	The carboxyl domain of BKI1 is necessary and sufficient to interact with BRI1-s kinase domain in yeast.
2807	16861711_MI:0018	Light dependent interaction of FHL and phyA in yeast cells.
2808	16861711_MI:0018	The C-terminus of FHY1 and FHL contains a phyA binding site.
2809	16862148_MI:0018	We isolated the full-length cDNA of a protein that was identified seven times as an interactor of the carboxyl terminus (repeats 21-24) of FLNa in a yeast two-hybrid screen of a human spleen cDNA library.
2810	16868027_MI:0018	All but one of these belonged to the 14-3-3 protein family, including isoforms beta (), zeta () and tau (). The remaining clone consisted of unidentifiable genomic sequence. Recovered 14-3-3 plasmid DNA or empty library vector pPC86 were re-introduced into yeast with either pDBLeu, pDBLeu-ADAM22v1 cytoplasmic domain or pDBLeu- ADAM22v4 cytoplasmic domain bait constructs. These yeast transformants were then assayed against the three reporter genes His3, lacZ and URA3 to confirm interactions in the yeast two-hybrid system
2811	16868027_MI:0018	Sequential transformations of pDBLeu-ADAM22v1 cytoplasmic domain and a human brain cDNA library into yeast cells resulted in an estimated 6.2 106 transformants, which were subsequently screened for His3 reporter gene activation. The 23 clones deemed positive for His3 selection were then subjected to second round screening for lacZ reporter activation by X-gal assay, resulting in 13 positive clones. Sequencing of yeast plasmid DNA recovered in E. coli revealed the identity of 10 clones. All but one of these belonged to the 14-3-3 protein family, including isoforms beta(), zeta ()and tau ()
2812	16888242_MI:0018	a yeast 2-hybrid screening was performed with human SK1 as bait in conjunction with a human heart cDNA library. After screening 2.4 106 clones, a total of 15 positive clones were identified, 3 of which encoded a full-length cDNA of the cardiacrestricted LIM-only factor, FHL2.
2813	16888242_MI:0018	Coexpression of pGAD-FHL2 and pGBD-SK1 resulted in a 5.1-fold increase in -galactosidase activity compared with coexpression of pGBD and pGAD-FHL2
2814	16888242_MI:0018	cotransfection of the vectors encoding Gal4 DBD-SK1 with FHL2-VP16 resulted in a substantial increase in Gal4-dependent transcriptional activity, indicating interaction of SK1 and FHL2 in mammalian cells.
2815	16892067_MI:0018	Using an activated RAPL mutant as the bait, we isolated cDNA encoding human MST1 or MST2 by yeast two-hybrid screening
2816	16897494_MI:0018	At-CPSF100 appears to interact with all of the proteins tested.
2817	16899217_MI:0018	Identification of Fyn as a magicin-specific binding protein in the yeast two-hybrid assay
2818	16919237_MI:0018	Full-length BRMS1 was used as bait and human mammary gland (or prostate or placenta) cDNA library as prey. Six genetic interactors of BRMS1 were identified in addition to the previously reported mSDS3 (SAP45, suppressor of defective silencing, Sin3 associated protein) and RBBP1 (Rbbinding protein)
2819	16919237_MI:0018	The six novel interactors are not part of the mSin3 core complex and include NMI (N-myc interactor), MRJ (Hsp40-related chaperone) [27], CCG1 (TAFII250, a protein essential for progression of G phase), SMTN (Smoothelin, a cytoskeletal protein specific to smooth muscles) [28], KPNA5 (karyopherin a 5) [29], and BAF 57 (BRG1 associated factor)
2820	16923016_MI:0018	Interaction of Arabidopsis ETFa and ETFb in a yeast two-hybrid experiment.
2821	16925602_MI:0018	A petunia ovary specific cDNA expression library was screened by the yeast two hybrid GAL4 system with FBP11 (Angenent et al 1995; Colombo et al 1995) as  bait to identify interacting partners for this ovule specific MADS-domain protein (Immink et al 2002).One of the interacting partners identified was a truncated MADS-domian protein, designated FLORAL BINDING PROTEIN 24 (FBP24).
2822	16949368_MI:0018	Specific interaction between the zinc finger domain of CTCF and the carboxyl-terminal region of CHD8 in yeast two-hybrid assay.
2823	16949368_MI:0018	To identify proteins that interact with CTCF, we performed a yeast two-hybrid screen using the zinc finger domain (CZ) (amino acids 268-577) as bait (Figure 1A). From a screening of not, vert, similar1.5 × 106 independent transformants of a mouse E11.5 whole embryo cDNA library, we isolated six positive clones that include the clone encoding the carboxyl-terminal region of CHD8 (amino acids 2240-2582).
2824	16957774_MI:0018	Characterisation of the AtBARD1 and AtBRCA1 interaction by yeast two-hybrid assay
2825	16962094_MI:0018	ank1.9 isoform binds the C-terminal region of obscurin in two-hybrid assays, similarly to ank1.5.
2826	16963744_MI:0018	Several clones were identified to interact with BHRF1 specifically and reproducibly. One of them contains cDNA sequence corresponding to the coding sequence of the VRK2 protein
2827	16963744_MI:0018	The two hybrid interaction assays showed that co-transformation of cells with BHRF1 and VRK2 resulted in activation of the HIS3 and lacZ reporter genes, as indicated by growth of the transformants on an SC-Trp, Ura, Leu, Lys, His plate (a His2 plate) and the formation of blue colonies on the colony-lift filter with a b-galactosidase assay.
2828	16963744_MI:0018	whereas formation of faint blue colonies was not observed within the first 8 h when BHRF1 was replaced by Bcl-2.
2829	16966434_MI:0018	In addition to atrophin-1, a cDNA encoding the 61COOH-terminal amino acids of a previously uncharacterized protein ZNF652 was identified.
2830	16982639_MI:0018	Interaction of XE7 with ZNF265
2831	16990133_MI:0018	Every transformant expressing Sst2-N-UbG and Ste2-C-Ub-LV showed robust reporter-gene expression at a level equivalent to that of the positive control (Figure 4D). For this control, cells were cotransformed with an Ste2-N-UbI chimera that binds Ste2-C-Ub-LV for two reasons: N-UbI interacts constitutively with C-Ub, and Ste2 self-associates to form dimers (Overton et al., 2003). Most importantly, like the negative control expressing N-UbG alone, no reporter expression was seen when Sst2-N-UbG carried any Q304 mutation
2832	16997270_MI:0018	To gain further insight into the function of Pof3, we performed a yeast two-hybrid screen to identify Pof3-interacting proteins. Using the full-length Pof3 as bait, we screened 2.7x10.6 colonies and isolated 16 candidate plasmids, which were able to confer growth on plates lacking histidine specifically in the presence of Pof3. Sequencing revealed that 12 of these plasmids contained the known Pof3-binding partner Skp1 and therefore served as positive controls for the screening conditions. Two of the plasmids encoded a previously not described open reading frame and two corresponded to an N-terminal truncated version of Mcl1. Cloning full-length Mcl1 into the pGAN6 vector confirmed that Pof3 and Mcl1 interact, as cells could only grow in the absence of histidine when both plasmids were present (Fig. 1A).
2833	17007873_MI:0018	In contrast, MYPT-75D failed to bind PP1&#946;9CY304X suggesting that residues 304-330 of PP1c are critical for binding.
2834	17007873_MI:0018	Interaction between two-hybrid positives and different isoforms and variants of PP1c
2835	17016471_MI:0018	However, dissection of the protein sequence with the help of the Blocks software (Henikoff et al, 2000) revealed the presence of a putative F-box between residues 172 and 214. To test this possibility, a Gal4-AD (Gal4 activation domain) fusion protein bearing deletion of the first 14 residues (172-186) of the predicted F-box was constructed and tested against Skp1 in the two-hybrid system. Figure 1A- C shows that in spite of similar expression levels, only the full-length protein retained ability to interact with Skp1.
2836	17016471_MI:0018	To gain insight into the function of Pof14, a second twohybrid screen with Pof14 as bait was performed and 61 candidates representing five proteins were isolated (Supplementary Table II).
2837	17016471_MI:0018	To gain insight into the function of Pof14, a second twohybrid screen with Pof14 as bait was performed and 61 candidates representing five proteins were isolated (Supplementary Table II). Two clones were recovered at similar high frequency: Skp1, as expected, and Erg9 (Figure 2A and B). Erg9 is the squalene synthase, a membrane-bound enzyme that plays a pivotal role in sterol metabolism. Analysis of overlapping interacting clones revealed that the C-terminal part of Erg9 was sufficient for interaction with Pof14 (Figure 2B).
2838	17016471_MI:0018	We screened 107 clones from a fission yeast two-hybrid cDNA library using Skp1 as bait. Ninety-four positive candidates representing 19 proteins (Supplementary Table I) were isolated.
2839	17055998_MI:0018	One clone contained a fragment of cDNA for nebulin, a muscle structural protein
2840	17055998_MI:0018	Ten other clones contained fragments of cDNA for glycogenin-1 encoding carboxy-terminal parts of the protein corresponding to residues 301-333, 297-333 and 263-333.
2841	17055998_MI:0018	Two-hybrid analysis of glycogenin-interacting regions in glycogen synthase
2842	17088979_MI:0018	The results of this study indicated that only RNF2 cDNA is a true positive interactor with the linker region.
2843	17092312_MI:0018	Series of truncations of each protein were performed to define the interacting domains of AKRP and EMB506. The results presented in Figure 1 demonstrate that the two proteins bind through their ANK domains, and that binding is independent of the type of Gal4 domains used for the fusion.
2844	17092312_MI:0018	we used the yeast two-hybrid screen to search for proteins interacting with EMB506. The EMB506 protein lacking the chloroplast targeting signal peptide was fused to the Gal4 activation domain to serve as bait. Nineteen cDNA clones were identified among a cDNA library constructed with RNA from immature siliques (Kroj et al., 2003). These positive clones corresponded to transcription products of the same gene. blast searches in databases identified the gene as At5g66055, which codes for AKRP (ankyrin repeat protein)
2845	17095503_MI:0018	To identify additional POSH-binding partners, we performed a yeast twohybrid analysis using POSH cloned into a bait vector as previously described (18). One clone corresponded to Nix, a proapoptotic BH3-only protein
2846	17112379_MI:0018	As expected, the positive control, Snf1/Snf4 was also able to confer HIS prototrophy
2847	17112379_MI:0018	A two-hybrid screen identifies Abp1 as a protein interacting with Cdc23
2848	17113272_MI:0018	By changing Y142 to phenylalanine (Y142F) the necessity of the free hydroxyl group of Y142 was determined. Y142F had no significant effect on the binding of bcatenin to either BCL9, BCL9-2 or a-catenin
2849	17137291_MI:0018	Eighteen clones selected from a pool of positive candidates interacted specifically with the MHD upon reconstitution analysis.
2850	17137291_MI:0018	The MHD of MAGE-C1 (CT7) was used as bait to screen a human testis cDNA library. This study identified NY-ESO-1 (CT6) as a MAGE-C1 binding partner.
2851	17138694_MI:0018	However, the interaction analysis showed that SUF4 binds to both FRI and FRL1
2852	17138694_MI:0018	In addition, SUF4 and FRI showed homodimerization activity
2853	17138694_MI:0018	LD protein bound to SUF4 but not to FRI or FRL1 in yeast two-hybrid analysis
2854	17138694_MI:0018	SUF4 and FRI showed homodimerization activity
2855	17138694_MI:0018	When the bait and prey were changed, the yeast cells grew slowly but confirmed the interaction of LD and SUF4
2856	17142478_MI:0018	SEF interacts with ARP6
2857	17157259_MI:0018	We performed a yeast two-hybrid screen with full-length SNIP1 and a HeLa cDNA library to identify SNIP1 partners. Nine of 21 strong positive clones encoded c-Myc, which did not interact with the N terminus of SNIP1 also used as bait.
2858	17183697_MI:0018	The Cno-Dsh interaction, however, mapped to two different domains of Cno: the PDZ domain and the Ras-binding domain (Fig. 5C and 5D). To distinguish which domains in Dsh bound the Ras-associating and PDZ motifs of Cno, different Dsh constructs were tested. A Dsh fragment containing the DIX (DIshevelled, aXin) and PDZ domains (DSH-DIZ) only bound Cno constructs containing the Ras-binding domain, as did the Ras positive control (Fig. 5C and 5D). In contrast, the Dsh fragment containing the DEP (Dsh, egl-10, pleckstrin) domain (DSH-DEP) only bound Cno constructs containing the PDZ domain plus some of the adjacent Myosin-V (Myo)-like domain
2859	17183697_MI:0018	To characterize the domains implicated in the binding, diverse deletion constructs of Cno, N and Dsh were tested in yeast two-hybrid assays (Fig. 5C and 5D). Only Cno constructs comprising the PDZ domain strongly interacted with both proximal (Notch-ICN1) and distal (Notch-ICN2) regions of the N intracellular domain
2860	17189269_MI:0018	After screening human brain cDNA library, we identified that Fyn tyrosine kinase interacted with the CT of 5- HT6R.
2861	17189269_MI:0018	To confirm this specific interaction, we carried out a yeast two-hybrid assay using CT cDNA (bait) transformed in the AH109 yeast strain and full-length Fyn cDNA (prey) transformed into the Y187 yeast strain as shown Fig. 1A.
2862	17189287_MI:0018	FWA interacted with FWA itself (Fig. 6A), suggesting homodimer formation.
2863	17189287_MI:0018	FWA protein can interact with FT protein
2864	17196367_MI:0018	VAMP2, the vesicle-localized v-SNARE, was later identified as a novel binding partner of PKD3 through yeast two-hybrid screening.
2865	17202144_MI:0018	These data indicate that the AR C terminus interacts with Foxo1 in a hormone-dependent manner.
2866	17209125_MI:0018	To analyze whether the Arabidopsis WEE1 kinase might be responsible for the observed Tyr phosphorylation of CDKA;1, both proteins were tested for their interaction using the yeast two-hybrid system. CDKA;1 and CDKB1;1 in fusion with the GAL4 DNA binding domain were cotransformed in an appropriate yeast reporter strain with an empty control vector or a vector encoding a fusion protein between the GAL4 transactivation domain and WEE1. Transformants were streaked on medium with or without His. Cells expressing CDKA;1 and WEE1 grew in the absence of His, indicating that both gene products interacted. No association was observed between CDKB1;1 and WEE1
2867	17210579_MI:0018	The interaction of ASK1 with the cloned full-length version of mouse ASK2 was confirmed by the yeast two-hybrid assay (Fig. 1C).
2868	17210579_MI:0018	To identify molecules that interact with ASK1, we employed the yeast two-hybrid system using a deletion mutant of ASK1
2869	17210637_MI:0018	A human brain cDNA library was used in this screen because merlin is highly expressed in the brain (44, 58). An N-terminal portion (amino acids 1 to 374) of merlin was cloned into the EcoRI and BamHI sites of pJK202 to create the bait pNLexA-NF2N. Three clones that specifically interacted with the bait were identified. Sequence analysis revealed that two of the clones contained overlapping sequences of a cDNA (26). The largest clone contained a 243-amino-acid open reading frame with a conserved GTP-binding domain named NGB (NF2-associated GTP binding protein)
2870	17210637_MI:0018	The binding region of NGB was mapped to the G-protein homology domain
2871	17210637_MI:0018	Yeast two-hybrid tests of interaction revealed that the amino (aa 1 to 52) and carboxyl (aa 288 to 344) termini of merlin are required for binding to NGB (Fig. 2I).
2872	17213653_MI:0018	By both co-immunoprecipitation and yeast two-hybrid experiments, specific interaction between Rcr1 and the ubiquitin ligase Rsp5 was found.
2873	17216128_MI:0018	We applied yeast two-hybrid screening and identified that a novel WD-repeat protein WDR6 was able to interact with LKB1.
2874	17220200_MI:0018	Truncated derivatives of PIP5K9 consisting of the MORN motif and the dimerization domain, or the dimerization and catalytic domains, were used as baits to screen an Arabidopsis cDNA library. We did not obtain any positive clone after screening of >4.5 x 106 transformants with a bait containing the MORN motif and the dimerization domain. On the other hand, we obtained several positive clones using the PIP5K9 dimerization and catalytic domains after screening of >3 x 106 transformants. Sequence analysis of the confirmed clones revealed one gene encoding a putative cytosolic invertase, which was assigned as CINV1.
2875	17220200_MI:0018	Two-hybrid analysis showed that the interaction with CINV1 activated the reporter HIS3 gene (even in the presence of 12 mM 3-amino-1,2,4-triazole, a competitive inhibitor of the HIS3 protein) and &#945;-galactosidase (with whole CINV1 protein) (Figure 4A), indicating a strong interaction between PIP5K9 and CINV1.
2876	17223078_MI:0018	Interestingly, cells co-expressing RAN1-MBDs with CCHD or ATX1 grow in the absence of histidine or adenine indicating a RAN1-chaperone interaction.
2877	17223078_MI:0018	These results demonstrate that RAN1 is able to interact with ATX1-like Cu chaperones in vivo
2878	17227544_MI:0018	A protein-protein interaction between AtRad54 and AtRad51 was revealed using the yeast two-hybrid system
2879	17229891_MI:0018	An initial yeast two-hybrid analysis of the 14-3-3B interaction with a panel of DYRK1A deletion mutants pointed to the involvement of the DYRK1A C-terminal region (Supp. Figure S1).
2880	17229891_MI:0018	To identify DYRK1A interacting proteins, we performed a yeast two-hybrid screen of a human fetal brain cDNA library, using the human DYRK1A full-length open reading frame (754 amino-acid isoform) as the bait. One of the positive clones encoded the protein 14-3-3&#946;,
2881	17237231_MI:0018	Rat HK3 Isoform Is a Ligand of hSR-A
2882	17237354_MI:0018	These results support the notion that PGP19 and PIN1 can interact and that PGP19-PIN interactions may be more specific than PGP1-PIN1 interactions
2883	17237354_MI:0018	When PIN1 and PIN2 were used as bait, an interaction with PGP19 was observed in both growth and a-galactosidase activity assays
2884	17255092_MI:0018	SRG3 interacted directly with SNF5, BRG1, and BAF60a.
2885	17259181_MI:0018	In contrast to the interaction of Zat7 with WRKY70 and HASTY (Table 1, Fig. 5A), Zat7delta or Zat7m did not interact with WRKY70 or HASTY in a directed yeast two-hybrid interaction assay
2886	17259181_MI:0018	In contrast to the interaction of Zat7 with WRKY70 and HASTY (Table 1, Fig. 5A), Zat7 or Zat7m did not interact with WRKY70 or HASTY in a directed yeast two-hybrid interaction assay
2887	17259181_MI:0018	Proteins that interact with Zat7 and/or the last 25 aa of Zat7 in a yeast two-hybrid screen
2888	17267444_MI:0018	ABI4 interacted only with ARP3.
2889	17267444_MI:0018	constitutively active ROP11 interacted with AtSCAR1, AtSCAR2 and AtSCAR4
2890	17267444_MI:0018	Furthermore, AtSCAR1 and AtSCAR2 have been found to interact with ARPC3. AtSCAR4, AtSCAR-LIKE
2891	17267444_MI:0018	Interaction could be detected between HSPC300/BRICK1 and AtSCAR1, 2 and 3,
2892	17267444_MI:0018	Interaction with all four ABI proteins was found in the case of AtSCAR3 only.
2893	17267444_MI:0018	Our data indicate additionally direct contact between ARP2 and ARP3.
2894	17267444_MI:0018	ROP8 interacted in both forms with AtSCAR2 and AtSCAR3, whereas only the unmodified form interacted with AtSCAR1,
2895	17267444_MI:0018	The unmodified ROP5 interacted with AtSCAR1, AtSCAR2 and AtSCAR4;
2896	17267444_MI:0018	We found that BRICK1 homodimerises, and physically interacts with all four ABI proteins.
2897	17267444_MI:0018	We further found that NAP1 also homodimerises and interacts with two ABI proteins (ABI 1 and 2) and with SRA1
2898	17267444_MI:0018	We identified interactions between both ARP3 and ARPC3 and AtSCAR3, HSPC300/BRICK1 and ABI1 and 2.
2899	17287892_MI:0018	Two positive clones were identified, and one of them encodes for a cinnamyl alcohol dehydrogenase that was designated as AtCAD5
2900	17289665_MI:0018	Cytoplasmic Dynein Light Chain, DYNLT3, Interacts with the Spindle Checkpoint Protein, Bub3
2901	17292860_MI:0018	We performed a genetic screen in yeast to identify proteins that interact with Notch3 in the cytoplasm, using the yeast SOS-rescue screen [11]. The most frequently identified gene encoded PSMA1, a subunit of the 20S proteasome complex.
2902	17310983_MI:0018	full-length cDNAs of MDM2 and S7 were cloned into pGBKT7 and pGADT7 vectors, respectively, and co-transformed into the yeast host strain AH109. As expected, transformants had the capacity to grow on the yeast Minimal Synthetic Dropout (SD) plate, which lacked adenine (Ade), histidine (His), leucine (Leu) and tryptophan (Trp) (SD/-Ade/-His/-Leu/-Trp)
2903	17310983_MI:0018	we conducted a yeast two-hybrid assay using full-length MDM2 to screen a human prostate MATCHMAKER cDNA library (BD Biosciences, Clontech, Mountain View, CA, USA). Sequence analysis of the candidate MDM2 interacting proteins identified RPL11 (Dai et al., 2006) and RPL23 (Dai et al., 2004), which have previously been shown to bind to MDM2. In addition, we identified 11 clones that encode a protein corresponding to full-length human S7.
2904	17310990_MI:0018	A library of cDNAs prepared from human lymphocytes immortalized with EBV (Durfee et al., 1993) was screened by the two-hybrid method using INT6 fused to the GAL4DNA-bi nding domain as bait. This led to isolation of partial cDNAs encoding the p110 subunit of eIF3 and Rfp, as reported previously (Morris-Desbois et al., 1999), but also to clones corresponding to the C-terminal part of MCM7, the shortest one encoding the C-terminal 205 amino acids of the protein
2905	17310990_MI:0018	Similarly, various pieces of the C-terminal domain of MCM7 were associated with the GAL4-activation domain and tested by the twohybrid assay with INT6 as bait. On the N-terminal side, deletion from amino acid 579-610 led to loss of the interaction (Figure 1f), whereas at the C-terminal end removal of amino acid 595-575 impaired the interaction (Figure 1f). These results show that the part of MCM7 mediating the interaction with INT6 is located between amino acids 579 and 595, outside the MCM box.
2906	17310990_MI:0018	the two-hybrid assay was used with MCM7 fused to the GAL4DNA binding domain as bait and INT6 deleted either on the N-terminal or C-terminal side fused to the GAL4-activation domain. At the C-terminus, removal of amino acids 395-331 led to loss of the binding of INT6 to MCM7 (Figure 1e). On the other hand, each construct deleted at the N-terminal end, up to amino acid 350, led to a positive result (Figure 1e). These data indicate that the MCM7-binding domain of INT6 is located between amino acids 351 and 395.
2907	17314099_MI:0018	Previously, a screen for NM23-H1-interacting proteins that could potentially modulate its activity identified serine-threonine kinase receptor-associated protein (STRAP), a transforming growth factor (TGF)-beta receptor-interacting protein.
2908	17314511_MI:0018	we analyzed selected interactions using a yeast two&#8209;hybrid assay. Thereby, the interactions of c&#8209;MYC with DBC&#8209;1, MCM7, ZNF281, and FBX29 were confirmed
2909	17322342_MI:0018	The data shown in Figures 1 to 4 establish roles for GCR1, GPA1, PRN1, NF-Y-A5, NF-Y-B9, and potentiallyexperiments (Fig. 6) indicate that PRN1 has the potential for a specific interaction with both NF-Y-B9 and NF-Y-B6.
2910	17324924_MI:0018	in order to determine the region within Int6 that is essential for HIF-2; binding, we constructed a vector containing the activated domain (AD) fused to HIF-2; fragment (amino acids 571-828). (indicated in Fig. 1D) and introduced this into yeast along with a vector expressing the DBD fused to an Int6 mutant fragments. The C-terminal HIF-2; fragment also binds the N-terminal region (amino acids 4-128) of Int6
2911	17324924_MI:0018	interactions between the N-terminal of Int6 and truncated HIF-2 in yeast that were analyzed by a quantitative -galactosidase assay. The N-terminal of Int6 (Int6-N; amino acids 4-150) retained its  -galactosidase activity in HIF-2 constructs that contained amino acids 571-828, 641-828, and 571-700. Constructs with amino acids 701-828 exhibited no activity.
2912	17324924_MI:0018	The Int6 fragment bound to HIF-2, but neither to HIF-1 nor HIF-3; this indicated subtype specificity (Fig. 1B)
2913	17324924_MI:0018	The Int6 fragment bound to HIF-2, but neither to HIF-1 nor HIF-3; this indicated subtype specificity (Fig. 1B).
2914	17324924_MI:0018	yeast two-hybrid analysis was performed using the C-terminal region of HIF-2 (amino acids 571-828) as bait; this region represents the region of greatest sequence divergence between the HIF- proteins and is devoid of autoactivity (55). From a total of 1.2  106 cDNA clones in the initial screen of the human heart cDNA library, 326 were positive clones when assayed for -galactosidase expression for the first screen. An N-terminal Int6 fragment (amino acids 4 128, accession number U94175) was identified in 3 of the 28 clones in a high-stringency screening.
2915	17329248_MI:0018	Yeast Two-hybrid Screening for PDE2A Interaction Partners and Identification of XAP2
2916	17347654_MI:0018	This interaction was confirmed by inverse transformation of yeast cells with GAL4AD-PRB and GAL4DBD-CUEDC2
2917	17347654_MI:0018	we performed a yeast two-hybrid screen using the IF domain of PR as bait to screen a human mammary cDNA library. We identified two interacting clones containing a complete open reading frame (681 bp) for a 26 000 Da molecular weight gene product that has 100% amino acid identity to human CUEDC2.
2918	17350572_MI:0018	Yeast two hybrid assay showing that human ALIX binds endophilins-1 and -2, and that the interactions are inhibited by the ALIX RP757,758AA mutation.
2919	17353003_MI:0018	Besides identiWcation of known AR-interacting proteins, like beta-actin [17], HSP90 [18], and SRC1a [19], additional AR-associated proteins (ARAPs) were found
2920	17353003_MI:0018	By using a fragment of the human AR (aa 325-919) as bait in a yeast two-hybrid screen, a region of the human JMJD1C gene was identiWed as interacting with AR.
2921	17353262_MI:0018	APLF interacts with the DNA strand break repair proteins XRCC1 and XRCC4. Indeed, APLF interacted with both of these proteins in yeast two-hybrid analyses
2922	17355907_MI:0018	The interaction between NADE and TSC1-CCD was confirmed by -gal assay and a selection assay on auxotrophy for adenine and histidine
2923	17355907_MI:0018	To identify an interactor for hamartin, the entire span of CCD (amino acid residues 674-1084) was used as a pray (Fig. 1A) and human fetal brain and placenta cDNA libraries were screened as baits by yeast two-hybrid method. Thirteen positive clones from human fetal brain cDNA and 147 positive clones from human placenta cDNA were obtained. Baits sequences from these clones were analyzed with BLAST to seek for homology with known genes. Sequences identical to those encoding for NADE were found to yield positive results and NADE was therefore considered a candidate protein
2924	17369373_MI:0018	After mating, colonies were selected and sequenced. The full-length cDNAs of selected candidate proteins were isolated, and the interaction with WRKY53 was tested in the yeast two-hybrid system. For 10 proteins, the interaction with WRKY53 could be confirmed for the full-length c-DNA clones also including putative transcription factors. One of the proteins (At1g54040) was an epithiospecifying protein (ESP)
2925	17369373_MI:0018	Interaction of WRKY53 and ESR in Vivo
2926	17374643_MI:0018	we performed a yeast two-hybrid screen and identified the alpha-isoform of the regulatory subunit A of protein phosphatase 2A (PR65alpha) as a new interaction partner of HRSL3.
2927	17376809_MI:0018	Of note was PHV (AtHB9; At1g30490), which was independently isolated eight times, based on cDNA termini sequences. All isolated PHV clones encoded C-terminal parts of the protein, extending maximally from amino acid 754 to the last amino acid, 841.
2928	17395368_MI:0018	the full-length U19/EAF2 is not suitable to be used as the bait in the screening. Previously we determined that the exon III (from AA68 to AA114) region of U19/EAF2 is essential for the apoptotic activity of U19/EAF2 [2,19]. As a result, this region was chosen as the bait in a yeast-two-hybrid system. One of the clones isolated was FB1, which is a E2A fusion partner in childhood leukemia
2929	17395368_MI:0018	To verify the interaction of FB1 with U19/EAF2 and to exclude the possibility that FB1 might activate reporters by itself, pAD-FB1 with pLexA-U19/EAF2(III), pLexA-U19/EAF2, and/or pLexA vectors were retransformed into yeast. These assays confirmed the specificity of the interaction of FB1 with U19/EAF2(III) and U19/EAF2 in the yeast-two-hybrid system.
2930	17397508_MI:0018	Histidine prototrophy was restored only in the presence of NtTGA2.2 (data not shown), indicating that the gene product of At1g28480 is recruited to the as-1 element only in the presence of NtTGA2.2.
2931	17397508_MI:0018	In planta two hybrid system documenting the interaction between NtTGA2.2 and GRX480.
2932	17397508_MI:0018	Therefore, a yeast 'bridge assay' was carried out with BD-GRX480 and AD-NPR1 fusion proteins expressed together with NtTGA2.2. Growth under selective conditions occurred only when NtTGA2.2 was provided as a bridging component
2933	17403664_MI:0018	Both Def-6 and Swap-70 Bind Specifically to the Cytoplasmic Part of the Integrin 7A Subunit
2934	17418788_MI:0018	Nup57 GLFG domain (BD-Nup57) interacted with itself and with the GLFG domains of Nup100 and Nup116
2935	17418788_MI:0018	the Nup116 GLFG domain (BD-Nup116) interacted with itself and with the GLFG domains of Nup100 and Nup57
2936	17419841_MI:0018	QQT1 interacts with QQT2 in a yeast two-hybrid assay
2937	17446396_MI:0018	In yeast cells, SHR and SCR interact directly
2938	17446396_MI:0018	SHR and SCR interact via the central domain (CD).
2939	17446396_MI:0018	Yeast two-hybrid assay examining the interaction between OsSHR1 or OsSHR2 with OsSCR1, as well as their interaction with SHR and SCR
2940	17446396_MI:0018	Yeast two-hybrid assay showing direct interaction between SHR and SCR.
2941	17468262_MI:0018	These isolated prey plasmids were retransformed into the alpha mating type of PJ694 and validated in a mating and selection assay with the Arabidopsis SKD1 bait, the empty bait vector, and unrelated baits. Out of seven confirmed positive clones, three were found to encode a predicted protein of 421 amino acids (At4g26750).
2942	17470967_MI:0018	and PIE1-N interacted with the three H2AZs (HTA8, HTA9, HTA11) but not with the other proteins tested
2943	17470967_MI:0018	AtSWC2 also interacted with all three H2AZs
2944	17470967_MI:0018	PIE1-C interacted with both SUF3 and AtSWC6
2945	17470967_MI:0018	The results showed that AtSWC6 interacts with SUF3 and AtSWC2, and revealed homodimerization of AtSWC6
2946	17482142_MI:0018	the alpha-galactosidase reporter gene was turned on producing blue colored colonies on plates containing chromogenic substrate X-alpha-gal (Fig. 3D). Thus, PBK and p53 interactions were tested positive with a different genetic approach in agreement with the biochemical experiment.
2947	17510388_MI:0018	Full-length DJ-1 cDNA was used to screen the library and identified a region of AR (Fig. 1B). The AR fragment contained a region of the NH2-terminal activation domain, the entire DNA binding domain, and a portion of the ligand binding domain
2948	17510388_MI:0018	high-stringency selection showed that neither the bait (DJ-1) nor prey (AR) plasmid was capable of activating reporter genes individually,but the combination produced an interaction and activation of the reporters.
2949	17511879_MI:0018	We performed a yeast two-hybrid study to identify proteins that interact with exon11 of BRCA1 and identified Protein Phosphatase (PP1), an isoform of the serine threonine phosphatase, PP1.
2950	17513499_MI:0018	NUA self interacts and interacts with ESD4 in yeast two-hybrid assays
2951	17513499_MI:0018	NUA self interacts and interacts with ESD4 in yeast two-hybrid assays.
2952	17513757_MI:0018	Using yeast two-hybrid screening of a human thymus cDNA library, PRP4, a serine/threonine protein kinase, was identified as a KLF13-binding protein.
2953	17517622_MI:0018	Interactions between full-length proteins were confirmed by direct two-hybrid analysis (Fig. 1).
2954	17517622_MI:0018	Interactions between full-length proteins were confirmed by direct yeast two-hybrid analysis (Fig. 1).
2955	17517622_MI:0018	Yeast two-hybrid screening of PFTK1 protein
2956	17535810_MI:0018	To address this possibility, we subjected atTic110 and atTic40 to yeast two-hybrid interaction analysis. As shown in Fig. 6 (A and B), the results provided clear evidence of a significant, if rather weak, interaction between the proteins.
2957	17535810_MI:0018	Vigorous growth of  cells carrying the pGBD-p53 plus pGAD-SV40T control plasmids indicated a  very strong interaction between murine p53 and SV40 large T-antigen, as  expected.
2958	17535814_MI:0018	HsNUF2 Is a Novel CENP-E-binding Partner
2959	17535814_MI:0018	To verify the specificity of interaction between HsNUF2 and CENP-E and to define further the domain(s) that mediates the interaction between them, we took advantage of yeast genetics and sought to perform additional yeast two-hybrid screens to map the binding interface(s).
2960	17543119_MI:0018	in a two-hybrid system, the FRB domain of AtTOR can bind to ScFKBP12.
2961	17550895_MI:0018	Growth was observed for AtCCMA-B1, -B3, -B5, and -B7 combinations but not the others
2962	17551920_MI:0018	Applying Sperm protein 17 (Sp17) as the bait in a yeast 2-hybrid system of a testicular cDNA library, 17 interacting clones were isolated and all encoded Ropporin, a spermatogenic cell-specific protein that serves as an anchoring protein for the A-kinase anchoring protein, AKAP110.
2963	17553790_MI:0018	Yeast two-hybrid screening identified integrin-linked kinase (ILK), a serine/threonine kinase, and an actin-binding protein as an interacting partner with the N-terminal domain of kAE1.
2964	17565979_MI:0018	this interaction was specific as indicated by the growth, in restrictive media lacking adenine, histidine, leucine, and tryptophan, of yeast transformed just with the combination of P-Rex DEP-DEP and mTOR prey
2965	17565979_MI:0018	We found that in yeast P-Rex1 DEP-DEP interacted with the carboxyl-terminal region, including the kinase domain, of mTOR
2966	17575050_MI:0018	MOS4 interacts in yeast with AtCDC5, an atypical R2R3 Myb transcription factor homologous to human CDC5L
2967	17575050_MI:0018	Using a yeast two-hybrid assay, we showed that AtCDC5 interacted directly with PRL1
2968	17577629_MI:0018	Full-length human Akt1 was used as bait for screening in a HeLa cDNA library. In this library, cDNAs are fused to the GAL4 activation domain in pGADT7. Of 106 transformants, 30 conferred to pGBKT7- Akt1-baits cells the ability to grow on His-plates and to produce b-galactosidase. Of these, 20 were true positives that could not induce His- or b-galactosidase production when transformed into Y190/pGBKT7 cells. One clone encoding the N-terminal amino acids (aa) 221-546 of human SETDB1 was isolated
2969	17577629_MI:0018	yeast cells expressing Akt1 together with SETDB1 could grow on both plates, suggesting the true interaction between Akt1 and SETDB1
2970	17587183_MI:0018	According to the growth of the yeast strains on selective medium, the WRKY53 protein could interact with the MEKK1 protein using MEKK1 either as bait or prey construct
2971	17588663_MI:0018	PKCtheta: PKCzeta complex formation was observed in a Lex A yeast two hybrid system via the COOH-terminal catalytic domain
2972	17620405_MI:0018	we performed a systematic yeast two-hybrid screening in which the cDNA fragment harboring the RHD of p65 (amino acids 1-312) was used as bait. Several positive clones were identified to encode full-length UXT
2973	17631528_MI:0018	Coexpression of GBD:BAP2 with GAD:BON1A conferred growth to the yeast host strain on medium selecting for protein-protein interactions, similarly to that of GBD:BAP1 and GAD: BON1A (Fig. 1D), indicating a direct interaction between the BON1 and BAP2 proteins.
2974	17631528_MI:0018	It thus appears that each member of the BON family can interact with each member of the BAP family.
2975	17635584_MI:0018	pKGIRp produces a GAL4 DNA-binding domain (DBD)Rp protein which interacts with mCtBP2 in yeast AH109 cells
2976	17637675_MI:0018	Likewise, using MYC2 truncated derivatives we demonstrated that JAI3 interacts with the N terminus of MYC2 (Fig. 3c). Yeast two-hybrid assays further confirmed MYC2-JAI3 interaction (Fig. 3d).
2977	17637677_MI:0018	Furthermore, the jasmonoyl-isoleucine (JA-Ile) conjugate, but not other jasmonate-derivatives such as jasmonate, 12-oxo-phytodienoic acid, or methyl-jasmonate, promotes physical interaction between COI1 and JAZ1 proteins in the absence of other plant proteins.
2978	17637677_MI:0018	Interaction between tomato COI1 and JAZ1 in yeast was also dependent on the presence of JA-Ile, and was not stimulated by jasmonate, MeJA or OPDA
2979	17644729_MI:0018	WER protein physically interacts with either of the GL3 or EGL3 proteins in yeast cells
2980	17657516_MI:0018	STK25, FAP-1, and STK24 were identified as bait-dependent interactors of CCM3.
2981	17681130_MI:0018	14-3-3&#955; interacts with BZR2 in yeast two-hybrid assays. pACT2 is the empty prey vector as a negative control.
2982	17681130_MI:0018	Further yeast two-hybrid assays indicated that 14-3-3&#955; interacts with BZR1, bzr1-1D, and the C-termini (amino acids 90-336) of BZR1 and bzr1-1D, but not with BRI1, BIN2 or bin2-1 (Figure 2A).
2983	17681130_MI:0018	To further understand the molecular mechanisms of BZR1 regulation, we performed yeast two-hybrid screen for BZR1-interacting proteins. Out of 98 positive clones identified, 80 clones encode members of the 14-3-3 protein family. They represent five of the 12 isoforms in Arabidopsis (Sehnke et al., 2002), namely 14-3-3&#955;, 14-3-3&#954;, 14-3-3&#949;, 14-3-3&#981; and 14-3-3&#969;
2984	17693260_MI:0018	Our two-hybrid screens using 39 residues of the rhodopsin cytoplasmic C terminus as a bait repeatedly isolated a bovine cDNA clone encoding an open reading frame with 97% identity to the C-terminal half (C627-V1323) of human SARA (Figure 1C).
2985	17702749_MI:0018	Approximately 108 independent clones were screened, and 12 potential L-UT-interacting candidate clones were identified, including snapin.
2986	17702749_MI:0018	As shown in Fig. 1B (panel c), mating with various baits of UT-A1 and snapin led to expression of the reporter gene, confirming the interaction between snapin and L-UT in yeast. Specificity of the UT-A1-snapin association was shown by transformations of control bait and prey plasmids.
2987	17704763_MI:0018	Quantitative two-hybrid assays with full-length ZTL confirmed this interaction (Fig. 2b). We observed a similar degree of interaction between GI and LKP2,
2988	17704763_MI:0018	Quantitative two-hybrid assays with full-length ZTL confirmed this interaction (Fig. 2b). We observed a similar degree of interaction between GI and LKP2, but not between FKF1 and GI in this system
2989	17704763_MI:0018	We tested different ZTL domains and found extremely strong binding of GI to the LOV domain (Fig. 2c), a flavin binding region implicated in blue-light signalling in these and other molecules
2990	17712600_MI:0018	Sequencing the cDNA inserts of eight randomly chosen potential CBF5 interaction partners and subsequent database searches revealed that they all matched to At1g03530, a previously uncharacterized protein of 801aa and a predicted molecular weight of 88.8 kD.
2991	17719007_MI:0018	AtbZIP34 and AtbZIP61 could not form homodimer but could form heterodimers with AtbZIP51 (a member of bZIP I group) and AtbZIP43 (a member of S group).
2992	17719007_MI:0018	We also found AtbZIP43, a member of bZIP S group,vcould interact with AtbZIP34 and AtbZIP61
2993	17719007_MI:0018	We got the mutants in which proline was replaced by alanine in leucine region of AtbZIP34 and AtbZIP61, these two mutants were called AtbZIP34m and AtbZIP61m. The yeast cells with co-expressing BDAtbZIP34DNm/ADAtb-ZIP34m grew well in SD/-Trp-Leu-His-Ade selective medium(Fig. 2). The similar result was also got for AtbZIP61m.
2994	17728244_MI:0018	Co-transformation of AH109 yeast cells with the vIRF-3-C/pAS2 bait and the human leukocyte cDNA library resulted in 42 positive colonies that grew on selection medium lacking Trp, Leu, His, and Ade. 22 of 42 His/ Ade-positive transformants formed blue colonies. Plasmids rescued from these positive colonies were analyzed using restriction enzymes, and their inserts were sequenced. One clone, termed C19, contained partial cDNA for human MM-1
2995	17762870_MI:0018	Interaction between AtPRD1 and AtSPO11-1 in yeast two-hybrid assay
2996	17785451_MI:0018	Further tests found that NDPK2 interacted with SnRK3.15 but not SnRK3.13 or SnRK3.5
2997	17785451_MI:0018	interaction of SOS2 with both CAT2 and CAT3 was confirmed by yeast two hybrid assays
2998	17785451_MI:0018	interaction of SOS2 with both CAT2 and CAT3 was confirmed by yeasttwo hybrid assays
2999	17785451_MI:0018	SOS2 interacts with NDPK2.
3000	17785451_MI:0018	Using a yeast two-hybrid approach, we screened a &#955;-ACT Arabidopsis seedling cDNA library for proteins that interacted with the bait protein SOS2. One of the interacting clones was found to encode NDPK2.
3001	17785527_MI:0018	In pairwise combinations we found that SHR interacted with JKD1 and MGP1
3002	17785527_MI:0018	JKD1 could interact with itself and with both SCR
3003	17785527_MI:0018	JKD1 could interact with itself and with both SCR and MGP1.
3004	17785527_MI:0018	JKD1 could interact with itself and with both SCR and MGP1. We detected weak interaction between SCR and MGP1 but no self interaction for MGP and SCR.
3005	17785527_MI:0018	Next, we confirmed that SHR interacted strongly with SCR
3006	17785527_MI:0018	We detected weak interaction between SCR and MGP1
3007	17825054_MI:0018	Interaction of CBL10 and CIPK24 as shown by yeast two-hybrid assays.
3008	17855368_MI:0018	To identify novel Id-1 interacting proteins, we used a full-length Id-1 cDNA as a bait to screen a cDNA library derived from an immortalized human nonmalignant prostatic epithelial cell line, Hpr-1, using the yeast two-hybrid technique. Sixteen positive clones were selected (data not shown). Sequence analysis and data base comparison revealed that one positive clone had 100% identity to the Homo sapiens caveolin-1 mRNA coding sequence
3009	17855426_MI:0018	The HEC proteins do not form either homodimers or heterodimers in yeast, but each is capable of heterodimerizing with SPT (Fig. 5G,H).
3010	17872410_MI:0018	Interaction between FKF1 and GI proteins in yeast. LOV+F contains LOV and F-box domains. F+kelch contains F-box and kelch repeat domains
3011	17872410_MI:0018	Interaction between FKF1 and GI proteins in yeast. LOV+F contains LOV and F-box domains. F+kelch contains F-box and kelch repeat domains (7). ASK2 is known to interact with F-box domain.
3012	17872410_MI:0018	Interaction between GI and CDF1 in yeast and in vitro.
3013	17875708_MI:0018	we screened a cDNA library using a yeast two-hybrid system to search for interacting protein(s) and report on the finding of poly(ADP-ribose) polymerase-14 (PARP-14) to be a binding partner with PGI/AMF.
3014	17875927_MI:0018	To confirm the interaction between VHA-B proteins and SOS2, the entire open reading frames of VHA-B1 and VHA-B2 were fused with the GAL4 activation domain in the prey plasmid pACT2 and cotransformed with the bait plasmid pAS-SOS2, pAS-SOS2 K40N, or pAS-SOS1 (33) into the yeast strain Y190. SOS2 interacted with both of the VHA-B subunits, as indicated by the &#946;-galactosidase activity produced
3015	17893151_MI:0018	we used a yeast two-hybrid approach to screen a mouse embryonic cDNA library with a sequence encoding the first 111 amino acids of rat PKC; as bait. This sequence encodes the N-terminal tail, the pseudosubstrate sequence, and C1A domain of PKC;. Five positive clones were obtained from approximately 100,000 screened. One of these encoded a 72 amino acid sequence which database analysis revealed was part of a novel gene predicted to encode a RING finger domain-containing protein. We named the putative protein RINCK for RING finger protein that interacts with C Kinase
3016	17898163_MI:0018	Among the five PP2CA subfamily members tested (ABI1, ABI2, HAB1, HAB2, and a novel member, At1g07430), only the novel member interacted with AKT1
3017	17898163_MI:0018	Interestingly, despite the low overall sequence similarity in the three CIPK proteins, they interacted with the same members of the CBL family,including CBL1, CBL2, CBL3, and CBL9
3018	17898163_MI:0018	These experiments revealed that, in addition to CIPK23, at least two other CIPKs, CIPK6 and CIPK16, interacted with the C terminus of AKT1
3019	17898163_MI:0018	The yeast two-hybrid results indicated that AIP1 (but not other PP2CAs) interacted with CIPK23 that also interacts with AKT1.
3020	17911168_MI:0018	Of these, only three were confirmed to be able to interact with POT1A as fusions with both the DNA-binding and the activation domain of GAL4 (Fig. 2). These three positives include an N-terminal region of the telomerase, a CBL-interacting protein kinase (CIPK21) and a plant-specific protein of unknown function. Furthermore, these interactions were specific to POT1A, because no growth occurred when tested with POT1B or the telomeric protein KU80
3021	17911168_MI:0018	Only those cells containing POT1A in combination with both TERT-V(I8) or TERT1-323 were able to grow on media depleted of histidine and adenine (Fig. 4B), indicating that the interaction was specific to the N-terminal domain.
3022	17911168_MI:0018	TERT-V(I8), a variant form of TERT, interacts with POT1A
3023	17922164_MI:0018	Here we present the identification of SEPT14 by yeast two-hybrid as a novel septin family member and interacting protein of SEPT9
3024	17934516_MI:0018	we screened a human placenta library using a fragment encompassing the SRA domain of ICBP90 (that is, amino acids 356-635; Figure 1 and Materials and methods). We identified 154 clones by histidine nutritional selection and b-galactosidase (b-gal) activity. The inserts from the isolated clones were sequenced, leading to the identification of 11 overlapping clones that encode a region of a protein named DNMT1 for DNA methyltransferase 1. The overlapping sequences of the yeast two-hybrid DNMT1 preys encompass a peptide that extends between residues 401-615 of human DNMT1.
3025	17944809_MI:0018	However, although HBT interacts with itself, neither CDC27A homodimerization nor heterodimerization of CDC27A with HBT was detected in yeast two-hybrid assays
3026	17944809_MI:0018	Interaction of HBT with Cdc20.4 and Ccs52A2 is clear but detectable only in the absence of the quantitative inhibitor
3027	17944809_MI:0018	In yeast two-hybrid assays both CDC27A and HBT interact with APC10, suggesting their incorporation into the APC/C complex
3028	17944809_MI:0018	The strongest binding of HBT occurs with Cdc20.1 and Cdc20.2, followed by Ccs52A1, Ccs52B and Cdc20.5.
3029	17944809_MI:0018	The strongest binding of HBT occurs with Cdc20.1 and Cdc20.2, followed by Ccs52A1, Ccs52B and Cdc20.5. Interaction of HBT with Cdc20.4 and Ccs52A2 is clear but detectable only in the absence of the quantitative inhibitor
3030	17951453_MI:0018	Results from the ONPG assays revealed that yeast expressing CO fused to the activation domain with either 14-3-3 fused to the DNA-binding domain exhibited &#946;-galactosidase activity at higher levels than background
3031	17951453_MI:0018	The yeast line expressing 14-3-3 (upsilon) fused to the DNA-binding domain and 14-3-3 fused to the activation domain also resulted in &#946;-galactosidase levels higher than background,
3032	17956734_MI:0018	Directed yeast two-hybrid analyses of the isolated clone 337 (Y2H 337) as a prey with syndapin I as a bait (E) as well as Y2H 337 as a bait and Abp1 as a prey (F), respectively,
3033	17965023_MI:0018	109 IRS-1 interacting candidates were identified. Among them, 33 clones included cDNAs encoding 14-3-3 isoforms
3034	17965023_MI:0018	109 IRS-1 interacting candidates were identified. Among them, 33 clones included cDNAs encoding 14-3-3 isoforms (,, and),which were previously shown to interact with IRS-1 or IRS-2 (36). In addition to the various clones identified, two contained the same insert, a region of ASPP2 cDNA sequence corresponding to amino acid residues 881-1128
3035	17965023_MI:0018	When pAS-IRS-1 was transformed into Y190 along with pACT-53BP2S, transformants turned blue in the -galactosidase assay, indicating that IRS-1 and 53BP2S specifically interact with each other
3036	17965270_MI:0018	Together, these results suggest that the basic zipper domain in HY5 and the B-boxes in STH2 are important for the HY5-STH2 interaction.
3037	17967441_MI:0018	During the last years several hMLH1-interacting partners have been identified by yeast two-hybrid. To circum-vent the limitations inherent to the yeast system, like delicate identification of nuclear proteins, we applied a bacterial two-hybrid screening. We now report the identification of Tb4, an actin-binding, and cell motility regulating protein
3038	17982713_MI:0018	A cDNA library of 6.3 x 105 clones was screened by means of the yeast two-hybrid system with PLPA as bait. To construct the cDNA library, a mixture of RNAs prepared from rosette leaves of A. thaliana plants that had been subjected to salt stress and dehydration stress was used, because PLP mRNA was markedly expressed in plants exposed to those stress treatments (Fig. 2). As a result, five clones were isolated for PLP-interacting proteins. Three of them were partial clones for VITAMIN C DEFECTIVE 2 (VTC2, Jander et al. 2002), and two others were those for VTC2 paralog (VTC2L) and BEL1-LIKE HOMEODOMAIN 10 (BLH10) (Hackbusch et al. 2005).
3039	17982713_MI:0018	Interactions of PLPA and PLPB with the fulllength proteins of VTC2, VTC2L, BLH10A, and BLH10B were also examined using the yeast two-hybrid system (Fig. 3). PLPA interacted with all four proteins,
3040	17982713_MI:0018	while PLPB interacted with VTC2 and VTC2L
3041	17983804_MI:0018	Only the mutant encoding amino acids 951-1301 of Topo IIgreek small letter alpha (highlighted in red) in combination with &#946;-catenin showed a significant increase of luciferase activity
3042	17986458_MI:0018	All HIF1/2a fragments spanned one of the two critical prolyl residues and mediated an interaction with pVHL that was entirely dependent on PHD3, ELB and ELC
3043	17986458_MI:0018	Among the true-positive interactors, multiple full-length cDNAs of ELC and ELB were identified that mediated a PHD3-independent interaction with pVHL
3044	17986458_MI:0018	In a proof-of-principle Y2H screen, we identified the known substrates HIF1/2a and new candidate substrates including diacylglycerol kinase iota, demonstrating that our strategy allows detection of stable interactions between pVHL and otherwise elusive cellular targets.
3045	17986458_MI:0018	we observed a robust interaction between pVHL and HIF1a that was strictly dependent on the presence of one of the three PHDs
3046	17986458_MI:0018	While full-length DGKi1-1065 interacted with pVHL in a PHD3- and ELB/ELC-dependent manner (Figure 4b), C-terminally truncated variants lacking the LxxLAP motif at Pro903 failed to interact, demonstrating that the C-terminal LxxLAP motif is required for the interaction with pVHL.
3047	17991437_MI:0018	follistatin was identified as a binding partner of angiogenin by a yeast two-hybrid screen
3048	17991437_MI:0018	To reconfirm the interaction between angiogenin and follistatin, yeast cells were co-transformed with pDBLeu or pDBLeu-ANG along with pPC86 or pPC86-FS. Transformants turned blue in X-gal analysis only when angiogenin and follistatin were simultaneously expressed
3049	18000879_MI:0018	Full length EEF1a1 and PCM1 proteins interacted with BBS1, BBS2, and BBS4. The results of experiments performed on full length clones are summarized in Table II
3050	18000879_MI:0018	Full length EEF1a1 and PCM1 proteins interacted with BBS1, BBS2, and BBS4. The results of experiments performed on full length clones are summarized in Table II.
3051	18000879_MI:0018	Subsequently, we addressed the question whether these clones will interact also with BBS2 and BBS7. Therefore, the coding sequences of BBS2 and BBS7 were cloned into pGBKT7, followed by sequencing analysis and the same control experiments as described above.
3052	18000879_MI:0018	To identify cellular factors that interact with selected BBS proteins (BBS1, BBS2, BBS4, BBS7 we applied a stepwise approach: First, yeast two-hybrid screening was performed with BBS1 and BBS4 fused to the C terminus of the DNA binding domain of GAL4(BD) as bait.
3053	18024891_MI:0018	Among five BGLF4-interacting cDNA clones identified, one contained the coding region, aa 509-835, of XPC
3054	18024891_MI:0018	The interaction of XPC (aa 509-835) with full-length (S300P) BGLF4, its N terminus (aa 1-293) and C terminus (aa 201-429) was reproduced in a yeast two-hybrid system
3055	18025262_MI:0018	Activation of the reporter gene was only detected when BTF3 was coexpressed with the A/B domain of ERa.
3056	18025262_MI:0018	These data indicate that BTF3b binds specifically to the region of the ER containing the AF-1 function.
3057	18025262_MI:0018	We have used the yeast two-hybrid system to isolate a cDNA coding for a protein that binds specifically to the AF-1 region of human ERA. This cDNA codes for the transcription factor basal transcription factor 3 (BTF3).
3058	18029035_MI:0018	To identify proteins binding to Ymer, we performed yeast two-hybrid screening using full-length human Ymer cDNA as a bait. Eight positive cDNA clones isolated from 1.8 106 transformants were several types of ubiquitin cDNA.
3059	18029035_MI:0018	Using a yeast two-hybrid system to search for proteins interacting with A20, we identified one novel binding protein, Ymer.
3060	18029035_MI:0018	we constructed a fulllength A20 cDNA in pBTM116 for yeast two-hybrid screening using a human B cell cDNA library. Sixty positive clones were isolated on Leu-Trp-His-deficient medium from 2.5 106 transformants. Several previously reported proteins including, 14-3-3, 14-3-3 and ABIN-1/2 [20,21], and one novel protein, Ymer (accession number: AJ416916), were isolated.
3061	18055606_MI:0018	Strong b-gal activity in yeast colonies that expressed both TOC1 and PRR3 indicated a physical interaction between these proteins
3062	18056989_MI:0018	we employed a yeast two-hybrid screening to identify cellular proteins that are associated with Pim-1L and we found the ABC transporter BCRP/ABCG2 as one of the potential interacting partners of Pim-1L.
3063	18056989_MI:0018	we employed a yeast two-hybrid screening to identify cellular proteins that were associated with Pim-1L, and we found the ABC transporter BCRP/ABCG2 as one of the potential interacting partners of Pim-1L
3064	18065690_MI:0018	HSP90-1 and RAR1 still interacted with SGT1beta3 tested in a yeast two-hybrid assay
3065	18086875_MI:0018	A total of 10 clones, encoding seven potential Wrch1-interacting proteins, were isolated. Three of the clones encoded Pyk2
3066	18093972_MI:0018	theCterminus of HIPK2-(503-1189) was utilized as bait for the screening of mouse embryonic match-maker cDNA libraries. Among the several cellular proteins that were identified and sequenced, a clone showed identity to WSB-1, a subunit of E3 ubiquitin ligase
3067	18165900_MI:0018	In order to search for new proteins that interact with TRAIL-R1/DR4 and could affect its signaling, we performed a yeast two-hybrid (Y2H) screening of several cDNA expression libraries using the intracellular part of DR4 (ICP, amino acids 246-445) as a bait. Two fusion proteins specifically interacting with DR4(ICP) contained a C-terminal part of ARAP1 (centaurin d2), an adapter protein with multiple domains and Arf and Rho GAP activities
3068	18165900_MI:0018	The presence of exon 30 in the ARAP1 C-terminus abolished its interaction with the intracellular part of DR4.
3069	18178112_MI:0018	To identify new proteins which could be involved in MT nucleation, the yeast two-hybrid method was used to screen a 3-week-old Arabidopsis seedling cDNA library (Clontech) with the full-length AtGCP3 as a bait. An efficient mating strategy on semi-dry filters was followed by direct plating on selective media (Fromont-Racine et al., 1997). Sixteen cDNA clones, corresponding to the full-length coding sequence of the AT4g09550 gene, were positive both for nutritional selection and in b-galactosidase assay.
3070	18178112_MI:0018	To identify new proteins which could be involved in MT nucleation, the yeast two-hybrid method was used to screen a 3-week-old Arabidopsis seedling cDNA library (Clontech) with the full-length AtGCP3 as a bait. An efficient mating strategy on semi-dry filters was followed by direct plating on selective media (Fromont-Racine et al., 1997). Sixteen cDNA clones, corresponding to the full-length coding sequence of the AT4g09550 gene, were positive both for nutritional selection and in b-galactosidase assay.Yeast co-transformation was performed with rescued library plasmids to confirm the interaction.
3071	18188704_MI:0018	To identify proteins that associate with the human HIPPI protein, we performed a yeast two hybrid cDNA library screen with HIPPI as a bait. We identified a protein of 99 amino acids in length that was identical to the protein BLOC1S2
3072	18218967_MI:0018	MYB72 interacts with EIL3 in a yeast twohybrid assay.
3073	18223036_MI:0018	Interactions between DDB1a and Arabidopsis DWD Proteins Detected by Yeast Two-Hybrid Assays.
3074	18230339_MI:0018	Luciferase activity was reduced by the TAT-p53-C-ter peptide in a dose-dependent manner, indicating that it was able to interfere with the binding between PARC-CPH and p53
3075	18250314_MI:0018	Initially, we did not detect any interaction between EMS1 and TPD1 using the entire EMS1 LRR domain (Fig. 2 A and B). LePRK2 contains 5 LRRs with a low potential for glycosylation, whereas EMS1 has 29 LRRs with 11 potential N-linked glycosylation sites that may have interfered with protein interaction (42). Therefore, we cloned a series of shortened cDNAs that encode truncated EMS1 LRRs (Fig. 2A). We found that one small fragment interacts with TPD1 (Fig. 2 A-C, SI Fig. 8). We named this small fragment the TPD1-interacting region (TIR).
3076	18267075_MI:0018	Therefore, NRIP1 and N(TIR) interact directly in a yeast two-hybrid assay
3077	18267075_MI:0018	To search for novel proteins that mediate the association between the N immune receptor with the p50 effector, we conducted a yeast two-hybrid screen with the TIR domain of N as bait. We identified N receptor-interacting protein 1 (NRIP1), which was represented by six identical, independent clones in the screen
3078	18267075_MI:0018	We found that yeast carrying p50 as bait and NRIP1 as prey activated expression of the LEU2 reporter gene (Figure 3A), suggesting that p50 and NRIP1 interact directly in a yeast two-hybrid assay.
3079	18268542_MI:0018	FIT interacts with AtbHLH38 or AtbHLH39
3080	18287201_MI:0018	Interaction of LFY and UFO in yeast two-hybrid assays. The AD-LFY/BD-UFO interaction shows a significant increase in -gal activity over background controls. This interaction is enhanced 8.6-fold when the F-box is deleted in the AD-LFY/BD-FUFO combination compared with that of AD-LFY/BD-UFO. AD-FUFO and BD-LFY also shows a significant interaction, while AD-UFO and BD-LFY shows a background level of -gal activity. AD, Gal4 activation domain; BD, Gal4 DNA-binding domain. Bars represent mean±s.e.m. for five replicates
3081	18296627_MI:0018	COP1 contains the distinguishing N-terminal RING finger and coiled-coil region (COP1{Delta}283-675) and the C-terminal WD40 repeat domain (COP1{Delta}1-209) (Deng et al., 1992Go), the latter of which is required for the interaction with HY5 (Ang et al., 1998Go) and CRY1 (Yang et al., 2001Go). To define which domain is required for the interaction with CO, we conducted a yeast two-hybrid assay using CO{Delta}1-105 as bait and COP1{Delta}283-675 and COP1{Delta}1-209 as preys. We found that CO{Delta}1-105 interacted with COP1{Delta}1-209 (Figure 2D, sample 2) but did not interact with COP1{Delta}283-675 (Figure 2D, sample 1). This result demonstrated that COP1-CO interaction might require the C-terminal WD40 repeat domain of COP1.
3082	18296627_MI:0018	However, &#946;-galactosidase activity increased dramatically when the CO{Delta}1-105 or CO{Delta}1-168 bait was coexpressed with the COP1 prey (Figure 2B, samples 3 and 5), indicating interaction between these domains of CO with COP1. The bait construct expressing CO lacking amino acids 1 to 183 (CO{Delta}1-183) showed little background in the plate assay, and clear interaction was observed between CO{Delta}1-183 and COP1 (Figure 2C). The N-terminal domain of CO lacking the CCT motif (CO{Delta}184-374) did not interact with COP1. These data indicated that CO-COP1 interaction might require the CCT domain of CO.
3083	18298670_MI:0018	However, we found that PCFS4 did interact with another putative polyadenylation factor, CLp1p-similar protein 3
3084	18303029_MI:0018	each GAL4-DBD-SWI/SNF component was cotransformed with GAL4-AD-p53. On average, about one thousand colonies appeared only in BAF60a construct
3085	18313049_MI:0018	Among them we paid our attention to one clone (number 13584) that showedstrong interactionwith RNF43 asmeasured by a -galactosidase assay (Fig. 6A). This clone harbored a contiguous open reading frame of HAP95
3086	18332111_MI:0018	One of these prey clones encoded amino acids 552 to 912 of actinin-4 and specifically bound to JRAB/MICAL-L2-MN in the same two-hybrid assay
3087	18332111_MI:0018	Three independent clones coding for proteins that specifically interacted with JRAB/MICAL-L2-MN were isolated. These positive clones contained sequences identical to actinin-4 cDNA (accession no. NM_021895).
3088	18339839_MI:0018	We observed growth of colonies with rictor fragments 1 and 5 (Fig. 1D), showing that NH2-terminal and COOH-terminal portions of rictor interact directly with full-length ILK and the COOHterminal ILK kinase domain, but not with the ankyrin repeat domain of ILK
3089	18344519_MI:0018	As an initial step to elucidate the mechanism that regulates TIMP-3, we used a yeast two-hybrid system to screen a human ovary cDNA library for a novel TIMP-3 interacting partner. Here, we identified human angiotensin II type 2 receptor (AGTR2) as such a partner
3090	18344519_MI:0018	b-galactosidase activity indicated interactions between TIMP-3 and AGTR2
3091	18344519_MI:0018	In the two-hybrid system, cells containing TIMP-3 deletion mutant (Met1-Asn144) with AGTR2 deletion mutant (Arg235-Ser363) only grew on the Ura, His, Trp and Leu deficient plates, whereas the other combination deletion mutants failed to grow.
3092	18347058_MI:0018	we isolated the zinc finger domain of EWS as a specific RASSF1A binding partner
3093	18390592_MI:0018	A yeast two-hybrid screen using PLP3a as the bait yielded 89 candidate interactors out of 1.2 million clones from an Arabidopsis cDNA library. Six of these clones corresponded to three different isoforms of Arabidopsis b-tubulin (Figure 6A). In all cases, the clones contained fusions between the GAL4 activation domain and the C-terminal region of b-tubulin, suggesting that the interaction with PLP3a occurs within this region (amino acids 300 or 302 to stop for TUB2; 237 or 292 to stop for TUB3; 370 to end for TUB4 and 351 to end for TUB5).
3094	18390806_MI:0018	A strong interaction was detected between full-length LUH-AD and SEU(ND)-BD
3095	18408009_MI:0018	co-expression of the HPV-16E7 and the C-terminal of USP11 (USP11-C) rendered the yeast strain CG1945/Y187 able to grow on SD/-Leu/-Trp/-His/-Ade minimal plates
3096	18408009_MI:0018	The cDNA library from HeLa cell was screened using intact HPV-16E7 (amino acids 1-97) as bait. One of the cDNA encoding the carboxyl-terminal domain of USP11 was repeatedly isolated
3097	18430956_MI:0018	AtRad54 interacted with yeast Rad51
3098	18430956_MI:0018	The plant proteins AtRad54 and AtRad51 also showed significant interaction
3099	18430956_MI:0018	The plant proteins AtRad54 and AtRad51 also showed significant interaction, as did their yeast homologs Rad54 and Rad51
3100	18430956_MI:0018	yeast Rad54 interacted with AtRad51
3101	18445131_MI:0018	Although the yeast cells carrying NAC11-199 fused to the GAL4-BD (GAL4-BD-NAC11-199) grew on the selective medium lacking histidine when co-transformed with NAC11-199 fused to the GAL4 transactivating domain (GAL4-AD-NAC11-199), as previously reported by Xie et al. (2000), GAL4-BD-NAC11-199 co-transformed with other VNDNTERM proteins fused to GAL4-AD or CUC21-228-GAL4- AD failed to grow on the selective medium
3102	18445131_MI:0018	These data suggest that VND7 might homodimerize and heterodimerize with other VND members. In contrast, the transformants carrying GAL4-BDVND6 1-186 showed strong reporter expression only with co-transformed GAL4-AD-VND61-186
3103	18445131_MI:0018	The transformants co-expressing GAL4-BD-VND71-188 along with any of the GAL4-AD-VNDNTERM constructs all grew on the selective medium, though co-expression with GAL4-ADVND1 1-187, VND21-188 and VND31-192 exhibited better growth than other VNDNTERM proteins (Figure 4). However, transformants expressing GAL4-BD-VND71-188 with GAL4-ADNAC1 1-199 or CUC21-228 failed to grow on the selective medium (Figure 4).
3104	18466301_MI:0018	the possibility of a weak or transient interaction between AtCBK2 and AtHSFA1a.
3105	18466301_MI:0018	Thus AtCBK3 can interact with AtHSFA1a but AtCBK1 cannot,
3106	18466309_MI:0018	BIF2 interacts with BA1 in yeast and in vitro
3107	18466309_MI:0018	To define the regions of BIF2 sufficient for interaction, truncations of BIF2 were generated and assayed for interaction with BA1 by growth on selective media (Figure 2a). Constructs lacking the conserved kinase domain of BIF2 did not interact with BA1, suggesting that the kinase domain is required for interaction, or that such extensive deletions did not allow BIF2 to fold properly (Figure 2a). Furthermore, a construct lacking just 59 amino acids of the C terminus of BIF2 did not interact with BA1, indicating that the C terminus of BIF2 may play a role in the interaction with BA1 (Figure 2a).
3108	18467451_MI:0018	AtFLS1, 3, and 5 interacted with AtCHS when they were fused to the GAL4 activation domain, but not when fused to the bait domain.
3109	18467451_MI:0018	AtFLS1 also interacted with AtF3H and AtDFR in both configurations.
3110	18467451_MI:0018	The only other positive result was for AtFLS5 fused to the GAL4 bait domain with AtDFR.
3111	18492870_MI:0018	we observed three pairs of strongly interacting subunits: EXO70A1/ SEC3a, SEC15b/SEC10, and SEC6/SEC8
3112	18494853_MI:0018	Protein interactions were signalled by the growth of transformant colonies on histidine-free medium. AtPolg interacted with PCNA1, PCNA2 and yeast PCNA, but more weakly than yeast, Polg interacted with yeast PCNA (Figure 4a).
3113	18500650_MI:0018	It is interesting to notice that SCL23, the most closely related to SCR among the members, was also able to interact with SHR
3114	18500650_MI:0018	We confirmed the interaction between SHR and SCR, which plays an important role in the regulation of SHR movement as recently reported
3115	18504434_MI:0018	Chfr were used as baits to screen a cDNA library obtained from a 6 to 8-week-old human embryo. One of the positive clones isolated was the translationally controlled tumor protein (TCTP).
3116	18504434_MI:0018	Mating assays subsequently confirmed an interaction between LexA-Chfr and TCTP.
3117	18505803_MI:0018	One strongly interacting clone was obtained (Figure 7A), which was identified as encoding At FIP37
3118	18505803_MI:0018	We sought to identify potential interacting partners of the Arabidopsis MTA by screening an Arabidopsis yeast two-hybrid library prepared from anther tissues, in which MTA is highly expressed (a gift from Z. Wilson). One strongly interacting clone was obtained (Figure 7A), which was identified as encoding At FIP37
3119	18532977_MI:0018	Protein-protein interaction between AtMYB2 and TT8
3120	18532977_MI:0018	TT8 forms a homodimer
3121	18532977_MI:0018	TT8 interacts with PAP1
3122	18541146_MI:0018	The LNL[E/D]L motif of AtMYB3 specifically interacts with AtCPL1640-967 of AtCPL1
3123	18541146_MI:0018	To identify proteins that interact with the defined C-terminal region (640-967) in AtCPL1, yeast two-hybrid screen was performed by using an AtCPL1640-967 bait clone and an Arabidopsis cDNA prey library. Fifty unique clones were identified as CPL1-interacting proteins after secondary confirmation and sequencing analysis. Among these, eight clones including two transcription factors, ANAC019 (At1g52890) and AtMYB3 (At1g22640), are predicted to be nuclear proteins (Table 1), and exhibited specific interactions with AtCPL1640-967 in yeast two-hybrid assay (Supplementary Fig. S1).
3124	18550827_MI:0018	Consistent with this finding, the eta2-1 mutation completely abolished the ability of CAND1 to interact with CUL1 in a yeast 2-hybrid assay
3125	18550827_MI:0018	In a yeast 2-hybrid assay, however, axr6-2 caused only a moderate reduction in the ability to interact with ASK1
3126	18552202_MI:0018	Identification of DRIP1 and DRIP2 Interaction with DREB2A via Yeast Two-Hybrid Analysis.
3127	18557765_MI:0018	One of the novel proteins that we found to robustly interact with necdin in yeast corresponded to the full-length 187 amino acid EID-1 protein.
3128	18567673_MI:0018	A third cDNA (AM883105) has been isolated from a spinach library by screening with the AtNIP1 cDNA clone. The corresponding protein was named SoNIP.
3129	18577522_MI:0018	We found through the examination of additional truncated versions of the ETR1 and ETR2 receptors that the GAF domain was sufficient to mediate their interaction, although based on the LacZ reporter analysis the strength of this interaction was reduced compared to that observed with the entire soluble domains
3130	18587275_MI:0018	The binding of OBF4 to CO in yeast cells was strong, and comparable to FOS-JUN and OBF4-OBP3 interactions
3131	18587275_MI:0018	To determine the specificity of the OBF4 interaction with CO, we performed yeast two-hybrid interaction tests using five other TGA factors (not TGA2) and CO as bait and prey, respectively, co-transformed into host cell pJ69- 4A. The interaction with CO was specific to OBF4
3132	18587275_MI:0018	To elucidate the biochemical function of OBF4, a yeast two-hybrid library screen was carried out using Gal4 DNA-binding domain (BD)-OBF4 as bait. An Arabidopsis transcription factor library was introduced into yeast cells harboring the bait construct. Positive colonies (n = 120) from approximately 3.2 × 105 transformants were plated onto SD agar medium lacking Trp, Leu, Ade, and His. One clone that expressed CONSTANS (CO) and two clones that expressed OBP1 (OBF4-binding protein 1) and OBP3 were obtained after eliminating false positive clones by &#946;-galactosidase assays and retransformation experiments.
3133	18591351_MI:0018	In yeast two-hybrid assays, WIT1 interacted with WPP1 and WPP2 but not with WPP3 (Figure 2A). WIT1 also bound to full-length RanGAP1 and RanGAP2 and to the WPP domain of RanGAP1 (RanGAP1DC, amino acids 1 to 119) but not RanGAP1DN (amino acids 120 to 535, RanGAP1 without the WPP domain)
3134	18599455_MI:0018	A full-length ARF2 clone was independently verified to interact with BIN2 (Fig. 2A)
3135	18599455_MI:0018	A yeast two-hybrid screen using the GSK3-type kinase BIN2 as bait provided the first potential molecular link between the auxin and BR pathways. A fragment of ARF2 was isolated as a BIN2-interacting protein. The ARF2 region interacting with BIN2 is restricted to the 540 aa in C terminus, encompassing the ARF-Aux/IAA dimerization domain
3136	18599653_MI:0018	we performed directed yeast two-hybrid assays using full-length AGL61 fused with the GAL4 DNA-binding domain (AGL61-BD) or the GAL4 activation domain (AGL61-AD) and full-length AGL80 fused with these domains (AGL80-BD and AGL80-AD). Figure 5 shows that AGL61-BD and AGL61-AD interacted with AGL80-AD and AGL80-BD, respectively, to stimulate transcription of the HIS3 and ADE2 reporter genes
3137	18632581_MI:0018	DDL was found to interact with an N-terminal portion (amino acids 1-833), but not a C-terminal portion (amino acids 814-1909), of DCL1 in the yeast two-hybrid assay
3138	18644794_MI:0018	The activation of reporter genes was observed when the CCMH-D1 AD construct was co-transformed with CcmFN1 domain 5 and with CcmFN2 domain 2 BD constructs but not with CcmFN1 domain 3 and CcmFC domain 6 BD constructs
3139	18644794_MI:0018	The activation of reporter genes was observed whenthe CCMH-D1 AD construct was co-transformed with CcmFN1 domain 5 and with CcmFN2 domain 2 BD constructs but not with CcmFN1 domain 3 and CcmFC domain 6 BD constructs
3140	18649364_MI:0018	Our results showed that only the human TSPY[151-308] and rat Tspy[185-334] interacted with eEF1A1 [305-462] in yeast (Fig. 1b).
3141	18676877_MI:0018	To elucidate the function of PDI5 in endothelial cell vacuoles, we screened two Arabidopsis cDNA libraries for proteins interacting with PDI5 bait using the yeast two-hybrid system. The principal isolates were clones encoding the following three Cys proteases: RD21 (NM_103612),CP43 (NM_123672), andCP19 (NM_112826), which represented 66, 31, and 3.8% of the total recombinants isolated, respectively.
3142	18703495_MI:0018	An Arabidopsis root cell cDNA library with the tail region of MYA2, aa1049-aa1505 (f1), lacking the coiled-0coil domain, as shown schematically in Fig. 1A was screened. After screening 1.2x106 clones, DNA fragments encoding AtRabD1 and AtRabC2a, members of the small GTPase Rab family, were identified.
3143	18703495_MI:0018	By contrast, AtRabC2a interacted only with a full-length MYA2 tail (f1), but not with its truncated forms, where 55 amino acids from the C-terminus or 146 amino acids from N-terminus were deleted. Therefore, both tail termini appear to be necessary for the interaction with AtRabC2a.
3144	18703495_MI:0018	To determine the region in the MYA2 tail responsible for the interaction with each AtRab, their interaction with a series of deletion forms of the MYA2 tail, aa1049-aa1450 (f2 in Fig. 1A), aa900-aa1221 (f3 in Fig. 1A), in which the coiled-coil domain was included, and aa1195-aa1505 (f4 in Fig. 1A) was examined. The association of each AtRab to each truncation of the MYA2 tail is summarized in Fig. 1B. AtRabD1 interacted with a truncation of MYA2 tail, aa1049-aa1450 (f2) lacking 55 amino acids in the C-terminus
3145	18713402_MI:0018	Among them, 22 clones were reconfirmed in the secondary test. One of these clones, ACI1, was studied in detail because it has a nuclear localization signal (NLS) which means that it may co-localize with ALC. ACI1 (At5g01370) is predicated to encode a protein of 427 amino acids containing a lysine-rich domain, a helix-turn-helix (HTH) DNA-binding motif, a nuclear localization signal and eight proline residues in tandem at its N-terminus
3146	18713402_MI:0018	To investigate which domain of ACI1 contributes to the ACI1- ALC interaction, serial truncations of ACI1 were constructed into pGBKT7 and co-transformed with the bait vector of the ALC Nterminus, respectively. Deletion experiments showed that both the lysine-rich domain and the C-terminal of ACI1 are able to interact with ALC in yeast cells, but the latter has lower affinity, indicating that ACI1 interacts with ALC via its lysine-rich domain (Figure 1C).
3147	18713950_MI:0018	Analysis of the interactions revealed that DIA interacts both as prey and as bait with theMg-type proteins AGL80, PHE1, AGL38 (PHE2), and AGL86,
3148	18724936_MI:0018	Consistent with this idea, by a directed Y2H approach, we detected physical interactions between Get3 and several additional secretory pathway TA proteins, including the SNAREs Tlg2 and Sec22 and the peroxisomal TA protein Pex15.
3149	18724936_MI:0018	Yeast two-hybrid assay with Get3 as bait and Sed5197-340 (the strongest hit from the Y2H screen) as prey (in the presence or absence of its TMD).
3150	18775314_MI:0018	To identify proteins that bind the longin domain of VAMP7, a yeast two-hybrid cDNA library screen using the longin domain as the bait protein was carried out. In this screen, 37 out of 39 positive clones encoded part of the AP3 complex &#948; subunit trunk domain.
3151	18775314_MI:0018	To test the specificity of the interaction between the longin domain of VAMP7 and Hrb, we first used the yeast two-hybrid system t
3152	18776063_MI:0018	In these screens, we used a fusion protein of WRKY62 with the human homolog of yeast cdc25, hSOS, as bait. The temperature-sensitive yeast strain transformed with the bait construct failed to grow at the restrictive temperature (378C). We screened >107 independent transformants of a cDNA prey library generated from SA-treated Arabidopsis plants. The screens yielded one group of cDNAs that all encoded HDA19
3153	18776063_MI:0018	WRKY62 interaction with HDA19 in yeast. Yeast cdc25H cells containing the indicated plasmids were grown on synthetic minimal medium containing glucose or galactose at 25°C or 37°C. The pictures were taken after 4 days of growth.
3154	18796637_MI:0018	Finally, we examined whether STH3 could interact with HYH, the bZIP protein most closely related to HY5 in Arabidopsis, in yeast two-hybrid assays.We found a 30-fold increase in relative b-Gal activity, indicating that STH3 indeed could interact also with HYH
3155	18796637_MI:0018	STH3 Interacts with HY5 in Yeast, and the bZIP Domain of HY5 and the Second B-Box in STH3 Are Important for the Interaction.
3156	18812496_MI:0018	The IMS Regions of ARC6 and PDV2 Interact
3157	18830673_MI:0018	Amongst these clones in each case were those encoding several protein kinases, metabolic enzymes and proteins with unknown function, and for the screen with DRN, PHAVOLUTA
3158	18830673_MI:0018	lthough random-primed cDNA synthesis gave rise to the yeast two hybrid library, all BIM1 clones clustered to the C-terminus and did not contain the bHLH DNA-binding/dimerization motif. The shortest clone for the screen with DRN and DRNL encoded 104 or 100 C-terminal amino acids, respectively, thus identifying a protein interaction complex involving the BIM1 C-terminus, a region showing patchy homology between BIM1, BIM2 and BIM3
3159	18835996_MI:0018	The result indicated that the DOR specifically interacts with ASK14 protein
3160	18836139_MI:0018	As shown in Fig. 1Aa, the GAL4(DB)-ACBP4 fusion interacted with GAL4(TA)-AtEBP, as indicated by the blue colour arising from the production of significant levels of b-galactosidase.
3161	18836139_MI:0018	Kelch-motif containing ACBP4 was used as bait in yeast two-hybrid screens from which an interactor (AtEBP) was retrieved
3162	18836139_MI:0018	Results from analysis using the BLAST revealed that only one clone was in-frame and it encoded a full-length actin-depolymerizing factor 3 (ADF3, At5g59880) protein. However, this was not investigated further in this study because it did not bind ACBP4 in subsequent co-immunoprecipitation,
3163	18845687_MI:0018	CYP20-3 Physically Interacts with SAT1.
3164	18845687_MI:0018	These results indicate that the full-length SAT1 interacts with CYP20-3 in the yeast two-hybrid system.
3165	18849490_MI:0018	We examined the physical interaction between UBC1/2 and HUB1/2 in yeast. It was found that HUB1 and HUB2 interacted with UBC1 and UBC2 in yeast, as indicated by the growth of yeast strains cotransformed with HUB1 or HUB2 and UBC1 or UBC2 on highstringency selection medium
3166	18849490_MI:0018	we tested for a physical interaction between HUB1 and HUB2 by yeast twohybrid assay. HUB1 and HUB2 were able to self-associate and to interact in a pairwise fashion (Figure 2A), suggesting that they form both homodimers and heterodimers.
3167	18854162_MI:0018	Amino acid residues 46-80 of OMA-1 are both necessary and sufficient for interaction with TAF-4.
3168	18854162_MI:0018	In yeast two-hybrid screens for OMA-1 interacting proteins, using the N-terminal 117 amino acids of OMA-1 (OMA-1-N) as bait, we isolated multiple TAF-4 partial cDNAs.
3169	18930710_MI:0018	We screened a human fetal brain cDNA library using hRap2A as bait and isolated two hMINK clones (pACT2-hMINK-A and -B)
3170	18948957_MI:0018	Among these only KRP4, KRP6 and KRP7 showed clear binding to FBL17 in yeast
3171	18948957_MI:0018	FBL17 interacts with ASK1 through its F-box domain.
3172	18948957_MI:0018	Yeast two-hybrid analysis of the binding of FBL17 to KRP6 and KRP7
3173	18974936_MI:0018	All results clearly prove a specific interaction of HIPP26 with ATHB29, a zinc-finger homeodomain box transcription factor
3174	18974936_MI:0018	in addition to HIPP26, also strongly interacts with HIPP20, HIPP21, HIPP23, HIPP24, HIPP27 and HIPP30
3175	18974936_MI:0018	The only other interactions detected were between HIPP30 and ATHB21 and ATHB30.
3176	19000167_MI:0018	IBR5 interacts specifically with MPK12 in yeast.
3177	19011118_MI:0018	Yeast two-hybrid assay showing direct interaction between SVP and FLC.
3178	19118534_MI:0018	AtGSTF10 was identified as a BAK1 interactor.
3179	19118534_MI:0018	Compared to the interaction of full-length GST and BAK1, we found that only GST(1-59), containing the N-terminal region prior to the start of the G-site, showed a specific interaction with similar strength to intact GST.
3180	7664335_MI:0018	The interaction between CSA and CSB proteins was confirmed in vivo by the use of the two-hybrid genetic system
3181	7759517_MI:0018	It should be noted that wild-type MEK5 also interacted with ERK5, although we did not isolate any ERK5 clones from the initial yeast two-hybrid screen.
3182	7923370_MI:0018	This activation construct, which proved to contain a portion of a known murine gene, mBRG7 (see below), was termed GalA-mBRG1. Control experiments showed that the RB-mBRG1 interaction
3183	7954795_MI:0018	We found that nearly full-length Su(H) protein associates with an intracellular segment of the N protein that includes all six cdcl O/ankyrin repeats
3184	8062390_MI:0018	By two-hybrid analysis, Ste11, Ste7, and Fus3 associate with different domains of Ste5, while Kss1, another MAPK, associates with the same domain as Fus3
3185	8062390_MI:0018	in the two-hybrid system (Table1).  Ste7 ineracts with both Fus3 and Kss1
3186	8062390_MI:0018	in the two-hybrid system (Table1).  Ste7 interacts with both Fus3 and Kss1
3187	8062390_MI:0018	Ste11 also interacts dtrongly with both Fus3 and Kss1
3188	8062390_MI:0018	Ste11 also interacts strongly with both Fus3 and Kss1
3189	8062390_MI:0018	Ste11 also interacts weakly with itself,
3190	8062390_MI:0018	Ste11 and Ste7 each interact with Ste5, Fus3 and Kss1,
3191	8062390_MI:0018	Ste11 and Ste7 each interact with Ste5, Fus3, and Kss1
3192	8062390_MI:0018	Ste11 and Ste7 each interact with Ste, Fus3 and Kss1,
3193	8062390_MI:0018	Ste, Ste7, and Fus3 were each found to interact with a different portion of Ste5
3194	8417317_MI:0018	We found that yeast transformants containing either of the DB-ETR1 constructs together with the AD-CTR153-568 construct were His1 (histidine prototrophs) and produced blue color in the presence of the b-galactosidase substrate X-Gal, indicating that the histidine kinase region of ETR1 can interact with the amino-terminal domain of CTR1 (Fig. 1B).
3195	8552194_MI:0018	Potential targets of Cdc2 kinase in the fission yeast Schizosaccharomyces pombe were identified using two-hybrid screen in the budding yeast S. cerevisiae. A screen of 2 x 10-7 fission yeast cDNA clones yielded 112 positives representing seven genes. One, orp2+ (ORC2 related in pombe), encodes a protein which is 22% identical to  the Orc2 subunit of S. cerevisiae ORC (Fig. 1).
3196	8604139_MI:0018	We found that the N-terminal 45 amino acid residues of FliG were not required for the FliG/FliM two-hybrid interaction (Figure 3).
3197	8617797_MI:0018	An additional B`alpha cDNA was isolated in an independent screen of a mouse T-lymphocyte library for proteins that interact with the A subunit of PP2A using the yeast two-hybrid assay. One of the cDNAs that interacted with the GAL4 DNA binding domain-A subunit fusion protein was a mouse homolog of human B`alpha.
3198	8617797_MI:0018	GAL4 DNA binding domain fusions of human B`alpha, p53, and the A subunit were tested for binding specificity with GAL4 activation domain fusions of the A and C subunits of PP2A.
3199	8663349_MI:0018	To confirm the interactions detected in the yeast two-hybrid assay, we showed that the amino-terminal domain of LBR bound to HP1Hsalpha  and HP1Hsgamma  in vitro
3200	8749394_MI:0018	After screening one million transformants by the galactosidase colony filter-lift assay, we isolated five plasmids, four of which encoded previously uncharacterized proteins and will be described elsewhere. One of the cDNA clones we isolated turned out to encode a segment of mNotch1
3201	8749394_MI:0018	he carboxy-terminal fragments of dNotch [1 769-1 880] - dNotch [1 799-1 847], dNotch [1 799-1 880] and dNotch [1 826-1 880] - showed a much weaker interaction with Su(H)
3202	8749394_MI:0018	RBP-J&#954; interacted with mNotch1 [1 751-1 850] and mNotch1 [1 751-2 026],
3203	8749394_MI:0018	RSu(H) associated with mRAM23 and mNotch1 [1 751-1 806], but not with mNotch1 [1 807-1 850] (Table 1).
3204	9016654_MI:0018	Using the yeast two-hybrid system, we have isolated an 835 amino acid RING finger (C3HC4 zinc finger)protein, TIF1b (also named KAP-1), that specifically interacts with the KRAB domain of the human zinc finger factor KOX1/ZNF10.
3205	9076992_MI:0018	interaction of heterologous OAS-TL/SATA
3206	9076992_MI:0018	self association of OAS-TL  in the two hybrid system could only be demonstrated after prolonged growth of transformed cells.
3207	9076992_MI:0018	The lowermost section presents the interaction of full-length SAT-A/TA and SATA/DB.
3208	9115279_MI:0018	One gene for which 10 independent isolates were obtained is represented by the positive clone pACT-JL21, which interacted specifically with the Gal4(1-147)Cdc2 fusion protein in the presence of 25 mM 3-aminotriazole (Fig. 1).
3209	9144171_MI:0018	RIN1, like RAF1, interacts well with both wild-type and the constitutively active mutant form of RAS (H-RASV12).
3210	9144171_MI:0018	The putative RAS effector RalGDS had an interaction profile identical to RIN1 (Table 1; ref. 28).
3211	9144171_MI:0018	We asked whether the RBD of RIN1 is also involved in other protein-protein interactions. Using the two hybrid procedure (41), we isolated eight distinct clones from a murine cDNA library. One of the most frequently isolated cDNAs encodes the epsilon isoform of 14-3-3.
3212	9144171_MI:0018	We tested the ability of RIN1 to interact with H-RAS effector domain mutants using the two-hybrid detection system (Table 1).
3213	9154825_MI:0018	As shown in Fig. 6A, plasmids encoding LexA-Mcm2, LexAMcm6, or LexA-Cdc47 produce a strong blue color in cells which also produce the Gal4-Mcm10 fusion protein.
3214	9173976_MI:0018	The two-hybrid assay was used to assess the ability of mSUG1 to bind to the wild-type and XP11BE mutant XPB protein and the other core subunits of TFII
3215	9173976_MI:0018	The wild-type human XPB (aa 31-742) was fused to the GAL4 DNA-binding domain (DBD) (aa 1-47) and used as bait in a two-hybrid screen for interacting proteins encoded by a library of cDNAs (mouse)
3216	9194697_MI:0018	Two-hybrid analyses of the in vivo interactions of Tps1, Tps2, TsI1, and Tps3, a protein with high homology to TsI1, revealed that both TsI1 and Tps3 can interact with Tps1 and Tps2; the latter two proteins also interact with each other.
3217	9235916_MI:0018	cDNA encoding a fragment (amino acids 141-291) of mouse p110 termed Rip36 (Ras-interacting protein) was identified by screening a mouse embryo library using Ha-RasV12 as bait in the yeast two-hybrid system.
3218	9271422_MI:0018	The N-terminal half of DIS1 protein specifically interacts with the C-terminal half of SIR4.
3219	9271422_MI:0018	To test DIS1-DIS1 interaction further, we took advantage of the two-hybrid system in yeast (26), which uses reporter gene activation as an indirect assay of protein-protein interactions
3220	9276444_MI:0018	Specific interaction of Cks1At with Cdc2aAt
3221	9276444_MI:0018	Specific interaction of Cks1At with Cdc2aAt (top) and Cdc2bAt (bottom)
3222	9341137_MI:0018	Both VAMP1 and VAMP2 interacted strongly with Syn1A, whereas a weaker interaction was detected with cellubrevin (Fig. 5B).
3223	9341137_MI:0018	Deletion of the carboxyl-terminal CXC prenylation signal in Rab3A (Rab3A(Delta CXC), and Rab3A(Q81L,Delta CXC)), and the last two cysteines in Rab1 (Rab1(Delta CC)) completely abrogated PRA1 interaction (Fig. 4).
3224	9341137_MI:0018	Fig. 5A shows that PRA1 interacted with VAMP2 but not with closely related VAMP1 or the ubiquitous cellubrevin.
3225	9341137_MI:0018	Our initial analysis from the yeast two-hybrid screen indicates that PRA1 interacts with both Rab3A and Rab1.
3226	9341137_MI:0018	This VAMP2-VAMP1 chimera showed a positive beta -galactosidase reaction when tested against PRA1.
3227	9367441_MI:0018	The Filamin DNA-binding domain fusion failed to interact with activation domain fusions for Pelle, Dorsal and Cactus, but had a readily detectable interaction (five-fold above background) with a Tube activation domain fusion
3228	9367441_MI:0018	The Toll/IL-1 receptor homology domain appears to be both necessary and sufficient for the interaction of Toll with Filamin
3229	9367441_MI:0018	Toll829-1036 interacting clones encode portions of a Drosophila homolog of ABP280 or Filamin, an actin-binding protein that localizes to the inner surface of the cell membrane
3230	9367441_MI:0018	we confirmed the interactions between Tube and Pelle and between Dorsal and Cactus
3231	9395480_MI:0018	Munc18-1-interacting domain, residues 226-314 of Mint1 as the minimal Munc18-1-interacting sequence tested
3232	9396801_MI:0018	The Rad51-Pir51 interaction was observed when either protein was fused to Gal4 DNA-binding or activation domain,
3233	9396801_MI:0018	We used human Rad51 protein as a bait in a two-hybrid screen of a cDNA library prepared from human HeLa cells.
3234	9409784_MI:0018	it appears that mUBC9 sequences necessary for interaction with human E12 in yeast include the C-terminal 12 residues of mUBC9.
3235	9409784_MI:0018	The C-terminal truncation to residues 442 to 564 eliminates reactivity with mUBC9.
3236	9409784_MI:0018	Using the yeast two-hybrid system, we have cloned 1.0- and 2.5-kb cDNAs encoding the identical murine E2, or ubiquitin conjugating enzyme by virtue of its interaction with the E2A transcription factor.
3237	9464541_MI:0018	Eight cDNAs encoding proteins that specifically interacted with the N-terminus of p130 were isolated in the two-hybrid assay.
3238	9464541_MI:0018	one cDNA encoded the mouse paired-like homeodomain protein, MHox
3239	9472012_MI:0018	To map the cyclin binding domain in p25rum1 we used the two hybrid interaction system. p25rum1 strongly interacts with p56cdc13 cyclin. cyclin. Indeed, expression of either rum1+ or cdc13+ individually in S. cerevisiae from the ADH promoter is lethal but cells co-expressing rum1+ (or certain deletions of rum1+) and cdc13+ are alive. Using different deletions of the rum1+ gene we have mapped the interaction domain between p25rum1 and p56cdc13 to a central region in p25rum1 extending from amino acids 67 to 147 (Fig. 9B).
3240	9515927_MI:0018	DnaQ49 fusion protein showed a sixfold-weaker interaction with DnaE than did wild-type DnaQ.
3241	9515927_MI:0018	The results in Table 2 indicate that the DnaE fusion protein is able to interact specifically with the DnaQ fusion protein. Also, the DnaQ fusion protein binds tightly to the HolE fusion protein.
3242	9556555_MI:0018	Consistent with an idea that p50 interacts with SRC-D, coexpression of a B42 fusion to the full-length p50 further stimulated the LexA/SRC-Dmediated LacZ expression, whereas coexpression of a B42 fusion to the full-length p65 was without any effects
3243	9556555_MI:0018	These interactions were further characterized in the yeast two-hybrid tests (42), in which formations of p50-p50 homodimer and p50-p65 heterodimer were readily detected as previously reported
3244	9560288_MI:0018	We found that yeast transformants containing either of the DB-ETR1 constructs together with the AD-CTR153-568 construct were His1 (histidine prototrophs) and produced blue color in the presence of the b-galactosidase substrate X-Gal, indicating that the histidine kinase region of ETR1 can interact with the amino-terminal domain of CTR1
3245	9560288_MI:0018	We tested for a two-hybrid interaction between AD-CTR153-568 and a fusion of DB to the ERS histidine kinase domain (DB-ERS261-613) as described for ETR1. Again, the yeast transformants were His1 and blue (Fig. 1B).
3246	9580671_MI:0018	Coiled-coil predictions and mapping of the interacting domains of hamartin and tuberin in the yeast two-hybrid system.
3247	9616122_MI:0018	Yeast two-hybrid assay showing specific interaction of dCLOCK with dBMAL1.
3248	9659918_MI:0018	The N-terminal 77 amino acids of HY5are essential and sufficient for COP1 interaction in yeast.
3249	9660868_MI:0018	We detect in a yeast two-hybrid screen that the PDZ domain of hCASK binds to the heparan sulfate proteoglycan syndecan-2
3250	9685490_MI:0018	We also observed a 6.5 fold decrease in the interaction between GAD Rsc6 and LexA Swh3ts16 compared with LexA Swh3.
3251	9697699_MI:0018	To test for a possible interaction between Bog and Rb, we used the yeast two-hybrid system (Fig. 2a). The intensity of X-gal staining for Rb and Bog as compared with Rb and SV40 large T suggested a similar degree of interaction.
3252	9724822_MI:0018	Interactions of CCA1 and CKB1, CKB2, and CKB3 in yeast.
3253	9742395_MI:0018	These results showed that Byr4 fusion proteins interacted with Cdc16 or Spg1 fusion proteins to increase b-galactosidase activity at least 60-fold (Table 1).
3254	9753775_MI:0018	Among the 68 ICK (Interactors of Cdc2 Kinase) clones identified using Cdc2a as the bait ( Wang et al. 1997), 55 represented various lengths of ICK1, seven of ICK2 and six of ICK3.
3255	9753775_MI:0018	The most significant reduction in &#946;-galactosidase activity for the interaction of ICK1 with CycD3 resulted from the deletion of amino acids 109-153, whereas the deletion of amino acids 176-191 had a more detrimental effect on the interaction with Cdc2a.
3256	9755158_MI:0018	COP1 dimerizes through the Coil domain
3257	9755158_MI:0018	Interaction between HY5 and COP1 domain-deletion mutant forms in the yeast two-hybrid system
3258	9761791_MI:0018	At left, interaction of full-length U1-70K protein with SRZ proteins.
3259	9761791_MI:0018	These results clearly demonstrate in vivo interaction of SRZ-22 and SRZ-21 proteins with U1-70K.
3260	9763420_MI:0018	The kinetochore binding domain was used in a yeast two-hybrid screen to isolate interacting proteins that included the kinetochore proteins CENP-E, CENP-F, and hBUBR1, a BUB1-related kinase that was found to be mutated in some colorectal carcinomas
3261	9763420_MI:0018	The third interactor (isolated twice) within this group encoded amino acids 1,989-2,353 of CENP-E. As this portion of CENP-E lies within the CENP-E1958- 2662(J) bait, elements within this region must specify self-association.
3262	9763420_MI:0018	We attempted to localize the portion of CENP-E1958- 2662(J) that specified interactions with CENP-F1804-2104 by using the yeast two-hybrid assay.
3263	9765207_MI:0018	The His- phenotype of yeast strains carrying an ATHKAP2-fused activation domain in combination with the Gal4p DNA-binding domain either alone or in fusion with unrelated proteins (NPK5, PIP-M, and PIP-N; Fig. 7b) showed that the PRL1-ATHKAP2 interaction was specific.
3264	9765207_MI:0018	To screen for Arabidopsis cDNAs encoding PRL1-interacting proteins (PIPs), the full-length PRL1 protein and an amino-terminal PRL1 segment of 321 amino acids were expressed as baits carrying the Gal4p DNA-binding domain in yeast using the two-hybrid vector pAS2 (Durfee et al. 1993). From 18.4 x 107 transformants obtained with a cDNA expression library prepared from an Arabidopsis cell suspension in pACT2 (Durfee et al. 1993), 342 clones showed His+ and LacZ+ phenotype indicating an interaction between the PRL1 baits and cDNA encoded proteins fused to the activation domain in pACT2 (Fig. 7a). Classification of PIP clones identified a family of 62 cDNAs coding for carboxy-terminal segments of PIP-B corresponding to a novel class of Arabidopsis alpha -importins, ATHKAP2.
3265	9771897_MI:0018	Henceforth, the previously characterized AtDBP was designated as AtDBP1 (Clone-A and -B), whereas the newly identified homologue was designated as AtDBP2 (Clone-C). In any case, these results are convincing enough for us to believe that these fishes are not false positives, and that the identified AtDBPs may exhibit an ability to interact with ARR4.
3266	9771897_MI:0018	In contrast to the case of ARR4, neither the intact ARR3 nor the truncated ARR4-&#916;C lacking the C-terminal region were not functional, as judged by the histidine-autotrophy. These results suggested that the common (or highly conserved) receiver domain is not sufficient for the presumed ARR4-AtDBP1 interaction, and that the unique C-terminal region of ARR4 is responsible for the interaction
3267	9801140_MI:0018	The yeast two-hybrid system detects an AtHSF1-E388 interaction with AtTBP1 in vivo
3268	9804171_MI:0018	As shown in Table 1, interaction between ATMPK4 and MEK1 was detected, based on both growth on His-lacking medium and &#946;-galactosidase activity
3269	9804171_MI:0018	Interaction between ATMEKK1 and MEK1 was detected, based on both growth on His-lacking medium and &#946;-galactosidase activity
3270	9807817_MI:0018	The interaction between AtFkbp12 and JD9 (AtFIP37) in the yeast two hybrid system.
3271	9811788_MI:0018	AJH1 Interacts with FUS6 but Not COP9 in the Yeast Two-Hybrid Assay.
3272	9824680_MI:0018	During a search for SCL binding partners using the yeast 2-hybrid system, we isolated two independent cDNA clones (clone L51 and clone V3) of the human DRG homologue from human fetal liver and human thymus cDNA libraries.
3273	9824680_MI:0018	growth on the SCL/ITF-2 sextant serves as a positive control
3274	9824680_MI:0018	Most of the clones encoded the E-proteins ITF-1, ITF-2, or HEB, which are bHLH proteins known to interact with SCL.
3275	9824680_MI:0018	The specific interaction between human SCL and DRG was displayed by the expression of the HIS3 and lacZ genes driven by a functionally reconstituted GAL4 in yeast cells
3276	9840943_MI:0018	All three CIP/KIP inhibitors interact with cyclin E2 as determined by the two-hybrid assay in yeast cells,
3277	9840943_MI:0018	In addition, a novel protein, encoded by clone HT376, was identifed and confrmed to strongly interact with CDK2K33M after re-transformation of the rescued plasmid into yeast cells with CDK2K33M as bait (Figure 1a).
3278	9840943_MI:0018	We used a catalytically inactive mutant of CDK2, CDK2K33M, to search for additional CDK2-interacting protein(s) by the yeast two-hybrid assay.
3279	9840943_MI:0018	When tested in yeast cells, both the catalytically inactive CDK3K33M mutant and wild type CDK3 interact with cyclin E2 (Figure 1a), suggesting that cyclin E2 could potentially function as an activating cyclin subunit of CDK3 and that CDK3-cyclin E2 is functionally distinct from the CDK2-cyclin E2 complex.
3280	9864360_MI:0018	Pex18p and Pex21p interact with Pex7p in the yeast two-hybrid assay.
3281	9867828_MI:0018	The mouse MRP8 and MRP14 readily form homodimeric molecules, although this interaction was significantly weaker than the heterodimeric complex formation.
3282	9891085_MI:0018	Nip7p interacts with Rrp43p and Nop8p.
3283	9989503_MI:0018	By using the yeast two-hybrid system, we found that the Stat5b region between residues 232 and 321 was sufficient for its interaction with Nmi
3284	9989503_MI:0018	Nmi Interacts with Stat5
3285	imex:IM-11847_MI:0018	we performed a yeast two-hybrid analysis. These experiments suggested that RSA-2 could directly bind to both RSA-1 and the core PCM protein SPD-5
3286	imex:IM-11906_MI:0018	additional yeast two-hybrid analyses were performed. Interaction between PGRL1 and Fd were found to require the C-terminal loop of the former (see -C-PGRL1- in Figure 5B).
3287	imex:IM-11906_MI:0018	PGR5 interacts in yeast two-hybrid assays with Fd
3288	imex:IM-11920_MI:0018	To test whether either protein is able to form a homodimer, we again first deleted the self-activating LCRs to create Gsm1269-934 and Gsp1356-1037 and then prepared bait and prey constructs using these or further deletion constructs (Figure 4D, sets with bars).
3289	imex:IM-11920_MI:0018	We therefore used two in vitro approaches-a yeast-two-hybrid assay and a GST pull-down assay-to ask whether Gsm1 and Gsp1 also form heterodimers.
3290	imex:IM-11926_MI:0018	Directional yeast two-hybrid approach to detect direct interaction of Ronin, Ronin-C, and Ronin-N with candidate interacting proteins identified by mass spectometry. Direct interaction of Ronin-C with HCF-1
3291	imex:IM-11926_MI:0018	Identification of Ronin by Yeast Two-Hybrid Screening
3292	imex:IM-11936_MI:0018	To explore the role of IpaB delivered into epithelial cells during Shigella infection of intestine, we performed yeast two-hybrid screening of HeLa cDNA library and found that IpaB interacted with Mad2L2, an APC inhibitor
3293	imex:IM-11943_MI:0018	A two-hybrid screen confirmed the physical interaction between VPS35a and the other two retromer components, VPS26a and VPS29
3294	imex:IM-11952_MI:0018	in specific yeast two-hybrid assays. Homospecific interactions were detected between Smf and full-size BsRecA
3295	imex:IM-11952_MI:0018	the AD fusion in which the first 27 residues of SpRecA are missing interacts with DprA.
3296	imex:IM-11952_MI:0018	Yeast two-hybrid assays revealing DprA and Smf self-interactions.
3297	imex:IM-11959_MI:0018	only Rad17 directly interacts with Rad18
3298	imex:IM-11959_MI:0018	the level of interaction is comparable to that of Pol30 with Rad18
3299	imex:IM-11993_MI:0018	We found that Sgs1 interacts with Ubc9 and SUMO in the yeast two-hybrid system
3300	imex:IM-12018_MI:0018	Yeast two-hybrid assays show the interaction of Borealin10-109 with Survivin
3301	imex:IM-12018_MI:0018	Yeast two-hybrid assays show the interaction of Borealin10-109 with Survivin and INCENP (via its N-terminal 58 residues
3302	imex:IM-12034_MI:0018	assays revealed that full length Bcl-3 indeed interacted with Cyld and that the binding site for Bcl-3 on Cyld corresponded to the C-terminal part of the protein
3303	imex:IM-12131_MI:0018	We determined whether Mre11H129N protein maintains the ability to homodimerize by using the yeast two-hybrid system.
3304	imex:IM-12132_MI:0018	However, although the monomeric single variants L77K and L154D interact with Nbs1 and Rad50, the salt-bridge L77K/L154D dimer is defective in these interactions
3305	imex:IM-12132_MI:0018	To probe the Mre11-Mre11 interface, we substituted charged residues for Leu77 and Leu154 in S. pombe Mre11 (P. furiosus Mre11 Leu61 and Leu97; Figure S1). Two-hybrid analysis shows that wild-type Mre11 had a robust self-interaction,
3306	11018022_MI:0019	Indeed, PHIP could be readily detected in anti-IRS-2 immunoprecipitates,
3307	11018022_MI:0019	To investigate the interaction of PHIP and IRS-1 in vivo, lysates from NIH/IR cells (NIH3T3 cells overexpressing the insulin receptor) were immunoprecipitated with anti-IRS-1 Abs directed against the C terminus of IRS-1
3308	11684708_MI:0019	Using the rabbit anti-TRADD antibody, we precipitated complexes containing TRADD proteins from 1% NP-40 soluble fraction of HMEC lysates (Fig. 4B). TRADD was immunoprecipitated with anti-TRADD antibody, but not with control rabbit IgG. K18 was coimmunoprecipitated with TRADD, using the anti-TRADD antibody.
3309	11684708_MI:0019	We next checked the binding of TRADD with K18 after TNF treatment by immunoprecipitation (Fig. 5 B). Lysates prepared from HMEC treated for 20 min with various doses of TNF, or left untreated, were immunoprecipitated with anti-TRADD antibody, and the presence of K18 or TNFR1 in the TRADD immune complex was examined. Coprecipitating K18 was readily detected in lysates from untreated (control) cells and physiological dose TNF (3 ng/ml)-treated cells but was barely visible in the 100 ng/ml TNF-treated samples.
3310	12072504_MI:0019	FIG. 9. HPV16 E7 mRNA-CK7 interaction in squamous cervical cancer SiHa cell lysate.
3311	15936270_MI:0019	association between the Wsh3 and Tea1 proteins in cell lysates was detected by coprecipitation experiments (Figure 4B).
3312	16286473_MI:0019	These data indicate that DGK is the predominant isotype that binds to pRB.
3313	16306047_MI:0019	The possibility that inhibition was related to the interaction of 
-catenin with PS1 was also investigated. Both proteins were co-immunoprecipitated either in SW-480 cells or in RWP1 cells
3314	16306047_MI:0019	The possibility that inhibition was related to the interaction of 
-catenin with PS1 was also investigated. Both proteins were co-immunoprecipitated either in SW-480 cells or in RWP1 cells (Fig. 3). We detected that PS1 also interacted with the 
-catenin homologue plakoglobin in both cell lines.
3315	16306047_MI:0019	Transfection of PS1 increased the amount of 
-catenin that could be precipitated with wild-type Tcf-4, but the increase was only very modest with Tcf-4 S60E (Fig. 6C). Better PS1 stimulation was observed when binding of Tcf-4 to plakoglobin was analyzed.
3316	16710422_MI:0019	Identifying the amino acid residue(s) mediating 14-3-3 binding to K17 should help to define the role of this interaction with regards to protein synthesis. Two consensus 14-3-3-binding sites, threonine 9 (Thr 9) and serine 44 (Ser 44), are present in the non-helical head domain of K17 (Supplementary Fig. 4a). We mutated these sites to alanine residues and transfected the mutant DNA constructs into BHK fibroblasts. Relative to wild-type K17, T9A and S44A single mutants and the double mutant T9A/S44A show significantly reduced 14-3-3 binding (Supplementary Fig. 4b). The similar loss of binding observed for all mutants implies that Thr 9 and Ser 44 both contribute to binding to 14-3-3 (ref. 25).
3317	16710422_MI:0019	To identify K17-binding proteins that might provide mechanistic insight into this growth defect, we set up a biochemical screen using a reversible chemical crosslinker in cultured skin keratinocytes. We identified 14-3-3sigma (also known as stratifin), an epithelial-specific isoform of 14-3-3 (ref. 16), as a specific K17-binding protein in keratinocytes (Supplementary Fig. 3a).
3318	16760425_MI:0019	To determine whether CP110 and CaM interact before mitosis, we synchronized cells by serum deprivation and immunoprecipitated CP110 from extracts of cells synchronously traversing the cell cycle. CP110 and CaM were coimmunoprecipitated from extracts  of cells in G, G, S, and G(Figure 2B). Interestingly, although CP110 levels vary during the cell cycle, the amount of immunoprecipitated CaM remains relatively unchanged (Figure 2B), suggesting that the levels of centrosomal CaM associated with CP110 may be constant throughout the cell cycle.
3319	18000879_MI:0019	Radioactive in vitro translation of pGBKT7-p53 and pGADT7-T followed by coimmunoprecipitation using anti-c-myc-antibodies and protein A beads (BD Biosciences) served as positive control for the biochemical verification of selected BBS protein-prey interactions (Fig. 2).
3320	imex:IM-11856_MI:0019	KDR could be phosphorylated by VEGF-C and heterodimerized with Flt-4 in THP-1 leukemia cells
3321	10512628_MI:0027	the N-tube/N-pelle mixture was considered as a 1:1 heteromeric complex, evidence for which comes from the sedimentation equilibrium experiments
3322	10954706_MI:0027	Incubation in filament assembly buffer induced a rapid polymerization of K8 and K18 (Fig. 2A, lanes 1). Recombinant GST (which served as a control) did not sediment in the presence of K8/K18 (Fig. 2, A and B, lanes 3).
3323	10954706_MI:0027	Recombinant GST (which served as a control) did not sediment in the presence of K8/K18 (Fig. 2, A and B, lanes 3). In the absence of K8/18, GST-Mrj did not sediment (Fig. 2, A and B, lanes 4); but in the presence of K8/18, a substantial portion of GST-Mrj was precipitated with K8/18 (lanes 5).
3324	11684708_MI:0027	Incubation in filament assembly buffer induced a rapid polymerization of K8 and K18 (Fig. 2A, lanes 1). As a control, recombinant GST was not sedimented in the presence of K8/18 (Fig. 2 A and B, lane 3).
3325	11684708_MI:0027	In the absence of K8/18, GST-TRADD was not sedimented (Fig. 2 A and B, lane 4), but in the presence of K8/18, a substantial portion of GST-TRADD was precipitated (Fig. 2 A and B, lane 5). Because TRADD interacted with K18, but not with K8 in the two-hybrid analysis, the TRADD sedimenting with K8/18 was thought to be associated with the K8/18 polymer via direct binding to K18. In addition, TRADD did not sediment with vimentin (Fig. 2 A and B, lane 6) or desmin (Fig. 2 A and B, lane 7), findings consistent with results obtained using the two-hybrid method.
3326	12119386_MI:0027	Erg26p/Erg28p and Erg27p/Erg28p Comigrate in the Same Complex.
3327	14508515_MI:0027	this further confirms that menin associates tightly with NMHC II-A and remains bound to it upon myosin release from actin after addition of ATP.
3328	16142218_MI:0027	Analysis of cytoplasmic extracts prepared from human HEK293 cells showed that Dicer and TRBP, co-sediment in a region corresponding to a molecular mass of 250 kDa.Notably, miR-17, an abundant miRNA in HEK293 cells, was also enriched in this region
3329	16142218_MI:0027	Analysis of cytoplasmic extracts prepared from mouse teratoma P19 cells showed that Dicer and TRBP, or their mouse counterparts, co-sediment in a region corresponding to a molecular mass of 250 kDa. Notably, miR-17, an abundant miRNA in HEK293 cells, was also enriched in this region.
3330	16260786_MI:0027	We then demonstrated that the FliI -(2-91)-FliH-(117-258) complex is very stable in solution and can be isolated and purified by gel filtration chromatography (Fig. 6).
3331	16641999_MI:0027	endogenous TMP21 from mouse brain, neuron-like SHSY-5Y cells and human embryonic kidney (HEK-293) cells could be co-immunoprecipitated with endogenous nicastrin, aph-1, pen-2 and PS1 (Fig. 1a, and Supplementary Fig. 1a) and that it had an overlapping size distribution with presenilin complex components in high-molecular-mass (more than 650-kDa) fractions on glycerol velocity gradients
3332	17055431_MI:0027	The cosedimentation suggests that these proteins form a complex. This complex was isolated and analyzed by laser-light scattering. The molecular mass of the complex was 154.6 kDa (Figures 5D and 5E). This corresponds well to the calculated molecular mass of 155 kDa of a 1:1:1 complex of P3H1, CRTAP, and Cyclophilin B.
3333	17113138_MI:0027	Wapl was detected in 8S fractions, and only a small amount was detected after long exposures in 14S fractions where cohesin sediments (Figure 2A and data not shown). The interaction between Wapl and cohesin may therefore not be stable enough to persist during the 18 hr centrifugation step. Pds5A also sediments corresponding to 8S
3334	17113138_MI:0027	When we peptide eluted proteins bound to Wapl antibodies and separated them in density gradients, we also found that Wapl and Pds5A cosedimented in 8S fractions (Figure 2C).
3335	18064632_MI:0027	GRP78 colocalized with Raf-1 mainly in the mitochondrial fractions
3336	18191223_MI:0027	ADP promotes the dimerization of Ire1cyto
3337	18692470_MI:0027	smaller complexes, such as Sec13-31 cuboctahedrons, can only be recovered by sedimentation at high speed
3338	18692470_MI:0027	Using this simple approach for self-assembly, we looked at the sedimentation behavior of Sec13-31 and Sec23-24 when coincubated in solution.
3339	8206846_MI:0027	An in vitro binding assay showed that FliG cosedimented with the MS ring complex at a FliG/FliF molar ratio of between 1:3 and 1:1 (Fig. 4B, lanes 2).
3340	8206846_MI:0027	The amount of FliM bound to the MS ring complex was estimated from SDS gels to be at a FliM/FliF molar ratio of around 1:5 or less (Fig. 4B, lanes 3, and Fig. 5).
3341	9214646_MI:0027	The six MCM/P1 proteins are present in a high molecular weight complex.
3342	10591219_MI:0028	Amino-terminal amino acid sequencing of the smaller RCAF subunits revealed that they are Drosophila histones H3 and H4. Furthermore, this microsequencing analysis indicated that the Lys 5 and Lys 12 of RCAF H4 were acetylated, whereas Lys 8 was not detectably acetylated. Similarly, Lys 14 of RCAF H3 was fully acetylated, whereas Lys 4 and Lys 9 were not detectably acetylated.
3343	10591219_MI:0028	Three polypeptides were correlated with the peak of RCAF activity through the three final purification steps
3344	10600387_MI:0028	In the presence of AcCoA the sedimentation profile of Hpa2 could best be fit by a single species model yielding a molecular weight of 71,454
3345	10864495_MI:0028	The fit of the absorbance versus radius profile for sedimentation equilibrium corresponds to a single molecular species with a molecular mass of 55.9(±1.0) kDa. This corresponds to a trimer with stochiometry SpoIIAB2:&#963;1F (calculated molecular MASS=58.1 kDa).
3346	12482983_MI:0028	dADA2a in fractions containing complexes with molecular masses between 400 and 800 kDa (Fig. 4B, fractions 6 to 12) which also contained a portion of dGCN5, TAF9, TAF10, and TBP, together with detectable levels of dADA2b
3347	12482983_MI:0028	In the fractions which correspond to masses greater than 2 MDa (fractions 16 to 20), dADA2b cosedimented with the second peak of dGCN5, TBP, and all the other TAFs tested
3348	12756240_MI:0028	Quantitative analysis indicated that at least 40% of Isu1 protein co-localized with Jac1.
3349	12756240_MI:0028	When Isu1 was incubated with Ssq1 in the presence of ADP, about 23% of Isu1 co-migrated with Ssq1 in fractions 13-17, indicating that Isu1 and Ssq1 could interact (Fig. 3D).
3350	14555658_MI:0028	ADP binding of wild type and mutant isocitrate dehydrogenases
3351	15225636_MI:0028	Distribution of the &#945;-subunits in soluble extracts of HEK 293 cells.
3352	15696166_MI:0028	MeCP2 cofractionated with Brm, which is presumed to be part of the larger SWI/SNF complex (Fig. 1a). Western-blot analysis of nuclear extracts also showed that BAF57 and INI1 cofractionated with MeCP2, suggesting that MeCP2 associates in vivo with the Brm-containing SWI/SNF complex.
3353	16239229_MI:0028	In a control experiment, 1 mol of free wild type GroEL or GroEL(L309K) (without GroES, nucleotide and BeFx) bound 2 mol of rhodanese (lanes 1 and 2).
3354	16239229_MI:0028	The GroEL(L309K) complex, formed in the presence of ADP and BeFx, had an apparent composition of 1:1:2 (GroEL(L309K)
GroES
rhodanese)
3355	16319076_MI:0028	Although we have identified several potential profilin 2 binding sites along the PRD, the question remains whether all these sites are occupied in the profilin 2-dynamin 1 complex. To determine the stoichiometry of the complex in vitro we performed velocity sedimentation using an analytical ultracentrifuge.
3356	16615894_MI:0028	Sedimentation velocity studies of the EI[Delta]UEV-A complex indicated the presence of two species having corrected sedimentation coefficients of approximately 3.6 and 4.8 S (Fig. 1C).
3357	16892067_MI:0028	Subcellular fractionation by continuous sucrose density gradient centrifugation showed that RAPL and Mst1 fractionated together exclusively in light fractions (fractions 2 and 3), which contained early (EEA1and Rab5) and late (Rab11) endosomal marker proteins, but lacked beta-COP and transferrin receptor, indicative of the Golgi-derived vesicles and recycling endosomes, respectively (Fig. 7b).
3358	17442384_MI:0028	Sedimentation equilibrium centrifugation analysis revealed that full-length ESCRT-I sample has an experimental molecular mass of 117 kDa
3359	17662939_MI:0028	Velocity sedimentation analysis of the Met928-InlB321 complex
3360	17662939_MI:0028	Velocity sedimentation analysis of the Met928-InlBfl complex (2 &#956;M) with a 2-fold excess of dp12 heparin.
3361	19135897_MI:0028	Indeed, when a construct encoding only the N-terminal motor domain of KHC was coexpressed with Miro they exhibited Ca2+-dependent coprecipitation (Figures 6G and 6H).
3362	19135897_MI:0028	When KHC was coexpressed with milton and Miro, however, Ca2+ caused a substantial shift of KHC, together with the adaptor proteins, to the soluble fraction.
3363	350874_MI:0028	Thus, the aggregate alpha6beta6 has a molecular weight of approximately 2.4 X l06, for which a sedimentation coefficient of approximately 44 S was obtained.
3364	9488738_MI:0028	Purification of recombinant human RFC from Sf9 cells
3365	imex:IM-11883_MI:0028	In contrast, BV6 induced dimerization of c-IAP1 BIR2-BIR3,
3366	imex:IM-12018_MI:0028	By analytical ultracentrifugation, Survivin-Borealin10-109-INCENP1-58 sedimented at a molecular mass of 35 kDa (Figure 2D), consistent with a complex of 1:1:1 stoichiometry (calculated molecular weight 34.7 kDa)
3367	10428848_MI:0029	The sedimentation coefficient of the Cet1(201-549)p-Ceg1p complex was 7.3. This value suggested a heterotrimeric subunit structure which, given that Cet1(201-549)p per se sediments as a dimer, whereas Ceg1p alone is monomeric (see below), likely consists of two molecules of Cet1(201-549)p and one molecule of Ceg1p.
3368	10490612_MI:0029	SBF ran at 180 kDa, a size which is close to the predicted size of a heterodimer of Swi4 (123 kDa) and Swi6 (91 kDa).
3369	10716984_MI:0029	Analyses of the oligomeric structure of the small RNR subunits composed of H6Rnr2p (Fig. 4A), Rnr4p, or coexpressed H6Rnr2p/Rnr4p complex by sucrose gradient centrifugation showed that all three proteins clearly sedimented as dimers with sedimentation coefficients of 5.6 S.
3370	10716984_MI:0029	Next, we determined the oligomeric structure of the active yeast RNR complex with Rnr1p and H6Rnr2p/Rnr4p.
3371	10770926_MI:0029	stable complexes that included Mcm2/3/4/5/6/7, Mcm2/4/6/7, Mcm4/6/7, Mcm3/5,
3372	11907036_MI:0029	Migration of PEK in either condition was significantly higher than its monomeric size of 125,000, indicating that PEK oligomerized
3373	12071968_MI:0029	Briefly, after their dissociation from the GroEL complex, proteins were separated by SDS/PAGE, electroblotted onto poly(vinylidene difluoride) membranes, and subjected to N-terminal sequencing. The amino-acid sequences of proteins X and Y were identified in the Swiss-Prot databank as GatY and UP12
3374	12107167_MI:0029	in all cell types examined, LDH localized to the bottom of the sucrose gradients, consistent with its association with mRNA being actively translated. In addition, direct association of LDH with AUF1 was demonstrated.
3375	12392552_MI:0029	S-tagged Ydr116c, Img1, Ynl177c, Img2, Ypr100w and Ynr022c proteins were localized in the large subunit.
3376	12392552_MI:0029	S-tagged Ypl013c, Ymr188c, Ygr165w proteins were detected in fractions of the small subunit,
3377	14623880_MI:0029	Purified material was subjected to centrifugation through a glycerol gradient and studied by Western blot analysis after SDS-PAGE to estimate the size of Kv4.2*KChIP2 channels.
3378	15148393_MI:0029	Sucrose gradient sedimentation of the wild-type extracts was performed (Fig. 2C). Cti1 exhibited a broad sedimentation profile ranging between 4.5S and 15S, overlapped with the peak of 13S holocondensin complex
3379	16043509_MI:0029	The Ski2/3/8 complex sediments at 380-Kda, consistent with a stoichiometry of 1:1:1.
3380	16369483_MI:0029	Western blotting revealed that mutant SOD1 had a distribution pattern similar to chromogranins, the trans golgi marker adaptin and the SNARE protein syntaxin-1.
3381	17314511_MI:0029	c&#8209;MYC was detected in fractions 4 to 20 (of 23 fractions in total). Therefore, c&#8209;MYC is present in a large number of protein complexes with a broad range of molecular weights. As expected its obligate dimerization partner MAX was detected in the majority of these fractions (3 to 19). Interestingly, RNA polymerase II was mainly present in fractions 13 to 15, whereas the replication associated protein MCM7 was detected in fractions 6-14. The distribution of DBC-1 overlapped largely with the distribution of MCM7, whereas U5&#8209;116kD was present in fractions 6-8 as well as fractions 17-19 and therefore presumably forms an additional c&#8209;MYC containing complex.
3382	17314511_MI:0029	U5-116kD was present in fractions 6-8 as well as fractions 17-19 and therefore presumably forms an additional c&#8209;MYC containing complex.
3383	18358808_MI:0029	We found that pontin and reptin participate in large complexes, which overlap the size distributions of both endogenous telomerase and Flag-TERT by glycerol gradient sedimentation (Figure 1A).
3384	18420585_MI:0029	BimEL distributed along with DLC1 and -tubulin
3385	18420585_MI:0029	both DLC1 and BimEL shifted from the heavier to the lighter fractions 16-20 (peaked at 18-19 and 18-20 for BimEL and DLC1, respectively), and corresponded to the sedimentation positions of mitochondrial outer membrane protein, Tom20
3386	18692471_MI:0029	SNAP-23 and syntaxin 4 were detected in the membrane raft fractions before and after Fcvar epsilonRI stimulation
3387	18805096_MI:0029	These sedimentation experiments suggest that FMRP, CYFIP, and eIF4E might reside in a common complex, perhaps with mRNA.
3388	8062390_MI:0029	Ste5, Ste11, Ste7, and Fus3 Cosediment in a Glycerol Gradient
3389	8668140_MI:0029	In order to prove that Bul1 and Rsp5 physically interact in vivo, we attempted to detect a complex of Bul1 and Rsp5 by centrifuging the cell lysates through a sucrose density gradient.
3390	8756677_MI:0029	Colocalization of Sst2 and Gpa1.
3391	8756677_MI:0029	the a-factor receptor (Ste2), a plasma membrane protein, and Ste4, another component of the receptor-coupled G protein, showed the same specific enrichment in fractions 10 and 11
3392	imex:IM-11815_MI:0029	The scans were corrected for baseline and were best fit to a single species model (-) with a molecular weight of 105,700 (252), which is close to the calculated molecular weight of 101,247.15 for the combined sequence of each protein for a 1:1 complex.
3393	imex:IM-11971_MI:0029	Hrd1p, Hrd3p, Usa1p, and Der1p are present in a large complex, which we will refer to as the Hrd1p core complex.
3394	11230138_MI:0030	In the mixture of A29C and I441C mutant proteins, however (Figure 6E, lane 12), a discrete dimer-length product was observed
3395	11853560_MI:0030	Covalent cross-linkage of biotinylated CaM to a human EGFR complex
3396	11853560_MI:0030	Covalent cross-linkage of biotinylated CaM to a human EGFR complex.
3397	11853560_MI:0030	To determine whether CaM could be associated with the EGFR,we performed cross-linkage experiments using the immunoprecipitated receptor from A431 tumour cells (Figure 2A) and EGFR-T17 fibroblasts (Figure 2B).
3398	11909951_MI:0030	To understand the biochemical function of Hbs1p, the prediction that it would be capable of binding GTP was investigated by UV cross-linking of radiolabeled GTP to E. coli-purified, GST-tagged-Hbs1p.
3399	12107167_MI:0030	a single 36-kDa protein capable of binding the ARE of GM-CSF RNA in the context of full-length RNA was observed, which colocalized with hnRNP A1. In DP28-9 and CB7 cytosols, (Fig. 1, B and C),
3400	12107167_MI:0030	The 36-kDa protein in the 1 M poly(U) fraction resolved as a single band on 15% SDS-PAGE that was excised, digested in situ with trypsin, and analyzed by matrix-assisted laser desorption/ionizationmass spectrometry.
3401	12107167_MI:0030	To verify that the p36 RNA binding activity in the CB3 cytosol was LDH, a rabbit polyclonal anti-LDH antibody was used to immunoprecipitate the radiolabeled RNA-protein complex from UV cross-linked CB3 cytoplasmic lysates (Fig. 2D).
3402	12217076_MI:0030	It was found that DSS cross-linked ALB3 to the cpSecY complex, as both proteins were present in the immunoprecipitated crosslinked product
3403	12237468_MI:0030	After crosslinking the complex still migrated in BNE at 1 MD. In the second (SDS) dimension the band at 32 kD was replaced by a new band at approximately 70 kD (illustrated for sBID in Fig. 1BGo). Peptide mass fingerprinting showed this new band to contain both PHB1 and PHB2
3404	12493774_MI:0030	Physical interactions between Nep98p and Jem1p were confirmed by cross-linking.
3405	14726512_MI:0030	To address whether the human small Tims directly interact with translocation intermediates of carriers during import into mammalian mitochondria, human ANT3 was subjected to chemical cross-linking.
3406	15236960_MI:0030	Lane 4 shows the DMS-treated mixture of helicase and CTD. The circled band was shown to contain both helicase RhlB and CTD using in-gel protease digestion and MALDI-mass spectrometry analysis.
3407	15696166_MI:0030	we cross-linked cells with formaldehyde, lysed them and carried out immunoprecipitations for MeCP2 and Brm followed by western-blot analysis. Antibody to Brm immunoprecipitated MeCP2 from soluble cross-linked protein extracts (Fig. 1g); conversely, antibodies to MeCP2 immunoprecipitated Brm.
3408	15797382_MI:0030	Tim21 can be crosslinked to Tim23.
3409	15805487_MI:0030	After treatment with formaldehyde, a novel high molecular mass band, approximately twice as high as that of the Myc-CRY1 monomer, recognized by anti-Myc antibody, was observed after SDS-PAGE separation of the protein extracts prepared from dark-grown and blue light-grown, and blue light-irradiated seedlings expressing Myc-CRY1
3410	16239229_MI:0030	To investigate whether or not the GXXLE region is in contact with GroES in the E. coli GroEL
GroES complex, we conducted a series of cross-linking experiments using mutants of E. coli GroEL and GroES.
3411	16497658_MI:0030	Figure 4 (lane 1) demonstrates that AtCyp59 could be efficiently cross-linked to RNA in vitro.
3412	17719542_MI:0030	hCAS/CSE1L protein could be detected in immunoprecipitates of Ad-p53 from extracts of crosslinked H1299 cells, and a weak signal above background was even detected in uncrosslinked cell lysates (Figure 2A).
3413	17719542_MI:0030	Isolation and identification of hCAS/CSE1L polypeptide from p53-associated rapidly sedimenting crosslinked protein complexes are described in Experimental Procedures and Figure S1
3414	17803912_MI:0030	the LPS-bound TLR4- MD-2 formed a band consistent with the size of the TLR4-MD-2 heterotetramer after crosslinking with glutaraldehyde and SDS gel electrophoresis
3415	17934213_MI:0030	cross-linking is essential for the detection of the interaction between APP and LINGO-1 by co-IP.
3416	18272596_MI:0030	APP association with NgCAM. Western blots with antibodies against NgCAM after immunoprecipitating for AP tag.
3417	18319262_MI:0030	Fhit complexes were purified through the His6-tag and co-purified proteins were detected with antisera against Hsp60, Hsp10 and Fdxr; Hsp60 and Fdxr were detected only in lysates of cells exposed to DSP (Fig. 2A,C), while Hsp10 was also detectable without cross-linking
3418	18455986_MI:0030	Supp Fig. 2
3419	18805092_MI:0030	Consistent with closed structures, introduction of each Cys pair into unmodified Cul1-Rbx1 allows substantial intermolecular, DTT-reducible disulfide crosslinking of Cul1 and Rbx1 under oxidizing conditions (Figures 4B and S9)
3420	18854156_MI:0030	Soj forms a complex with DnaA-His12
3421	18976803_MI:0030	Yeast cells expressing Mup1-FLAG and/or Art1-HA were stimulated with methionine, treated with crosslinkers, and TCA precipitated.
3422	2839507_MI:0030	a-factor cross-linked to the truncated form of STE2 protein.
3423	8618836_MI:0030	amount of crosslinked GroEL7 and GroEL7GroES7 species and, in contrast, a native GroEL14(GroES7)2 particle produces only GroEL7GroES7, with no GroEL7 crosslinked species (Table 1, Fig. 1A).
3424	9425043_MI:0030	The cross-linkage was carried out in the presence of Ca2+, and the GST-HER(645-660)-calmodulin complex was visualized as a double band by Coomassie Blue staining after electrophoresis run in the presence of either Ca2+ or EGTA in the sample buffer.
3425	imex:IM-12024_MI:0030	GCC185 is also dimeric
3426	imex:IM-12128_MI:0030	Recombinant wild-type NML or its mutants were mixed with 3H-labeled SAM and crosslinked by UV irradiation.
3427	16717101_MI:0038	Thus, the Sir4-CC domain alone or in complex with Sir3-(464-978) assembles into higher order protein arrays in the absence of DNA, albeit at high protein concentrations.
3428	10888666_MI:0040	AtTLG2a and AtTLG2b colocalize with AtVPS45
3429	10888666_MI:0040	AtVPS45 colocalizes with AtELP, and not with AtPEP12, on ultrathin cryosections of Arabidopsis roots.
3430	12051897_MI:0040	Phosphofructokinase is an octamer composed of 4alpha and 4betasubunits arranged in a dihedral point group symmetry D2.
3431	12217076_MI:0040	Electron microscopy of double-immunogold-labelled ultrathin sections of chloroplasts from Arabidopsis leaves was performed to verify further an interaction ofALB3 with the cpSecY complex. ALB3 and cpSecY were visualized using secondary antibodies conjugated to 5 nm and 10 nm gold particles respectively. In all cross-reactions of different sections analysed, the gold particles were attached to the thylakoid membrane and showed a similar labelling pattern
3432	15182174_MI:0040	The intermolecular distance between 15 nm gold particles (detecting SCP-2) and 6 nm gold particles (detecting caveolin-1) determined in six examples from several cells ranged from about 100-240 Å.
3433	15467741_MI:0040	Colocalization of merlin and magicin in the cortex of a CAD cell determined by electron microscopy.
3434	16286452_MI:0040	Electron microscopy analysis of the PrP82-146 flowing solution detected globular particles with a diameter of 31  11 nm (mean  S.D.; range, 8 -56 nm; Fig. 1a).
3435	16286452_MI:0040	Electron microscopy analysis of the PrP82-146 flowing solution detected globular particles with a diameter of 31  11 nm (mean  S.D.; range, 8 -56 nm; Fig. 1a). These poorly defined sphere-shaped species were identified as PrP82-146 by immunogold labeling (Fig. 1b).
3436	16286452_MI:0040	Small round shaped material, often organized to form little chains, was present in the solution of A42 immobilized on sensor chip as an internal control (Fig. 1d). For A42, however, the globular units appeared smaller (8  2 nm; range, 3-15 nm).
3437	16301313_MI:0040	at 2-fold excess of  RavA (3.24 M RavA and 1.8 M LdcI in the presence of 3 mM ADP or ATP
S), the background became clean, individual LdcI views virtually disappeared, and most of the protein was present as an amazingly large and apparently homogeneous RavA
LdcI complex.
3438	16314420_MI:0040	The representative electron micrograph of double immunogold labeling demonstrates co-localization of Neu1 and EBP on the cell surface of ASMCs
3439	16369483_MI:0040	Double immunohistochemistry using secondary antibodies conjugated with different gold particles (5nm and 10nm)provided frequent detection of cluster complexes comprising SOD1 and chromogranins.
3440	17468262_MI:0040	We then performed double immunogold labeling with antibodies against Arabidopsis SKD1 and against the three Rab5-type GTPases (Figures 6D to 6F). In all cases, the immunogold results support the partial colocalization of SKD1 and the three endosomal Rab GTPases on MVBs shown in the confocal analysis of the fluorescent proteins.
3441	17662947_MI:0040	Electron micrographs of FtsZ assembled in the presence and absence of UgtP suggest that UgtP interferes with stabilizing lateral interactions between single-stranded protofilaments. In the absence of UgtP, FtsZ formed large bundled structures, the consequence of lateral interactions between protofilaments (Figure 3E).
3442	17662947_MI:0040	However, we observed very few bundles at a 1:2 ratio of UgtP to FtsZ, and protofilaments were significantly shorter, consistent with a decrease in polymer stability (Figure 3F).
3443	17662947_MI:0040	Intriguingly, UgtP itself formed higher order structures in FtsZ assembly buffer (Figures 3G and 3H). These structures, which appear to consist of closely stacked spirals of UgtP monomers (seven or eight per turn), were less prevalent in the presence of FtsZ (Figure 3F), suggesting that UgtP inhibition of FtsZ assembly occurs at the expense of UgtP self-assembly.
3444	18191225_MI:0040	Immuno-EM of plasma membrane sheet shows colabeling of Cav1-GFP (6 nm gold) with PTRF-RFP (2 nm gold; arrowheads) in cotransfected BHK cells.
3445	18676877_MI:0040	PDI5 and RD21 colocalized in ER cisternae (Figures 8A and 8D), LVs (Figure 8B),PSVs (Figure 8C), the Golgi, trans-Golgi network (TGN), and vesicles (Figure 8D) of endothelial cells.
3446	18692470_MI:0040	COPII coats were prepared for cryo-EM analysis by preserving the samples in vitreous ice
3447	350874_MI:0040	Micrograph of fatty acid synthetase from yeast negatively stained with methylamine tungstate: x 200,000.
3448	imex:IM-11979_MI:0040	Immunoelectron microscopy confirmed the localization of p62 in the cytoplasmic aggregated structures (Figures 3D, top panel, and S5).
3449	imex:IM-11979_MI:0040	Immunofluorescence analysis of cellular localization of ubiquitin, p62, and LC3 in autophagy-deficient hepatocytes.
3450	imex:IM-12005_MI:0040	As the next step in the structural characterization of TRAPP I, we examined the morphology of rTRAPP I by single-particle electron microscopy (EM).
3451	imex:IM-12140_MI:0040	Electron Microscopic Analysis of Assembly Intermediates
3452	10075709_MI:0047	Pol II purified from HeLa cell nuclear pellet was separated by SDS-PAGE, transferred to polyvinylidene difluoride membrane, renatured, and probed with 35S-labeled p160. As shown in Fig. 5A, a clear band of ~200 kDa, which co-migrates with the largest subunit of pol II, was detected. p160 also reacted with GST-p14 protein which was similarly blotted onto the membrane.
3453	10393905_MI:0047	A modified dot-blot immuno analysis was performed to test the binding between GST fusions (KAPP mutants) and MBP fusions (MBP, KIK1 and K558E).
3454	10409688_MI:0047	Far Western analysis has also been used to examine the ability of eIF4G1 to bind to eIF4E
3455	10488241_MI:0047	Confirmation of the MFP1-MAF1 interaction by protein overlay analysis.
3456	10764785_MI:0047	Five of the mutations (R275Q, R293Q, E295K, R297S, and A302D) were greatly reduced in their ability to bind sigma 70.
3457	10809665_MI:0047	Following denaturation and renaturation, the membrane was probed with radiolabeled Zeste (Fig. 6B). Autoradiography of the blot revealed that Zeste directly bound to a number of BAPs, most notably MOR, BAP170, and p400. Somewhat less prominent binding was observed to BAP111 and OSA.
3458	10809665_MI:0047	When radiolabeled MOR was used as a probe in a far-Western assay, the pattern of binding was very different (Fig. 6B, lane 4). MOR bound to BRM and itself, as was previously reported (Crosby et al. 1999), as well as to BAP111, BAP60 and to either BAP47 or BAP45.
3459	11157757_MI:0047	a far western blot containing several FTZ deletion constructs probed with 35S-labeled FTZ-F1. The full-length FTZ polypeptide is recognized well by the radiolabeled FTZ-F1 probe
3460	11157757_MI:0047	The C-terminal half of FTZ-F1 (A+LBD) binds well to the FTZ probe (Figure 5A, lane 1), as previously shown in Figure 3B.
3461	11402167_MI:0047	The labeled FISL peptide was overlaid onto a protein blot of SOS3 and control proteins. Figures 2B and 2C show that FISL was able to bind to GST-SOS3. This binding is not dependent on Ca2+, because similar results were obtained when the reaction was depleted of Ca2+
3462	11853560_MI:0047	For this purpose, we overlaid the immunoprecipitated EGFR using biotinylated CaM (see Figure 5).
3463	11988016_MI:0047	we then expressed the PCD17 peptides as a bacterial GST fusion protein separated by SDS-PAGE, and separated GST alone by SDS-PAGE as a control. These proteins were blotted onto a PVDF membrane and probed with the purified carboxyl terminal region of MRG X tagged with FLAG; Western blotting was then carried out using anti-FLAG M2 antibody. As shown in Fig. 3, a specific interaction was seen with GST-PCD17
3464	12486115_MI:0047	Mps3p interacts with Cdc31p.
3465	12907755_MI:0047	we observed efficient binding of PTP-H1, PTP-1B, TC-PTP, and Sap1 to GH-induced GHR
3466	15080792_MI:0047	To determine whether ErbB2 could be responsible at least in part for the high-molecular-mass signal observed in overlay experiments with biotinylated CaM using whole cell extracts, we repeated the experiment using immunoprecipitated ErbB2.
3467	15153109_MI:0047	GST-eIF4E-1 (Fig. 6A, lanes 1-3) was found to interact with all three (His)6-tagged 4E-BP isoforms (Fig. 6B, lanes 1-3, 4E-BP1; lanes 4-6, 4E-BP2; lanes 7-9, 4E-BP3) to a similar extent
3468	15153109_MI:0047	GST-eIF4E-2 (Fig. 6A, lanes 4-6) was found to interact with all three forms of (His)6-tagged 4E-BPs
3469	15316289_MI:0047	AtBT1 is a Ca2+-dependent CaM-binding protein.
3470	15316289_MI:0047	To verify this prediction, the full length cds of all five AtBT genes were cloned into expression vector pET32b (Figure 5A) for a 35S CaM-binding assay. The CaM-binding assay was performed in the presence of Ca2+ and demonstrated that all five AtBTs are Ca2+/CaMbinding proteins.
3471	15467741_MI:0047	Blot overlay assays were then employed to test a direct interaction between magicin and Grb2
3472	15743878_MI:0047	VAN3 bound to phosphatidylinositol (PtdIns)
3473	15743878_MI:0047	VAN3 bound to phosphatidylinositol (PtdIns), phosphatidylinositol 4-monophosphate (PtdIns4P)
3474	15743878_MI:0047	VAN3 bound to phosphatidylinositol (PtdIns), phosphatidylinositol 4-monophosphate (PtdIns4P) and PtdIns(4,5)P2,
3475	15806159_MI:0047	Figure 2a shows that when proteins from SK-BR-3 cells extract were overlaid with biotinylated CaM, a specific signal was detected in the presence but not in the absence of Ca2+ (presence of EGTA) (right panel).
3476	15806159_MI:0047	Moreover, Figure 2c (top panel) shows that recombinant Grb7 interacts with biotinylated CaM in the presence but not in the absence of Ca2+ (presence of EGTA).
3477	16003391_MI:0047	AtBAG3 and AtBAG5 bound to the AtHSC70,
3478	16003391_MI:0047	Four recombinant proteins (D0, D2, D3, and CDD) containing the putative CaMBD interacted with AtCaM2::HRP,
3479	16109709_MI:0047	Both nonphosphorylated (ammonia-grown) and fully phosphorylated (nitrogen-starved) PII could interact with GST-PamA-(475-680) but not with GST (Fig. 3A).
3480	16109709_MI:0047	Cell lysates prepared from GT cells were incubated with this filter, and endogenous PamA, interacting with the filter bound PII, was detected with the PamA antiserum.
3481	16267044_MI:0047	Cam binding to wild type and mutated N terminal of ACA8 measured by CaM overlay assay.
3482	16288713_MI:0047	As can be seen from the color intensity that eF2a-, but not b-, and g-subunits, interacts with PERK
3483	16766265_MI:0047	we carried out Far-Western analyses in which we probed HMGA2 on pRB immunoprecipitates from cell lysates overexpressing wild-type and different mutant forms of the pRB protein (Figures 2B and 2C). Interestingly, HMGA2 was found to bind to the pRB mutant expressing only the pocket region (lane 5) as efficiently as to the wild-type pRB (lane 1). It did not bind to the naturally occurring mutant pRBD21 that carries a deletion of exon 21 and encodes a portion of the pocket region
3484	16899217_MI:0047	In order to test whether phospho-magicin and the SH2 domain of Grb2 directly interact, and to avoid phosphorylation-independent interaction with the SH3 domains of Grb2, we carried out blot overlay experiments employing phosphorylated magicin and GST-Grb2(SH2).
3485	17137328_MI:0047	Furthermore, a far-Western blotting technique was applied to investigate whether OmpW could be bound with the other proteins in the complex. Our result indicated that the bait protein is FrdB when OmpW was used as the prey protein
3486	17142482_MI:0047	Overlay assay reveals that Arabidopsis CaM protein interacts with the C-terminal region of AtBI-1.
3487	17196169_MI:0047	Stronger signal intensity of bio-ALG-2 binding was observed with FLAG-Sec31A-1 than with positive control FLAG-Alix
3488	17353262_MI:0047	Similar results were observed by far-Western blotting, in which the CK2-phosphorylated XRCC1-His protein probe detected His-APLF and His-APLF1-166, but not His-APLF360-511, proteins present on renatured Western blots (Fig. 3D).
3489	17587183_MI:0047	South-Western analysis confirmed the DNAprotein interaction with the recombinant protein in the E. coli extract of the correct size whereas the E. coli proteins did not show any DNA-binding activity to the WP1- fragment
3490	17681130_MI:0047	To determine if 14-3-3 binding requires phosphorylation of BZR1 by BIN2, purified MBP-BZR1 fusion protein was phosphorylated by a GST-BIN2 protein in vitro, separated on a SDS-PAGE gel, and blotted to nitrocellulose membrane. Incubation of the blot with GST-14-3-3&#955; and anti-GST antibodies detected strong binding to the phosphorylated MBP-BZR1 and very weak binding to the unphosphorylated form
3491	18502764_MI:0047	a blot overlay was used to demonstrate a direct interaction between EHD2 and myoferlin.
3492	9349713_MI:0047	This is in agreement with the data obtained from the interaction trap experiments, which indicates that AFT1 and OMT1 could interact with each other both in vivo and in vitro.
3493	9570409_MI:0047	Results from this experiment showed that CesD bound to EspD, but not to EspB or to EspA
3494	9660868_MI:0047	In a blot overlay assay, a 125I-labeled 30-kD fragment of protein 4.1 was incubated with fusion proteins GSThCASK,
3495	9701578_MI:0047	Interaction was observed only between the KI domain and the active, phosphorylated CLV1 kinase domain
3496	9761791_MI:0047	Blot Overlay Assay Showing the in Vitro Interaction of SRZ-22 and SRZ-21 Proteins with the Plant U1-70K Protein.
3497	9764821_MI:0047	32P- labeled MDL-1 will only associate with MXL-1
3498	9764821_MI:0047	These experiments revealed that 32P-labeled MXL-1 will only associate with MDL-1
3499	imex:IM-11956_MI:0047	equal amounts of baculovirus-produced and purified FLAG-Upf1(WT) and FLAG-Upf1(G495R/G497E) (Figure 5E) were used in far-western analyses to probe blots of purified HeLa cell eIF3
3500	imex:IM-11961_MI:0047	ATP binding to the CASK CaM-kinase domain
3501	10531384_MI:0049	Binding of 35S-labeled AtCaMs to 1.5 C KCBP.
3502	11006339_MI:0049	SOS3 Binds 45Ca2+.
3503	11230138_MI:0049	the blunt end 0.20 RNA and the 5&#8242;-extended 5.20 RNA have nearly identical affinities for the polymerase
3504	11826307_MI:0049	Next, we performed protein overlay analysis (Harlow and Lane, 1988; Chen and Evans, 1995) using recombinant OsDr1 and OsDrAp1
3505	12107167_MI:0049	Nitrocellulose filter binding assays examined the ability of LDH to bind specifically to the ARE of GM-CSF RNA independent of cross-linking. LDH/GM-CSF RNA complex formation plateaued at 750 nM with 75% of input RNA bound (Fig. 3).
3506	12869544_MI:0049	At 100 nM [{alpha}-32P]GTP both Toc33-wt and Toc33-R130A bound [{alpha}-32P]GTP with similar efficiency (Fig. 2A). The binding appeared to be specific as a bovine serum albumin control failed to retain [{alpha}-32P]GTP. These results suggest that both Toc33-wt and Toc33-R130A bind GTP with high affinity.
3507	15350535_MI:0049	The purified, recombinantly expressed Wrch1 proteins were first loaded with [3H]-GTP.
3508	15806159_MI:0049	Figure 7b demonstrates that, in the presence of EGTA, wild-type Grb7 binds to immobilized phosphoinositides (center subpanel), and that Grb7Delta has lower phosphoinositide binding capacity, although it significantly retains the ability to associate to phosphatidyl-3-phosphate, and phosphatidyl-3,5-bisphosphate (right subpanel).
3509	16275660_MI:0049	Also an association with AMFR, only found very recently to interact with VCP (43), was detected (Table I).
3510	16275660_MI:0049	Here we show that CHIP interacts with a domain at the carboxyl terminus of Tau (aa 685 756) that is located downstream of the tubulin-binding domains (aa 559 684).
3511	16275660_MI:0049	interaction partners Hsp70, Hsc70, and Hsp90 were detected by the GST-CHIP overlay assay (Table I and Supplemental Fig. 2)
3512	16275660_MI:0049	Overlay experiments with the SH3 domain of amphiphysin II allowed the identification of the known interaction partner dynamin (Table I).
3513	16275660_MI:0049	Overlay experiments with VCP (Supplemental Fig. 1) led to the identification of the well known interaction partner p47
3514	16275660_MI:0049	the proteins Discs large-associated protein 4 (DLP4), XRCC4 (DNA repair protein), and fructose-1,6-bisphosphatase (FBP) (Table I) were identified as novel amphiphysin II interaction partners
3515	16275660_MI:0049	uncharacterized ubiquitin-conjugating enzyme E2Q as well as the disease protein caytaxin (45) interact with CHIP in the overlay screen (Table I).
3516	16278217_MI:0049	the combination of the MALDI-TOF fingerprint data and the migration pattern in SDS-PAGE (Fig. 2; for identification of the bands see Ref. 22) led to the assignment presented in Table 1, concluding that both collagen I-chains are targets for FOG.
3517	16316992_MI:0049	The binding of MAGI-3 PDZ1 to various point-mutated versions of beta1-AR-CT was examined in overlay experiments (Fig. 2A, lanes 1-6).
3518	16319056_MI:0049	ligand blot analysis employing biotinylated Glu-plasminogen of purified variant PAM proteins. Lane 1, NS696 M1 protein; lane 2, PAMNS265; lane 3, PAMNS455; lane 4, PAMNS1133; lane 5, PAMNS53; lane 6, PAMNS13
3519	16525503_MI:0049	VCP significantly enhanced the formation of SDS-insoluble protein aggregates in comparison to the control protein ovalbumin. Interestingly, the assembly of protein aggregates was significantly reduced when the protein GST-Atx68Q(242 360)282HNHH, which does not contain a functional VBM, was incubated with VCP and PP (Figure 5A).
3520	17210637_MI:0049	NGB binds to GTPS within 2 min.
3521	17353262_MI:0049	Whereas both His-APLF and His-APLF1-166 preferentially interacted with CK2-phosphorylated XRCC1-His (Fig. 3C, top left and middle panels), neither protein bound to control slots blotted with CK2 reaction products lacking XRCC1-His (Fig. 3C, bottom left panel).
3522	17693260_MI:0049	SARA specifically bound to PI3P in phospholipid filter binding assays.
3523	17719543_MI:0049	the Smurf2 C2 domain interacted with phosphatidyl mono-, bi-, and triphosphates (PtdIns(3)P, PtdIns(4)P, PtdIns(5)P, PtdIns(3,4)P2, PtdIns(3,5)P2, PtdIns(4,5)P2 and PtdIns(3,4,5)P3) and with phosphatidic acid (PA) in a Ca2+-independent manner
3524	17951432_MI:0049	Human G
oA had a kobs value of 0.09 min1 in this GTPS-binding assay
3525	17951432_MI:0049	indicating that AtGPA1 is selective toward guanine nucleotides and is a bona fide GTPbinding protein.
3526	19135895_MI:0049	Both GTG1 and GTG2 show saturable ABA binding with increasing concentrations of 3H-ABA.
3527	8816473_MI:0049	The Msh2p-Msh6p complex specifically binds to duplex oligonucleotides containing GT, 11, 112PAL, and 114PAL mismatches.
3528	9263453_MI:0049	The maize and Arabidopsis KI domains bind to the catalytic domains of KIK1, Arabidopsis TMK1 (Chang et al., 1992), Brassica SRK-A14 (Glavin et al., 1994), Arabidopsis RLK5 (Horn and Walker, 1994), and Arabidopsis RLK4 (Walker, 1993), but not to the kinase domains of maize CRINKLY4 (Becraft et aL, 1996), or maize ZmPK1
3529	9294234_MI:0049	The resulting GST-KI protein interacted with GST-CKD (Fig. 4A) in a filter binding assay. GST-KI did not bind to either GST-CKD1-1 or GST-CKDK720E at detectable levels (Fig. 4A), suggesting that the introduced mutations alter residues or structures that are required for the interaction, or that the CLV1/KAPP interaction is dependent on phosphorylation of the CLV1 kinase domain.
3530	15252009_MI:0051	EGFP-tagged FBP17 and FLAG-tagged dynamin-1 were coexpressed in COS-1 cells.
3531	15800064_MI:0051	As shown in Figure 2C (top), in early and midmitotic cells, Mto2p-YFP colocalized with Cdc11p-CFP at the SPB.
3532	15800064_MI:0051	To ascertain that Mto2p localizes along cytoplasmic microtubules, we performed colocalization analyses in strains that expressed CFP-Atb2p and Mto2p-YFP by live imaging.
3533	16845383_MI:0051	immunofluorescence microscopy analysis indicated that both endogenous Daxx and Mdm2 were found mainly in the nucleus, and their colocalization in subnuclear structures was evident when cells were treated with ALLN to stabilize Mdm2
3534	17474147_MI:0051	Representative binding curves of fluoresceinlabeled peptides (shown here for SOS1 and HPK1) to purified (His)6-PLCg1 SH3 domain based on fluorescence polarization measurements.
3535	17560331_MI:0051	We identified three consecutive peptides that displayed significantly elevated anisotropy in the presence of the MYND domain (Figure 1D) and share the common sequence motif NPPPLI, corresponding to SMRT residues 1104-1109.
3536	17951432_MI:0051	To verify this result by using an independent approach, we measured GTPS binding to AtGPA1 by using intrinsic tryptophan fluorescence, and comparable kinetic data were obtained
3537	18555782_MI:0051	ATP-bound Sse1p accelerated the dissociation of the fluorescent nucleotide MABA-ADP from Ssa1N or full-length Ssa1p to a similar extent, indicating that the interaction of cytosolic Hsp110s with the NBD of Hsp70 is sufficient for binding and nucleotide exchange (Figure S1B).
3538	18555782_MI:0051	The fluorescent probe MABA-ADP was bound to 2.5 &#956;M Hsp70N, and mixed in a stopped-flow apparatus with a solution containing 250 &#956;M ATP and 2.5 &#956;M Sse1p variant or no protein (spontaneous)
3539	18794331_MI:0051	As expected, Cdc14-Myc and Net1-Myc were localized exclusively to the nucleolus in all HU-arrested preanaphase wild-type cells (Fig. 6 A, panels a' and d').
3540	19135892_MI:0051	However, when Vps25 was added to membrane-bound Vps2061-NBD, a large additional increase of NBD emission intensity was observed that was Vps25 dependent (Figures 2D-2F).
3541	19135892_MI:0051	Interestingly, the spectral data indicate that Vps20 binds similarly to both free and membrane-bound Snf7.
3542	19135895_MI:0051	Confirming binding specificity, both GTG proteins showed efficient binding with BODIPY-GDP
3543	19135895_MI:0051	GTG1 has specific GTP-binding activity.
3544	19135895_MI:0051	GTG2 has specific GTP-binding activity.
3545	imex:IM-11954_MI:0052	Normalized fluorescence autocorrelation amplitude G () of free and chaperonin bound DM-MBP.
3546	17981123_MI:0053	Binding of DegS or the isolated PDZ domain of DegS to a fluorescein-modified YYF peptide was monitored by changes in fluorescence anisotropy.
3547	18835031_MI:0053	FP assay of binding of Bcl-2 BH3 peptide to Bcl-XL.
3548	18835031_MI:0053	We next used fluorescence polarization (FP) assays to determine whether NuBCP-9s bind Bcl-2.
3549	imex:IM-11854_MI:0053	Also distinct is BFL-1. While it binds BID and BIM, it binds only PUMA among the sensitizers tested.
3550	imex:IM-11854_MI:0053	BCL-XL may be distinguished from BCL-2 and BCL-w by its much greater affinity for HRK BH3.
3551	imex:IM-11854_MI:0053	It is also notable that the activators BID and BIM BH3 are bound by all of the antiapoptotics tested,
3552	imex:IM-11854_MI:0053	It is significant that, while the other four proteins interact with neither of the NOXA BH3 domains tested, MCL-1 interacts with both.
3553	imex:IM-11854_MI:0053	NOXA A BH3 efficiently displaces BIM from MCL-1
3554	imex:IM-11859_MI:0053	The Kds after unfolding for the oligo(U) tail and stem/loop I were 26.6 ± 5.0 nM and 51.1 ± 4.1 nM, respectively.
3555	imex:IM-11859_MI:0053	We found that the MRP1/ MRP2 complex binds the stem/loop II (oligo I) and stem/loop I + stem/loop II (oligo II) of gND7-506 (Figure 3B) with apparent binding affinities (Kds) of 7.0 ± 0.5 nM and 5.5 ± 0.9 nM, respectively, at salt concentrations of 50mM NaCl.
3556	imex:IM-11954_MI:0053	To obtain insight into how GroEL binding affects local protein mobility, we performed steady-state anisotropy measurements with the dye Atto532 attached to single-cysteine residues positioned throughout the DM-MBP sequence.
3557	imex:IM-12147_MI:0053	fluorescence polarization assays using nucleotides labeled with BODIPY-fluorescein showed that A. aeolicus DnaC AAA+ is competent to bind both ADP and ATP analogs
3558	14507921_MI:0054	Wild type ATREGFP-expressing cells bound PA and displayed a linear relationship between the amount of receptor expressed and the amount of PA bound (Fig. 2A).
3559	15383453_MI:0054	Importantly, binding of SIRPb2-D1D2-IgG to Jurkat consistently yielded a lower median fluorescence intensity than did binding of SIRPb2-D1D2-IgG in flow cytometry, suggesting that the affinity of SIRPb2 for CD47 is lower that that of SIRPa(Figure 5).
3560	15383453_MI:0054	we hypothesized that SIRPb2 may be involved in cell-cell adhesion rather than inhibitory or activating signaling. To test this, we mixed BW cells transfected with SIRPb2(BW-SIRPb2) with Jurkat or Jurkat-CD470. After 30 minutes of incubation at 37°C we measured formation of conjugates by 2-color flow cytometry. Under these conditions, BW-SIRPb2 made abundant conjugates with Jurkat but not with Jurkat-CD470 (Figure 6A). Conjugate formation was partially blocked by anti-SIRP and anti-CD47 antibodies, confirming the specificity of the interaction. In contrast, antibodies against CD18 (Figure 6A) or CD11a (data not shown) did not significantly block cell conjugation, suggesting that SIRP
2-CD47 interaction mediates cell conjugation by a mechanism that is independent of leukocyte function-associated molecule-1 (LFA-1). To corroborate that SIRP
2-CD47 interaction mediates cell-cell adhesion, we compared the ability of Jurkat, which expresses both CD47 and SIRP
2, and JurkatCD470, which expresses only SIRP
2, to form conjugates either alone or in combination with each other. Jurkat-CD470 formed fewer conjugates with itself than when mixed with Jurkat, and fewer than Jurkat formed with itself (Figure 6B).
3561	16272158_MI:0054	Binding of PAI-1 to AGP on cell membranes.
3562	16293625_MI:0054	The alternative mutation in the FG loop of domain 3 PLAF440-443HNHY abolished both SSL7 binding (MFI  4.7  0.2, mock  4.3  0.2) and FcRI-Ig binding to levels equivalent to that of the mock transfections (Fig. 4C). Mutation of residues Leu-257 and Leu-258 in the C2 AB helix/loop of IgA Fc also affected both SSL7 (MFI  35  3, 9% of WT) and FcRI-Ig binding (MFI  8.1  0.8, 7% of WT). Mutation of the N-linked glycosylation site (N263T) did not affect SSL7 binding (MFI  330  19, 94  6% of WT) and only modestly reduced FcRI-Ig binding (MFI242, 80 6% of WT).by staining with anti-IgA FITC (Fig. 2A) and the rSSL7 (Fig. 2B), and FcRI-Ig (Fig. 2C) binding to the same transfectants was also determined. In agreement with our previous data the binding of FcRI-Ig to WT IgA Fc fusion protein expressing cells (mean fluorescent intensity (MFI)38.62) was inhibited 90% in the presence of 2M (40g/ml) rSSL7 (MFI82, background staining MFI51, Fig. 2D).
3563	16293625_MI:0054	The surface expression of the WT and mutant IgA fusion proteins was determinedby staining with anti-IgA FITC (Fig. 2A) and the rSSL7 (Fig. 2B), and FcRI-Ig (Fig. 2C) binding to the same transfectants was also determined. In agreement with our previous data the binding of FcRI-Ig to WT IgA Fc fusion protein expressing cells (mean fluorescent intensity (MFI)38.62) was inhibited 90% in the presence of 2M (40g/ml) rSSL7 (MFI82, background staining MFI51, Fig. 2D).
3564	16354665_MI:0054	To demonstrate that the mutants indeed exhibit different binding affinities for transferrin, the cells were incubated with ferri-Tf-FITC and analyzed by flow cytometry.
3565	imex:IM-11914_MI:0054	Nectin-1-Ig fusion protein bound cells expressing gD
3566	imex:IM-11914_MI:0054	Specific binding of human PILRalpha to gB.
3567	11891322_MI:0055	the bHLHZip domains of Myc and of Max were fused to the N termini of CFP (MycCFP) and YFP (MaxYFP), respectively. The fusions were expressed in E. coli, purified, and allowed to dimerize, followed by excitation of CFP at wave 433 nm. Dimerization generated a FRET spectrum characterized by a strong emission signal of YFP at 525 nm and a weaker emission signal of CFP at 475 nm.
3568	12065423_MI:0055	Fluorescence emission of ScpA-YFP is therefore due to excitation by fluorescence of ScpB-CFP, which is only possible if both protein fusions are in close proximity (10-100 &#8491;) within the cell
3569	12741847_MI:0055	Direct evidence for the existence of a Cph1 monomer/dimer equilibrium was obtained from the increase in anisotropy when PEB/PEB homo dimers were diluted.
3570	15171681_MI:0055	The reductions of lifetime resulted from energy transfer from donor to acceptor, and thus indicated a close association between S100A1 and S100P or S100A1 and S100A1 in vivo.
3571	15182174_MI:0055	caveolin-1 detected by sensitized emission appeared distributed mostly at the plasma membranes of L-cells, clearly indicating that at the plasma membrane the SCP-2 molecules were very close to caveolin- 1 (i.e., within less than 100 Å, the limit of FRET sensitivity)
3572	15548744_MI:0055	The areas where BRI1/BRI1 homodimers in the plasma membrane occur do not appear to be organized but are fairly frequent (note the dark orange areas indicated by arrowheads in Figure 4D).
3573	15548744_MI:0055	We conclude that BRI1-AtSERK3 heterodimerization is nonuniformly distributed in the plasma membrane and appears to coincide with developing endocytic compartments that contain both receptors.
3574	15592873_MI:0055	The FRET energy transfer efficiency was calculated from the emission intensity ratios between Fig. 6a, b and is roughly 23%. These results show that at the plasma membrane AtSERK1 and GF14 can interact.
3575	16288713_MI:0055	FRET analysis suggests that the energy transfer is occuring from PERK to eIF2a (inset in Fig. 5).
3576	16293632_MI:0055	FRET results indicate that only TRPV4-A and TRPV4-D efficiently assemble into homomeric channel complexes. To check whether TRPV4 channels oligomerize in the ER we
3577	16293632_MI:0055	Using TRPV4-A-YFP as the FRETacceptor and CFP-fused TRPV4-B-E variants as donors, a high FRET efficency of 21.7  3.5 could only be demonstrated for the heteromeric channel formation between TRPV4-A and TRPV4-D subunits.
3578	16317008_MI:0055	in the cytoplasm: the 6-7% intramolecular FRET efficiency of the doubly labeled constructs (CFP-beta1a-YFP or YFP-beta1a-CFP) expressed in dysgenic myotubes indicates that the N and C termini of cytoplasmic beta1a subunits are likely separated by <10 nm. Fourth, within junctions: there was no measurable intermolecular FRET for 1:1 mixtures of CFP-beta1a + YFP-beta1a, beta1a-CFP + beta1a-YFP, or CFP-beta1a + beta1a-YFP expressed in beta-null myotubes. This result is consistent with the idea that then N and C termini of adjacent beta1a subunits are >10 nm apart, which would occur if they were oriented away from the center of tetrads.
3579	16339850_MI:0055	As shown in the top panels of Figure 2E, a nucleus coexpressing YFP-COL3 and CFP-COP1 excited with 514- and 405-nm lasers resulted in the emission of YFP and CFP, respectively, before the 514-nm bleach of the region of interest. After the bleach, emission from YFP-COL3 in the region of interest was reduced dramatically, whereas we saw a clear increase in the emission of CFP-COP1 in the region of interest (Figure 2E, bottom panels), indicating that FRET had occurred.
3580	16522632_MI:0055	a FRET control by co-producing Ctr1:CFP and Ctr1:YFP in yeast
3581	16522632_MI:0055	The FRET spectra from the combination of Fet3:CFP and Ftr1:YFP
3582	16621602_MI:0055	For comparison we also used the SERK1-CrFP and SERK1-YFP pair (Fig. 3H, Table 1) conWrming the formation of SERK1 homodimers as shown previously
3583	16621602_MI:0055	Our results show that the SERK1-protein and CDC48A physically interact close to and/or at the plasma membrane in living cells. Because CDC48 proteins are not integral membrane proteins, this interaction either occurs when the receptor is at the PM or when the receptors are localized in the vesicle-like compartments close to the PM
3584	16740636_MI:0055	FRET Analysis of CatSper1 and Cav3.3 Interaction on Human Sperm Tail
3585	16854975_MI:0055	FRET analysis by photoacceptor bleaching further confirms that SPA1 and CO interact in planta.
3586	17098811_MI:0055	One homolog, SMR2, was shown to interact with CYCD2;1,
3587	17098811_MI:0055	We observed that SIM interacted with the D-type cyclins CYCD2;1, CYCD3;2, and CYCD4;1 and with CDKA;1
3588	17693538_MI:0055	As reported previously, coexpression of CDC48A-CrFP and SERK1-YFP resulted in a reduction of the fluorescence lifetime in a punctuate pattern at the membrane
3589	17693538_MI:0055	Oligomerization of CDC48A at Locations with SERK1 Interaction
3590	17693538_MI:0055	The combination of CrFP and YFP-CDC48C showed a lifetime of 2.44 6 0.1 ns (Cr-C/Y-C; Fig. 4P; Table I), a significant reduction compared to the donor alone.
3591	17951432_MI:0055	Here we show, by using FRET, that D-glucose alters the interaction between the AtGPA1 and AtRGS1 in vivo.
3592	17965270_MI:0055	To this end, we examined whether fluorescence resonance energy transfer (FRET) occurred between the two fusion proteins using the acceptor photobleaching technique. Here, we coexpressed CFP-STH2 with Yellow Fluorescent Protein (YFP)-fused HY5 and excited them with 405- and 514-nm lasers. Both CFP and YFP fluorescence were detected before the bleach
3593	17981115_MI:0055	FRET analysis, showing that PlGF induced dimerization of Npn1 using PAE cells overexpressing Npn1-ECFP and Npn1-EYFP
3594	17991437_MI:0055	FRET analysis demonstrates that angiogenin interacts with follistatin in HeLa cell nucleus.
3595	18191225_MI:0055	fluorescence resonance energy transfer (FRET) to examine whether PTRF and caveolin are in close proximity.
3596	18296627_MI:0055	To further confirm CO-COP1 interaction in vivo, we transiently expressed CFP-COP1 and CO-YFP, either individually or together, in Arabidopsis protoplasts and conducted fluorescence resonance energy transfer (FRET) analysis. Clear real FRET (rFRET) signal was observed for protoplasts coexpressing CFP-COP1 and CO-YFP but not for those coexpressing CFP-COP1 and CO-N-YFP
3597	18326491_MI:0055	The presence of FRET between L-CFP-G&#945;, YFP-G&#947;1 and YFP-G&#946; (Fig. 3D and 3I) supports the inference that the subunits of Arabidopsis G protein form a heterotrimer in vivo.
3598	18326491_MI:0055	This result clearly shows that FRET occurs in the plasma membrane between CFP-G&#946; and YFP-G&#947;1. We conclude that G&#946; and G&#947;1 form a complex, which is required for membrane localization of the G&#946; protein.
3599	18326491_MI:0055	We detected FRET signal and a spectral shift in protoplasts transfected with L-CFP-G&#945;-(35S)-G&#946;-(35S)-YFP-G&#947;1 (Fig. 3F and 3I), but not in protoplasts transfected with the L-CFP-G&#945;-(35S)-YFP-G&#946;-(35S)-G&#947;1 construct (Fig. 3E and 3I).
3600	18429938_MI:0055	Dimerization of MYA1 coiled-coil constructs in tobacco leaf epidermis measured by FRET.
3601	18429938_MI:0055	When YFP-CC and Cerulean-CC were co-expressed in Arabidopsis leaf epidermis, only a weak Nfret signal was detected, which was much lower than that of the specific positive control but about three times as high as that of the negative control
3602	18429938_MI:0055	YFP-KCA1CCGT and Cerulean-KCA1CCGT, both of which include the KCA1 coiled-coil region (KCA1CC) and the MYA1 globular tail (GT). As expected, this specific positive control showed an Nfret value that was lower than that of the general positive control (YFP-Cerulean) but significantly higher than that of the negative control
3603	18466301_MI:0055	The corrected FRET images show interaction between CFP and YFP, and indicate that AtHSFA1a and AtCBK3 interact in vivo.
3604	18796637_MI:0055	STH3 Is a Nuclear Protein and Colocalizes with HY5 in Plant Cells
3605	18836139_MI:0055	Confocal images indicating co-localization of ACBP4:DsRed and GFP:AtEBP fusion proteins transiently-expressed in tobacco leaves.
3606	19135892_MI:0055	The association of Snf7 into polymeric assemblies was detected directly through the use of a variation of the fluorescence resonance energy transfer (FRET) technique involving two samples of Snf7 E81C, one labeled with an NBD donor dye and the other with a Rh acceptor dye.
3607	imex:IM-11954_MI:0055	DM-MBP (175-298) (Figure 1E [2]), on the other hand, exhibited a very broad fE distribution when bound to GroEL, with only a small fraction of molecules being in the expanded state.
3608	imex:IM-11954_MI:0055	Dye modification did not affect the folding rates of the cysteine mutants or the ability of the refolded proteins to bind maltose and folding was typically accelerated not, vert, similar6-fold by GroEL/GroES
3609	imex:IM-11954_MI:0055	In the case of DM-MBP (175-298), FRET efficiencies were also measured upon addition of maltose to the free and chaperonin-enclosed native states.
3610	imex:IM-11954_MI:0055	To obtain the binding kinetics of GroES to GroEL under these conditions, FRET was monitored between Atto532-labeled GroEL E315C and Atto647N labeled GroES 98C
3611	imex:IM-9153_MI:0055	Constructs p-ECFPAPPL1-EYFPADIPOR1 and p-ECFPAPPL1-EYFPADIPOR2 displayed positive interaction FRETN mirroring the fusion value
3612	imex:IM-9153_MI:0055	Flow cytometry further validated positive interactions by detecting EYFP fluorescent cell populations in pFer-YcAPPL1-YnADIPOR1 transfected HeLa cells
3613	imex:IM-9153_MI:0055	FRET investigation with pT7-ECFPADIPOR1-EYFPADIPOR1 resulted in the identification of a novel receptor interaction
3614	10512628_MI:0065	the interaction between N-tube and N-pelle was characterized using isothermal titration microcalorimetry (ITC)
3615	11567028_MI:0065	Thermodynamic parameters for the interactions between sFcgamma RIIb and homogeneous glycoforms of IgG1-Fc by ITC at 30 °C
3616	11567028_MI:0065	Thermodynamics of the interaction between IgG (Cri) and sFcgamma RIIb by ITC
3617	14691232_MI:0065	The binding isotherm for the thrombin-mAb interaction (Fig. 3A,BGo) is characteristic of an exothermic single binding site interaction
3618	16293619_MI:0065	Most interestingly, the presence of the C-tail appears to weaken the affinity of axin slightly, at most 7-fold (compare 
-cat-arm to 
-cat-arm-Ct), and has a somewhat stronger effect on APC-R3, changing the affinity by up to 20-fold.
3619	16293619_MI:0065	The affinities of 
-catenin ligands vary over a wide range (Table 1) and can be classified into three groups. APC-R3 and axin belong to the low affinity group with dissociation constants in the single micromolar range
3620	16293619_MI:0065	The affinities of 
-catenin ligands vary over a wide range (Table 1) and can be classified into three groups. APC-R3 and axin belong to the low affinity group with dissociation constants in the single micromolar range, whereas Ecyto, Lef-1-(1-61), Lef-1-(1-131), phosphoAPC, ICAT, and ICAT-h have KD values in the range of tens of nanomolar.
3621	16293619_MI:0065	The affinities of 
-catenin ligands vary over a wide range (Table 1) and can be classified into three groups. APC-R3 and axin belong to the low affinity group with dissociation constants in the single micromolar range, whereas Ecyto, Lef-1-(1-61), Lef-1-(1-131), phosphoAPC, ICAT, and ICAT-h have KD values in the range of tens of nanomolar. PhosphoEcyto is an exceptionally avid ligand, with a KD of 52 pM.
3622	16293619_MI:0065	The data show that the presence or absence of either or both 
-catenin tail regions has no significant effect on binding to the strong ligands Ecyto, phosphoAPC, Lef-1, and ICAT-h.
3623	16330538_MI:0065	A recombinant protein consisting of residues 1-124 of C4BP 
-chain (see Fig. 1C, C4BP12), His-tagged at the C terminus, was expressed in E. coli and refolded. ITC was used (Fig. 1D) to measure the binding affinity between C4BP12 and a dimerised peptide corresponding to the hypervariable region of M4 (residues 1-45 of M4 protein with a C-terminal Cys added.
3624	17560331_MI:0065	Isothermal titration calorimetry (ITC) was employed to determine the stoichiometry and binding affinity between the MYND domain and the SMRT and N-CoR peptides
3625	17947231_MI:0065	different affinities between binding sites. Binding of two CP12-2 molecules to each A4-GAPDH tetramer
3626	17947231_MI:0065	Thermodynamic parameters of the interaction between PRK and (A4-GAPDH)-(CP12-2)2 were also determined by ITC
3627	18001825_MI:0065	The binding of RNF8 FHA domain (residues 13-146) to its optimal phosphopeptide ELKpTERY was measured by isothermal titration calorimetry.
3628	18001825_MI:0065	The RNF8 FHA domain shows significant binding affinities for four putative phosphorylation sites on MDC1.
3629	18022369_MI:0065	Binding Inhibition of the Alkaline Phosphatase Signal Peptide to SecA
3630	18022369_MI:0065	Binding isotherms of the calorimetric titration of the KRR-LamB signal peptide to SecA
3631	18191223_MI:0065	We observed that hyperphosphorylated Ire1cyto displays a significant ADP binding signal
3632	18243101_MI:0065	for the type II IL-13 complex, IL-13 first binds IL-13Ra1 with an affinity of Kd = 30 nM(similar to previous BIAcore studies [Kd = 34 nM]; Andrews et al., 2002) and this binary complex then recruits IL-4Ra
3633	18243101_MI:0065	For the type II IL-4 complex, IL-4 again first binds to IL-4Ra followed by recruitment of IL-13Ra1
3634	18243101_MI:0065	we find in the type I complex that IL-4 first binds to IL-4Ra, followed by recruitment of gc to form a ternary complex
3635	18775314_MI:0065	Using residues 1-176 of Hrb and the VAMP7 longin domain in isothermal titration calorimetry (ITC), the KD for the interaction was measured as 10.5 &#956;M
3636	imex:IM-11845_MI:0065	the talin (W359A) mutant, which inhibits binding of the MD site of the b3 tail, reduced the affinity 1000- fold,
3637	imex:IM-12024_MI:0065	titrations of Rab6-GTP and Rab9-GTP into buffer (upper-panel insets) or into GST (lower panel insets) resulted in heats comparable to baseline values in the GCC185 binding reaction.
3638	12124176_MI:0067	none of the hMSH2-hMSH6 missense mutant proteins retain the maximum binding (Bmax) of the wild-type protein. Moreover, between a 2- and 8-fold reduction in KD(G/T) was observed
3639	16286452_MI:0067	When examined by quasi-elastic laser light scattering, the PrP82-146 -flowing solution- contained species with an average hydrodynamic radius (RH, by cumulant analysis) of 250 nm.Multiexponential analysis of the correlation function decay (Fig. 2A) showed that most of these species (99% by number) had average RH  12 nm, corresponding to small oligomers.
3640	16990134_MI:0067	After deleting five residues from the N terminus of LuxP, a modification shown to stabilize the AI-2 bound state in vivo (Neiditch et al., 2005), liganded LuxPQp displayed a hydrodynamic radius of 4.0 ± 0.1 nm.
3641	16990134_MI:0067	The hydrodynamic radius (RH), a measure of molecular size and shape, was 3.4 ± 0.1 nm in the absence of AI-2 but increased to 3.8 ± 0.1 nm in the presence of AI-2. While the RH of unliganded LuxPQp is in excellent agreement with calculations based on the crystal structure (Neiditch et al., 2005), the RH after AI-2 addition is significantly larger. The measured value (3.8 nm) is intermediate between those predicted for LuxPQp monomers (3.4 nm) and (LuxPQp)2 dimers (4.3 nm) and probably reflects an equilibrium mixture of monomers and dimers.
3642	17662947_MI:0067	FtsZ assembly was measured using a 90 degree angle light-scattering assay (Mukherjee and Lutkenhaus, 1999).
3643	17662947_MI:0067	To test whether UgtP inhibits FtsZ assembly directly, we examined the effect of UgtP on FtsZ assembly in vitro. For these experiments we employed native B. subtilis FtsZ and a Thioredoxin-UgtP-6XHis fusion protein (Thio-UgtP). FtsZ assembly was measured using a 90 degree angle light-scattering assay (Mukherjee and Lutkenhaus, 1999). Using this approach we determined that UgtP inhibited FtsZ assembly in a concentration-dependent manner with 90% inhibition at a 1:1 ratio of Thio-UgtP to FtsZ (Figures 3A and 3B). Thio-UgtP was able to inhibit FtsZ assembly at ratios as low as 1:5 (Figure 3B). The absence of UgtP's substrate, UDP-Glc, resulted in a small but statistically significant reduction in its ability to inhibit FtsZ assembly in vitro (Figure 3C). Adding 6 mM Thioredoxin-6XHis (Thio) or BSA had no effect on FtsZ assembly (Figure 3D).
3644	17947231_MI:0067	Since MALS data are independent of protein conformational effects, they do suggest that two CP12-2 molecules can bind to one A4-GAPDH tetramer giving rise to an (A4-GAPDH)-(CP12-2)2 binary complex (calculated Mr = 166 kDa, Table 1).
3645	10869553_MI:0069	Direct evidence for the S100A4/S100A1 heterodimerization was obtained in vitro by ESI-FTICR mass spectrometry.
3646	15236960_MI:0069	Addition of Peptide D to PNPase in stoichiometric excess gave evidence for a charge series corresponding to a species with a molecular mass of 497,442(±15) Da, (Figure 9, red trace, series D). This is consistent with a dimer of PNPase trimers with six peptide D molecules bound, which equates to one peptide D per PNPase monomer (theoretical mass of 496,950 Da).
3647	15236960_MI:0069	Confirmation of the stoichiometric ratio of R-domain to helicase RhlB came from nanoflow-ES mass spectrometry (Figure 6).
3648	15236960_MI:0069	Nanoflow-ESI mass spectra of enolase and peptide C recorded under non-dissociating conditions.
3649	16293620_MI:0069	When two mutated, oligomerization-deficient forms of PA are combined in the presence of LFN (31), a ternary complex is formed containing one molecule of each species.
3650	10077571_MI:0071	Nondenaturing electrophoresis of GroEL GroES complexes containing radiolabeled GroES.
3651	10207046_MI:0071	CpSecY and cpSecE cofractionate during gel filtration analysis.
3652	10436016_MI:0071	Gel filtration analysis reveals two discrete pools of Mad2p, one of which co-fractionates with Mad1p.
3653	10464305_MI:0071	Heterodimer formation of the 50-kDa protein and mtHSP70 in vitro.
3654	10480939_MI:0071	cpSRP54 elutes as a monomer with an estimated molecular mass of 55,000 Da. B, cpSRP43 elutes as a dimer with an estimated molecular mass of 70,000 Da
3655	10490601_MI:0071	Mass spectrometry identified the four ADA subunits as Ada2, Ada3, Gcn5, and Ahc1.
3656	10490601_MI:0071	The Western blot results in Fig. 3 demonstrate that Ada2 and Ada3 cofractionated, as expected, with the ADA and SAGA complexes.
3657	10512628_MI:0071	the protein complex elutes from the column in a single peak (lanes 8-12) separated from the slight excess of the N-tube monomer (lanes 15-16). This shows that the two proteins form a complex on mixing, most likely a heterodimer
3658	10757791_MI:0071	We found that HA-ESC and E(Z) cofractionate in complexes of about 600 kDa
3659	10864495_MI:0071	These samples were concentrated (lane 5) and then subjected to gel filtration, which separated SpoIIAB-&#963;F complex (lanes 6-9)
3660	11029466_MI:0071	eIF3e and eIF3b are part of a protein complex larger than the COP9 signalosome.
3661	11029466_MI:0071	To determine if eIF3e and eIF3b are found in a large molecular weight complex, total soluble proteins from cauliflower buds and Arabidopsis roots were separated by gel filtration chromatography, and the fractions were subjected to Western blot analysis with alpha -eIF3e and alpha -eIF3b antibodies. In both tissues, the peak elutions of eIF3e and eIF3b were in a large molecular weight species, which is larger than the COP9 signalosome, as shown by the elution profile of CSN7 (Fig. 6).
3662	11124122_MI:0071	A small proportion of p55 co-fractionates with FLAG-ESC and E(Z) in fraction 18-20.
3663	11124122_MI:0071	FLAG-ESC and E(Z) co-fractionate on a Superose 6 gel filtration column with identical peaks at ~600 kDa
3664	11435442_MI:0071	To establish that Elp4, Elp5, and Elp6 are bona fide subunits of Elongator, the purified complex was analyzed by gel filtration chromatography. All six Elongator proteins exactly co-eluted from this resin
3665	11483513_MI:0071	Gel filtration analysis of this fraction after thrombin cleavage suggested that the complex of co-expressed Tim9 and Tim10 had the same size as the endogenous TIM10 complex from the IMS (Figure 1B).
3666	11545742_MI:0071	In I, PCNA is alone (5 &#956;g, not, vert, similar0.2 nmol); in II, the mixture of Pol&#951; (5 &#956;g, not, vert, similar0.05 nmol) and PCNA (5 &#956;g, not, vert, similar0.2 nmol) were gel filtered.
3667	11701877_MI:0071	Cofractionation of the putative COP9 signalosome subunit 6 (CSN6) with CSN1 and CSN8 on a Superose 6 H/R gel filtration column
3668	11726501_MI:0071	As shown in Figure 4A, we found that Mad2, Mad3, Bub1myc18, Bub3HA3 and Cdc20myc18 co-fractionated in two peaks (corresponding to fractions 2-6 and 14-19, respectively), which might identify two distinct complexes, both eluting with apparent molecular weights >670 kDa.
3669	11731480_MI:0071	To determine the apparent molecular mass of Sas2-, Sas4-, and Sas5-containing complexes in yeast, whole cell lysates of strains expressing myc-tagged versions of Sas2 and Sas4 and HA-tagged Sas5 were applied directly to a Sephacryl S-300 gel-filtration column.
3670	11854419_MI:0071	Instead, most of CSN4 and CSN7 are in the fractions of 250-300 kDa, and a small portion is in the fraction corresponding to the monomeric size
3671	11854419_MI:0071	We examined the gel filtration profiles of CSN4, CSN5, CSN7, and CSN8 in the crude extract of fus6 by immunoblots. Whereas the wildtype extract contains all four subunits in the fractions corresponding to CSN complex of 500 kDa (Figure 1, marked by  asterisks), the fus6 mutant lacks this 500-kDa peak for all of the subunits examined.
3672	12039038_MI:0071	dSAP18-containing complexes range in mass from not, vert, similar1100 to not, vert, similar450 kDa ( Fig. 4, bottom; fractions 22-30). These results are consistent with inclusion of dSAP18 in the ESC-E(Z) complex.
3673	12217076_MI:0071	As shown in Figure 1(A), most ALB3 and cpSecY eluted from the gel ®ltration column as higher-molecularmass species of approx. 200 kDa. This molecular mass is close to that ofC180 kDa determined previously for the cpSecY complex
3674	12368503_MI:0071	Immunoblotting of column fractions with anti-HA and anti-c-Myc antibodies revealed that SPDS2-HA and SPDS1-myc eluted between 650 to 750 kD, whereas SPMS-myc was detected in overlapping fractions between 700 and 750 kD. Because the expected size of protein dimers was 80 kD, these results indicate that the Arabidopsis spermidine and spermine synthases described here occur in multiprotein complexes in vivo.
3675	12441347_MI:0071	As summarized in Fig. 2B, these data show that during the night all four clock-related proteins were mainly co-frac-tionated in 
400-600-kDa portions, whereas they separated into different fractions during the daytime, especially at ZT 10.
3676	12482963_MI:0071	Whole-cell extract from strain YTT642 was separated by size exclusion chromatography. Isw1p, Ioc2p, and Ioc3p were detected by Western blotting using &#945;-FLAG, &#945;-MYC, and &#945;-HA antibodies, respectively.
3677	12482983_MI:0071	ADA2a eluted from the Superose 6 column a between 0.2 and 0.7 MDa, and in fractions 14 to 17 it coeluted with GCN5
3678	12482983_MI:0071	ADA2b, together with the tested TAFs and GCN5, eluted from the column as a large multiprotein complex with a molecular mass larger than 2 MDa
3679	12527904_MI:0071	hRPA was purified as a trimeric complex of three polypeptides, 70, 34 and 14 kDa in size
3680	12533794_MI:0071	Overexpression of ESC results in greater accumulation of the 600-kDa complex.
3681	12724535_MI:0071	CSN and SCFCOI1 Form a Large Complex in Vivo, as Shown by Gel-Filtration Analyses.
3682	14555658_MI:0071	Gel filtration of purified wild type and mutant enzymes.
3683	14726512_MI:0071	Native complex sizes of Tim9, Tim10a, and Tim10b. HeLa cell mitochondria were solubilized in 0.5% digitonin (A and B, left panels) or in 0.5% Triton X-100 (A and B, right panels) and subjected to gel filtration on a Superose 12 column.
3684	15078334_MI:0071	Gel filtration of solubilized plasma membrane proteins from normal cultivar rice
3685	15165234_MI:0071	By comparison with molecular mass markers, this corresponds to a size of 180 kDa (Fig. 4); with the monomeric size of the ArgB polypeptide of 32 kDa, this would correspond to a multimeric structure composed of four to six subunits.
3686	15165234_MI:0071	The size and composition of the complex that is formed between PII and NAG kinase was analysed by fast protein liquid chromatography (FPLC) gel filtration experiments.
3687	15236960_MI:0071	The native-CTD-enolase complex eluted from a S200 gel-filtration column as a single peak and was identified as one species on a native gel (Figure 7A).
3688	15236960_MI:0071	This C-terminally truncated helicase RhlB was also found to form a stable complex with the R-domain ( Figure 5B) in an approximate 1 : 1 stoichiometry (Figure 5B inset), indicating that the highly basic tail is not required for this protein-protein interaction.
3689	15485833_MI:0071	Yeast extracts were analyzed on a SE1000 gel filtration column, and 0.5-ml fractions were collected. Every other fraction of fractions 15-37 were resolved by 12.5% SDS-PAGE and immunoblotted using antibodies against yeast Arp2, Arp3, Arc18 (ARPC3), and Arc15 (ARPC5).
3690	15805487_MI:0071	To further confirm the homodimerization of CRY1 in vivo, we generated transgenic plants expressing an N-terminal fusion of the TAPa tag to the CRY1 protein (TAPa-CRY1) (Saijo et al., 2003; Rubio et al., 2005) in the wild-type background and conducted gel filtration studies. In both dark and blue light conditions, approximately equal amounts of dimer and monomer of the native CRY1 were obtained (Figure 4C), whereas the TAPa-CRY1 was found almost all as a dimer.
3691	15879521_MI:0071	In one of the peaks, Mad2 cofractionated with the Bub3, Mad3, Cdc20, and Cdc27 complex,
3692	15879521_MI:0071	The fractionation profiles, Fig. 1D, demonstrate that Bub3, Mad3, Cdc20, and Cdc27 comigrated as a large multiprotein complex (670 kDa) when extracts were prepared from cells grown in the presence of nocodazole to activate the spindle checkpoint.
3693	15916958_MI:0071	We conclude that LuxP and LuxQp form heterodimers both in the presence and absence of AI-2. Furthermore, performing these gel filtration experiments over a range of protein concentrations demonstrated that the affinity of apoLuxP for LuxQ is similar to the affinity of holoLuxP for LuxQ
3694	16239229_MI:0071	In the absence of denatured MDH, GroEL(L309K) formed a complex with GroESCy3 (Fig. 5C).
3695	16239229_MI:0071	we sought to analyze further the properties of GroEL(L309K). The mutant protein was mixed with denaturedMDHCy3 and analyzed using gel filtration HPLC with elution in a buffer containing ATP (Fig. 5A).
3696	16278218_MI:0071	Role of serine 121 in HSF1-HSP90 binding.
3697	16301313_MI:0071	A mixture of 10 M LdcI with excess RavA (18 M) results in a large shift in the migration of both species indicating a strong interaction (Fig. 6B, panel 3). A range of higher order oligomers are formed, with the predominant complex (boxed) migrating at or near the void volume of the column, suggesting a size of 50 MDa or greater.
3698	16301313_MI:0071	LdcI binds to 3M RavA in the absence and presence of ATP(Fig. 6C, panels 4 and 5), however, the size of the complex is smaller in the absence of ATP as compared with when ATP is present.
3699	16301313_MI:0071	The predominant complex formed changes if 18 M RavA is incubated with 2-fold excess of LdcI (40 M).
3700	16474402_MI:0071	The interaction was disrupted by addition of the USP7-binding fragment of EBNA1 (395-450) to the binding reaction. This fragment formed a complex with the USP7 NTD
3701	16474402_MI:0071	We also examined the interaction of MDM21-160 with the USP7 NTD by gel-filtration analysis (Fig. 3c). In keeping with the pull-down results, a complex was formed between the two proteins that comigrated on the gel-filtration column. The interaction was disrupted by addition of the USP7-binding fragment of EBNA1 (395-450) to the binding reaction.
3702	16615894_MI:0071	This study commenced with the expression and characterization of a recombinant form of the yeast ESCRT-I complex, referred to here as EI[Delta]UEV-A, in which the UEV domain of Vps23, residues 1-161, was deleted (Fig. 1A).
3703	16905657_MI:0071	Clathrin was detected in a peak between 443 and 669kD(see Supplemetary Figure 1 online). Interestingly, VSR, the vacuolar cargo receptor, was eluted at the same postion.
3704	17055435_MI:0071	The methylated PP2A core enzyme coeluted with the B00/PR72 protein in a single peak, which corresponds to an apparent molecular mass of approximately 160 kDa (Figure 6A, top right panel). Importantly, the elution volume for this peak is smaller than that of the PP2A core enzyme or the B00/PR72 protein alone. This result unambiguously demonstrates that the methylated PP2A core enzyme forms a stable holoenzyme with the B00/PR72 protein. In contrast, the unmethylated PP2A core enzyme failed to form a stable complex with the B00/PR72 protein, as the PP2A core enzyme eluted from gel filtration at a volume identical to that of the free PP2A core enzyme
3705	17254966_MI:0071	The results of SEC showed that both unmodified p27 and Y88-phosphorylated p27 (pY88-p27) bound to recombinant cyclin A/Cdk2 (Figure 2A).
3706	17293877_MI:0071	The addition of a nearly equimolar amount of human CIA I 172AA to the solution caused the histone H3 H4 tetramer to disappear. The emerging new molecular species had a molecular weight of 49,600
3707	17293877_MI:0071	The histone H3 H4 complex existed as a tetramer in solution with an estimated molecular weight of 57,290 plusminus 760 Da
3708	17298945_MI:0071	when Cul7-CPH is preincubated with an excess of p53-TD at high protein concentrations (2 mg/ml), Cul7-CPH co-eluted with p53-TD as a Cul7-CPH/p53-TD complex
3709	17442384_MI:0071	The full-length heterotetrameric ESCRT-I complex consisting of intact Vps23, Vps28, Vps37, and Mvb12 runs on gel filtration chromatography with an apparent molecular weight of 340 kDa
3710	17704303_MI:0071	The majority of TRF3 elutes in fractions smaller than 67 kDa, but a significant portion of TRF3 coelutes with TAF3 at ~150-200 kDa (Fig. 4A).
3711	17709393_MI:0071	in cells treated with DFO, there was a displacement toward the high molecular size fractions of JNK (including pJNK) and other proteins of the signalosome, including JIP1, TAK1, and MKK7 and their phosphorylated forms
3712	17803912_MI:0071	LPS bound TLR4-MD-2 eluted earlier in gel filtration chromatography and shifted upwards in native gel electrophoresis. The elution volume of the LPS-bound protein complex in the gel filtration chromatography was consistent with the predicted elution volume of a TLR4-MD-2 heterotetramer
3713	17947231_MI:0071	In vitro reconstitution of (A4-GAPDH)/(CP12-2) binary complexes with wild type and site-specific mutants of CP12-2.
3714	18022368_MI:0071	The Mad2-p31comet complex has a native molecular mass of 53 kD as determined by equilibrium sedimentation and gel filtration chromatography (Figure S2C), indicating that it exists predominantly as a 1:1 heterodimer in solution with a calculated molecular mass of 51 kD.
3715	18083099_MI:0071	As shown in Figure 2I and 2J, both Set1 and Cps60 coelute on analytical size exclusion column at about the same fractions near the 670 kDa molecular weight marker (Figure 2I and 2J, fractions 23-27)
3716	18083099_MI:0071	Both Set1 and Cps35 from WT strains coelute from size exclusion at about the same fractions near the 670 kDa molecular weight marker (Figure 3)
3717	18243101_MI:0071	Full length IL-13R ectodomain forms binary complex with IL-13 on gel filtration.
3718	18243101_MI:0071	Truncated IL-13R1 D2D3 ectodomain forms ternary complex with IL-4 on gel filtration.
3719	18286207_MI:0071	In the case of endogenous JIP1 also smaller complexes were detected, but they contain bound endogenous VRK2A, which is not detected free (Fig. 8A).
3720	18286207_MI:0071	The cell extracts were fractionated and complexes at high molecular weigh containing the proteins JIP1, TAK1, TAB1, MKK7 and JNK were detected, suggesting that when the phosphorylation cascade is activated
3721	18492870_MI:0071	Importantly, cofractionation of five exocyst subunits (SEC3, SEC5, SEC6, SEC8, and EXO70A1) was maintained through all three steps of purification.
3722	18500823_MI:0071	Evi1 as well as Mbd3b appeared to be present in closely related high-molecular mass fractions of approximately 1&#8722;1.5 MDa (32) (Figure 5B).
3723	18504434_MI:0071	Gel filtration performed on interphase extracts showed that a small amount of endogenous TCTP coeluted with Chfr.
3724	18555782_MI:0071	Interaction of Sse1p mutants with Ssa1N analyzed by size exclusion chromatography.
3725	18555782_MI:0071	Sse1p or Sse1-&#916;loop were mixed with Hsp70N (17.2 &#956;M each) in presence of 40 &#956;M ATP and applied to a Superose-12 size exclusion chromatography column
3726	18567673_MI:0071	This result suggests that both proteins exist in a very large complex together with additional proteins that are not yet identified or as multidimers comprising several NIP and RPOTmp molecules. Although we do not know yet the exact composition of this complex, the result confirms interaction between NIP and RPOTmp.
3727	18656546_MI:0071	The collected fractions from the HeLa cell extract separation were analyzed by blotting using antibodies specific for p97 and Ubxd1 as indicated.
3728	1961752_MI:0071	For purification, the protein was precipitated from the soluble fraction of HeLa lysate by ammonium sulfate, dissolved in 100 mM sodium phosphate (pH 7.0), incubated with GDP to obtain uniform nucleotide binding, and gel-filtered on Sephacryl S-200 (Fig. 3). Purification to homogeneity was achieved on hydroxylapatite (Fig. 4).
3729	9837904_MI:0071	We fractionated yeast cell extracts according to molecular mass of the proteins using Superose 6 FPLC, and we used Western blot analysis to detect the presence of the protein components of the trehalose synthase complex after separation of all proteins in each fraction by SDS gel electrophoresis (Figs. 4-6).
3730	imex:IM-11815_MI:0071	Analytical gel filtration of Kar3/Vik1, Kar3/Cik1, dimeric conventional kinesin K401, and Kar3MD with the Mr predicted based on amino acid sequence. Stokes radius of Kar3/Vik1 = 4.1 nm, Kar3/Cik1 = 3.9 nm, K401 = 3.8 nm, Kar3MD = 3.4 nm.
3731	imex:IM-11815_MI:0071	This truncated version of Kar3/Vik1 contains much of the coiled-coil dimerization region and the C-terminal globular domains of Kar3 and Vik1 (Figure 1 and Figure S1). This construct was designed based on sequence analyses and proteolysis experiments of Kar3, Vik1, and Cik1 to identify the minimal length of coiled-coil that allows the C-terminal globular domains of Vik1 and Cik1 to heterodimerize with the motor domain of Kar3. The dimeric state of this complex was confirmed by analytical gel filtration and equilibrium centrifugation
3732	imex:IM-11885_MI:0071	A stoichiometric combination of Mad2LL and Mad2wt-MBP1 generated a Mad2LL-Mad2wt-MBP1 complex eluting near the 44 kDa marker (Figure 1A).
3733	imex:IM-11885_MI:0071	The shoulder in the elution peak of the Mad2L13A indicates that at 40 &#956;M this mutant is a mixture of monomers and dimers.
3734	imex:IM-11984_MI:0071	Sec13-Nup145C heterodimers that contained either yeast (Figure 1C) or human (Figure 1D) full-length Sec13 formed higher-order oligomers in a concentration-dependent fashion.
3735	imex:IM-11984_MI:0071	The expressed Seh1-Nup85 complex was purified and analyzed by SEC. We found that the Seh1-Nup85 complex forms a dynamic equilibrium between heterotetramers and hetero-octamers
3736	imex:IM-12005_MI:0071	all six yeast proteins were coexpressed, a stable complex was formed. Quantitation of the bands on the SDS gel indicated a stoichiometry of 2:1:1:1:1:1 with respect to Bet3p:Trs33p:Trs31p:Trs23p:Trs20p:Bet5p
3737	imex:IM-12005_MI:0071	However, we could coexpress and purify the heterotetramer Bet5p-Trs23p-Bet3p-Trs31p
3738	imex:IM-12005_MI:0071	Incubation of trs23 with the bet3-trs33-bet5 complex resulted in the production of a four-subunit complex. Gel filtration followed by electrophoretic analysis of the mixture indicated that one copy of bet5 in the three-subunit complex was slowly replaced by trs23 (Figure 1B).
3739	imex:IM-12005_MI:0071	Quantitation of the bands on the gel indicates a 1:1:1 stoichiometry for the bet3-trs31-sedlin complex and a 1:1:2 stoichiometry for the bet3-trs33-bet5 complex, consistent with their molecular sizes on a size-exclusion column (51 kDa and 71 kDa, respectively; (1B)
3740	imex:IM-12005_MI:0071	upon coexpression of TRAPP I subunits, stable Bet3p-Trs33p-Bet5p and Bet3p-Trs31p-Trs20p complexes were produced (Figure 1C). Quantitation of the bands on the SDS gels indicated a 1:1:1 stoichiometry for both subcomplexes.
3741	imex:IM-12005_MI:0071	When each trimeric complex was coexpressed with Trs23p, stable tetrameric complexes of Bet3p-Trs33p-Bet5p-Trs23p and Bet3p-Trs31p-Trs20p-Trs23p were formed (Figure 1D), and both exhibited a 1:1:1:1 stoichiometry.
3742	imex:IM-12009_MI:0071	Densitometry of Coomassie-stained gel filtration fractions indicated stoichiometric amounts of NDC-80, Nuf2HIM-10, and KNL-3 (Figure 2B; data not shown). KBP-1, KBP-2, Spc24KBP-4, and Spc25KBP-3 were also stoichiometric relative to each other in peak fractions. For KNL-1, where a series of lower molecular weight species are present, stoichiometry measurements were not possible. MIS-12 was present at a lower stoichiometry relative to the other proteins but was clearly present in the peak fractions
3743	imex:IM-12009_MI:0071	If KNL-1-6xHis and untagged KNL-3/MIS-12/KBP-1/KBP-2 were expressed together, all of the expressed proteins copurified
3744	imex:IM-12009_MI:0071	KBP-1, KBP-2, and MIS-12 copurified with KNL-3-6xHis from bacteria through multiple purification steps
3745	imex:IM-12009_MI:0071	KBP-1,KBP-2, and MIS-12 copurified with KNL-3-6xHis from bacteria through multiple purification steps
3746	imex:IM-12009_MI:0071	KBP-4 copurified with the other subunits through multiple purification steps resulting in a nearly homogenous 4-subunit NDC-80 complex
3747	imex:IM-12009_MI:0071	we copurified the two homologous subunits of the human Ndc80 complex: Hec1/hNdc80 and hNuf2
3748	imex:IM-12009_MI:0071	we isolated untagged NDC-80/Nuf2HIM-10 dimer by using a similar coexpression and purification strategy to the intact NDC-80 complex and by exploiting an intrinsic affinity for nickel agarose independently of an introduced tag
3749	imex:IM-12018_MI:0071	Gel filtration profiles of Survivin-Borealin10-109
3750	imex:IM-12018_MI:0071	Gel filtration profiles of Survivin-Borealin10-109 (in red, peak 1) and of Survivin-Borealin10-109-INCENP1-58, (blue, peak 2) formed in the presence of an excess of INCENP1-58 (blue, peak 3).
3751	imex:IM-12024_MI:0071	GCC185 is also dimeric
3752	imex:IM-12055_MI:0071	Pax3 was monoubiquitinated whether the reaction was carried out in the presence of UbK0 (as expected) or WT ubiquitin (Ub)
3753	imex:IM-12055_MI:0071	These assay conditions resulted in polyubiquitination of p21CIP1 in the presence of Ub,
3754	imex:IM-12140_MI:0071	E/F/G eluted as a separate entity
3755	imex:IM-12140_MI:0071	However, when pICln was incubated with a mixture of the Sm hetero-oligomers D1/D2 and E/F/G, a stable complex was formed (Figure 2C) with an identical elution profile to the 6S complex
3756	imex:IM-12140_MI:0071	ICln formed a second stable unit with the unmethylated D3/B hetero-oligomer
3757	imex:IM-12140_MI:0071	pICln formed a homogenous complex with D1/D2, as evident by the strict coelution of the three proteins in identical fractions from the column (Figure 2A)
3758	imex:IM-12140_MI:0071	Reconstitution of the 7S Complex
3759	imex:IM-12140_MI:0071	Reconstitution of the 8S Complex (Gemin2/SMN&#916;C/pICln/D1/D2/ E/F/G)
3760	imex:IM-12140_MI:0071	The Sm protein D1 had an elution profile very similar to pICln
3761	imex:IM-12140_MI:0071	The Sm protein D1 had an elution profile very similar to pICln, whereas PRMT5 and B-B&#8242; were predominantly found in the 20S peak.
3762	imex:IM-12152_MI:0071	Immunoblots of DT40 cell extracts fractionated on a Superose 6 gel-filtration column and probed using antibodies against anti-CENP-H or CENP-T.
3763	10409688_MI:0077	eIF4G1393-490 exists as an unfolded protein in the absence of eIF4E and becomes folded in the presence of eIF4E.
3764	11060015_MI:0077	solution structure of the second protein-protein complex of the Escherichia coli phosphoenolpyruvate: sugar phosphotransferase system, that between histidine-containing phosphocarrier protein (HPr) and glucose-specific enzyme IIAGlucose (IIAGlc), has been determined by NMR spectroscopy
3765	12540855_MI:0077	NMR studies (see Supplementary Information) indicated that a histone peptide containing mono-methylated Lys 4 was better ordered in complex with SET7/9 than unmodified peptide.
3766	15890360_MI:0077	NMR data further support the results of SPR and limited proteolysis experiments, by showing that a 13 amino acid residue peptide corresponding to domain 1 of p27 bound to cyclin A and Cdk2/cylin A but not to Cdk5/p25.
3767	16166382_MI:0077	both eIF4A domains play a role in binding the middle domain of eIF4G (eIF4G-m, amino acids 745-1003), the main interaction surface is located on the C-terminal domain. We use NMR spectroscopy to define the binding site
3768	16317001_MI:0077	To further test the ability of CRC-N to serve as a calcium sensor, experiments were performed to characterize CRC-N binding of a peptide fragment of Sfi1 corresponding to the seventh centrin binding repeat.
3769	16326715_MI:0077	Aliquots of each peptide solution were added to the sample solution of the 15N-labeled tandem SH3 domains of p47phox, and the two-dimensional 1H-15N HSQC spectra were analyzed (Fig. 1). We found that many of the signals decreased and finally disappeared as the concentration of p22phox-(149-162) increased (Fig. 1a). Notably, three of five tryptophan signals disappeared, leaving only two observed signals (indicated by asterisks in Fig. 1a). This shows that a structural change occurs in the tandem SH3 domains upon complex formation. This produces an intermediate slow-exchange limit in the NMR spectra so that some signals cannot be observed because of exchange broadening. In contrast, an increase in concentration of p22phox-(149 -168) caused changes in the chemical shifts for a number of resonance
3770	16326715_MI:0077	The solution structure of p47phox-(151-286) complexed with p22phox-(149-168) was determined using an ARIA/CNS protocol.
3771	16330538_MI:0077	Significant changes in the 15N-1H HSQC spectrum of C4BP12 occurred upon addition of M4-N
3772	16474402_MI:0077	we performed NMR titration experiments with WT p53 and EBNA1 peptides on uniformly 15N-labeled USP7 NTD with mutated Trp165. In both experiments, negligible changes were observed compared to those seen for WT USP7 NTD
3773	16603186_MI:0077	The three-dimensional structure of the tertiary complex of vSET with cofactor SAH and H3-K27me peptide.
3774	16837009_MI:0077	The addition of RAFtide but not PYE causes an improvement in line width and the appearance of new peaks.
3775	16837009_MI:0077	We noticed a dramatic change in the spectral properties of the kinase domain upon the addition of a large molar excess of LIMKtide (Figure 2(b)) with smaller line widths, an increase in intensity of weak peaks, and the appearance of new peaks.
3776	16885027_MI:0077	Chemical shift changes of four CoREST SANT2 residues are plotted against the molar ratio of DNA/SANT2. Kd of SANT2 DNA and the standard deviation are indicated.
3777	17254966_MI:0077	We used solution NMR spectroscopy to elucidate the structural consequences of pY88 phosphorylation.
3778	17298945_MI:0077	Chemical shift perturbation of the p53 oligomers upon binding to Cul7-CPH domain.
3779	17298945_MI:0077	The free and bound forms of the protein are in fast exchange on the NMR time scale, suggesting that the affinity between CPH and p53-TD is likely in the micromolar range.
3780	17560331_MI:0077	We confirmed that an aa 1031-1273 SMRT polypeptide bound the MYND domain by HSQC titration
3781	17719543_MI:0077	addition of Smurf2 C2 domain to 15N-labeled HECT domain resulted in numerous chemical shift changes in the 1H,15N-HSQC spectrum of the HECT domain
3782	17719543_MI:0077	titration of the HECT domain to the 15N-labeled C2 domain also resulted in significant chemical shift changes in the 1H,15N-HSQC spectrum of the C2 domain
3783	17719543_MI:0077	Using NMR titrations with unlabeled Ins(1,3,5)P3 and 15N-labeled Smurf2 C2 domain (Figure S2C), we mapped the phospholipid binding surface to hydrophobic and positively charged C2 domain residues in the b1-b2 loop, the b5-b6 loop including helix aI, and the b7-b8 loop
3784	17719543_MI:0077	we obtained high-quality 1H,13C-correlation (HMQC) methyl spectra that could be used for chemical shift mapping studies (Figure 3C). This approach is thus a useful alternative to 1H,15N-based chemical shift perturbation studies for proteins with limited stability and/or solubility. As in the 1H,15N-based chemical shift titration (Figure 1B), a subset of resonances of the Smurf2 HECT domain changed in the methyl HMQC spectra upon stepwise addition of the C2 domain
3785	18022369_MI:0077	The lowest-energy structure of SecA bound to the KRR-LamB signal peptide
3786	imex:IM-11845_MI:0077	a synthetic chimeric peptide comprised of b3-integrin tail residues on the N-terminal side of the critical tryptophan and PIPKIg residues on the C-terminal side would yield a peptide ligand with higher affinity and better solubility that would be suitable for high-resolution studies of the F3-MP interaction. The sequence of the designed chimeric peptide is shown in Figure 1A. NMR experiments showed that this chimeric peptide does indeed bind to talin and forms a tight, highly soluble 1:1 complex.
3787	imex:IM-11845_MI:0077	NMR studies of the interaction with full-length b3 cytoplasmic tails were more challenging. The off rates of the complex correspond to an "intermediate exchange" regime, with peaks broadening and disappearing rather than changing position. It was possible, however, to define perturbed residues by plotting the percentage decrease in peak height upon addition of the peptide
3788	imex:IM-11845_MI:0077	The Structure of the Talin F3/Peptide Complex Reveals a Binding Interface with the MP Site The structure of the complex was calculated from NMR data using a total of 2187 experimental restraints, 138 of which were unambiguous intermolecular nuclear Overhauser effects
3789	imex:IM-11845_MI:0077	Weighted shift maps (see Experimental Procedures) of induced chemical shifts seen in 1H-15N-HSQC spectra when the (B) MP peptide and (C) MD peptides are added to the talin F3 subdomain.
3790	imex:IM-11994_MI:0077	The portion of the zzTM making interchain contacts (colored yellow and green) comprises almost the entire TM domain (20 of 23 TM residues
3791	16275660_MI:0081	In FBP, the peptides RKARGTGELTQLLNS (aa 22 36) and GTIFGIYRKKSTDEP (aa 130 147) were detected by overlay screens (Fig. 4, C and D).
3792	16275660_MI:0081	Interestingly in XRCC4 arginine- and lysine-rich sequences were found to be critical for the association with the SH3 domain (Fig. 4, C-E). Besides the Arg/Lys-rich sequence in XRCC4 (aa 259-285; Fig. 4E) also the peptide KISRIHLVSEPSITH (aa 4-18) gave a signal above background (Fig. 4, C and D)
3793	16275660_MI:0081	We found that in the protein DLP4, besides a proline-rich motif (aa 915-941; Fig. 4E) with a well known PXXP core element (49), also the sequences RRDGYWFLKLLQAET (aa 798-812) and KQRQEARKRLLAAKRAASVRQNSA (aa 948-971) were recognized by the SH3 domain of amphiphysin II (Fig. 4, C and D).
3794	16316992_MI:0081	To gain a panoramic view of beta1-adrenergic receptor (beta AR) interactions with PDZ scaffolds, the beta1AR carboxyl terminus was screened against a newly developed proteomic array of PDZ domains.
3795	16319076_MI:0081	To identify the exact binding sites of profilin 2 within the PRD and to compare these with the docking sites of other known dynamin 1 ligands we made use of a SPOT peptide array covering the entire PRD.
3796	16446437_MI:0081	Detection of Tau-A
 Interaction Sites on Membrane-Bound Peptide Arrays.
3797	16525503_MI:0081	Figure 4A shows that binding peptide 43 (BP43; TSEELRKRREAYFEK, aa 277 291) interacted most strongly with the His VCP protein, suggesting that it contains the amino acids crucial for the association with His-VCP.
3798	14531730_MI:0084	To identify potential Pax8 interactors, immunological screening of a rat thyroid cDNA expression library was performed, using the fusion protein GST-Pax8 as bait.
3799	17875722_MI:0084	Phage DNA was prepared and the variable region was sequenced. The results showed that 7 of 10 MDMX-selected and 4 of 10 MDM2- selected phages contain the same insert (LTFEHYWAQLTS; Table 1). This peptide was named pDI for peptide dual inhibitor.
3800	17875722_MI:0084	Phage DNA was prepared and the variable region was sequenced. The results showed that 7 of 10 MDMX-selected and 4 of 10 MDM2-selected phages contain the same insert (LTFEHYWAQLTS; Table 1). This peptide was named pDI for peptide dual inhibitor.
3801	imex:IM-11849_MI:0089	By probing with the Cy3-labeled MukE and DnaQ proteins, we successfully detected known PPIs, MukE-MukF
3802	imex:IM-11849_MI:0089	By probing with the Cy3-labeled MukE and DnaQ proteins, we successfully detected known PPIs, MukE-MukF (the S/N ratio was 3.1), DnaQ-DnaE (2.7), and DnaQ-HolE (5.0) on the E. coli proteome chips
3803	15781858_MI:0090	Bimolecular fluorescence complementation analysis of AtOFP1 and BLH1 interactions in vivo
3804	10564262_MI:0091	The peaks of clathrin heavy chain and Kex2p from wild-type cells occurred in fraction 42
3805	11435442_MI:0091	We purified Elongator to virtual homogeneity via a rapid three-step procedure based largely on affinity chromatography. The purified factor, holo-Elongator, is a labile six-subunit factor composed of two discrete subcomplexes: one comprised of the previously identified Elp1, Elp2, and Elp3 proteins and another comprised of three novel polypeptides, termed Elp4, Elp5, and Elp6.
3806	12186975_MI:0091	The SAGA proteins were abundant in fractions 38-39, whereas a very small amount of the SALSA Spt20 and Spt3 were present about seven fractions earlier.  However, in a spt7-217 strain the SALSA subunits were predominant.
3807	12186975_MI:0091	The SAGA proteins were not abundant, whereas SALSA Spt20 and Spt3 were present about seven fractions earlier were abundant.  However, in a strain with wild-type Spt7 the SAGA subunits were predominant.
3808	12186975_MI:0091	These SAGA proteins were abundant in fractions 38-39, whereas a very small amount of SALSA Spt20 and Spt3 were present about seven fractions earlier.  However, in a spt7-217 strain the SALSA subunits were predominant.
3809	12186975_MI:0091	These SAGA proteins were not abundant, whereas SALSA Spt20 and Spt3 were present about seven fractions earlier were abundant.  However, in a strain with wild-type Spt7 the SAGA subunits were predominant.
3810	12419231_MI:0091	The two bands, at 52 kDa and 75 kDa, were excised from the gel, and the proteins were identified by a combination of peptide mass fingerprinting using matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) and mass spectrometric sequencing using NanoES triple-quadrupole MS/MS. These analyses unambiguously identified the 52 kDa band as Ceg1p, the guanylyltransferase subunit of the yeast pre-mRNA capping enzyme, and the 75 kDa band as Cet1p, the RNA 5&#8242;-triphosphatase subunit of the yeast pre-mRNA capping enzyme.
3811	12644575_MI:0091	Mass measurements by ESI-MS and post-translational modifications of nuclear encoded subunits of bovine complex I
3812	12644575_MI:0091	Subunit compositions of subcomplexes of bovine complex I
3813	12644575_MI:0091	Table S1-2: Identification by Mass Spectrometry of Subunits Present in Subcomplex Ib
3814	16857963_MI:0091	Tandem mass spectrometry analyses, combined with native gel electrophoresis, immunoprecipitation, and immunoblotting, revealed the identification of 2 previously unrecognized functional partners in the intact cardiac 20S complexes: protein phosphatase 2A (PP2A), and protein kinase A (PKA).
3815	16857966_MI:0091	Figure 5. Verification of proteasome subunits expression in cardiomyocytes. A, Immunoblotting of proteasome subunits in myocytes, heart lysates, purified 20S proteasomes, and Hela cell lysate.
3816	16857966_MI:0091	LC/MS/MS Identified Murine Cardiac 19S Proteasome ATPase and Non-ATPase Subunits
3817	16857966_MI:0091	LC/MS/MS Identified Murine Cardiac 20S Proteasome Subunits
3818	17210637_MI:0091	Repeated experiments revealed that NGB was capable of hydrolyzing [-32P]GTP in the presence of an excess of unlabeled UTP but not GTP
3819	1961752_MI:0091	For purification, the protein was precipitated from the soluble fraction of HeLa lysate by ammonium sulfate, dissolved in 100 mM sodium phosphate (pH 7.0), incubated with GDP to obtain uniform nucleotide binding, and gel-filtered on Sephacryl S-200 (Fig. 3). Purification to homogeneity was achieved on hydroxylapatite (Fig. 4).
3820	350874_MI:0091	Tris-glycine sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the yeast synthetase gave two bands designated as alpha and beta.
3821	8206846_MI:0091	An in vitro binding assay showed that FliG cosedimented with the MS ring complex at a FliG/FliF molar ratio of between 1:3 and 1:1 (Fig. 4B, lanes 2).
3822	8206846_MI:0091	The amount of FliM bound to the MS ring complex was estimated from SDS gels to be at a FliM/FliF molar ratio of around 1:5 or less (Fig. 4B, lanes 3, and Fig. 5).
3823	8816473_MI:0091	SDS-PAGE (8%) analysis of protein fractions from the purification of an Msh2p-Msh6p heterodimer.
3824	9210376_MI:0091	Identification of the subunits of the Arp2/3 complex by mass spectrometry
3825	9214646_MI:0091	active RLF-M fractions contained all six MCM/P1 proteins (Figure 5C)
3826	9214646_MI:0091	On the Superose 6 (gel filtration) column, all six MCM/P1 proteins co-eluted in the same fractions with an apparent mol. wt of 400 600 kDa
3827	9735357_MI:0091	The proteins that consistently copurify with BRM have been designated BRM associated proteins BAPs and are referred to by their molecular mass in kDa BAP45, BAP47, BAP55, BAP60, BAP74, BAP111 and BAP155.
3828	10068665_MI:0096	An immunoblot of the GST-SH2 domain pull-down eluates, incubated with the anti-SHIP MoAb P1D7, showed a clear phosphorylation-dependent interaction of the p85 C-terminal SH2 domain with 145 kD SHIP (Fig 8, lanes 5 and 6). Identical immunoblots incubated with the monoclonal anti-SHIP antibody P2C6 also indicated an interaction of the p85 C-terminal SH2 domain with 145 kD SHIP
3829	10068665_MI:0096	An immunoblot of the GST-SH2 domain pull-down eluates, incubated with the anti-SHIP MoAb P1D7, showed a clear phosphorylation-dependent interaction of the p85 C-terminal SH2 domain with 145 kD SHIP (Fig 8, lanes 5 and 6). Identical immunoblots incubated with the monoclonal anti-SHIP antibody P2C6 also indicated an interaction of the p85 C-terminal SH2 domain with 145 kD SHIP, and a much weaker interaction of the SH2 domain with D183 SHIP
3830	10068665_MI:0096	the p85 N-terminal SH2 domain showed only a faint SHIP antibodyreactive band at 145 kD, which was similar in the unstimulated and the M-CSF-stimulated lysates
3831	10069336_MI:0096	Ena bound effectively to the D2 domain of DPTP69D
3832	10069336_MI:0096	Endogenous Abl protein expressed in S2 cell lysates associates specifically with GST fusion proteins that contain the cytoplasmic domain of Dlar, as visualized by Western blot with anti-Abl antibodies
3833	10069336_MI:0096	Purified, recombinant Drosophila Abl B or v Abl C binds to GST Dlar in vitro, as assessed by a pull down assay in which dAbl protein has been prelabeled with g32P ATP before mixing with the fusion proteins.
3834	10069336_MI:0096	Purified, recombinant Ena (arrow) binds to GST-Dlar D1-D2 (lane 2), and binds weakly to GST-DPTP10D
3835	10069336_MI:0096	Therefore, we repeated the GST pull down assays using purified, recombinant Ena protein in the absence of other Drosophila proteins. Purified Ena bound to the Dlar cytoplasmic domain (Figure 5B)
3836	10069336_MI:0096	We exposed equal amounts of different GST PTP fusion proteins to Drosophila S2 cell lysates and found that endogenous Ena protein associates with a Dlar full length cytoplasmic domain (GST Dlar D1 D2) or with D2 alone but not comparably with wild type D1
3837	10075709_MI:0096	The interaction was unaffected by the presence of 0.5% Nonidet P-40 and 1 M KCl (lane 6). Because p14 contains a putative zinc finger motif conserved among different species (13), we examined the effect of divalent cations (lane 4) and a high concentration of a chelating agent (lane 5). Even under these conditions, p160 efficiently bound to p14, suggesting that the zinc finger is not required for the interaction.
3838	10215621_MI:0096	we carried out GST pull-down experiments with 35S-labeled Exd proteins (Fig. 6). GST-Hth bound Exd
3839	10220404_MI:0096	Ena bound specifically to the Drosophila and murine Abl-SH3 domains and the murine src SH3 domain. Ena also bound to the C-terminal but not to the N-terminal SH3 domain of Drk.
3840	10220404_MI:0096	The Ena fusion protein precipitated chickadee from the fly lysate, unlike GST alone
3841	10220404_MI:0096	The optimal consensus binding motifs for Abl (Abl-Pro) and Src (Src-Pro) specifically blocked binding of Ena to the Abl or to the Src SH3 domains, respectively.
3842	10220464_MI:0096	To confirm that no yeast proteins were involved as mediators in the PRL1-AKIN interactions observed in the two-hybrid system, N-terminal GST fusions with AKIN10 and AKIN11 were constructed, purified, and immobilized on glutathione- Sepharose. [35S]Methione-labeled PRL1 protein was synthesized by coupled transcription-translation by using the cDNA as tem-plate and incubated with GST-AKIN10 and GST-AKIN11, as well as with control GST, and glutathione-Sepharose matrices. After stringent washes, the supernatant fractions and matrixbound proteins were resolved by SDSyPAGE and detected by autoradiography, demonstrating specific binding of PRL1 to both GST-AKIN10 and GST-AKIN11 in vitro
3843	10231394_MI:0096	SDS-PAGE analysis showed that mTIM (1 1196) binds to GST-mPER1 (135 638), which includes the PAS and CLD domains, but not to GST alone (Fig. 4A), indicating that mTIM and mPER1 directly associate with each other in vitro.
3844	10320477_MI:0096	Cdc2 and Cyclin A specifically bind to the E2F/DP complex in vitro.
3845	10369680_MI:0096	Ring1 binds RYBP and M33 through the same C-terminal domain, whereas the RYBP-M33 interaction takes place through an M33 domain not involved in Ring1 binding.
3846	10383400_MI:0096	Binding of p59fyn to theta PKC-V1 affinity sorbent
3847	10409688_MI:0096	binding of recombinant eIF4E to immobilized GST-eIF4G1 fusion proteins.
3848	10464305_MI:0096	Interaction between the 50-kDa protein and mtHSP70.
3849	10466729_MI:0096	Missense mutations in phytochrome B impair PIF3 binding.
3850	10466729_MI:0096	N and C terminal domains of phyB are both involved in PIF3 binding.
3851	10466729_MI:0096	Phytochrome B (phyB) binds to PIF3 as a biologically active conformer Pfr.
3852	10480939_MI:0096	The eluate from successive passes of the assembled complex over the two resins was quantitated by radioimaging, and the GST4354his ratio was determined to be 2:1 in two independent experiments. This ratio suggested that cpSRP is a trimer composed of one cpSRP43 dimer and one cpSRP54 monomer.
3853	10488108_MI:0096	The RING finger of COP1 interacts directly with the RING H2 finger of CIP8 in vitro.
3854	10490612_MI:0096	Binding of the C-terminal 144 amino acids of Swi4 to Swi6 and N-terminal regions of Swi4 in vitro.
3855	10498867_MI:0096	p65 interacted strongly with the ankyrin repeats and the SH3 domain of 53BP2
3856	10536025_MI:0096	A very small amount of CHS and F3H protein could be eluted reproducibly from the immobilized TRX-CHI by using lysates from wild-type seedlings
3857	10536025_MI:0096	Binding of CHI and F3H to TRX-CHS was also near the limit of detection.
3858	10564262_MI:0096	GST-Apl2p (1) bound clathrin heavy chain
3859	10590166_MI:0096	AtCBL1 Affinity Chromatography Purifies CIPK1 from Arabidopsis Plants
3860	10590166_MI:0096	We also found that Ca2 1 was required for the interaction between AtCBL1 and CIPK1. In the presence of EGTA to chelate Ca 2 1 , CIPK1-AtCBL1 interaction was not detected.
3861	10593939_MI:0096	As shown in Fig. 4B, SR33 and SR45 coprecipitated with U1-70K. T7.tag antibody-agarose beads did not bind to S.tag-fused SR33 or SR45 (data not shown). These results confirm the in vivo interaction data in yeast and the specificity of interaction between SR proteins and U1-70K.
3862	10593939_MI:0096	As shown in Fig. 6A, the nonphosphorylated form of SR33 interacts very efficiently with autophosphorylated AFC2 (lane 2), and no binding was detected between nonphosphorylated AFC2 and SR33 (Fig. 6A, lane 1). The phosphorylated SR33 protein showed a weak interaction with both forms of AFC2 (Fig. 6A, lanes 3 and 4). These results demonstrate direct interaction between SR33 and AFC2, and this interaction is modulated by the phosphorylation status of SR33 and AFC2.
3863	10593939_MI:0096	Similar studies with SRZ22 and SRZ21 also showed that direct interaction of phosphorylated and nonphosphorylated proteins takes place (Fig. 6B, data shown for SRZ22 only)
3864	10593939_MI:0096	These interactions were further confirmed by coprecipitation analysis. The SR33 on T7.tag antibody-agarose beads pulled down SR33 and SR45 proteins that are expressed as S tag fusions (Fig. 7B).
3865	10593939_MI:0096	The SR33 on T7.tag antibody-agarose beads pulled down SR33 and SR45 proteins that are expressed as S tag fusions (Fig. 7B).
3866	10594004_MI:0096	Analysis of the interacting domains in Sla1p, Pan1p, and End3p.
3867	10594004_MI:0096	Sla1p interacts with the first long repeat region of Pan1p and the N-terminal EH domain of End3p, thus leaving the Pan1p-End3p interaction, which requires the second long repeat of Pan1p and the C-terminal repeat region of End3p
3868	10611319_MI:0096	Binding of IP3 receptor fragments to human TRP3
3869	10611319_MI:0096	Using the whole C terminus of TRP3 as a probe, we then proceeded to narrow down the TRP3 interacting domain of IP3R. To our surprise, IP3R has not one but two TRP interacting sequences, F2q (Fig. 4 B) and F2g (Fig. 4 C). Of these, a subfragment of F2g, F2t (IP3R3[768 805]), was also positive for interaction with the C terminus of TRP3
3870	10625663_MI:0096	Deletion studies revealed that SNIP specifically interacts with the Nbut not the C-terminal coiled-coil domain of SNAP-25
3871	10633111_MI:0096	The VirB10 fusion bound to both the GST-VirB10 and GST-VirB9 fusions
3872	10633111_MI:0096	The VirB10 fusion bound to both the GST-VirB10 and GST-VirB9 fusions (lanes 2 and 4). A very low level of binding of VirB10 to GST-VirB8 was also observed
3873	10656681_MI:0096	To demonstrate in vitro binding, TRX, ALL-1 and ASH1 polypeptides spanning the SET domains were linked to GST, expressed in bacteria, and bound to glutathione-Sepharose beads. TRX, ALL-1 and ASH1 SET fragments were synthesized and radiolabeled in a coupled transcription /translation system and examined for binding to the GST chimera polypeptides and to GST alone
3874	10662555_MI:0096	The interaction between MAGOH and RBM8 was demonstrated by both yeast two-hybrid and GST fusion protein pull-down assays
3875	10669747_MI:0096	To confirm and extend the observation of schwannomin-SCHIP-1 interaction in the yeast two-hybrid system, we tested the interaction between the two proteins by in vitro GST pull-down experiments.
3876	10669747_MI:0096	We therefore tested the ability of SCHIP-1 to self-associate.
3877	10704439_MI:0096	Fig 5 d shows that radiolabeled Bub3p bound efficiently to the Mad3-GST fusion and that amino acids 176-409 of Mad3p (containing homology region II) were sufficient for this interaction.
3878	10704852_MI:0096	In the present study, we determined which part of HTH is required for interaction with EXD. GST EXD can pull down full length HTH
3879	10716984_MI:0096	Interestingly, the H6Rnr2p bound to a Ni-NTA agarose retained the Rnr4p in 2 M KCl, but not in 4 M urea, indicating that the complex of H6Rnr2p/Rnr4p formed in bacteria was stable and could not be disrupted by high salt concentrations.
3880	10717484_MI:0096	GST-Bin3 interacts with Bicoid.
3881	10764785_MI:0096	mutations R275Q, E295K, and A302D caused defects in binding sigma 70 in both log and stationary phase samples (Fig. 4C). Also reduced in Esigma 70 formation were N266D in both log and stationary phase samples and R297S in log phase samples. Q300E again showed properties of binding sigma 70 better than wild type.
3882	10798620_MI:0096	On a western blot, a monoclonal anti-GFP antibody revealed a single 50 kDa protein corresponding in size to GFPAtROP4 if beads carrying GST-AtRhoGDI1 were applied to the cell extracts (Figure 8, lane 3). GST alone did not retain GFP-AtROP4 (lane 4).
3883	10801826_MI:0096	PECAM-1 tyrosine phosphorylation had no effect on gamma -catenin recruitment, suggesting that neither gamma -catenin (Fig. 1B) or PECAM-1 (Fig. 1C) tyrosine phosphorylation is necessary for their interaction. Interestingly, although gamma -catenin was mainly present in the pellet fraction, beta -catenin was unable to interact with PECAM-1 and was mainly detected in the supernatant fraction (Fig. 1C, second panel), suggesting that under these conditions gamma -catenin but not beta -catenin is the major PECAM-1 partner, and in agreement with our previous IP experiments
3884	10809665_MI:0096	The domain structure of MOR and its interaction domains with itself, BRM
3885	10809665_MI:0096	We were able to further narrow the Zeste binding domain of MOR to amino acids 171 to 410 (Fig. 6C, lanes 6-8).
3886	10864495_MI:0096	Lane 3 illustrates that SpoIIAB co-purified with His6-&#963;F, suggesting that the complex indeed formed in vivo.
3887	10888666_MI:0096	In each case, the His-tagged t-SNARE bound to the Ni21-agarose column and was eluted with imidazole. AtVPS45 was seen to bind only to the t-SNAREs AtTLG2a and -b
3888	10903443_MI:0096	The recombinant GST-Dazl1 peptide is able to form homomeric complexes in vitro.
3889	10915743_MI:0096	Bacterial-produced GST-E12 (aa 210-360), but not GST alone, was able to bind directly to several variants of the HHM protein that contained the HLH domain (DHHM [1-184], DHHM [150-360], and the full-length HHM [1-360])
3890	10915743_MI:0096	Bacterial-produced GST-E12 (aa 210-360), but not GST alone, was able to bind directly to several variants of the HHM protein that contained the HLH domain (DHHM [1-184], DHHM [150-360], and the full-length HHM [1-360]) as well as positive controls (Id2, MyoD, and E12)
3891	10930412_MI:0096	[35S]Methionine-labeled full-length HBO1 protein bound to GST-AR fusion proteins was analyzed by SDS-PAGE and detected by autoradiography. As seen in Fig. 3A, a strong retention of HBO1 protein was specifically observed for the samples with GST-AR containing both the DBD and LBD (505-919 amino acids) in the presence of DHT. A weak interaction was also observed for the full LBD (676-919 amino acids)
3892	10930412_MI:0096	the C terminus of HBO1 strongly precipitated in vitro-translated AR protein.
3893	10982829_MI:0096	A strong binding of endogenous SHP-2 to pY2, but not to Y3 and pY3, was detected in COS-1 cells,
3894	10982829_MI:0096	baculovirus-produced b-ST3- FL, b-ST3-DN1H, and b-ST3-DN4H (deleting four a-helices) were purified, and their receptor-binding abilities were analyzed by the peptide-binding assay. Similar to the results obtained in vivo (Fig. 4), we observed a strong interaction between wild-type Stat3 and the gp130-derived phosphopeptide pY3, but not Y3 (Fig. 7, lanes 1 and 2). The binding was significantly diminished for b-ST3-DN1H
3895	10982829_MI:0096	The phosphorylated peptide-containing sequences surrounding the third tyrosine (pY3), coprecipitated with full-length Stat3 as well as the N-domain mutant ST3-DN. Surprisingly, binding was diminished in ST3-DN1H and was totally abolished in ST3-DN2H, ST3-DN3H, and ST3-DN4H
3896	10990452_MI:0096	Figure 3B shows that Ric1p again copurified with Ypt6p, and that it could be released by addition of GTP-gammaS in the lysis buffer. GDP also released Ric1p, but less efficiently.
3897	10990452_MI:0096	Ric1p forms a complex with Rgp1p in vivo.
3898	10990452_MI:0096	We conclude that the Ric1p-Rgp1p complex can bind to Ypt6p, and that it interacts preferentially with the nucleotide-free form and, to a lesser extent, with the GDP form, but not with the GTP form.
3899	11003656_MI:0096	Daxx was retained on immobilized GST-Fas-DD
3900	11003656_MI:0096	HaHSP27-EE interacted with the Daxx protein encoded by clone 55.1 much more efficiently than HaHSP27-AA
3901	11003656_MI:0096	HSP27 was retained on GST-HSP27
3902	11003656_MI:0096	In extracts from transfected 293 cells, HaHSP27-AA and HaHSP27-EE interacted efficiently with immobilized GSTHuHSP27
3903	11003656_MI:0096	The interaction between Daxx and Ask1 was confirmed by showing that Ask1 from extracts of 293 cells was retained on immobilized GST-55.1
3904	11003656_MI:0096	The interaction between Daxx and HSP27 was confirmed in a GST pull-down assay.
3905	11006275_MI:0096	The full-length RIP140 interacts with both HDAC 1 and 3
3906	11029466_MI:0096	As shown in Fig. 3A the amount of GST-eIF3e protein that was -pulled down- increased as the amount of His6-CSN7 protein increased, whereas the control failed to pull down GST-eIF3e. Similar results were obtained in a pull-down experiment using equal amounts of His6-eIF3c and increasing amounts of GST-eIF3e on glutathione-Sepharose beads (Fig. 3B).
3907	11029584_MI:0096	Full-length GST-Brn-2 1±443 fusion protein was immobilized on glutathione agarose beads and incubated with 35S-radiolabelled full-length native, p300, TFIIB and TBP general transcription factors. Each of these proteins was found to be capable of binding to beads containing GST-Brn-2 but not with the GST protein alone
3908	11029584_MI:0096	Testing of 35S-radiolabelled full-length native, Sox10, Pax3 and Brn-2 itself also showed each protein was capable of direct interaction with the immobilized GST-Brn-2
3909	11029584_MI:0096	Testing of 35S-radiolabelled full-length native, Sox10, Pax3 and Brn-2 itself also showed each protein was capable of direct interaction with the immobilized GST-Brn-2 1-443 fusion protein but not GST
3910	11029584_MI:0096	when GST-Sox10 fusion protein was immobilized on glutathione agarose beads each of the 35S-radiolabelled Sox10, Pax3 and Brn-2 proteins bound selectively compared to immobolized GST protein alone confirming the direct interaction of each of these molecules.
3911	11030144_MI:0096	GST pull-down experiments showed (Figure 1c) that GST-p55CDC (lanes 3 and 4), but not GST alone (lanes 5 and 6) or GST-Tyro3 (lane 1 and 2) used as a negative control, brought down the BUBR1 antigen.
3912	11030144_MI:0096	Proteins interacting with His6-BUBR1 or resins were blotted for p55CDC (a), CDC16 (b), CDC27 (c) and BUBR1
3913	11042198_MI:0096	None of the residue substitutions appears to have any gross conformational effect on holoenzyme structure, since both subunits copurify when only one subunit is affinity-tagged.
3914	11046044_MI:0096	To confirm the interaction between IFN-RßL and RACK-1, we performed "pull-down" experiments. GST constructs containing the entire cytoplasmic domain of IFN-RßL bound RACK-1 in IFN-stimulated or unstimulated cell lysates (Fig. 2A).
3915	11069292_MI:0096	In initial studies using this procedure, we found that full-length phyB bound strongly and specifically to PIF3 in the Pfr form as expected
3916	11069292_MI:0096	PhyA also bound selectively to PIF3 in the Pfr form,
3917	11069292_MI:0096	The PAS domain of PIF3 is necessary but not sufficient for phyB binding
3918	11073942_MI:0096	GST-Rag A efficiently pulled down the in vitro synthesized C-terminal portion of Rag C (Fig. 5d, lane 6).
3919	11073942_MI:0096	GST-Rag C efficiently pulled down the in vitro synthesized C-terminal portion of Rag A protein (Fig. 5d, lane 4).
3920	11112409_MI:0096	Interaction of GST-sentrin with in vitro translated Daxx.
3921	11121078_MI:0096	Our results show that, when AGG1 is present in the matrix, it shows a strong ability to bind 35S-labeled AGB1, whereas GST alone is not able to bind any detectable AGB1
3922	11124122_MI:0096	As shown in Fig. 5B, GST-E(Z)1-73 pulls down RPD3, p55 and ESC
3923	11124122_MI:0096	GST-EED1-81 pulls down HDAC1, HDAC2 and RbAp48 from HeLa cell nuclear extract
3924	11124122_MI:0096	GST-EED1-81, which contains the corresponding N-terminal region of EED (Schumacher et al., 1996), binds directly to in vitro translated EED
3925	11124122_MI:0096	GST-ESC1-60 fusion protein encoding just the N-terminal 60 residues of ESC is sufficient to pull down full-length in vitro translated ESC
3926	11124122_MI:0096	GST-ESC1- 60 specifically pulls down the ESC complex.
3927	11124122_MI:0096	GST-ESC and GST-E(Z) directly interacts with RPD3
3928	11124122_MI:0096	GST-p55 was used to pull down in vitro translated full-length ESC, E(Z) and RPD3.
3929	11124122_MI:0096	pull-down assay indicates that GST-RPD3 can pull down E(Z), p55 and ESC from nuclear extract
3930	11148284_MI:0096	In Vitro Interaction of FIE and MEA Polycomb Proteins.
3931	11157980_MI:0096	This shows that native KEULE from plant extracts is capable of binding T7-KNOLLE-loaded beads in these assays
3932	11162467_MI:0096	GST-d was able to pull-down pRb from mitotic HeLa cell extracts, as well as from G2 and G1 cells
3933	11169732_MI:0096	As shown in Figure 2a, p150 was detected in the eluates from both GST-hPrt1(129-873) and GST-K7(325-468) columns (lanes 3 and 5 from the left) but not from the GST control columns (lanes 2 and 4 from the left), indicating that the interactions between p150 and hPrt1(129-873), and between p150 and K7(325-468) are specific.
3934	11172717_MI:0096	We found that while GST alone shows no interaction with components of the HDA1 complex ( Figure 4, lane 2), GST-TUP1 interacts with both HDA1 and HDA3, but not HDA2 ( Figure 4, lane 3).
3935	11178989_MI:0096	Addition of E2 could enhance the binding of GST-ERa to MDM2, however, this interaction was much weaker than that between GSTp53NM and MDM2 protein
3936	11178989_MI:0096	in vitro translated MDM2 protein interacted specifically with ERa both in the absence or presence of E2. Addition of E2 could enhance the binding of GST-ERa to MDM2,
3937	11230129_MI:0096	As shown in Figure 1C (right panel), full-length AtCIPK1 (Kin), KinD1 and KinD4, but not KinD6 and KinD9, interacted with AtCBL2-His6 in vitro
3938	11256608_MI:0096	A GST SAP18 fusion protein was shown to interact very efficiently with recombinant GAGA
3939	11256608_MI:0096	As seen in Figure 1D, only the GAGA519 species appears to bind to GST dSAP18 with some efficiency.
3940	11256608_MI:0096	Furthermore, a GST-POZ245 fusion was found to bind both GAGA forms indistinctly and much more efficiently
3941	11266362_MI:0096	dAF10::HP1 interaction via pull-down assays involving a GST-HP1 fusion protein and in vitro translated, labelled dAF10. HP1 binds via its chromo shadow domain to full-size dAF10 and to the subfragment that contains the PLVVL motif
3942	11274188_MI:0096	The related MAGUKs SAP90/PSD95, PSD93/chapsyn-110, SAP97, and SAP102 all bound to the COOH-terminal tail of PMCA4b, whereas only the first three bound to the tail of PMCA2b.
3943	11274204_MI:0096	purified Net1(1-341)-His6 (1 nmol) was incubated for 30 min at 4 C with GST and GST-Cdc14 affinity matrices containing 0.25 nmol of each protein.
3944	11275986_MI:0096	about 10% of input p73a or p73b protein was retained on the E6-conjugated Sepharose beads, confirming that p73 binding to HPV E6 is direct.
3945	11278976_MI:0096	In vitro, GST-Mgc-N fusion protein actually binds to the carboxyl-terminal domain of Tat1. The Tat1 COOH-terminal region also interacts with the full-length MgcRacGAP protein, but not with the GAP domain (Fig. 8B, lanes 2-4).
3946	11283335_MI:0096	The coding region of pUGT1f was cloned downstream from the glutathione S-transferase (GST) coding region, and the fusion protein was expressed in Escherichia coli and purified using glutathione-agarose beads. The SA2 domain of phragmoplastin was labeled with 35S-methionine in an in vitro transcription/translation system (Zhang et al., 2000). The radiolabeled phragmoplastin peptide was pulled down effectively by the recombinant fusion protein (Figure 1B), suggesting that the interaction between the phragmoplastin and UGT1 also occurs under in vitro conditions and that no additional protein is required for this interaction.
3947	11283335_MI:0096	When UGT1 was fused to GST and purified with the beads, it interacted quantitatively with 35S-labeled Rop1 and brought down the radiolabeled product to the pellet
3948	11302744_MI:0096	GST-menin bound nm23
3949	11302744_MI:0096	GST-nm23 bound menin
3950	11302744_MI:0096	GST-nm23 bound menin protein expressed in COS-7 cells
3951	11306572_MI:0096	Fig. 3B shows that cpSRP54-(371-564) is specifically co-precipitated by GST-cpSRP43 and GST-cpSRP43-(259-350) and not by the unfused GST protein
3952	11306572_MI:0096	First, we verified that the region of cpSRP43 containing the third and fourth ankyrin repeat (cpSRP43-(190-258)) is able to form homodimers.
3953	11353774_MI:0096	In the GST pull-down assay, FKHR only weakly interacted with ER both in the absence of hormone (Fig. 2B, lane 2) and the presence of Tam (Fig. 2B, lane 4). E2 treatment enhanced the interaction by 2-3-fold (Fig. 2B, lane 3). GST alone did not interact with FKHR even in the presence of E2 (Fig. 2B, lane 5), indicating the specific interaction between ER and FKHR.
3954	11353774_MI:0096	the known ER-interacting protein AIB1 interacted with ER only in the presence of E2
3955	11356022_MI:0096	In vitro translated mNkd1, similar to fly Nkd, specifically bound glutathione sepharose beads to which a GST-Dsh fusion protein was attached (Fig. 3B).
3956	11356864_MI:0096	Neurofibromin was precipitated specifically by a GST fusion of syndecan-2 (amino acid residue 33-211) containing part of the extracellular domain, plus complete transmembrane and cytoplasmic domains of rat syndecan-2 (Fig. 1B; data not shown). GST-syndecan-2D65, which lacks the C-terminal 65 amino acid residues corresponding to the transmembrane and cytoplasmic domains of syndecan-2, was unable to pull down neurofibromin from rat brain extract
3957	11377421_MI:0096	GST pull-down assay of CASK and rabphilin3a.
3958	11397012_MI:0096	To verify the two-hybrid interaction between ASX and TAN, a GST pull-down assay was employed.
3959	11431700_MI:0096	deletion of the N-terminal domain of Tbx5 abrogated its binding ability to Nkx2-5
3960	11431700_MI:0096	Full-length protein, proteins with a deletion of the amino-terminal or carboxy-terminal domains outside the homeodomain, and the homeodomain of Nkx2-5 itself, all associated with Tbx5
3961	11449057_MI:0096	CDKA;1 was detected in the flow-through fraction, but a significant amount also was bound to the column, indicating again a stable interaction between KRP3 and CDKA;1
3962	11455422_MI:0096	(Fig. 2A) show that interaction with Bin1 does not require the Bicoid acidic activation domain (AD), or the polyglutamine (Q) or polyalanine (A) domains.
3963	11477570_MI:0096	We confirmed the binding of SART3 to RNPS1 in vitro using a recombinant SART3-glutathione-S-transferase fusion protein (GST-SART3) with the cell extract of FLAG-RNPS1-transfected 293T cells.
3964	11483513_MI:0096	To test for a direct interaction between Tim9 and Tim10, the soluble fraction, after disruption with French Press, was bound onto glutathione S-Sepharose beads.
3965	11513956_MI:0096	In vitro binding of AGB1 to the AGG2:GST fusion protein.
3966	11543633_MI:0096	we used a GST pull-down assay with biotinylated in vitro translated LASS2 and GST fusion proteins of AGPRH1, AGPRH2, VPL, and the C-terminal half of OCT1 (amino acids 306-544). Confirming the interactions identified in the twohybrid assay, we found that LASS2 bound to GST-AGPRH1, GST-AGPRH2, GST-VPL, and GST-OCT1 (amino acids 306-504), but not to GST alone
3967	11564868_MI:0096	HEK293T cell extracts were incubated with microcystin-LR-Sepharose (labeled Mcyst pulldown) to isolate cellular PP1/GADD34 complexes, and GADD34 was detected by Western immunoblotting
3968	11564868_MI:0096	Immunoblotting the I-1-bound proteins with an anti-FLAG antibody established that all GADD34 polypeptides, including the full-length protein, were concentrated by the I-1 beads (Fig. 4D)
3969	11564868_MI:0096	To establish whether PP1 was required to recruit I-1 to GADD34 or whether the two proteins bound independently to GADD34, we expressed hexahistidine-tagged GADD34(233-674) and analyzed its association in vitro with recombinant human I-1 coupled to CNBr-activated Sepharose
3970	11577348_MI:0096	IBtk was efficiently bound by GST-Btk (aa 1-659) and GSTPHBM (aa 25-173; this region includes the PH domain and the unique Btk motif (BM) from aa 139 to 173, which is common to the Btk family of tyrosine kinases22) (Fig. 3a, lanes 1, 4). IBtk was bound weakly by GST-SH2 (aa 281-372, Fig. 3a, lane 2) and not at all by GST-SH3 (aa 219-268) or by GST
3971	11577348_MI:0096	We next tested GST-IBtk fusion proteins for binding to endogenous Btk using a pull-down assay. Btk proteins were specifically recovered from MC3 lysates after binding to GST-IBtk
3972	11606059_MI:0096	These data show that the interaction of ALG-2 and Fas is Ca21-dependent and the PEF domain is sufficient to allow the binding.
3973	11683500_MI:0096	To determine whether Byr1 and Bob1 associate in fission yeast, plasmids were constructed for expressing Byr1 as a glutathione S-transferase (GST) fusion protein (GST-Byr1) and Bob1 as a c-Myc epitope-tagged protein (CM-Bob1) in S. pombe cells. Lysates were prepared from cells coexpressing CM-Bob1 with either GST or GST-Byr1, and GST complexes were isolated using glutathione agarose beads and resolved by SDS-PAGE and immunoblot analysis. CM-Bob1 was found to be associated with GST-Byr1, but not with GST, providing evidence that Bob1 forms a complex with Byr1 in S. pombe cells (Fig. 2B).
3974	11690648_MI:0096	His-tagged SnwA coprecipitates myc-tagged CypE in a colysis experiment in Dictyostelium.
3975	11690648_MI:0096	nd the His-CypE dependent precipitation of endogenous SnwA was identified by 8% Tris-glycine sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) using anti-SnwA antibody (Fig. 3A a
3976	11713520_MI:0096	Applied auxin also promoted the SCFTIR1±AUX/IAA interaction in a dose-dependent manner (Fig. 5b). Auxin treatment enhanced the SCFTIR1±AXR2/AXR3 interaction at concentrations as low as 0.5 mM.
3977	11713520_MI:0096	Auxin treatment enhanced the SCFTIR1±AXR2/AXR3 interaction at concentrations as low as 0.5micro molar.
3978	11713520_MI:0096	TIR1±Myc and AtCUL1 both co-puri®ed with the GST±AXR2 fusion protein but were absent in control pulldown assays using GST alone
3979	11713520_MI:0096	TIR1 was able to interact, albeit at a reduced level, with a GST±AXR2 fusion protein containing only domain II (AXR271±100). In contrast, when a short deletion was introduced into the highly conserved core of domain II, this mutant derivative of AXR2 (AXR2D86±88) interacted very weakly with TIR1 (Fig. 4d). These data demonstrate that domain II is both necessary and suf®cient to bind SCFTIR1.
3980	11713520_MI:0096	To determine whether SCFTIR1 interacts with additional AUX/ IAA proteins, we tested GST±AXR3 in pull-down assays. Similar to the results obtained with AXR2, GST±AXR3 co-puri®ed with TIR1 protein and the axr3-1 mutation substantially disrupted this interaction
3981	11786550_MI:0096	Protein pull-down and coimmunoprecipitation experiments using recombinant PMCA2b and PMCA4b as well as NHERF1 and NHERF2 showed that the interaction of PMCA2b with NHERF2 was specific and selective.
3982	11793469_MI:0096	The interaction of the IVTT-MLH1 with the control wild-type GST-PMS2 fusion proteins was confirmed as IVTT-MLH1 was retained (lane 4). However, the gene alterations in GST-PMS2, P511K, T597S, and M622I substantially reduced interaction (lanes 5, 6, and 7 respectively), as indicated by the presence of less MLH1.
3983	11909642_MI:0096	MEK2 interacts with A-Raf in vitro.
3984	11909951_MI:0096	Twenty micrograms of protein extracts was prepared from yeast strain TKY514 expressing Dom34p-triple-HA-tag (HA3) and either the full-length, aa-1-to-161, or aa-162-to-611 form of GST-tagged Hbs1p, incubated with 20 &#956;l of 50% glutathione Sepharose 4B slurry, washed three times with 150 mM KCl buffer, and analyzed by Western blotting.
3985	11914126_MI:0096	Fu binds specifically to the GST-Cos2 fusion protein but not to the GST protein alone
3986	11914126_MI:0096	In vitro assays between the GST-Cos2 fusion protein and radiolabeled Ci revealed a direct specific interaction between these proteins
3987	11919189_MI:0096	In an independent approach to corroborate these results, we incubated recombinant His-tagged ICAP-1alpha  bound to a cobalt chelating resin with a solution of purified recombinant nm23-H2 protein or with HeLa cell lysates containing endogenous nm23-H2 (Fig. 2B).
3988	11932251_MI:0096	We now report that RanBP3 associates with the Ran-specific guanine nucleotide exchange factor, regulator of chromosome condensation 1 (RCC1).
3989	11943170_MI:0096	Thus, the results of the pull-down assays confirmed the direct and specific interaction of SibI with the Sig1R4.
3990	11959851_MI:0096	Fig. 2A, the NHD of Dlxin-1 (DXN-NHD) specifically bound to GST-Praja1
3991	11959851_MI:0096	Necdin also bound to Praja1, but much less efficiently than did Dlxin-1 (Fig. 2A
3992	11973328_MI:0096	OmpR molecules bind to EnvZc monomers stoichiometrically in a 1:1 ratio
3993	11976948_MI:0096	Radiolabeled Dcyp33 could be affinity precipitated by GST-trxPHD1-3 and GST-trxPHD3, but not GST-trxPHD2, GST-trxPHD1 or GST alone
3994	11976948_MI:0096	Radiolabeled Dcyp33 was pulled down by Gst-MLL-PHD1-3 and human Cyp33 was pulled down by Gst-trxPHD1-3
3995	12007189_MI:0096	GST pull-down assays showing that the RAB3IP and SSX2IP proteins interact in vitro with SSX2
3996	12007405_MI:0096	Neither GST nor GST-BRI1 kinase interacted with BES1 or mutant bes1; however, a BIN2-GST fusion pulled down significant amounts of BES1 or bes1 (Figure 5C). These results indicate that BIN2 interacts in vitro with both wild-type and mutant BES1 proteins.
3997	12011449_MI:0096	Also, GST-Siva-1 and GST-BCL-XL proteins were used to pull down GFP-BCL-XL and GFP-Siva-1, respectively, from 293T cell lysates (Fig. 2B).
3998	12011449_MI:0096	GST-Siva-1 but not GST alone coprecipitated BCL-XL with increasing amounts of soluble BCL-XL, demonstrating direct interaction between Siva-1 and BCL-XL.
3999	12011449_MI:0096	Immunoblotting with anti-GFP antibodies revealed that GST-Siva-1 but not GST-Siva-2 or GST is able to coprecipitate GFP-BCL-XL from the double transfectants, and GFP is unable to associate with any of the GST fusion proteins (Fig. 2C;
4000	12015115_MI:0096	We tested the ability of either a fusion between UNC-112 and maltose binding protein (MBP), or MBP alone, to bind to purified GST::PAT-4/ILK in vitro.
4001	12032852_MI:0096	JAB1 interacted with GST-DTrc8562 - 809 and GST-DTrc8562 - 744, both of which include the highly conserved segment (55% identity/73% similarity) of 109 amino acids encompassing the RING-H2 finger
4002	12039038_MI:0096	Following extensive washing, bound proteins were examined by SDS-PAGE and subsequent autoradiography. 35S-E(Z) bound to His6-dSAP18
4003	12039038_MI:0096	Thus, dSAP18 is capable of binding independently to two non-contiguous E(Z) regions: aa 377-446 and aa 512-605.
4004	12050667_MI:0096	GST-SNS(I) pulled down the GFP-p11 fusion proteins specifically and efficiently in an GST pull-down assay
4005	12080051_MI:0096	GST-SPHK1 specifically pulled down SKIP,
4006	12084833_MI:0096	These results clearly indicate that TGA2CT and NPR1 form a complex in wild-type plants resulting in the dominant-negative effect of TGA2CT, and this complex is disrupted in the npr1-2 mutant, abolishing the dominantnegative effect
4007	12107167_MI:0096	LDH and AUF1 associate in vivo and in vitro.
4008	12165861_MI:0096	Both GST-LSM7 and GST-SmG fusion proteins were able to precipitate TACC1l
4009	12167173_MI:0096	To determine whether phosphorylated Rum1p interacts with Pop1p and Pop2p, protein lysate was prepared from cells co-overexpressing epitope-tagged combinations of Pop1p and Pop2p. Upon affinity purification on Ni-NTA resin, HA-Pop1p/His-Myc-Pop2p complexes were incubated with bacterially expressed, phosphorylated Rum1p. In this reaction, Pop1p-Pop2p complexes specifically bound phosphorylated Rum1p (Fig. 2B, lane 1). Consistent with the genetic data His-Myc-Pop1p and His- Myc-Pop2p individually purified upon overexpression in pop1 pop2 double mutants exhibited no Rum1p binding above background (Fig. 2B, lanes 2 and 3).
4010	12196526_MI:0096	extracts of p65PI3K- and p85-expressing CTLL2 cells were prepared and incubated with the Ras peptide-specific column or a control column. p65PI3K and p85 were both retained in the Ras column, with slightly greater retention of p85 than of p65PI3K
4011	12223483_MI:0096	An in vitro binding assay was then performed by using a 35S-labeled AAT-1alpha  synthesized in vitro with GST-AMY-1 or GST expressed in and prepared from E. coli.
4012	12223483_MI:0096	To first determine the possibility that AAT-1alpha binds to S-AKAP84, in vitro pull-down assays using various 35S-labeled fragments of S-AKAP84 synthesized in vitro with GST-AAT-1alpha  or GST were carried out (Fig. 5A).
4013	12354775_MI:0096	The mutant proteins, Nkd-D201A and Nkd-D213V, can both interact with Dsh in the yeast two-hybrid (Fig. 5A) and GST pull-down assays (Fig. 5B)
4014	12368503_MI:0096	The results of these GST pulldown experiments demonstrated that GST-SPDS2 recruited SPDS1 and SPMS, whereas GST-SPMS bound SPDS1 in vitro.
4015	12383081_MI:0096	NIM1/NPR1 interacts with TGA2 and TGA5 in vitro
4016	12393858_MI:0096	Inh2 binds to KPI-2-(1099-1503) with or without PP1C.
4017	12411502_MI:0096	These studies revealed that Mex67p-Mtr2p binds efficiently to GST-Sac3p-N + M, but only marginally to GST-Sac3p-C (Figure 6B).
4018	12421915_MI:0096	To confirm the identity of the 230-kDa protein, Western blot analysis with an Ab against NMMHC-IIA was performed in Peer T cells (Fig. 2A) and PBL (Fig. 2B) lysates pulled-down with GST-CXCR4-Ct.
4019	12441357_MI:0096	Cells-In order to determine whether Pax8 and TTF-1 could physically associate, recombinant GST-Pax8 protein was purified from bacteria and used in pull-down experiments with total protein extracts prepared from thyroid and non-thyroid cells.
4020	12441357_MI:0096	To investigate the possibility that Pax8 and TTF-1 interact directly, pull-down experiments were performed using the fusion protein GST-Pax8 and bacterial TTF-1 protein affinitypurified.
4021	12511573_MI:0096	To test if the Pof6 F-box protein is part of an SCF, a TAP fusion protein was expressed from the endogenous pof6 locus. After tandem affinity purification (45), the eluate was separated on lithium dodecyl sulfate-PAGE and silver-stained revealing several bands (Fig. 4A). The 19-kDa band represents Skp1 as demonstrated by Western blot analysis (Fig. 4A).
4022	12527904_MI:0096	as the concentration of immobilized GST-BRCA2 was increased, there was a corresponding increase in the recovery of hRPA in the eluted fractions
4023	12527904_MI:0096	The acidic domain of BRCA2 was also able to bind hRPA present in cell extract (lane 5) and, as seen above with purified proteins, the Y42C mutation reduced this binding markedly
4024	12529400_MI:0096	The interaction between HIPK1 and Daxx was further verified by means of an in vitro pulldown assay (Fig. 2C). Radiolabeled HIPK1 preferentially associated with a Daxx-GST fusion protein over GST alone.
4025	12553664_MI:0096	A small amount of Ivy1- HAp (compared to GST-Ypt7p) is found attached to GST-Ypt6p.
4026	12553664_MI:0096	Ivy1-HAp is found on washed Sepharose matrices containing GST-Ypt7p, GST-Vps33p and GST-Ivy1p.
4027	12553664_MI:0096	VSV-tagged Vps33p binds to GST-Ivy1p but not to GSTalone.
4028	12602868_MI:0096	To assay interactions, the co-purification of GST fusion proteins with CBP fusion proteins that were adsorbed to calmodulin affinity resin was measured. As shown in Figure 5D, the GST-PAP isoforms were retained on the immobilized calmodulin when incubated with the full-sized CPSF100-CBD protein extract
4029	12612082_MI:0096	GST-HEI10 incubated with noncycling Xenopus extracts developed an extensive ladder of higher migrating species. The modified forms were most abundant in interphase extracts, although they were observed in mitotic extracts as well. The periodicity of molecular masses observed approximated the 9-kDa ladder characteristic of ubiquitin modification; in fact, reprobing of lanes with antibody to ubiquitin (Fig. 6B) showed significant reactivity in lanes containing GST-HEI10
4030	12612082_MI:0096	GST-HEI10 is ubiquitinated in the presence of UbcH7 but not in the presence of either of the other E2 proteins.
4031	12620624_MI:0096	Co purification of wild-type FliC from lysates of E. coli co expressing His tagged FliS by affinity chromatography on Ni NTA.
4032	12620624_MI:0096	To confirm that the C-terminal D0 domain is sufficient for FliS interaction in the absence of the remaining 454 amino acids, GST fusion GST-C&#916;1-454 (Fig. 4) was co-expressed with untagged FliS in E. coli BL21.
4033	12646039_MI:0096	Western-blot analysis of the affinitybound material showed that MBP-RHA2a(1±155) was recovered in the bound fraction, whereas MBP, also reacting with the antibody used for detection, was not
4034	12646258_MI:0096	MT2A was bound to GST-ECRG2
4035	12674497_MI:0096	Next we performed in vitro pull-down assays to verify the observed interactions between AUF1 and the proteins NSAP-1, NSEP-2, IMP-2 and UBCE2I.All four proteins interacted in vitro with AUF1p37.
4036	12711603_MI:0096	Here we show that histone H3 methylase Suv39h1 and the methyl lysine-binding protein HP1 directly interact with MBD of MBD1 in vitro and in cells.
4037	12740913_MI:0096	only full-length GST-2TK-p14ARF could precipitate EBNA-5 from the lysates. Neither the N- nor the C-terminus deleted constructs, which lack amino acids 1-55 and 65-132, respectively, bound EBNA-5
4038	12757932_MI:0096	Ataxin-1 539-816 proteins labeled with [35S]-methionine interacted with the GST-p80 coilin 266-576 fusion protein
4039	12788081_MI:0096	As shown in Fig. 1B, the GST-p250GAPTH2 fusion protein specifically precipitated a constitutively active form of Fyn (FynY531F), indicating that p250GAP interacts directly with Fyn in vitro.
4040	12820899_MI:0096	Pull-down assay for &#945;II-&#946;II2 interaction
4041	12827204_MI:0096	As expected, COP1 interacted with CIP8 (ref. 15) but not luciferase (Fig. 1b) and, under the same conditions, LAF1 translated in vitro purified together with COP1 (Fig. 1b).
4042	12827204_MI:0096	The interaction between LAF1 and COP1 also occurred in vivo, as confirmed by co-purification experiments
4043	12837948_MI:0096	In vitro protein interaction between AtPirin1 and GPA1.
4044	12857813_MI:0096	Mitotic cyclins are also possible partners of CDKB2; thus, we applied the same assay as above to CYCA2;2 and CYCB2;1. The results showed that both mitotic cyclins bound to CDKB2;1, and the binding efficiency was the same or rather lower compared with the case of CYCD1;1 or CYCD4;1
4045	12857813_MI:0096	Next, we determined the type of CDK that interacts with CYCD1;1 or CYCD4;1 in the pull-down assay. For this purpose, CDKA;1, CDKB1;1, and CDKB2;1 were fused to GST and immobilized on the beads. As shown in Figure 3, CYCD1;1 was retained on any of the CDKs to almost the same extent,
4046	12857813_MI:0096	whereas CYCD4;1 tightly bound to CDKA;1 and CDKB2;1 but very weakly to CDKB1;1.
4047	12857813_MI:0096	whereas only a small amount of CYCD2;1 and CYCD3;1 was retained on the GST-CDKB2;1 resin
4048	12857841_MI:0096	Calcium dependency of the in vitro interaction between PBP1 or TCH3 and PID.
4049	12864730_MI:0096	fulllength DDC interacts with all domains of AR
4050	12869544_MI:0096	In the pull-down assay, Toc33-wt (Fig. 6A, lanes 1-4) bound more efficiently to soluble [35S]Toc159 (~5% of the total radioactive protein) than Toc33-R130A (~2% of the total radioactive protein) (Fig. 6A, lanes 5-8) suggesting that heterodimerization of Toc33 and Toc159 may also require Arg130 of Toc33 (Fig. 6, A and B).
4051	12869544_MI:0096	Whereas recombinant Toc33-wt pulled down around 20% of the synthetic, radioactive wild-type protein ([35S]wt) (Fig. 5A, lanes 1-6), recombinant Toc33-R130A pulled down only trace amounts of its radioactive equivalent
4052	12874278_MI:0096	As positive controls, we used in vitro translated human T-cell lymphotrophic virus-1 Tax and rhotekin, two previously described binding partners of TIP-1
4053	12874278_MI:0096	the readily observed interaction between 
-catenin and TIP-1 was almost completely abolished by the removal of the DTDL sequence from the C terminus of 
-catenin
4054	12874278_MI:0096	we performed pull-down assays with purified GSTTIP- 1 in the presence of in vitro translated 
-catenin. As positive controls, we used in vitro translated human T-cell lymphotrophic virus-1 Tax and rhotekin, two previously described binding partners of TIP-1
4055	12917342_MI:0096	As shown, N-terminal BAF60a also interacts with progesterone receptor b (PRb), ER alpha (ERalpha), and farnesoid receptor (FXR), and minimally with peroxisome proliferator-activated receptors gamma (PPARgamma), suggesting conservation of mechanism with the GR (Fig. 2B).
4056	12917342_MI:0096	In agreement with the in vivo coimmunoprecipitation results (Fig. 1B), the GR1-556 directly interacts with coactivators SRC-1 and SRC-3, but not histone deacetylase protein 1 (HDAC1), which is often found as part of a corepressor complex (Fig. 1C). Similar pull-down conditions were then applied to test whether the GR1-556 interacts with core catalytic BRG1 complex, BRG1, BAF170, and BAF155 (Fig. 1C)
4057	12917342_MI:0096	The N-terminal BAF60a interacts strongly only with BRG1, interacts to a lesser degree with BAF155, and interacts not at all with BAF170, whereas the C-terminal BAF60a interacts strongly with BAF170 and BAF155 but not with BRG1 (Fig. 2A).
4058	12917342_MI:0096	The results demonstrate that GR1-556 is similar to BRG1 in that it interacts with the N terminus of BAF60a but not the C terminus (Fig. 2A)
4059	12947415_MI:0096	55Fe was co-immunoprecipitated with Isu1 (Fig. 5),
4060	12947415_MI:0096	These findings show that Isu1-GST efficiently competed with native Isu1 for binding to Yfh1, Nfs1 and Ssq1, and therefore demonstrate further the specificity of these interactions.
4061	12947415_MI:0096	The two predominant proteins that precipitated with GST-Yfh1 were Isu1 and Nfs1 (Fig. 1A)
4062	12966087_MI:0096	In Vivo Interaction of Nse1 and Nse2 with Smc5 and Smc6
4063	1321833_MI:0096	Isolation of the EGF receptor by calmodulin affinity chromatography.
4064	14506250_MI:0096	GST pulldown assays were performed as indicated above using nuclear lysates from PAM14-HA-expressing EJ cells and subsequently immunoblotted with HA antibodies.
4065	14506250_MI:0096	MRGX interacts with Rb through the helix- loop-helix and leucine zipper regions.
4066	14507921_MI:0096	An aspartate residue at position 683 in PA is required for receptor binding.
4067	14508515_MI:0096	Menin interacts with NMHC II-A in vitro by GST pulldown.
4068	14508515_MI:0096	NMHCII-A bound to GST-menin but not to GST alone.
4069	14521924_MI:0096	Binding of hAATYKs-p35BPN169 to rat brain Cdk5/p35
4070	14531730_MI:0096	As shown in Figure 5(A) (lane 2), Pax8 bound specifically to the GST-WBP-2 fusion protein loaded on glutathione- Sepharose beads.
4071	14531730_MI:0096	When HeLa cells were transfected with Pax8 only, Pax8 was not pulled down in the co-immunoprecipitation (Figure 5B, lane 4), thus demonstrating that the interaction with WBP-2 is specific.
4072	14594812_MI:0096	Binding of G{alpha} with PLD{alpha}1 expressed in E. coli
4073	14594812_MI:0096	Binding of G{alpha} with PLD{alpha}1 from Arabidopsis leaf extracts
4074	14594812_MI:0096	The presence of PLD{alpha}1 in the precipitates was measured by immunoblotting with PLD{alpha}1-specific antibodies and assaying PLD{alpha}1 activity
4075	14627983_MI:0096	GST-Carom-1 captured Myc-MAGI-1-full and Myc-MAGI-V containing PDZ4 and PDZ5 (Figure 3Bb). GST-Carom-10 lacking the C-terminal PDZ-binding motif did not bind Myc-MAGI-1-V.
4076	14627983_MI:0096	How-ever, the addition of GST-CASK-Camk, but not GST inhibited the interaction between GST-MAGI-1-PDZ4+5 and GST-Carom-1 in a dose-dependent manner.
4077	14627983_MI:0096	In the reverse experiment, we prepared 35S-methionine-labeled Carom by in vitro transcription translation, and performed pulldowns with GST proteins containing various PDZ domains of MAGI-1.
4078	14627983_MI:0096	We incubated various Myc-tagged proteins of CASK with either GST or GST-Carom-1 (Figure 5Ca).
4079	14645129_MI:0096	Interestingly, Rig can also bind to a mutated FTZ-F1 E region that is missing the conserved activation domain 2 core motif located between amino acids 791-797
4080	14645129_MI:0096	Rig protein binds to DHR3, EcR, ßFTZ-F1, USP and SVP in vitro.
4081	14645241_MI:0096	radio-labeled ASC-2 readily interacted with GST fusion to Rb in the GST-pull down assays,
4082	14653779_MI:0096	Only IKKg could be detected in the complex pulled-down by GST-ABIN-2 (Figure 1A, lane 1).
4083	14653779_MI:0096	we constructed and expressed a series of deletion mutants of ABIN-2 and examined their abilities to bind IKKg (Figure 3A).
4084	14675452_MI:0096	Interaction of GFP-SR45 with U1-70K
4085	14685242_MI:0096	The ankyrin domain of IkappaB-alpha was required for association with Murr1, as were amino acids 1-160 of Murr1
4086	14701856_MI:0096	In vitro interactions between these various GST fusion proteins and a His-tagged version of the E domain of PPAR{gamma}, His-PPAR{gamma}E, were assayed in pull-down experiments. BAF60c1 and BAF60c2 full-length as well as the N-terminal part of BAF60c2 (BAF60c2Nt) interacted with His-PPAR{gamma}E
4087	14715275_MI:0096	DRpp20 was specifically retained on the beads by the GST-dSMN fusion protein
4088	14715275_MI:0096	In vitro binding results as shown in Fig. 2B demonstrates strong association of hRpp20 with GST-hSMN.
4089	14715275_MI:0096	Our results reveal that the most severe exon 6 mutant Y272C completely abolishes the binding between SMN and Rpp20 while less severe mutant T274I greatly reduces the binding activity. Milder forms of S262I and G279V mutants only slightly decrease the binding of SMN to Rpp20.
4090	14715275_MI:0096	self-association of dSMN protein as well as a direct interaction between dSMN and hSMN proteins by in vitro binding assays
4091	14718544_MI:0096	MTCBP-1 expressed in cells formed a complex with MT1-MMP and co-localized at the membrane.
4092	14729613_MI:0096	A GST fusion protein corresponding to full-length RASSF1A (1-340 amino acids) was created and incubated with in vitro translated E4F and p120E4F protein. E4F and wild-type p120E4F specifically bound to the GSTRASSF1A (1-340) fusion protein but not to the GST alone
4093	14764652_MI:0096	Both ER and ER were pulled down by full-length PP5
4094	14970209_MI:0096	Results of the binding reactions showed that TTF-1, 14, 3XFLAG-TF-1 proteins were specifically bound by GST
TAZ, whereas the  XFLAG--protein was not, thus demonstrating that physical interaction between TAZ and TTF-1 was mediated through the NH2-terminal domain of TTF-1 (Fig. 5A).
4095	14970237_MI:0096	The requirement of Cig2 phosphorylation for binding to Pop1 was, therefore, examined in the above binding assays by treating Cig2 with lambda-phosphatase. As shown in Fig. 4B, it was evident that binding between Pop1 and Cig2 was abolished by phosphatase treatment (lane 5). Phosphatase activity was required for this inhibition, as simultaneous inclusion of phosphatase inhibitors blocked its inhibitory effect (lane 6). This result suggests that the interaction between Pop1 and Cig2 is dependent on phosphorylation of Cig2.
4096	14970237_MI:0096	We next sought to examine binding characteristics between Cig2 and Pop1 using in vitro translation systems. At first, to assess binding capability and specificity, various full-length proteins were labeled with radioisotope, incubated with Cdc2 kinase, and then mixed with bacterially produced and purified GST-tagged Pop1 protein (GST-Pop1). The binding between radiolabeled proteins and GST-Pop1 was examined by pull-down with GSH-Sepharose beads. Proteins translated and labeled in these reactions included Cig2, Cig2/dm (Cig2 construct with a mutated destruction box), Cdc13, Cdc18, and Rum1 (Fig. 4A, lanes 1-6, and see -Experimental Procedures-). These pull-down experiments showed that GST-Pop1 bound Cig2 as efficiently as Cdc18 and Rum1 (lanes 7, 10, and 11), whereas GST-Pop1 did not bind Cdc13 (lane 9). Moreover, Cig2 was not pulled down by mock Sepharose beads (lane 12), indicating that the interaction depends on Pop1. Consistent with the independence of the APC/C in SCFPop1/Pop2-mediated Cig2 degradation, Cig2/dm was still capable of binding GST-Pop1 (lane 8).
4097	14970237_MI:0096	we sought to identify the domain within Cig2 that is necessary for an interaction with Pop1. For this purpose, various subclones of Cig2 that lack either N-terminal or C-terminal regions were expressed in the rabbit reticulocyte lysate system (Fig. 5A, lanes 3-6). Binding between translated proteins and GST-Pop1 was then examined as before. In the case of N-terminal truncations, subclones lacking 180 amino acid residues (Cig2-N180) as well as deletions of 60 and 121 residues were still capable of interacting with GST-Pop1 (Fig. 5A, lanes 12-15). Again, interaction was specific as Cig2 without GST-Pop1 or with GST alone did not pull down Cig2 (lanes 10 and 11), and only Cdc18 and Rum1, but not Cdc13, bound GST-Pop1 (lanes 16-18). This result shows that N-terminal 180 amino acid residues of Cig2 are dispensable for binding to Pop1. As for C-terminal truncations (Fig. 5B, lanes 1-5), two constructs (Cig2-C53 and -106, lanes 10 and 12) were still positive, although binding of Cig2-C106 was somewhat weaker. In contrast, the other two deletions (Cig2-85 and -190, lanes 11 and 13) did not bind Pop1. We do not know at present the reason that Cig2-85 was negative, whereas the  shorter Cig2-106 could bind Pop1. It is possible some structural abnormalities specifically created in Cig2-85 may  hinder an interaction with Pop1. To delineate further the minimal region of Cig2 for binding to Pop1, an internal fragment containing 181-358 was constructed and expressed (Fig. 5C, lane 4). As expected from the above results, this fragment was indeed capable of binding to Pop1 (lane 12). Then, this fragment was further divided into two regions, 181-283 and 284-385 (lanes 5 and 6, respectively), and binding of each fragment was examined. It was found that only the N-terminal region (181-283) was positive (lanes 13 and 14). Also, a shorter fragment consisting of 181-273 (lane 8) bound to Pop1 (lane 16). Taking these results together (see Fig. 5D for a summary of the binding assay), internal 93 amino acid residues of Cig2 (181-273) are necessary and sufficient for binding to Pop1.
4098	15016378_MI:0096	Both APPL1 and APPL2 strongly bound Rab5:GTP&#947;S but neither Rab5:GDP nor Rab4, Rab7, or Rab11 (Figure 1C), indicating that they are specific effectors of Rab5.
4099	15016378_MI:0096	n a search for new Rab5 effectors, mass spectrometry analysis revealed that one of the most abundant proteins (not, vert, similar80 kDa) affinity purified on a GST-Rab5:GTPS column (Figure 1A) corresponded to APPL
4100	15016378_MI:0096	We furthermore confirmed these interactions by GST pull-down experiments applying nuclear extracts to columns with immobilized GST alone or fused to APPL proteins (Figure 6D). PID/MTA2 and RbAp46 were specifically bound to GST-APPL1 but not GST alone. Interestingly, we also recovered these proteins on the GST-APPL2 column, suggesting that both APPL proteins can interact with the components of NuRD/MeCP1 in the nucleus.
4101	15020404_MI:0096	Western blot analyses of the eluants reveal that Chl1p bound specifi-cally to GST-Ctf7p (Figure 4).
4102	15044383_MI:0096	The results in Figure 7C show that XRCC1 binds only to the FHA domain of aprataxin. Interestingly, PARP-1 bound to the FHA, NL and HIT domains, and p53 bound to both the FHA and HIT domains. Since aprataxin co-localizes with nucleolin in the nucleoli and since nucleolin is implicated in the genotoxic stress response (27), we determined whether nucleolin also interacted with aprataxin.
4103	15063184_MI:0096	Recombinant GST-Ci76 fusion proteins were purified using Glutathione Sepharose 4B beads from bacterial extracts, and were incubated with in vitro translated 35S-labeled Su(fu) or Cos2 without or with increasing amounts of the corresponding competing protein. As shown in Fig. 6A, less Su(fu) was pulled down by GST-Ci76 in the presence of competing Cos2. Reciprocally, increasing amounts of Su(fu) decreased the amounts of Cos2 bound to GST-Ci76 (Fig. 6B).
4104	15080792_MI:0096	To determined whether or not ErbB2 could be isolated by CaM-affinity binding, we performed pull-down experiments using CaM-agarose.
4105	15133492_MI:0096	By measuring the ability of each E2F-7 derivative to bind to E2F-7 in vitro, we found that wild-type E2F-7 could bind to domain 1, and further that domain 1 could interact with either domain 1 or 2 (Figure 4c).
4106	15138274_MI:0096	Of all of the many combinations that were tested, only a direct interaction between Elp5 and Elp6 was detected.
4107	15147888_MI:0096	Moreover, His-Tag-CGI-99 and GST-CGI-99 fusion proteins were pulled down as detected by Western blotting ( Fig. 4C, lane 4), suggesting that CGI-99 indeed forms a dimer.
4108	15147888_MI:0096	The results of in vitro GST pull-down assay showed that GST-CGI-99 binds to His-Tag-hNinein (1617-2090 aa), but not His-Tag-hNinein (1617-1931 aa)
4109	15153109_MI:0096	4E-BP3 was found to copurify with S-tagged human eIF4E-1
4110	15153109_MI:0096	eIF4E-2 was found to bind 4E-BP3
4111	15153109_MI:0096	eIF4GI(159-614)(His)6, was found to copurify with S-tagged human eIF4E-1
4112	15153109_MI:0096	eIF4GI(159-614)(His)6 was found to copurify with S-tagged mouse eIF4E-3
4113	15159385_MI:0096	GST-BSEP and GST-MDR2 Fusion Proteins Bind HAX-1 in Rat Liver Homogenates.
4114	15165234_MI:0096	Complex formation of NAG kinase with PII
4115	15169888_MI:0096	A pulldown assay with biotinylated TPL-2398-467 peptide (2) coupled to streptavidin-agarose beads demonstrated that the isolated TPL-2 C terminus is sufficient for binding to ABIN-2-FL (Fig. 5E).
4116	15169888_MI:0096	A pulldown experiment with GST-p105497-968 protein (2) confirmed that the isolated C-terminal half of p105 was sufficient for binding to ABIN-2-FL (Fig. 5C).
4117	15169888_MI:0096	In contrast, Myc-A20 interacted with GST-ABIN-2251-429 but not GST-ABIN-21-250 (Fig. 6B),
4118	15169888_MI:0096	Mapping regions of ABIN-2 which interact with p105
4119	15169888_MI:0096	Pulldown assays revealed that the TPL-2 C terminus was required for interaction with GST-ABIN-21-429 (Fig. 5D).
4120	15169888_MI:0096	Pulldown experiments revealed that Myc-TPL-2 bound to a region containing amino acids 194 to 250 of ABIN-2 (Fig. 6C).
4121	15169888_MI:0096	These data indicate that GST-ABIN-2 preferentially forms a ternary complex with HA-p105 and TPL-2.
4122	15169888_MI:0096	To analyze the interaction of p105 with ABIN-2, 293 cells were transiently transfected with vectors encoding a panel of deletion and point mutants of HA-p105 (Fig. 5A)
4123	15169888_MI:0096	When expressed individually, GST-ABIN-2 interacted with TPL-2
4124	15197186_MI:0096	Furthermore, the pull-down assays showed that NDR2 with mutated Tyr-32 does not bind to hMOB1, whereas the binding of NDR2 with mutated Arg-42 and Arg-45 is not abolished (Fig. 5B).
4125	15225636_MI:0096	Fig. 2A, panel i shows that in vitro translated &#945;7 binds the six other GST-&#945; subunits and itself, confirming the result of the Y2H screen
4126	15256549_MI:0096	SseA selectively co-precipitates SseB and SseD, and this association is differentially affected by Triton X-100.
4127	15256549_MI:0096	These results were confirmed by GST co-precipitation assays (Fig. 4b). GST SseA1 31 precipitated a comparable amount of SseB as GST SseA3 108.
4128	15272023_MI:0096	Full-length MAGE-D1 (amino acids 1 775) and deletion mutants encompassing the MHD (amino acids 466 775 and 553 688) interacted with His-tagged necdin, indicating that necdin and MAGE-D1 form a heterodimer via the MHD.
4129	15272023_MI:0096	Msx1 and Msx2 bound to MBP-MAGE-D1 fusion proteins containing the WQXPXX repeats (amino acids 1 775, 1 479, and 291 441), but the deletion mutants lacking the repeat domain (amino acids 466 775 and 1 291) failed to interact with Msx1 and Msx2.
4130	15277686_MI:0096	To establish whether the two-hybrid interactions between LUG and SEU represented a direct physical contact in vitro, we carried out GST affinity chromatography. Immobilized GSTSEU was incubated with MBP, MBP-LUFS, and MBPLUFS+Q. In agreement with the two-hybrid data, GST-SEU (but not GST alone) interacted specifically with MBP-LUFS and MBP-LUFS+Q (Fig. 2), demonstrating a direct protein-protein interaction between LUG and SEU.
4131	15294869_MI:0096	In pull-down assays employing purified fulllength recombinant proteins, GST-tagged PIR interacted with ATNAP125
4132	15295098_MI:0096	Asynthetic AuxIAA domain II peptide was used in pull-down assays from extracts of tir1-1[TIR1myc] plants without and with auxin (10 M NAA) added in vitro. The recovery of TIR1myc on domain II peptide beads was assessed by immunoblotting with anti-c-Myc antibody
4133	15296760_MI:0096	In GST pull-down assays, GST-tagged ATSRA1 interacted physically with full-length GRL
4134	15299139_MI:0096	Mapping of the NZZ and INO interaction domains.
4135	15299139_MI:0096	NZZ and FIL interact in vitro.
4136	15299139_MI:0096	NZZ bound FIL (FIL, FILmyc), YAB3, and INO reproducibly and independently of GST.
4137	15299139_MI:0096	NZZ fused to glutathione S-transferase (NZZ), but not glutathione S-transferase (GST) alone, could bind FIL
4138	15316289_MI:0096	The results show that GST-AtBET10 recombinant protein pulled down a GUS(1-360)-AtBT1(1-192) recombinant protein band.
4139	15326298_MI:0096	Among the fragments containing the QLQ, WRC, or C-terminal domains of GRF1, only that containing the QLQ domain was able to bind to GIF1
4140	15326298_MI:0096	Only the SNH but not the QG domain of GIF1 was able to bind GRF1
4141	15331764_MI:0096	We have confirmed that Nse4 interacts with the Smc5 and Nse1 components of the Smc5+6 complex
4142	15350535_MI:0096	Interaction between Wrch1 and individual SH3 domains of NCKbeta.
4143	15358149_MI:0096	Effect of divalent cations on the interaction between KChIP2.1 and KvN.
4144	15358149_MI:0096	GST-KChIP2.1 (lane 3); and GST-KChIP2.2 (lane 4) were incubated with KChIP2.1-His-Bind resin complex in the presence of 10 mM Ca2+.
4145	15358149_MI:0096	It was found that KChIP2.2 could bind with KChIP1 and the interaction increased with increasing Ca2+ concentration.
4146	15358149_MI:0096	Moreover, pull down assay also revealed an interaction of KChIP2.2 with GST-KChIP2.
4147	15358149_MI:0096	Pull down assay of the binding of KChIP1 and KChIP2.2 with KvN-Sepharose.
4148	15358149_MI:0096	Pull down of KvN and KChIP2.2 using KChIP1-Sepharose beads
4149	15361138_MI:0096	IIIf including GL3 (data not shown). Selected interactions were confirmed by in vitro pulldown assays. GST-tagged PAP1 and PAP2, respectively, was purified from Escherichia coli and bound to GSH agarose beads. As a negative control beads were loaded with GST. The loaded beads were incubated with in vitro translated and radioactively labelled GL3, EGL3, TT8, AtBHLH012 and AtBHLH013, respectively. Both, PAP1 and PAP2, specifically interacted in vitro with all four R/B-like BHLH proteins from subgroup IIIf. No binding of the related AtBHLH013 from subgroup IIIe was detected, confirming the results of the yeast two-hybrid assays (Figure 1c).
4150	15361138_MI:0096	Selected interactions were confirmed by in vitro pulldown assays. GST-tagged PAP1 and PAP2, respectively, was purified from Escherichia coli and bound to GSH agarose beads. As a negative control beads were loaded with GST. The loaded beads were incubated with in vitro translated and radioactively labelled GL3, EGL3, TT8, AtBHLH012 and AtBHLH013, respectively. Both, PAP1 and PAP2, specifically interacted in vitro with all four R/B-like BHLH proteins from subgroup IIIf. No binding of the related AtBHLH013 from subgroup IIIe was detected, confirming the results of the yeast two-hybrid assays (Figure 1c).
4151	15377662_MI:0096	Purified cleaved p85 pro-tein bound best to Rab5 (no nucleotide), followed by Rab5-GTPS. Significant amounts of p85 also bound to the transition state analogue conformation of Rab5 (GDP-AlF4), and to Rab5-GDP. We found similar results using a pull-down assay with two Rab5 mutants. The Rab5S34N mutant preferentially binds GDP, whereas the Rab5Q79L mutant is unable to hydrolyze bound GTP. Purified cleaved p85 bound to both GSTRab5S34N and GST-RabQ79L preloaded with GDP and GTP, respectively, which were immobilized on glutathione-Sepharose beads
4152	15377662_MI:0096	The p85BH mutant only bound Rab5Q79L-GTP
4153	15377662_MI:0096	the p85R274A mutant only bound Rab5S34N-GDP.
4154	15380617_MI:0096	To evaluate the respective affinities of the different B' isoforms for Chk2, we developed an in vitro pulldown assay using recombinant Chk2 fused to glutathione S-transferase (GST).
4155	15448699_MI:0096	Morevoer, in vitro experiments using purified proteins showed that Sic1 binds directly to Hog1 (Fig. 3c).
4156	15456723_MI:0096	the HIS6-EMF2 VEFS protein bound to GST-CLF C5 (lane B) but not to GST alone (lane C), suggesting a direct physical interaction between the proteins. Thus, the CLF C5 domain and EMF2 VEFS domain bound to each other in vitro as well as in yeast.
4157	15456783_MI:0096	both Vangl1 and Vangl2-GST fusions can retain immunoreactive Dvl2 and Dvl3 present in embryonic extracts.
4158	15456783_MI:0096	we used protein extracts from HEK293 cells transfected with Dvl1 to monitor interaction with Vangl1GST and Vangl2-GST proteins. Results in Fig. 3A show that GST-Vangl1/2 can capture Dvl1 present in such extracts
4159	15467741_MI:0096	NP-40 lysates from CAD cells were incubated with GST or GST-magicin fusion proteins and bound proteins were detected with an anti-Grb2 antibody.
4160	15467741_MI:0096	NP40 lysates from COS-7 cells overexpressing HA-merlintA were incubated with various GST-merlin fusion proteins immobilized on glutathione Sepharose 4B beads.
4161	15485833_MI:0096	For binding Arp2/3 complex from yeast extract, 5 µl of GST-VCA beads were mixed with variable amounts of high speed extracts or purified Arp2/3 complex in a total volume of 200 µl. Kd was determined as described previously
4162	15485833_MI:0096	To test this hypothesis, recombinant baculovirus-expressed His6-HA-tagged Arc40 was used to test the interaction with GST-VCA from Bee1 and N-WASP and CA from yeast Myo5. Purified VCA and CA fragments were cross-linked to Affi-Gel beads and tested for interaction with purified Arc40 by bead pull-down assays
4163	15485833_MI:0096	yeast extracts prepared from wild-type and {Delta}arc40 strains were incubated with VCA beads, and unbound (Sup) and bound (Pellet) Arp2/3 complex was detected by immunoblot analysis using the anti-Arp2 antibody.
4164	15526038_MI:0096	Binding of WAT to PRAD-Sepharose.
4165	15592873_MI:0096	The AtSERK1 kinase domain interacts with AtCDC48 and GF14 in vitro
4166	15632444_MI:0096	Interaction of the chaperone ShcS1 with its cognate effector HopS1' in GST-pulldown experiments.
4167	15643072_MI:0096	An in vivo interaction between the N terminus of Pol1p and Mcl1-MHp was tested by expression of the first 180 amino acids of Pol1p C-terminally fused to GFP (Fig. 2B, bottom) and expressed under the regulation of its endogenous promoter from a plasmid (pTB19) in nmt41mcl1-MH cells. Purification of Mcl1-MHp with Talon resin recovered only a fraction of the GFP-NT chimera (Fig. 2B) from cell lysates when cells were grown in the absence of 10 mM thiamine (Fig. 2D, ON) but did not recover any detectable GFP-NT when the expression of Mcl1-MHp was repressed by 10 mM thiamine (Fig. 2D, OFF). Because DNA might have mediated this weak interaction, we digested the purified material while it was still on the Talon beads with DNase I, followed by extensive washes (Fig. 2D). This treatment was not sufficient to disrupt the weak Mcl1-MHp interaction with the GFP-NT protein fragment. Expression of GFP with Mcl1-MHp does not recover GFP with Mcl1-MHp, demonstrating that the Pol1p fragment interaction was not induced by nonspecific interaction between GFP and Mcl1-MHp.
4168	15643072_MI:0096	Cell lysates arrested by the mutations cdc25-22 (G2), cdc22- M45 (S phase), cdc21-M68 (S), or orp1-4 (pre-S) were used in this analysis (Fig. 2E). In G2 and pre-S-phase arrests (cdc25-22 and orp1-4, respectively), the majority of the GFP-NT remained unbound to Mcl1-MHp recovered by cobalt-immobilized resin, but during S phase nearly all of the GFP-NT in the cellular lysate was recovered with the Mcl1-MHp.
4169	15643072_MI:0096	Mcl1p interacts with the N terminus of Pol1p both in vitro and in vivo. Two epitope-tagged Mcl1 proteins (diagrammed in Fig. 2A) were highly enriched in material recovered from yeast cellular lysates bound to an affinity matrix composed of an N-terminal Pol1 protein fragment fused to GST (GST-NT in Fig. 2B and C). This protein fragment contains amino acids 118 to 634 of Pol1p (47). None of these tagged alleles of Mcl1p interacted strongly with the C-terminal GST-Pol1p protein chimera (GST-CT in Fig. 2B and C) or GST (Fig. 2C). Such GST pulldown assays from whole-cell lysates demonstrate a high-affinity interaction between Mcl1p and the N terminus of Pol1p.
4170	15643072_MI:0096	To test this result in a different way, we used the GST-Pol1NT118-634 bound to GSH-Sepharose to collect Mcl1-GFP from 3 mg of total protein in whole-cell extracts from the above arrested strains. This technique also showed that Mcl1-GFP interacts with Pol1p in the mcl1-GFP, cds1, and hsk1-1312 backgrounds. It was not, however, present when GST-Cds1p was overexpressed.
4171	15659634_MI:0096	Direct interaction of DIS3/SCAR2 and ARPC3 in a GST pull-down assay.
4172	15665379_MI:0096	The site of binding on Tea2 was investigated by measuring the binding of Mal3 to Tea2 constructs attached to a Ni-NTA column as His-tagged fusions with Trx as indicated in Fig. 2.
4173	15674350_MI:0096	GST-ER 338-379 captured both BRCA1 1-100 and BRCA1 101-200
4174	15674350_MI:0096	GST-ER 420-595 captured BRCA1 1-100 but not BRCA1 101-200
4175	15674350_MI:0096	the binding of BRCA1 mutant 1 to GST-ER 282-420 was significantly less than that of BRCA1 mutant 2, mutant 3, or wildtype protein (Figure 5c and d). Mutant 1 (which contains three leucine or isoleucine to alanine substitutions) yielded about 28% of the wild-type control binding; whereas mutants 2 and 3 (which contain one or two leucine/isoleucine to alanine substitutions) exhibited 80-90% of control binding.
4176	15674350_MI:0096	These studies revealed that most of the BRCA1 : ER-a interaction was mediated by aa 338-379 of ER-a; but a smaller amount of binding could be ascribed to aa 420-595 of ER-a
4177	15696166_MI:0096	To examine further whether MeCP2 directly interacts with Brm, we carried out glutathione S-transferase (GST) pull-down experiments using bacterially expressed MeCP2 and in vitro&#8722;translated recombinant SWI/SNF subunits. MeCP2 specifically interacted with Brm and INI1 (Fig. 1c),
4178	15721254_MI:0096	Although OS-9 bound to either hydroxylated or nonhydroxylated GST-HIF-1alpha, increasing amounts of OS-9  had no effect on the binding of VHL to hydroxylated GST-HIF-1alpha
4179	15721254_MI:0096	GST-HIF-1alpha(531-826) bound to in vitro-translated OS-9 isoform 1 (aa 1-667) ing OS-9 or PHD2. PHD2 was chosen for analysis beand isoform 2 (aa 1-533/589-667)
4180	15721254_MI:0096	HIF-1alpha   residues 531-826, 653-826, or 692-826 efficiently bound  to OS-9, whereas residues 1-329, 429-608, 531-610,  and 786-826 did not bind OS-9
4181	15721254_MI:0096	increasing amounts of OS-9  had no effect on the binding of VHL to hydroxylated  to GST-HIF-1alpha
4182	15721254_MI:0096	OS-9 bound to either hydroxylated or nonhydroxylated GST-HIF-1alpha
4183	15721254_MI:0096	Testing  of carboxy-terminal truncation mutants of isoform 1 in  the GST pull-down assay demonstrated binding of OS-9 aa 1-544 to HIF-1alpha, whereas OS-9 aa 1-235 and 1-158  did not bind.
4184	15721254_MI:0096	when 293 cell lysates were incubated with GST-HIF-1alpha(531-826) in vitro, the binding of PHD3  was dramatically increased by coexpression of V5-OS-9
4185	15741320_MI:0096	To further investigate HFR1-COP1 interaction, we carried out in vitro pull-down assays. Figure 2B shows that HFR1 interacted with the COP1 WD40 domain, but not the COP1 deletion mutant containing only the RING and coiled-coil domains, confirming results obtained with yeast two-hybrid assays.
4186	15797382_MI:0096	GST-Tom22IMS but not GST itself bound to immobilized Tim21IMS (Figure 2C). Thus, Tim21IMS interacts with the TOM complex via direct binding to Tom22IMS.
4187	15797382_MI:0096	Isolation of protein A-Tim23 from wild-type (wt) and tim21 yeast mitochondria lysed with digitonin.
4188	15797382_MI:0096	Ni-NTA agarose was left untreated (control) or loaded with purified Tim21IMS and Tim50IMS prior to incubation with Triton X-100 solubilized mitochondrial extracts.
4189	15797382_MI:0096	We expressed and purified Pam18N and incubated it with lysed mitochondria.
4190	15797382_MI:0096	We thus directly compared which components of TIM23-PAM were copurified with either tagged Tim23 or tagged Tim21 (Figure 3F).
4191	15797382_MI:0096	While the purification via tagged Tim23 yielded both TIM23core and TIM23*, the purification via tagged Tim21 yielded only TIM23* (Figure 3B),
4192	15799966_MI:0096	As was the case for COMMD1, most COMMD proteins were also capable of precipitating NF-{kappa}B complexes
4193	15799966_MI:0096	COMMD1-8 and COMMD10 could readily precipitate endogenous COMMD1
4194	15799966_MI:0096	COMMD1-RelA interactions are only detectable with full-length COMMD1
4195	15799966_MI:0096	homologous regions, present in the RHD of all five NF-{kappa}B subunits, were capable of binding to COMMD1.
4196	15799966_MI:0096	RHD of RelA was sufficient for binding to COMMD1, p50 or p105, and I{kappa}B-{alpha}.
4197	15799966_MI:0096	The carboxyl terminus of COMMD1 (exon 2-3), which contains the COMM domain, was found to be sufficient for interactions with COMMD1 and COMMD3.
4198	15800064_MI:0096	Further evidence of association was that bacterially produced GST-Mto2p specifically bound to Mto1p-MYC from S. pombe lysates (Figure 1B).
4199	15800615_MI:0096	A series of nine overlapping glutathione S-transferase (GST) fusion proteins designated B2-1 to B2-9 (ref. 30), spanning the entire coding region of BRCA2, were used to define the regions of BRCA2 that interact with RAD51 (Fig. 1a).
4200	15800615_MI:0096	The phosphorylation of TR2 was particularly interesting because the RAD51 interaction domain maps exclusively to TR2, as determined by pull-down assays (Fig. 2b, lane 3).
4201	15805487_MI:0096	Pulldown assay using these proteins showed that both CRY and CNT bound to CRY
4202	15806159_MI:0096	A CE (7.7 mg protein) from E. coli expressing recombinant Grb7 was subjected to CaM-affinity chromatography and processed as indicated above (top panel).
4203	15806159_MI:0096	Figure 1a shows that Grb7 can be isolated from the SK-BR-3 cytosolic fraction (CF) by Ca2+-dependent CaM-affinity chromatography upon EGTA ([ethylene bis(oxyethylenenitrilo)]-tetraacetic acid) elution (EGTA, fractions 1-3), while it is absent in the effluent before EGTA addition (Ca2+).
4204	15809031_MI:0096	Importantly, a bacterially expressed N-terminal fragment of for3p (6His-for3N) was able to bind tea4p in vitro (Figure 4B), showing that this interaction between for3p and tea4p is likely to be direct. In contrast, for3p did not bind to the C-terminal region of tea1p in this assay (Figure 4B), suggesting that the interaction between for3p and tea1p is probably indirect.
4205	15809031_MI:0096	We also noted that tea1C can dimerize through its coiled-coil region (Figure 1F).
4206	15809031_MI:0096	We then showed that tea1p and tea4p bind directly by using bacterially expressed 6His-tagged fragments in in vitro assays. The C-terminal half of tea4p specifically bound to MBP-tea1C, but not to MBP alone (Figure 1F).
4207	15855171_MI:0096	The pull-down assays showed strong binding of p53 with the FAK-NT domain of FAK
4208	15855171_MI:0096	we detected binding of the p53 protein in 293 cells with the GST-FAK-NT protein, and the binding of p53 with GST-FAK-NT was higher in 293-p53 cells that overexpressed p53 versus 293-vector cells
4209	15855171_MI:0096	We show that full-length FAK binds to GST-p53
4210	15907477_MI:0096	E1B-AP5 was labelled with [L-a-35S]methionine in in vitro transcription-translation assays and shown to interact with GST-p53
4211	15907477_MI:0096	It can be seen that p53 is bound by GST-E1B-AP5 to a comparable extent in all of the cell lines examined.
4212	15907477_MI:0096	It can be seen that p53 is bound by GST-E1B-AP5 to a comparable extent in all of the cell lines examined. It was isolated as a binding partner for E1B-AP5 from tumour cell lines expressing wild type (A549)
4213	15907477_MI:0096	It can be seen that p53 is bound by GST-E1B-AP5 to a comparable extent in all of the cell lines examined. It was isolated as a binding partner for E1B-AP5 from tumour cell lines expressing wild type (A549) and mutant protein (C33A) and from adenovirus transformed cell lines (Ad12E1HER2 cells and Ad5E1911 cells).
4214	15917470_MI:0096	As shown in Figure 3A, approximately 10% of input EWS protein was specifically retained on the Oct-4-conjugated Sepharose beads. Because EWS did not bind to GST alone (Fig. 3A, lane 2), the interaction was considered to be specific.
4215	15917470_MI:0096	bacterially produced GSTEWS protein interacts with recombinant Oct-4, suggesting that the Oct-4-EWS interaction does not require an adaptor protein.
4216	15917470_MI:0096	EWS bound to GST-Oct-4 (POU) but did not interact with GST-Oct-4 (NTD) or GST-Oct-4 (CTD)
4217	15917470_MI:0096	GST-Oct-4 beads, but not control GST beads, efficiently retained endogenous EWS
4218	15917470_MI:0096	In the reciprocal experiment, the GST-EWS fusion protein was also able to interact with endogenous Oct-4
4219	15917470_MI:0096	This result suggests that EWS has at least three sites (amino acids 70 through 163, GRP I, and GRP II and III) that can bind to Oct-4 independently.
4220	15935327_MI:0096	The association between DSCR1.4 and Raf-1 was conWrmed by immunoblot analysis with antibody against Raf-1 following pull-down analysis
4221	15935327_MI:0096	The interaction between DSCR1.4 and endogenous Raf-1 was again observed in pull-down experiments using the lysates prepared from GM7373 and MS-1 endothelial cells
4222	15935327_MI:0096	the results suggest that Raf-1 can associate with two regions of DSCR1.4: one in the N-terminal end (amino acids 1-84) and the other in the C-terminus (amino acids 134-156), and this is interfered with by amino acid sequence 115-133 of DSCR1.4.
4223	15936270_MI:0096	Interaction between Win1 MAPKKK and Wsh3 was also detected biochemically in S. pombe. Wsh3 was overexpressed from a plasmid with an N-terminal GST (glutathione S-transferase) tag, and isolation of GST-Wsh3 by glutathione-Sepharose led to coprecipitation of Win1 both before and after high osmolarity stress that activates  the Spc1 MAPK cascade (Figure 1B).
4224	15964553_MI:0096	The yeast two hybrid assay and GST fusion protein pull down experiment demonstrated that TSSK5 physically interacts with CREB in vitro.
4225	15976448_MI:0096	The GST-myosin 1c IQ4 tail binds to PHR1b and PHR1b.mid, but not to PHR1.JMD and PHR1a.AP.
4226	15990873_MI:0096	The interactions of MKS1 with W25 and W33 were also confirmed in vitro using His-tagged MKS1
4227	15990873_MI:0096	The MKS1 and MPK4 interaction was confirmed by in vitro binding assays. This showed that recombinant, N-terminal 6xHis-tagged MKS1 from Escherichia coli could pull down labeled MPK4, but not a control human lamin
4228	16002617_MI:0096	In vitro pull-down assay between FKF1, LKP2, and ZTL kelch domains and CDF proteins.
4229	16002617_MI:0096	To verify the interactions detected in yeast, we carried out binding studies using recombinant glutathione S-transferase (GST)-FKF1 and -LKP2 kelch fusions and the three His/T7-CDF proteins. The results of the in vitro pull-down assays were similar to those of the two-hybrid assays (Fig. 1C), validating the interactions observed in yeast.
4230	16027220_MI:0096	Mlp1p-protein A (PrA) could be reproducibly isolated in a complex exclusively with Mlp2p, indicating that the two proteins are able to bind directly to each other as previously proposed
4231	16043509_MI:0096	Full-length Ski2-myc associated specifically with GST-Ski8 only in the presence of full-length Ski3p, while no significant Ski2deltaN-myc signal was observed even in the presence of full-length Ski3p (Fig. 4A).
4232	16043509_MI:0096	Glutathione agarose beads were added to the cell extracts to pull down GST-Ski8, and anti-HA Western blotting was carried out to check the copurification of Ski3p.
4233	16053918_MI:0096	The interaction between KIAA0649 and 1A6/DRIM was first demonstrated by a GST-pull-down assay. The result showed that endogenous 1A6/DRIM protein presented in the nuclear extract of BGC823 cells could specifically bind to the GST-K2.1 fusion protein,
4234	16055635_MI:0096	The epitope-tagged E2FB and DPA proteins are likely to be functional in BY-2 cells because they form heterodimers (Figure 3C) and interact with the bacterially purified Arabidopsis RBR1
4235	16055635_MI:0096	To prove that the endogenous Arabidopsis E2FB is able to dimerize with DPA as well as to bind RBR1, we conducted pull-down experiments with glutathione S-transferase (GST)-tagged Arabidopsis DPA and RBR1 proteins and Arabidopsis cell extracts. We found that E2FB could associate with both RBR1 and DPA and therefore has the characteristics of the canonical E2F transcriptional complexe
4236	16091426_MI:0096	Fig. 2 shows that hSec23Ap can be specifically captured by immobilized GST-PCTAIRE (lane 2).
4237	16109709_MI:0096	Interaction of PII with PamA in Vitro-
4238	16166382_MI:0096	The binding between eIF4G-m and eIF4A-NTD was tested using His-tagged eIF4G-m and untagged eIF4A-NTD
4239	16179646_MI:0096	Therefore, we used pull-down assays of in vitro translated AtORC proteins with purified GST-tagged AtORC proteins. We found that AtORC2 and AtORC5 interact strongly with all AtORC subunits
4240	16203867_MI:0096	A macromolecular complex was formed between maltose binding protein (MBP)-C-CFTR, glutathione S-transferase (GST)-NHERF2, and LPA2 (Fig. 6 B).
4241	16203867_MI:0096	Flag-tagged LPA2 binds GST-NHERF2 with the highest affinity.
4242	16203867_MI:0096	GST-NHEFR2 binds directly to maltose-binding protein (MBP)-C-LPA2.
4243	16214168_MI:0096	These studies delineate the region required for the interaction with the HMG domain of Sox10 to residues 135 to 200 of Nmi.
4244	16214168_MI:0096	When expressed as a green fluorescent protein (GFP) fusion, amino acid residues 135 to 200 of Nmi were able to mediate binding to Sox10 in GST pulldown assays
4245	16221674_MI:0096	To examine this possibility, we performed a GST pull-down experiment by reacting GST-tagged TRAF6 and FLAG-tagged FLN29 and its deletion mutants (Fig. 6B).
4246	16221674_MI:0096	To explore the binding region in TRAF6 with FLN29, the reaction of His-tagged FLN29 and GST-tagged TRAF6 and its deletion mutants was examined.
4247	16223725_MI:0096	GST-Pin1 also binds Myc-tagged cyclin E.
4248	16223725_MI:0096	Pin1 might bind to the hetrodimer in a manner that requires an active CDK2 protein to catalyze the phosphorylation of Ser384 on cyclin E.
4249	16227626_MI:0096	Wild type and mutant 35S-labeled p53 proteins were subjected to pull-down assays with GST-LAP, GST-LIP, or GST alone immobilized on glutathione-Sepharose. The input of labeled protein is shown in the first of four lanes for each of the p53 variants.
4250	16229834_MI:0096	For this purpose, Par-4 was expressed as a GST-tagged fusion protein in E. coli, immobilized on glutathione sepharose beads and used as affinity matrix to bind 35S-methionine-labeled in-vitro-translated Amida.
4251	16230351_MI:0096	the ability of GST-POSH fusion proteins to pull down SIAH1
4252	16236155_MI:0096	As shown in the top panel of Figure 7(a), there was clear binding between the His6-tagged GRIP domain and GST-ARL1 in the presence of GTPcS. In the presence of GDP, no binding was observed.
4253	16242403_MI:0096	we have preliminary data that the extracellular domain of GOP can bind PDF using an in vitro assay (Supplemental Experimental Procedures; Figure S4). Moreover, this binding appears to be specific. It is competed by PDF but not by another neuropeptide, proctolin, and significant binding is not observed with an unrelated peptide (Figure S4).
4254	16246841_MI:0096	domain analysis of Spa33 involved in binding to MxiN, Spa32, or Spa47 by pull-down assay
4255	16246841_MI:0096	To test the possibility that Spa33 interacts with other translocating effectors, we used GST pull-down assays to investigate the capacity of Spa33 to interact with effectors, such as VirA, IcsB, IpaC, and IpgB1.
4256	16246841_MI:0096	We investigated the capacities of the Spa33 homologues SpaO, YscQ, and HrcQB to interact with MxiN and other Shigella-TTSM-associated proteins, i.e. MxiK, Spa32, Spa47, MxiG, and MxiJ, by GST-pull down assay.
4257	16249186_MI:0096	For these studies we carried out pull-down studies with E2F-(237-423) using wild-type, patch 1, and patch 2 mutants of GSTE7- E/D/CR3.
4258	16249186_MI:0096	To confirm that the CR3 region used for structure determination in this study is sufficient for pRb binding, we prepared GST-tagged 1AE7-(44-93) (called GST-1AE7-CR3) for use in aGST pull-down assay with pRb,
4259	16249186_MI:0096	To directly determine whether the CR3 region of E7 contributes to the disruption of pRbE2F complexes, we prepared a 1:1 complex of bacterially expressed His-tagged pRb large pocket (His-pRbABC) and a bacterially expressed E2F fragment harboring residues 237-423 that was previously shown to be sufficient for pRb binding
4260	16253999_MI:0096	GST pull-down assays, we confirmed that SPIN90-C-term also associates with the Arp2/3 complex
4261	16253999_MI:0096	The VCA domain of N-WASP was used as a positive control for Arp2/3 complex binding.
4262	16254079_MI:0096	A fragment containing PAH4 and most of the C-terminal domain of Sin3A (545-1157) pulled down endogenous Ebp1.
4263	16254079_MI:0096	GFP-Ebp1 was found associated with the E2F1 oligonucleotide. No GFP reactive proteins from lysates of cells that had not been transfected or cells that were transfected with the GFP vector alone (Figure 6B, upper panel) were found associated with the E2F1 oligo. Endogenous Ebp1 was also associated with the oligonucleotide, although binding was decreased in the GFP only transfected cells (Figure 6B, middle panel). Sin3A was found associated with the E2F1 consensus oligonucleotide in all three cell lysates.
4264	16254079_MI:0096	GST-Ebp1, but not GST, bound full-length in vitro translated Sin3A protein
4265	16254079_MI:0096	we incubated [35S] HDAC2 to GST-Sin3A. HDAC2 was able to bind to Sin3A directly
4266	16254079_MI:0096	we performed GST pull-down assays using HeLa cell lysates. Western blot analysis demonstrated that Sin3A specifically associated with GST-Ebp1
4267	16254079_MI:0096	we showed that domain 545-1157 bound to HDAC2
4268	16257957_MI:0096	In this study, we show that EBNA-3 interacts specifically with AhR
4269	16257957_MI:0096	In this study, we show that EBNA-3 interacts specifically with AhR.
4270	16260785_MI:0096	Next, we tried to reconstitute the interaction in vitro employing recombinant proteins. Arr4p N-terminally fused to a decahistidine tag was purified from E. coli by nickel chromatography.
4271	16260786_MI:0096	GST-pulldowns were conducted by using equimolar ratios of GST-FliH and each of the the respective purified FliI(2-91) mutant proteins.
4272	16260786_MI:0096	When tested for interactions with the four truncated FliH proteins (full-length FliH and FliH fragments 55-258, 94-258, and 117-258), FliI-(2-91) interacted with all of them by GST pulldown assay, and FliI-(19-91) interacted with none of them (Fig. 4,
4273	16275645_MI:0096	GST-Fbx4, but not GST, bound to in vitro synthesized 35S-Pin2 or -TRF1.
4274	16275645_MI:0096	GST-Pin2 bound to Fbx4 fragments, including amino acid residues 172-306. GST-Pin2 fragments encompassing residues 1-419, 48 -155, or 1-155 bound to Fbx4.
4275	16275660_MI:0096	As shown in Fig. 3A the recombinant proteins Tau, Hsc70, Hsp70, Hsp90, E2Q, and caytaxin interact with GST-CHIP in pull-down assays
4276	16275660_MI:0096	Fig. 2A shows the selective enrichment on the GST-VCP affinity matrix of a 35-kDa carboxyl-terminal His-tagged AMFR fragment from a crude E. coli protein extract. In strong contrast, no AMFR protein was bound to the matrix with the control protein GST.
4277	16275660_MI:0096	Overlay experiments with the SH3 domain of amphiphysin II allowed the identification of the known interaction partner dynamin (Table I). In addition, the proteins Discs large-associated protein 4 (DLP4), XRCC4 (DNA repair protein), and fructose-1,6-bisphosphatase (FBP) (Table I) were identified as novel amphiphysin II interaction partners and verified by in vitro pull-down and two-hybrid assays (Fig. 4, A and B).
4278	16275660_MI:0096	The VCP binding region in AMFR was mapped downstream of the Cue domain to the carboxyl terminus of the protein (aa 498-643) (Fig. 2, G and H).
4279	16275660_MI:0096	We found that the amino-terminal region of VCP (aa 1 199) is necessary and sufficient for the association with His-AMFR in vitro
4280	16278218_MI:0096	HSF1 is a direct substrate for phosphorylation by MK2 and that this phosphorylation may mediate the inhibitory effects of MK2
4281	16278218_MI:0096	MK2 Directly Phosphorylates HSF1
4282	16278681_MI:0096	To test whether CRIPak can bind directly to PAK1 in vitro, PAK1 was expressed as a GST fusion protein in bacteria and tested for interaction with in vitro-transcribed and -translated [35S] methionine-labeled CRIPak.
4283	16280327_MI:0096	Nickel-agarose-Bcl10 pull-down experiments were performed to identify the interaction of Bcl10 with Akt1.
4284	16282318_MI:0096	Specifically, GST-AtPAP[IV] copurified with MBP-FipN but not MBP.
4285	16282318_MI:0096	Thus, GSTFipN copurified with MBP-CstF77, MBP-CPSF30, MBP-PabN1, and CFI25-CBD after purification of the latter fusions on their respective affinity matrices
4286	16282325_MI:0096	First, we used the GST pulldown method to compare the ability of cIAP1, cIAP2, and XIAP to bind TRAF2 in vitro, employing fragments of cIAP1, cIAP2, and XIAP comprised of the three tandem BIR domains and using L-[35S]methioninelabeled TRAF2 prepared by in vitro translation (Fig. 3A).
4287	16282325_MI:0096	FLAGcIAP1 was immunoprecipitated using anti-FLAG antibody, and associated TRAF2 (and SMAC) were detected by immunoblotting.
4288	16282325_MI:0096	To verify that the E64 and R65 mutations directly affect BIR1-TRAF2 association, we used cIAP2 instead of cIAP1, and we produced recombinant single mutant E64R and double mutant E64A/R65A BIR1 proteins in bacteria and examined their interaction with TRAF2 in vitro.
4289	16282325_MI:0096	TRAF2 binding to FLAG-cIAP1 (first panel) or GST- cIAP2 BIR1 (second panel) was examined by SDS-PAGE and immunoblotting (IB) with antibodies against TRAF2. Themembranewas also probed with an anti-SMAC antibody
4290	16284401_MI:0096	In contrast to GST-wild type ARMS protein (7.2), a decrease in binding of C3G to CrkL was observed with GST-ARMSY1096F fusion protein (Fig. 7A).
4291	16284401_MI:0096	The tyrosine-phosphorylated GST-ARMS7.2 protein bound more CrkL protein compared with the non-phosphorylated protein (Fig. 2B, compare lanes 3 and 4).
4292	16284401_MI:0096	To confirm the participation of SH2 domain of CrkL in ARMS-CrkL interaction [35S]methionine CrkL proteins were synthesized and tested for association with ARMS.
4293	16286470_MI:0096	Fig. 2A shows that 
N-MKP-1 formed a complex with active ERK2, but 
N-MKP- 1(ANAP) did not; conversely, neither 
N-MKP-1 nor 
N-MKP- 1(ANAP) associated with unactive ERK2.
4294	16286473_MI:0096	Based on Western blot analysis, we conclude that the C terminus of pRB is the major binding site for DGK.
4295	16286473_MI:0096	DGK associates with pRB via its MARCKS-PSD.
4296	16286473_MI:0096	DGK binds to hypophosphorylated pRB
4297	16286473_MI:0096	DGK binds to pRB, p107, and p130 in vitro and in cells.
4298	16286473_MI:0096	To test whether the DGK-MARCKS-PSD was sufficient to mediate interaction with pRB, we used a biotinylated DGK-MARCKS-PSD peptide to affinity-purify pRB from MCF7 cell lysates.
4299	16288713_MI:0096	Interaction between recombinant wt and mutants of human eIF2a with purified recombinant PERK and PKR.
4300	16291744_MI:0096	As shown in Fig. 6B, the phosphorylated alpha-actinin peptide, but not the unphosphorylated peptide, captured Src,
4301	16291752_MI:0096	a comparatively weak interaction was seen between GST borealin and survivin 2beta.
4302	16291752_MI:0096	An intense interaction between GST-borealin and wild type survivin was observed
4303	16291752_MI:0096	Interactions of similar intensity were also seen between GST-auorora-B and survivin and GST-aurora-B and the isoforms.
4304	16291752_MI:0096	Interactions of similar intensity were also seen between GST-aurora-B and survivin and GST-aurora-B and the isoforms.
4305	16291752_MI:0096	In this assay both isoforms bound to GST-survivin, albeit survivin -deltaEx3 bound far less efficiently than wild type survivin.
4306	16291752_MI:0096	Survivin isoforms can form heterodimers with wild type survivin.
4307	16291753_MI:0096	Complex formation of ATF3Zip2 with p65 in vivo and in vitro.
4308	16291753_MI:0096	Counteraction between ATF3Zip2 andCBPinp65binding,
4309	16291753_MI:0096	Counteraction between ATF3Zip2 andCBPinp65binding, reporter assay,andcell death.
4310	16291755_MI:0096	Syk is recruited to the TNF receptor signaling complex following TNF-stimulation.
4311	16299177_MI:0096	Thus, our in vitro interaction assay indicated that AtCPK32 interacts with ABF4 in vitro.
4312	16301319_MI:0096	results suggest that Erbin interacts with Sur-8 in cells. Further analyses showed that Erbin interaction with Sur-8 requires the LRR domain.
4313	16301319_MI:0096	Sur-8 and RasV12 co-precipitated
4314	16306047_MI:0096	As observed in our assays, PS1 migrated in our SDS gels mainly as a band of 50 kDa, suggesting that it was not being processed in our cell lines. To determine whether this modification might alter PS1 binding to Tcf-4 and plakoglobin, we analyzed cellular extracts from cell lines in which PS1 was predominantly present in the processed form. As shown in Fig. 9, when binding of processed and unprocessed forms of PS1 to GST fusion proteins was analyzed, the PS1 carboxyl-terminal fragment bound with lower affinity to 
-catenin (5-fold lower, Fig. 9B) and plakoglobin (3-fold) than the 50-kDa form. Binding to Tcf-4 was barely detectable for the processed PS1
4315	16306047_MI:0096	PS1 associated with armadillo repeats 7-12 to the same extent as the complete central domain and with repeats 10-12 only slightly less, indicating that these repeats are the main binding site for PS1 (Fig. 4C). On the other hand, armadillo repeats 1-6 barely interact with PS1. Deletion of the 
-catenin amino-tail, which strengthens the interaction of the carboxyl- tail with the armadillo domain and reduces the interaction of this element with other
-catenin-binding proteins (41), decreases the affinity for PS1 (Fig. 4C). The effects of 
-catenin point mutants that modify  the interaction with other proteins were also studied. Tyr-654 3 Glu (Y654E), a mutant that mimics the phosphorylation of this residue by epidermal growth factor receptor or other tyrosine kinases, decreases 4-fold the association between 
-catenin and PS1,
4316	16306047_MI:0096	Pulldown assays using fragments of Tcf-4 fused to GST indicated that PS1 interacted through the same regions used by 
-catenin and plakoglobin, amino acids 1-50 and 51-80, respectively (Fig. 6B). Preincubation with either 
-catenin or plakoglobin increased the amount of PS1 retained by glutathione-Sepharose, suggesting that these proteins mediate the interaction of PS1 and Tcf-4. However, the effect was much stronger when plakoglobin was used (Fig. 6B), suggesting that binding of Tcf-4 to PS1 is mainly mediated by this protein. Moreover, plakoglobin also associated better with Tcf-4 when PS1 was present,
4317	16306047_MI:0096	The armadillo repeats involved in PS1 binding were identified as 1-6, suggesting that the interaction of PS1 with plakoglobin requires a more amino-terminal part of this domain than in the case of 
-catenin. This conclusion was reinforced by the fact that mutation of the plakoglobin equivalent resi-due to 
-catenin Tyr-654, Tyr-643, did not down-regulate PS1 binding but, to the contrary, increased it (Fig. 4F)
4318	16306047_MI:0096	The mechanism involved in stimulation of plakoglobin-Tcf-4 association by PS1 was further investigated. As shown in Fig. 6D, the armadillo repeat domain binds to Tcf-4 with a higher affinity than the full-length protein
4319	16306228_MI:0096	Analysis of a Coomassie-stained polyacrylamide gel of purified QSK and SIK indicated that a significant proportion of these enzymes were associated with 14-3-3 (Fig. 3D).
4320	16306228_MI:0096	Cell extracts derived from the different HeLa cell lines were incubated with 14-3-3{zeta} conjugated to Sepharose, and immunoblot analysis of 14-3-3-associated proteins revealed that QSK (Fig. 2C) and SIK (Fig. 2D) were associated with 14-3-3{zeta} derived from HeLa cells expressing wild-type LKB1, but not from LKB1-deficient control cells or cells expressing kinase-inactive LKB1.
4321	16306228_MI:0096	o further explore these observations, we generated HeLa lines that stably express GFP-TAP-14-3-3{zeta} in the presence or absence of LKB1. QSK and SIK were associated with purified TAP-14-3-3{zeta} in the HeLa cell line expressing wild-type LKB1, but not in LKB1-lacking cells (Fig. 2E).
4322	16306228_MI:0096	The phosphorylated QSK T-loop peptide interacted with 14-3-3{zeta} to a markedly greater extent than did the non-phosphopeptide (Fig. 3B)
4323	16306228_MI:0096	The RAF-phospho peptide LSQRQRSTS(P)TPNVHMV binds 14-3-3 with high affinity
4324	16316992_MI:0096	To examine the binding of beta1-AR-CT to full length MAGI-3 rather than simply the isolated PDZ1 domain, HEK-293 cells were transfected with full-length V5/His-tagged MAGI-3, and pull-down assays were performed using purified GST fusion proteins corresponding to beta1-AR-CT with the terminal Val residue mutated to either Ala, Ile, Met, or Leu (Fig. 2B).
4325	16316996_MI:0096	Epac2 specifically bound GTPS-loaded H-Ras.
4326	16319076_MI:0096	To test for direct binding, we expressed and purified recombinant dynamin 1 and performed binding studies using beads loaded with profilin 1 and profilin 2 (Fig. 1B).
4327	16326698_MI:0096	Therefore, BRCA1 associated with endogenous P-ACCA in mammalian cells.
4328	16326701_MI:0096	Purification of stable complexes f fUDG-A20 and fUDG-A20-Pol.
4329	16326715_MI:0096	These results indicate that the alpha-helical conformation of the region C-terminal to the p22phox PRR (amino acids 161-164) participates in the full interaction with p47phox-(151-286).
4330	16330544_MI:0096	Active Chk1 is associated with Hsp90.
4331	16331268_MI:0096	As shown in Figure 3c, the N-terminal domain of Daxx interacted with the DNA-binding domain of STAT3, while the central domain of Daxx showed weak binding to that of STAT3
4332	16331268_MI:0096	To delineate the domains in STAT3 that mediate the protein-protein interactions between STAT3 and Daxx, pull-down experiments were performed with a series of mutant GST-STAT3 proteins. As shown in Figure 3b, only the DNA-binding domain of STAT3 (320-493) showed a significant interaction with Daxx.
4333	16332538_MI:0096	Light-Regulated Interaction of FHY1 and phyA In Vitro and In Yeast
4334	16332688_MI:0096	These data indicated that Parkin directly binds to RanBP2 in vitro as well as in vivo, and the region spanning amino acid residues 78-170 appears to be important for its binding to RanBP2.
4335	16332960_MI:0096	TAZ was pulled down with a TBE oligonucleotide in the presence of TBX5
4336	16339145_MI:0096	The presence of both proteins during the expression and purification procedure was verified by Western blotting using the affinity-purified Pdx1 antibody and a monoclonal His tag antibody for the detection of Pdx2 (Fig. 3B).
4337	16339760_MI:0096	A GST fusion protein consisting of a HAP1 fragment (160-599 amino acids), but not 160-445 amino acids, precipitated KLC-2, confirming the yeast two-hybrid results
4338	16341228_MI:0096	This interaction was confirmed in vitro using glutathione S-transferase (GST)-tagged Sam68 (GST-Sam68) produced in Escherichia coli and in vitro-translated Brm
4339	16344550_MI:0096	Instead, both the N-terminal (amino acids 1-190) and C-terminal (amino acids 501-691) regions of CoCoA were capable of binding to -catenin. Thus, CoCoA has two independent -catenin binding sites.
4340	16344550_MI:0096	To test for binding in vitro, HA-tagged CoCoA (Fig. 1A, lane 1) or -catenin (lane 4) was expressed in COS-7 cells by transient transfection, and the COS-7 cell extracts were incubated with GST--catenin or GST-CoCoA, respectively.
4341	16352600_MI:0096	When incubated with brain extract from normal, non-infected hamsters (NHa) in sarkosyl-containing buffer (0.3%), both the GST·4OR and GST·16OR captured PrPC in the presence of copper ions at pH 7.5 with a half-maximal effect between 75 and 125 µM (Fig. 1A).
4342	16352600_MI:0096	When we incubated Sepharose-immobilized GST·OR fusion proteins with brain extract from ScHa in the presence of sarkosyl-containing buffer, we observed that only GST·16OR captured PrPSc at pH 7.5 in the absence of copper ions (Fig. 3, A and B), demonstrating selective interaction of the expanded OR domain with PrPSc.
4343	16354671_MI:0096	L10P co-eluted with LolA proteins adsorbed to a FLAG tag affinity column (F),
4344	16365431_MI:0096	293T cells were transfected with GST-STAP-2 SH2 and/or a series of Myc-tagged IKK- deletion mutants (Fig. 5E). The transfectants were lysed, pulled down with glutathione-Sepharose beads (GSH bound), and immunoblotted with an anti-Myc Ab. As shown in Fig. 5F, the LZ domain of IKK- alone failed to interact with the SH2-like domain of STAP-2, while both the kinase and HLH domains of IKK- retained strong binding to STAP-2.
4345	16365431_MI:0096	both the death domain and TIR domains of MyD88 interacted with the SH2-like domain of STAP-2.
4346	16373488_MI:0096	40LoVe was specifically associated with GST-hnRNP I and not GST-l (Fig. 4A, cf. lanes 1 and 2).
4347	16373488_MI:0096	and we tested if the two proteins can interact directly by using purified recombinant proteins. 6His-40LoVe was mixed with either GST-hnRNP I or GST-l, and then proteins bound to glutathione resin were analyzed by SDS-PAGE gel. 40LoVe could clearly be detected bound to GST-hnRNP I to a much greater extent than to GST-l, supporting direct hnRNP I- 40LoVe interaction (Fig. 4B, cf. lanes 3 and 7).
4348	16407827_MI:0096	GSTfusion protein of human Grb2 and a SH2-deficient Grb2 mutant, R86K, were created and tested for the ability to bind mycPLD2 in in vitro GST-pull-down assays. As shown in Figure 2a, purified GSTGrb2 interacts with mycPLD2.
4349	16415858_MI:0096	Autoradiography (AR) showing the direct interacion of a2N-35S with GST-ARNO(WT) d) via carboxy-terminus but not amino terminus of ARNO (e)
4350	16415858_MI:0096	Pull-down (PD) of the a2-isoform with recombinant ARNO(WT)-6His used as bait from (b) proximal tubule PMS and (c) isolated endosomes (Endo).
4351	16429262_MI:0096	AtSAP18 and ERF3 or ERF4 specifically interact in vitro.
4352	16429262_MI:0096	AtSAP18 and HDA19 specifically interact in vitro.
4353	16429262_MI:0096	Binding reactions between immobilized AtSAP18 and ERF3 or ERF4 by GST pull-down assays.
4354	16438971_MI:0096	Recombinant AtCPK11 interacts with AtDi19 in vitro
4355	16449236_MI:0096	deletion of the PITX2A HD ({Delta}39-98) ablated FOXC1 interactions.
4356	16449236_MI:0096	Full-length PITX2A bound to Ni2+-FOXC1 in these assays
4357	16461343_MI:0096	First, we tested the ability of various substrate trap mutants of PTPN22cd including D195A, C227S, D195A/Q274A, and DACS to pull down TCR{zeta} from Jurkat cell lysates.
4358	16461343_MI:0096	Identification of substrates of PTPN22.
4359	16461343_MI:0096	In contrast, ~54% of the phosphorylated cyto-TCR{zeta} was captured by the DACS mutant, whereas none was pulled down by wild type PTPN22cd (Fig. 4C, lanes 4-6),
4360	16461343_MI:0096	In contrast, ~70% of the phosphorylated Zap70 was captured by the DACS mutant (Fig. 2E, lanes 4-6), demonstrating that PTPN22cd binds directly to Zap70 in an interaction that requires phosphorylation at one or both tyrosines.
4361	16461343_MI:0096	In contrast, activated Lck (phosphorylated at tyrosine 394) did interact with PTPN22cd, as ~30% of the activated Lck was pulled down by the substrate trap mutant (Fig. 2B, lanes 7-9).
4362	16461343_MI:0096	proteins identified by mass spectrometry were confirmed in repeated substrate capture experiments by immunoblotting with antibodies specific for Zap70 (lanes 1 and 2), Lck (lanes 3 and 4), CD3{epsilon} (lanes 5 and 6), Vav (lanes 7 and 8), and phospho-TCR{zeta} (lanes 9 and 10).
4363	16461579_MI:0096	To test this idea, a series of WSIP1 truncations were tested in a GST pulldown assay for interaction with full-length WUS. Full-length WSIP1 and WSIP1&#916;1 retained the ability to interact with WUS, but all deletions in which the LisH domain was removed failed to interact (Figure 6C). These results demonstrate that the interaction between WSIP1 and WUS requires the C-terminal conserved domain of WUS and the N-terminal LisH domain of WSIP1.
4364	16474402_MI:0096	The crystal structures of the USP7 NTD bound to EBNA1, p53 and MDM2 peptides have shown that all these peptides contact USP7 residues Asp164 and Trp165 and that EBNA1 also specifically contacts Asn169 (ref. 11). We investigated the relative importance of these residues in peptide binding by generating point mutations in the USP7 NTD where each of these residues was individually mutated to alanine, as well as a fourth mutant where both Asp164 and Trp165 were mutated. Each mutant was also analyzed by 1H-15N HSQC NMR spectroscopy in order to confirm that the mutations did not affect the folding of the protein (data not shown). The USP7-binding regions of EBNA1, p53 and MDM2 were initially tested for binding to USP7 NTD mutants using GST pull-down assays (Fig. 5a-c, respectively). For all three peptides, the Trp165 mutation abrogated binding, the Asp164 mutation decreased binding and the Asn169 mutation had no obvious effect.
4365	16474402_MI:0096	The USP7-binding regions of EBNA1, p53 and MDM2 were initially tested for binding to USP7 NTD mutants using GST pull-down assays (Fig. 5a-c, respectively). For all three peptides, the Trp165 mutation abrogated binding, the Asp164 mutation decreased binding and the Asn169 mutation had no obvious effect.
4366	16474402_MI:0096	We examined whether this interaction is direct by pull-down assays using equimolar amounts of purified full-length USP7 and MDM2 fragments fused to GST. GST fusions containing MDM2 residues 1-280 or 1-160 each caused the retention of USP7 on glutathione resin, which was not seen with GST alone (Fig. 3a). This indicated that the MDM2-USP7 interaction is direct and is mediated by sequences between residues 1 and 160. To determine whether this interaction occurs through the USP7 NTD, we repeated the pull-down assay with GST-MDM21-160 and the USP7 NTD (Fig. 3b). The USP7 NTD was retained on the glutathione resin by MDM21-160, to a similar degree as by EBNA1.
4367	16476580_MI:0096	Using a GST-Pin1 fusion protein, in vitro GST pulldown assays were performed. Results showed that Myc- Nek6 protein associated with the GST-Pin1 fusion protein (Fig. 1B, lane 3)
4368	16480949_MI:0096	Our results indicate that GST-AICD, but not GST alone, is able to bind to the full-length flotillin-1 (Fig. 3A).
4369	16497658_MI:0096	all tested Arabidopsis SR proteins, including SCL33/SR33, were able to interact with AtCyp59 in vitro.
4370	16497658_MI:0096	Interaction between the two proteins was also studied by in vitro pull-down assays. To do so, the Arabidopsis CTD was overexpressed in E. coli as GST fusion and purified on glutathione Sepharose beads (Fig. 7B, left panel). Beads bound with GST-AtCTD were incubated with protein extracts prepared from either tobacco protoplasts transiently expressing AtCyp59-HA (Fig. 7B, upper right panel, lane 3) or E. coli cells expressing AtCyp59-HA (Fig. 7B, lower right panel, lane 3). As evident from Figure 7B (two right panels), AtCyp59-HA was able to bind recombinant CTD in vitro (lanes 3), thereby confirming interaction between these two proteins observed in the yeast two-hybrid assay.
4371	16525419_MI:0096	Identification of a phosphotyrosine-dependent interaction between nephrin and the Nck SH2/SH3 adaptor.
4372	16525503_MI:0096	GST-Atx22Q affinity matrix pulled down VCP from brain extracts in the presence and absence (apyrase treatment) of ATP. Moreover, the interaction was detected when the nonhydrolyzable ATP analog ATPgammaS was added to the binding reaction.
4373	16525503_MI:0096	In contrast, the well-characterized binding partner Ufd1 (Meyer et al, 2000) associated with VCP in the in vitro binding assay (Figure 1D).
4374	16525503_MI:0096	N-terminal VCP fragment (aa 1 199) is critical for the Atx-3 interaction, while the C-terminus containing the highly conserved ATP-binding domains D1 and D2 is not required.
4375	16525503_MI:0096	the GST-Atx22Q affinity matrix pulled down VCP from brain extracts in the presence and absence (apyrase treatment) of ATP. Moreover, the interaction was detected when the nonhydrolyzable ATP analog ATPgammaS was added to the binding reaction. In contrast, in the presence of ADP, VCP was not pulled down from the brain extract, suggesting that the addition of ADP changes the conformation of VCP and reduces the binding affinity for Atx-3. Similar results were obtained with reticulocyte lysate or when purified His-tagged VCP was used for in vitro binding assays (
4376	16525503_MI:0096	VCP was selectively enriched from brain extract by Atx-3
4377	16525503_MI:0096	when purified His-tagged VCP fusion protein was incubated with Atx-3 affinity matrices, indicating that VCP and Atx-3 interact directly with each other in vitro (Figure 1C)
4378	16533805_MI:0096	A, D-site peptides (triangle) were used to inhibit the ability of MKK7 to bind to GST-JNK1.
4379	16533805_MI:0096	In contrast, the isolated D-site from MKK4 (MKK4-(36-49)) bound reasonably well to JNK1 when tested in the same assay (Fig. 3, B and C).
4380	16533805_MI:0096	To ascertain if any of the D-sites were necessary for high affinity JNK binding, substitution mutations were introduced into D1, D2, and D3, either alone or in combination, in the context of MKK7-(1-85).
4381	16533805_MI:0096	To confirm that the MKK7beta N terminus was sufficient to bind JNK, and to evaluate whether systematic removal of the putative docking sites would compromise binding, fusions of GST to portions of the N terminus of MKK7 were tested for their ability to bind in vitro to 35S-labeled JNK1 (Fig. 2A).
4382	16543236_MI:0096	Immunoprecipitation revealed that the fraction of total HIF-1{alpha} co-precipitated with p300
4383	16547356_MI:0096	tail" peptides that represented either the non-modified or the me3K9-modified NH2-terminal region of H3 exhibited marginal binding to HP1beta at 0.3 M salt and did not compete with the full-length protein, even at a 200 molar excess.
4384	16547356_MI:0096	this fragment can be assigned to the stretch extending between amino acids 40-129, i.e. the so-called "histone fold" domain. Thus, at least under in vitro conditions, HP1beta has the capacity to bind histone H3 independently of post-translational modifications, associating primarily with the central, helical part of the molecule.
4385	16555005_MI:0096	In these experiments, Tre-GAP was pulled down by GST-Myl2 and GST-LOC91526 but not by GST alone
4386	16556936_MI:0096	GST-p37 AUF1 and His-PABP were expressed in E. coli and used at equimolar amounts for in vitro interaction analysis, then recovered by glutathione-Sepharose binding of GST-p37
4387	16556936_MI:0096	GST-PABP (purified and RNA-free) also bound strongly to full-length p37 AUF1 and apparently far more than the p37{Delta}N78 mutant protein (Fig. 4B).
4388	16556936_MI:0096	p37 AUF1 directly binds to the C terminus of eIF4G independently of ARE interaction.
4389	16556936_MI:0096	the C-terminal 45-amino acid domain of AUF1 is essential for interaction with eIF4G and PABP.
4390	16556936_MI:0096	The p37 AUF1 isoform interacted most strongly with the C terminus of eIF4G, followed by the p40 isoform (z30% that of p37). There was a weaker interaction detected between the p45 (z15%) and p42 (z20%) AUF1 isoforms and the C terminus of eIF4G, despite the nearly equivalent level of input AUF1 protein isoforms (Fig. 3).
4391	16601102_MI:0096	Western blots of bound proteins probed with anti-His antibody show that both PID and MPID bind PDK1
4392	16603732_MI:0096	Here we describe the identification of a novel protein complex, the MLL2 complex, consisting of MLL2, ASH2, RBQ3, and WDR5, which is required for ligand-dependent ER{alpha} transactivation
4393	16603732_MI:0096	These results suggest that ER{alpha} binds to the MLL2 complex through two LXXLL motifs in MLL2 (located between amino acids 4167 and 4780) in the presence of estrogen.
4394	16616919_MI:0096	We found that PRMT2 directly interacts with RB, in contrast to PRMT1, PRMT3 and PRMT4
4395	16619302_MI:0096	Lane 3 shows that precipitated GST-MVP co-precipitates 35[S]-methionine labeled GR.
4396	16622416_MI:0096	Endogenous AdipoR1 interacted with GST-APPL1c but not with GST control protein.
4397	16636664_MI:0096	Moreover, in vitro pull-down assay using bacteria expressed recombinant His-GSTP1-1 and the HEK293 cell lysates containing Flag-tagged TRAF2 or TRAF6 showed the same result.
4398	16643855_MI:0096	Identification of ZCCHC11 as a LPS-dependent TIFA-interacting protein
4399	16648843_MI:0096	The Mud 1825-1997 fragment from the Mud(2501) protein contains the NLM domain and is pelleted with GST-bound full-length Pins (amino acids 1-658; lanes 3,4) and GST-bound Pins amino-terminal TPR domain (amino acids 42-398; lanes 5,6)
4400	16648845_MI:0096	peptides representing the C-terminal 25 amino acids of Nek2A with or without the terminal MR dipeptide were used to bind the APC/C in CSF extracts. Again, the full-length peptide, but not the &#916;MR peptide, could bind Xenopus APC/C in untreated and Cdc20 (Fizzy)-depleted extracts equally well
4401	16678774_MI:0096	Since yeast two-hybrid analysis does not differentiate between direct and bridged protein interactions, we performed a GST pull-down assay using recombinant Inp2p and Myo2p tail made in Escherichia coli (Figure 4C)
4402	16682412_MI:0096	an interaction between GST-DNMT3A 477-617 and SETDB1 was observed (lane 4).
4403	16682412_MI:0096	GST-fused SETDB1 1-527 (Fig. 3B, staining panel) strongly bound to both exogenous and endogenous DNMT3A (lanes 4-6 and 10-12), indicating that amino acids 1-527 of SETDB1 are responsible for the recruitment of SETDB1 to DNMT3A.
4404	16682955_MI:0096	upon Dox induction of SNT-1 PTB, the involvement of Gab1 and Sos1 in the multiprotein complex with SNT-1 in FGF-dependent conditions was significantly decreased in Clone 29 cells but not in control cells. Thus, abrogation of the recruitment of multiple proteins to the C-terminus of wild-type SNT-1 confirmed the dominant negative action of the SNT-1 PTB domain in MCF-7 cells.
4405	16713566_MI:0096	This study indicates that OCA-B is required for pre-BCR and BCR signaling at multiple stages of B cell development through its nontranscriptional regulation of SYK.
4406	16717101_MI:0096	Both subunits of the Sir3 dimer are required to stabilize the complex with the Sir4 coiled-coil.
4407	16717101_MI:0096	Sir3 residues 464-522 are essential, but apparently not sufficient, for the interaction with Sir4. We conclude that Sir3-(464-728) is the minimal domain of Sir3 that stably interacts with Sir4.
4408	16717101_MI:0096	The efficient association of Sir3-(832-978) with both Sir3 fragments shows that the dimerization function of Sir3 is mediated by C-terminal residues 832-978 and Sir4-binding residues 464-728.
4409	16717101_MI:0096	These protein fragments bind specifically to Sir4-CC and fail to bind underivatized plates or a Sir4-CC(M1307N) point mutant that does not interact with full-length Sir3
4410	16740636_MI:0096	Identification of Cav3.3 as a CatSper1- and CatSper2-associated Protein from Human Sperm Extracts by GST Pulldown Approach
4411	16760425_MI:0096	Moreover, bacterially expressed GST-centrin incubated with 293T extracts associated with endogenous CP110, but not with a noncentrosomal protein, both in the absence (-Ca2+) and presence of calcium (+Ca2+; Figure 5D).
4412	16760425_MI:0096	To determine whether the interaction between CP110 and CaM is direct or is mediated by other proteins, we incubated in vitro-translated, radiolabeled CP110 with CaM agarose, and we observed robust binding (Figure 3A). No interaction was detected between CaM agarose and control proteins, strongly suggesting that the binding between CaM and CP110 is direct and specific (Figure 3A).
4413	16762630_MI:0096	The interaction of HCCR-1 and DP1 identified by the yeast 2-hybrid screen was confirmed by GST pull-down experiments
4414	16766265_MI:0096	These results are supported by in vitro binding experiments in which GST-pRB fusion proteins containing various pRB domains (Figure 2B) were incubated with a lysate from cells overexpressing HMGA2 (Figure 2D). pRB(379-928), which contains the entire wild-type pocket region of pRB plus the C-terminal region, was able to bind efficiently to HMGA2 (lane 1). In contrast, pRB(379-928)D21, which lacks the region corresponding to exon 21, only weakly associated with HMGA2 (lane 3). pRB(768-928) and pRB(834-928), which carry the C-terminal region plus a small region of the pocket and the C-terminal region only, respectively, did not bind to HMGA2 at all (lanes 5 and 6). Finally, pRB(1-379) and pRB(379-792), carrying the N-terminal region and the pocket region, respectively, were able to bind efficiently to HMGA2 (lanes 2 and 4).
4415	16766265_MI:0096	We used cell lysates expressing HA-HMGA2 mutants carrying serial deletions at the N and C terminus regions (Figure 2E) in a pull-down assay with a recombinant GST-pRB protein (Figure 2F, lanes 1-6). The only mutant that lost the capacity to bind to pRB was A2(1-44),
4416	16766694_MI:0096	No online version of this paper was available; therefore source text annotations are not entered.
4417	16777956_MI:0096	PKS1 interacts with phot1 and NPH3 in vitro
4418	16782065_MI:0096	SDS-PAGE analysis of purified proteins revealed that MhpE co-eluted with GST-MhpF (Fig. 2B), indicating that MhpE binds directly to MhpF.
4419	16792691_MI:0096	full-length and partial DDB1a proteins co-precipitated with GST:CUL41&#8722;453
4420	16792691_MI:0096	Interestingly, the partial proteins of GST:DDB1a300&#8722;666 and in vitro translated CUL41&#8722;453 were sufficient to permit interaction between the proteins
4421	16792691_MI:0096	myc-tDET1 co-precipitates with GST:CUL41)453 and GST:RBX1.
4422	16792691_MI:0096	o investigate the interaction of DDB1a-CUL4 with in planta expressed DDB1a we generated transgenic Arabidopsis plants that expressed DDB1a under the control of a 35S promoter (here referred to as 35S::myc-DDB1a; Figure 2h). The 35S::myc-DDB1a plants grew like wild-type plants, indicating that ectopic expression of DDB1a has no major impact on Arabidopsis development (data not shown). Using GST:CUL41&#8722;453 as bait, myc-tagged DDB1a was successfully pulled down from plant extracts
4423	16792691_MI:0096	The GST:DDB1a300&#8722;666 fusion protein was also used to successfully pull down CUL4 from plant extracts (Figure 2g). Detection of precipitated CUL4 was performed using a polyclonal antibody raised against a CUL4-specific N-terminal peptide.
4424	16792691_MI:0096	To investigate whether DDB1b can also interact with CUL4, a DDB1b fragment stretching from amino acids 300-694 (DDB1b300&#8722;694) was cloned and used for a pulldown assay since this region was sufficient for DDB1a-CUL4 association
4425	16809346_MI:0096	The result showed that FoxM1 bound to the S1/S2, S4, S6/S7, and S8 FHREs containing oligonucleotides
4426	16815998_MI:0096	The N-terminal domain of GW182 interacts with the PIWI domain of AGO1.Samples were analyzed by GST pull-down assays.
4427	16816948_MI:0096	We conWrmed the interaction between Cdc10p and Pol5p using an alternative method, an in vitro -pulldown- assay
4428	16828757_MI:0096	As shown in Fig. 1B, GST-PLZF was co-purified with His-CCS-3 at an approximate molar ratio of 1:1.
4429	16843263_MI:0096	higher levels of EGFR, Y1068 P-EGFR, Shc, and p85 coprecipitated with Myc in cells expressing the insertion mutant compared to HER2WT cells (Figure 4A, lanes 7-12). Higher levels of Y1289 P-HER3 and increased HER3:HER2 association were observed in HER2YVMA-expressing MCF10A cells but not in BEAS2B cells, probably as a result of the lower levels of HER3 in the latter cells
4430	16843263_MI:0096	To determine the activation status of ectopic HER2, Myc pull-downs were tested by P-Tyr and Y1248 P-HER2 immunoblots. Y1248 P-HER2 was only detected in the Myc precipitate from HER2YVMA-expressing cells. A much stronger P-Tyr band coprecipitated with Myc in these cells compared with HER2WT-expressing cells. The fainter P-Tyr band in HER2WT cells, where Y1248 P-HER2 was not detected in the Myc precipitates, suggests that HER2 is phosphorylated in tyrosines other than Y1248 in MCF10A/HER2WT cells. Finally, higher levels of EGFR, Y1068 P-EGFR, Shc, and p85 coprecipitated with Myc in cells expressing the insertion mutant compared to HER2WT cells (Figure 4A, lanes 7-12). Higher levels of Y1289 P-HER3 and increased HER3:HER2 association were observed in HER2YVMA-expressing MCF10A cells
4431	16843263_MI:0096	To determine the activation status of ectopic HER2, Myc pull-downs were tested by P-Tyr and Y1248 P-HER2 immunoblots. Y1248 P-HER2 was only detected in the Myc precipitate from HER2YVMA-expressing cells. A much stronger P-Tyr band coprecipitated with Myc in these cells compared with HER2WT-expressing cells. The fainter P-Tyr band in HER2WT cells, where Y1248 P-HER2 was not detected in the Myc precipitates, suggests that HER2 is phosphorylated in tyrosines other than Y1248 in MCF10A/HER2WT cells. Finally, higher levels of EGFR, Y1068 P-EGFR, Shc, and p85 coprecipitated with Myc in cells expressing the insertion mutant compared to HER2WT cells (Figure 4A, lanes 7-12). Higher levels of Y1289 P-HER3 and increased HER3:HER2 association were observed in HER2YVMA-expressing MCF10A cells but not in BEAS2B cells, probably as a result of the lower levels of HER3 in the latter cells
4432	16844784_MI:0096	we used the Y2H system and in vivo pull-down assays to: (i) independently verify the Cfp-10/ClpC1, Cfp-10/Pks13, Cfp-10/FtsQ Cfp-10/Rv2240c, and Cfp-10/Rv0686 interactions
4433	16845383_MI:0096	Daxx binds directly to Hausp, as shown by an in vitro pulldown assay with purified recombinant proteins
4434	16845383_MI:0096	HeLa S3 lysates were incubated with M2 beads (control) or M2 beads coated with recombinant Flag-Daxx. The bound proteins were resolved on SDS-PAGE and visualized by Coomassie blue staining. The 135 K protein band in the Flag-Daxx lane was identified as Hausp by mass spectrometry
4435	16845383_MI:0096	The Daxx-Mdm2 interaction is likely to be direct, as shown by an in vitro pulldown assay with recombinant proteins
4436	16845477_MI:0096	In vitro interaction between the Cterminal region of AtSWI3C and a GST fusion protein containing the domain II of BRM.
4437	16854969_MI:0096	An in vitro pull-down assay showing 35S-labeled AP1 and SEP3 proteins retained by GST-SEU
4438	16854969_MI:0096	SEU bridges an interaction between LUG and AP1/SEP3
4439	16857903_MI:0096	BKI1-6XHIS interacts with GST-BRI1-KD in vitro.
4440	16857903_MI:0096	BKI1 inhibits the interaction between the kinase domains of BRI1 and BAK1 in vitro
4441	16861711_MI:0096	Light regulated interaction of FHL with phyA in vitro
4442	16861711_MI:0096	phyA specifically binds to GST-tagged FHL and FHY but not GST alone
4443	16862148_MI:0096	The ultimate C-terminal FLNa repeats (23-24) exhibited strong FilGAP binding activity. Repeat 23 alone had some binding activity, but repeat 24 had none (Fig. 1c).
4444	16868027_MI:0096	we performed GST-14-3-3 fusion protein pull-down assays using HEK 293T cell lysates expressing the same ADAM22 wild-type and mutant proteins (Fig. 4B). Mutations of the first binding site similarly reduced the ability of GST-14-3-3 to pull down the ADAM22 precursor form. Mutation of the second site had very little effect, whereas double mutation or deletion of both binding sites abolished binding to the GST-14-3-3 protein.
4445	16892067_MI:0096	A fusion protein of glutathione S-transferase (GST) and the RAPL coiled-coil domain precipitated wildtype MST1 but not the MST1 mutant lacking the C-terminal regulatory region (Fig. 1b). These results indicate that the coiled-coil region of RAPL associates with the MST1 regulatory domain.
4446	16897494_MI:0096	As shown in Fig. 4C, At- CPSF100 was pulled-down by the fusion proteins of GST with AtCPSF160, AtCPSF73-I, AtCPSF73-II, AtCPSF30, and AtPAP(II), respectively.
4447	16897494_MI:0096	As shown in Fig. 4C, At-CPSF100 was pulled-down by the fusion proteins of GST with AtCPSF160, AtCPSF73-I, AtCPSF73-II, AtCPSF30, and AtPAP(II), respectively.
4448	16897494_MI:0096	The interaction between GST-AtCPSF30 and AtPAP(II) is demonstrated in Fig. 4D.
4449	16899217_MI:0096	Magicin interacts with the SH3 domains of Src family proteins.
4450	16899217_MI:0096	Pull-down (Fig 2A) and coimmunoprecipitation (Fig. 2B) experiments in CAD cells confirmed the interaction of CAD and Fyn
4451	16902409_MI:0096	14-3-3sigma is a p37 AUF1-interacting protein. (A) Recombinant His-tagged p37 protein was purified from E. coli by NTA resin and mixed with whole-cell HeLa lysate. His-p37 AUF1 was recovered by NTA resin chromatography, proteins resolved by SDS-PAGE, and visualized by silver stain. The 30 kDa band (arrow) was excised and sequenced by mass spectrometry.
4452	16902409_MI:0096	A 20 amino-acid sequence in the CTD of p37 AUF1 is critical for interaction with 14-3-3s.
4453	16902409_MI:0096	GST-14-3-3 was recovered by glutathione Sepharose-GSH resin chromatography, and the association of His-p37 AUF1 was examined by immunoblot analysis using anti-AUF1 antibody. In vitro binding analysis revealed that p37 AUF1 interacts with 14-3-3 directly, and does so in a dose-dependent manner (Figure 2A).
4454	16902409_MI:0096	the His-p37 recovery assay suggested that only the sigma isoform, but not the g or b/z isoforms, of 14-3-3 binds to p37 AUF1 (Figure 1C)
4455	16902409_MI:0096	the His-p37 recovery assay suggested that only the sigma isoform, but not the g or b/z isoforms, of 14-3-3 binds to p37 AUF1 (Figure 1C).
4456	16902409_MI:0096	The predominant isoform of AUF1 which bound to 14-3-3sigma was the p37 protein, and to a much lesser extent p40 AUF1. There was no detectable interaction between 14-3-3sigma and the two larger AUF1 isoforms, p42 and p45 (Figure 3B).
4457	16902409_MI:0096	Under identical binding conditions, recombinant purified p37 AUF1 was found to interact strongly with 14-3-3s, to a lesser extent with 14-3-3Z, but not with 14-3-3z (Figure 2B).
4458	16905657_MI:0096	ESPIN1 Binds to gamma-ADR
4459	16905657_MI:0096	ESPIN1 Binds to VSTI11
4460	16905657_MI:0096	ESPIN1 Binds VSR1 via the ENTH Domain
4461	16905657_MI:0096	GST:ESPIN1, but not GST alone, precipitated from plant extracts a 180kD protein species that was recognised by anti-clathrin antibody(Figure 4C), indicating that ESPIN1 bound clathrin.
4462	16905657_MI:0096	Interestingly, MBP:alphaADR(ear) also bound weakly to GST:ESPIN1.
4463	16919237_MI:0096	immuno-affinity chromatography identified two other chaperone proteins known to form a complex with Hsp40; Hsp90 and Hsp70
4464	16923726_MI:0096	Recombinant HisPEX19-1 bind to the C-terminus of PEX10.
4465	16949368_MI:0096	The carboxyl-terminal region of CHD8 specifically bound the CZ zinc finger region of CTCF, but not the CN, CC, and GST
4466	16962094_MI:0096	In agreement with the results obtained in yeast two-hybrid assays, binding to the C-terminal region of obscurin was observed with ank1.9-GST (relative binding: 61% ± 14.21 of the input, means ± SE, n = 4) and ank1.5-GST
4467	16962094_MI:0096	in vitro translated telethonin/T-cap was able to bind to the GST fusion protein containing domains ZIg1/2 of titin.
4468	16963448_MI:0096	Pulldown experiments in these stable cell lines using S-agarose beads showed that Chk1 only interacted with wild-type S-/FLAG-tagged Claspin but not the 3A mutant of Claspin
4469	16963448_MI:0096	To further investigate how human Claspin and Chk1 interact, we generated five internal deletions of ~200-300 amino acids within the full-length GST-Claspin (Fig. 3B) and investigated the interaction between these Claspin mutants and Myc-tagged Chk1.
4470	16963448_MI:0096	When insect cells were infected with baculoviruses expressing GST-Chk1 and FLAG-Claspin, we observed an interaction between Chk1 and Claspin by either pulldown with glutathione beads (Fig. 2A) or immunoprecipitation using anti-FLAG beads (Fig. 2B).
4471	16963744_MI:0096	HA-tagged VRK2 could be pulled down specifically by immobilized GST-BHRF1, but not by GST alone
4472	16987957_MI:0096	As shown in Figure 6B, the Phg2 core region bound to beads coated with GST-Adrm1, but not to beads coated with GST alone.
4473	16990133_MI:0096	endogenous Ste2 detergent solubilized from purified plasma membranes, regardless of its state of N-glycosylation, binds to c-Myc epitope-tagged Sst2 immobilized on beads using anti-myc mAb 9E10 (Figure 4A). Interaction was specific because no bound species were observed if beads lacked Sst2 or if membrane extracts were prepared from ste2Dcells. Most importantly, no Ste2 was retained when beads were coated with an equivalent amount of Sst2(Q304N)
4474	16990133_MI:0096	We found, second, that His6-Sst2 (produced by baculovirus expression and purified by FPLC) bound to FLAG-tagged Ste2 (detergent solubilized from plasma membranes of sst2D ste2D gpa1D ste4D cells) immobilized on beads with anti-FLAG epitope mAb
4475	16990252_MI:0096	FLAP1 also interacted with N- and C-terminus, but not with the middle region, of GRIP1.
4476	16990252_MI:0096	FLAP1 synthesized in vitro bound to GST-fused ß-catenin
4477	16990252_MI:0096	the N-terminal LRR fragment of Fli-I bound to the GRIP1 N-terminal region but not to any of the other GST fusion
4478	17041588_MI:0096	To determine whether the regulation of histone H3 methylation at K4 is unique to WDR5-RBBP5, we examined whether loss of L2DTL or other WDR proteins affects this methylation. We found that the loss of L2DTL or DDB2 did not significantly affect K4 methylation status (Fig. 5c).
4479	17055431_MI:0096	Further in vitro evidence that P3H1 and CRTAP could directly interact came from Western analysis on affinity chromatography eluted proteins after binding to either CRTAP or P3H1 antibody columns. In both cases, using the appropriate antibody, we were able to detect the corresponding protein supporting that CRTAP and P3H1 can form a stable complex
4480	17055998_MI:0096	Interaction of COOH-terminal fragments of glycogenin with mouse muscle glycogen synthase.
4481	17055998_MI:0096	Interaction of glycogenin and glycogen synthase expressed in COS cells.
4482	17088250_MI:0096	Phosphorylation of BII2-Spectrin C-terminal fragment inhibits its interaction with aII N-terminal fragment
4483	17095503_MI:0096	Nix binds directly to POSH
4484	17098746_MI:0096	35S-labeled in vitrotranslated FBXO11 bound to immobilized GST-p53 (lane 3) but not GST alone (lane 2).
4485	17098746_MI:0096	Specific p53-interacting protein bands were analyzed by mass spectrometry, and FBXO11 peptide sequences are presented.
4486	17142478_MI:0096	GST-SEF recombinant protein interacted with a HA-tagged ARP6 protein
4487	17142478_MI:0096	SEF, ARP6 and PIE1 proteins interact in vitro.
4488	17157259_MI:0096	Neither SNIP1-N (1-121) nor a SNIP1 construct that lacks the FHA domain-bound c-Myc.
4489	17157259_MI:0096	the fusion protein SNIP1 (215-321), which contains part of the FHA domain, bound to in vitro-translated c-Myc with the greatest affinity. The SNIP1 (215-321) construct also contains amino acids N terminal to the FHA domain. To test whether the FHA domain alone was sufficient to mediate binding, we used the GST fusion protein SNIP1 (274-349) containing only the FHA domain, and again showed binding to c-Myc, although this interaction is weaker compared to the 215-321 construct.
4490	17158449_MI:0096	TAK1 interacted with TAB2 mutants containing residues 516-693 or 574-693, but not with residues containing primarily the C-terminal zinc finger domain of TAB2-(653-693)
4491	17158449_MI:0096	The GFP fusion protein containing TAK1-C100 and TAK1-(479-553) interacted with both TAB2 and TAB3 by co-immunoprecipitation and GST fusion pull-down experiments
4492	17158449_MI:0096	we performed GST fusion pull-down experiments with either GST or GST-TAB2 and lysates from transiently transfected HEK293 cells programmed to express various TAK1 deletion mutants. Similar to the co-immunoprecipitation experiments, only TAK1-FL, TAK1-{Delta}5, and TAK1-{Delta}6 interacted with GST-TAB2
4493	17189269_MI:0096	Purified His-CT protein interacted with GSTSH3, but not GST or GST-SH2 (Fig. 2B).
4494	17189287_MI:0096	As shown in Fig. 6C, binding of the fulllength protein (FWA) and the N-terminally truncated protein (FWA
N) with FT protein was confirmed. Other truncated forms [FWA
C, FWA(STARTþC), FWA(ZLZ), FWA(C) and FWA(ZLZþC)] did not bind to FT.
4495	17194765_MI:0096	KEG interacts directly with ABI5
4496	17196169_MI:0096	we first performed a GST-ALG-2 pull down assay. Immunoblotting with anti-Sec31A pAb revealed doublet bands at 130 and  125 kDa positions corresponding to long and short isoforms of Sec31A, respectively, in HEK293 cell lysates
4497	17196367_MI:0096	Only the full-length GST-PKD3 showed positive interaction with Flag-VAMP2, GST and GST-PKD3-C1 domains did not show any binding activities to Flag-VAMP2
4498	17196367_MI:0096	Our results show hat GCT-VAMP2 was able to specifically pull down PKD3-GFP expressed in CHO cells (Fig. 4a).
4499	17229891_MI:0096	We confirmed DYRK1A and 14-3-3 interaction in mammalian cells by GST pull-down assays.
4500	17234752_MI:0096	binding in vitro transcribed and translated [35S]Topo I to a His-NKX3.1 fusion protein bound to a MagZ binding column and showed preferential binding to the fusion protein compared with a polyhistidine peptide alone
4501	17234752_MI:0096	NKX3.1 bound to GST-Topo D26 and GST-Topo 70 but not to GST-Topo A2
4502	17237231_MI:0096	the results of two different approaches: yeast two-hybrid assay and mass spectrometry analysis of hSR-A-CD-bound proteins, suggested that there was an interaction between hSR-A and a homologeous protein of hHK3 in rat alveolar macrophages
4503	17237231_MI:0096	These results indicate that overexpressed hHK3 interacts with the hSR-A cytoplasmic domain
4504	17255092_MI:0096	the SNF5 protein could bind to wild-type SRG3 (GST-SRG3), but not to the deletion mutant (GST-531-536) nor the double point mutant (GST-L531A/N533A).
4505	17280616_MI:0096	Comparison of silver staining of SDS-PAGE gels containing the pulled-down proteins identified an approximately 30 kDa protein in the lane corresponding to proteins pulled-down with WT-MELK but not in that corresponding to proteins pulled-down with D150A-MELK (Figure 3a). MALDITOF analysis showed this 30 kDa protein to be Bcl-G, a member of the Bcl-2 protein family
4506	17280616_MI:0096	we demonstrated that His-tagged WTMELK could pull-down with Bcl-GL but His-tagged D150AMELK could not, indicating that, in vitro, Bcl-GL interacts directly with WT-MELK but not with D150A-MELK
4507	17289665_MI:0096	Bub3 bound exclusively to DYNLT3
4508	17289665_MI:0096	Cytoplasmic Dynein Light Chain, DYNLT3, Interacts with the Spindle Checkpoint Protein, Bub3
4509	17289665_MI:0096	DYNLT3 from the mitotic extract bound to the Bub3 beads but not the GST beads. The dynein intermediate and heavy chains were also bound to the GST-Bub3 beads.
4510	17293877_MI:0096	The double mutation of residues in the primary binding site and Phe 100(H4) showed a significant effect on the complex formation with CIA/ASF1
4511	17296600_MI:0096	Specifically, we found the 16 murine homologs of all of the human PRC1 PcG proteins, i.e. Polycomb paralogs Pc3/Cbx8 and Pc2/Cbx4, M33/Cbx2; polyhomeotic paralogs, Phc1, Phc2, Phc3, and Ring1A/Ring1 and Scmh1 (19). Non PcG proteins found in PRC1, such as the heat shock 70 kDa protein 8 (Hspa8) and the ATPase Snf2h, were also identified (19). Other known Ring1/Ring1B interactors found here included Cbx7 (39), and Pcgf3, which are Polycomb and Bmi1/Pcgf4 paralogs, respectively. Cbx6, another Polycomb paralog about which very little is known, was found in one of the experiments. With regards to the E2F6.com-1 complex (25), all of its previously described components (Mga, Euhmt1, L3mbtl2, MBLR/Pcgf6, Myn, E2F6, DP1, HP1g/Cbx3, YAF2, and the Ring1A/Ring1, Ring1B/Rnf2 proteins) were identified in our analysis as well.
4512	17296600_MI:0096	specific binding of 35S-Fbxl10/Jmjd1B to GST-Ring1B,
4513	17296600_MI:0096	We first tested some of the known Ring1A/Rnf2 interactors in the PRC1 and E2F6.com-1 complexes, such as Bmi1/Pcgf4, PC3/Cbx8, YAF2 and HP1g/Cbx3.
4514	17310983_MI:0096	In vitro pull-down assays demonstrated direct binding between MDM2 and S7; no co-factors were required. As shown in Figure 1b, GST-MDM2 (b1) or GST-S7 (b2), but not GST, bound to in vitro translated S7 or MDM2, respectively.
4515	17310990_MI:0096	A signal corresponding to INT6 was clearly detected with beads including the MCM7 peptide, but not with those corresponding to GST alone
4516	17310990_MI:0096	The same experiment was performed with INT6 expressed in bacteria and purified to homogeneity. As before INT6 was seen with the beads bearing the MCM7 peptide, but not with the control beads
4517	17314099_MI:0096	293T cells were transfected with expression vectors for wild-type and mutant forms of STRAP, together with a GST fusion protein of a constitutively active form of the TGF-beta type 1 receptor, GST-TbetaR1(TD). Cell lysates were incubated with glutathione-Sepharose beads, and protein complexes were analyzed by immunoblot using an anti-FLAG antibody.
4518	17314099_MI:0096	As shown in Fig. 4F, no changes in the self-association of STRAP were detected in the presence of the STRAP mutants.
4519	17314099_MI:0096	FLAG-STRAP was detected in association with NM23-H1 only when coexpressed with GST-NM23-H1 (Fig. 1A, top).
4520	17314099_MI:0096	The expression of the NM23-H1 mutants NM23-H1(C4S), NM23-H1(C109S), and NM23-H1(C145S) had no effect on complex formation between NM23-H1 and NM23-H1 (Fig. 4A)
4521	17314099_MI:0096	The expression of the NM23-H1 mutants NM23-H1(C4S), NM23-H1(C109S), and NM23-H1(C145S) had no effect on complex formation between NM23-H1 and NM23-H1 (Fig. 4A) or NM23-H1 and NM23-H2 (Fig. 4B),
4522	17322342_MI:0096	The data shown in Figures 1 to 4 establish roles for GCR1, GPA1, PRN1, NF-Y-A5, NF-Y-B9, and potentiallyexperiments (Fig. 6) indicate that PRN1 has the potential for a specific interaction with both NF-Y-B9 and NF-Y-B6.
4523	17329248_MI:0096	The Carboxyl Terminus of XAP2 Is Required for Binding to PDE2A
4524	17329248_MI:0096	Two of these GST fusion proteins bound to PDE2A, and one of these was XAP2, a 330 amino acid protein of the immunophilin family
4525	17347654_MI:0096	Our results demonstrated that CUEDC2 expression did not affect the association of JDP-2 and SMRT with PR
4526	17347654_MI:0096	PRB binds full-length CUEDC2 and the two CUEDC2 fragments (1-180 and 100-226 aa) containing the CUE domain. In contrast, the CUEDC2 fragments (1-133 and D133-180 aa) lacking the CUE domain failed to interact with PRB.
4527	17347654_MI:0096	We performed a GST pull-down assay and found that the DNA domain of ER (180-282 aa) was essential for the interaction between CUEDC2 and ER. Notably, the interaction of CUECD2 with ER was ligand-independent and was similar to the interaction of PR
4528	17347654_MI:0096	we used a glutathione S-transferase (GST) pull-down assay. GST-CUEDC2 was expressed in bacteria and purified by glutathione-coupled beads. GSTCUEDC2 was then incubated with Myc-PRB protein expressed in 293T cells and subjected to SDS-PAGE and Western blot. Figure 1A shows that CUEDC2 interacts with PRB with or without progesterone in vitro.
4529	17350572_MI:0096	As expected, wild-type ALIXBro1 bound to a GST-CHMP4A fusion protein but not to GST alone (compare lanes 2 and 3). In contrast, the ALIXBro1,I212D mutant did not bind GST-CHMP4A detectably
4530	17350576_MI:0096	purified Arp2/3 complex bound directly to wild-type Coronin 1B, but did not bind to the phosphomimetic S2D Coronin 1B mutant
4531	17353003_MI:0096	No significant interaction between AR and GST alone could be observed (pAR/pGST), but very strong protein/protein interaction was observed between AR and the fragment of s-JMJD1C (pAR/pGST-s-JMJD1C) in independent experiments
4532	17355907_MI:0096	we expressed the TSC1-CCD as a GST-fused protein (TSC1-CCD-GST) in bacteria. The fusion product was immobilized by glutathione beads and further incubated with PC12h cell lysate. The protein pulled down by TSC1-CCD was subjected to coomasie blue staining and anti-NADE western blotting (Fig. 1C). NADE was pulled-down by TSC1-CCD-GST but not GST
4533	17374643_MI:0096	In a GST pull-down assay we used a GST-HREV1dC recombinant construct containing the truncated HRSL3 protein fused to glutathione and coupled to glutathione-Sepharose. With this approach, we were able to recover PR65alpha protein from cell  lysates thus confirming a direct interaction between the HRSL3 and PR65alpha proteins
4534	17441508_MI:0096	Here, full-length Mdy2 was fused with GST and mixed with recombinant Sgt2 and its fragments, and the polypeptides bound to GST-Mdy2 were isolated with glutathione-Sepharose.
4535	17441508_MI:0096	Purified Ydj1 was incubated with GST-Mdy2 or glutathione S-transferase (GST) immobilized on glutathione (GSH)-Sepharose with or without the addition of purified Sgt2.
4536	17441508_MI:0096	The results shown in Figure 6B demonstrated that GST-Sgt2 interacted with Mdy2, but that GST-sgt2(&#916;N) lost the capacity to form complexes with Mdy2.
4537	17468262_MI:0096	In vitro pull-down assay to confirm interactions between LIP5 and GST-SKD1 but not between LIP5 and GST alone.
4538	17474147_MI:0096	The GST-fused PLCg1 SH3 domain or a variant containing the mutation of Trp828 to Ala was used to pull-down PAG3, ABl2, Rin3, Shank2, Shank3, and HPK1, respectively, from lysate of cells expressing these proteins with appropriate tags
4539	17525340_MI:0096	Abraxas specifically bound to the BRCT repeats of wild-type BRCA1 (Fig. 1B), but not a cancer-causing BRCT mutant, M1775R
4540	17525340_MI:0096	Rap80 interacts specifically with the Brca1-BRCT domain in vitro.
4541	17525340_MI:0096	Synthetic peptides containing pSer406 bound GST-BRCA1-BRCT, whereas the pSer404 and unphosphorylated peptides did not
4542	17535814_MI:0096	To examine whether the recombinant HsNUF2 protein binds to the CENP-E protein directly, we carried out a pulldown assay in which GST-tagged recombinant HsNUF2 was purified on glutathione-agarose beads and used as an affinity matrix to absorb purified MBP-CENP-E1 in test tubes.
4543	17535814_MI:0096	we carried out a pulldown assay using bacterial recombinant GST-CENP-E protein as an affinity matrix to score the biochemical binding activity of the HsNUF2 protein and its deletion mutants.
4544	17540172_MI:0096	Autoradiography of interactions between immobilized H1b-K26me1 or H4-K20me1 peptides and full-length in-vitro-translated [35S]-labeled L3MBTL1, either wild-type or with P1a or P1b, P2a or P2b, or P3a or P3b point mutants (see Supplemental Data for details) in the first, second, and third MBT domain, respectively.
4545	17540172_MI:0096	GST-3MBT protein bound specifically to H4K20me1/2 but not to unmodified H4K20 or H4K20me3 (Figure 2A).
4546	17540172_MI:0096	His-3MBT protein bound to H4K20me1 in the presence of H1K26me3 peptides, but binding was completely inhibited by the presence of the H1K26me2 peptide (Figures 4D and 4E, right panels).
4547	17540172_MI:0096	Indeed, using an antibody that specifically recognizes H1bK26me2, we confirmed that G9a dimethylates H1K26 and that H1b dimethylated at K26 binds to GST-3MBT (Figure 4A).
4548	17540172_MI:0096	To determine if the interaction between L3MBTL1 and H1b is direct and if methylation of K26 is required, we initially used peptide-affinity chromatography.
4549	17540172_MI:0096	We expanded the binding studies and found that full-length in-vitro-translated L3MBTL1 protein bound mono- and dimethylated H1 peptides exclusively (Figure 3F and data not shown).
4550	17540175_MI:0096	Similar results were obtained in the reverse experiment, where full-length wild-type and mutant forms of p110alpha were mixed with GTP-bound GST-V12 H-Ras fusion protein (Figure 1C).
4551	17540175_MI:0096	We investigated whether GST-fusion proteins of the RBD of the mutant forms of p110alpha were capable of binding to Ras.
4552	17540176_MI:0096	GST-tagged ST was mixed with 293T cell lysates overexpressing a control vector (Vector), FLAG-tagged Aalpha or FLAG-tagged Abeta.
4553	17543119_MI:0096	Pull down of native AtTOR with recombinant His-tagged ScFKBP
4554	17553790_MI:0096	Consistent with formation of an ILK·kAE1 complex, kAE1 was present in the eluant, using anti-HA antibody when co-expressed with ILK as detected with anti-HA antibody
4555	17553790_MI:0096	These immunoblots revealed that endogenous paxillin and actopaxin associated with the complex of ILK·kAE1 (Fig. 8, lane 2)
4556	17565979_MI:0096	As seen in Fig. 4E, the interaction of both proteins (P-Rex1 and mTOR prey) was dramatically weakened by the expression of the DEP domains of P-Rex1, which compete with the endogenous domains of this protein.
4557	17565979_MI:0096	mTOR prey was detected associated with P-Rex1 DEP-DEP
4558	17565979_MI:0096	The carboxyl-terminal region of mTOR (mTOR prey) was detected associated with P-Rex1-DEP-DEP fused toGSTbut not withGSTused as control
4559	17565979_MI:0096	The GST pulldown assays proved thatmTORnot only interacts with P-Rex1 but also with P-Rex2a and P-Rex2b.
4560	17565979_MI:0096	Total cell lysates were analyzed (TCL, left), and affinity-purified proteins (AP, right) showed a specific interaction of the DEP-DEP domains of P-Rex1 with GST-mTOR prey and not with the GST alone used as control.
4561	17577629_MI:0096	GSTAkt1-bound SETDB1 proteins were detected by autoradiography.
4562	17577629_MI:0096	Myc-SETDB1 and GST-Akt1 or GST were co-expressed in HEK293T cells and GST-fused proteins were purified with glutathione sepharose 4B. As shown in Fig. 2C, SETDB1 could be copurified with GST-Akt1 but not GST alone.
4563	17629495_MI:0096	With GST-TRF1 as the bait protein, Tara was recovered in the prey complex
4564	17635584_MI:0096	GST pulldown assays were performed with combinations of bacterially expressed and 35S-methionine-labelled proteins and the results are shown in Fig. 3. These confirm that UXT binds Rp
4565	17637675_MI:0096	Analyses with truncated versions of JAI3 showed that COI1 interacts with the JAI3 N terminus (containing the ZIM domain), but not with its C terminus (containing the C-terminal domain)
4566	17637675_MI:0096	Consistent with this hypothesis, in vitro pull-down assays demonstrated a direct MYC2-JAI3 interaction (Fig. 3a-c). In contrast to COI1, MYC2 interacts with MBP-JAI3DeltaN, containing the C-terminal domain
4567	17637675_MI:0096	Consistent with this hypothesis, physical interaction between JAI3 and COI1 proteins was demonstrated by enrichment of [35S]JAI3 in amylose resins containing maltose binding protein (MBP-COI1 compared to MBP controls
4568	17637677_MI:0096	JA-Ile promoted the COI1-JAZ1 interaction in a dosedependent manner
4569	17657516_MI:0096	Both GST-CCM3 clones but not the controls were able to pull down Flag-CCM2 (Fig. 4b)
4570	17657516_MI:0096	Only GST-CCM3 was able to trap endogenous STK25 and FAP-1,
4571	17666011_MI:0096	A direct interaction was demonstrated between AtPRMT1a and AtPRMT1b as no other signal was detected by MBP monoclonal antibody in any of the control lanes
4572	17681130_MI:0096	When the binding site (RISNS, at position 169-173) was deleted (BZR1&#916;) or the serine 173 mutated to alanine (S173A) (Figure 2C), 14-3-3 binding was greatly reduced (Figure 2D). In contrast, deletion of isoleucine-170 (&#916;I170) of BZR1 that changes the sequence from a mode II to a mode I 14-3-3 binding site (Figure 2C) did not abolish 14-3-3 binding (Figure 2D). These results indicate that 14-3-3 proteins bind to BZR1 through the conserved binding site that contains phosphorylated serine 173.
4573	17693260_MI:0096	Pull-down assays were carried out by incubating purified His-SARA with either GST- or GST-Rho39-conjugated glutathione Sepharose.
4574	17693260_MI:0096	These experiments showed that purified His-SARA specifically bound to immobilized GST-syntaxin 3 (Figure 6C),
4575	17699755_MI:0096	GST-HFR1 interacted with MBP-COP1,
4576	17699755_MI:0096	HFR1 and LAF1 interact in vitro and in vivo.
4577	17699755_MI:0096	These results indicate that HFR1 can self-associate
4578	17699755_MI:0096	We also confirmed LAF1/HFR1 interaction using LAF1 synthesized by in vitro transcription/translation (Supplementary Fig. S1).
4579	17702749_MI:0096	As shown in Fig. 9, snapin detected UT-A1 and t-SNARE components (Syntaxin-4 and SNAP23) in the inner medulla.
4580	17702749_MI:0096	A strong interaction between GST-snapin and native UT-A1 was detected
4581	17702749_MI:0096	Snapin could be co-immunoprecipitated only with L-UT, whereas in the case of N-UT and C-UT, no snapin was detected in the immunoprecipitated complex (Fig. 2B).
4582	17702749_MI:0096	To further characterize the UT-A1-binding site within snapin, we generated six deletion mutants and one PKA phosphomimetic mutant (S50D) of snapin (Fig. 3A) and tested them for their interaction with UT-A1 by GST affinity chromatography (GST pulldown assay).
4583	17702749_MI:0096	We found that HA-snapin detects native UT-A1, suggesting an in vivo interaction between snapin and UT-A1 in kidney IMCD (Fig. 2C).
4584	17704303_MI:0096	In addition, our in vitro binding reactions using recombinant proteins indicate a direct interaction between TAF3 and TRF3 (Fig. 4C).
4585	17704763_MI:0096	In vitro interaction tests between 35S-labelled GI and glutathione S-transferase (GST)-tagged ZTL and the related family members, FLAVIN-BINDING, KELCH REPEAT, F-BOX (FKF1)9 and LOV KELCH REPEAT PROTEIN 2 (LKP2)10, showed a strong, specific interaction, when compared to GST alone or a negative control
4586	17709393_MI:0096	JIP1 stably interacts with TAK1 by a region located between residues 283 and 471.
4587	17709393_MI:0096	JIP1-TAK1 interaction could be affected by the presence of the TAB1 coactivator or the kinase activity of TAK1, for which a kinase-inactive (TAK1K63W) form was used.
4588	17709393_MI:0096	TAK1 variants interact by their N-terminal domains, the first 300 amino acids, with JIP1
4589	17709393_MI:0096	the amount of phosphorylated JNK increased in the presence of TAK1 and TAB1 in a dose dependent manner suggesting that TAK1 contributes to JNK activation.
4590	17709393_MI:0096	The endogenous TAK1 protein was brought down by GST-VRK2A (Fig. 6D,
4591	17709393_MI:0096	VRK2A interacted with the full-length and the N-terminal domain of TAK1 variant a (Fig. 6B, left) but did not interact with variant b (Fig. 6B, right) of TAK1, which contains an insertion of 27 residues in its C-terminal domain
4592	17709393_MI:0096	We clearly detected the interaction of the fulllength VRK2A (508 amino acids), as well as of a carboxyterminal construction of VRK2A (residues 364 to 508).
4593	17711851_MI:0096	GCP60 Interacts Preferentially with the Golgin-160-(140-311) Fragment in Vitro
4594	17719543_MI:0096	the Smurf2 C2 domain interacted with the HECT domain
4595	17719550_MI:0096	EphA4 interacted with the &#945;-chimerin C terminus that is common to both alpha1 and alpha2 isoforms.
4596	17728244_MI:0096	both c-Myc and vIRF-3 bound effectively to wtcdk4 promoter as well as 4XE-box sequences
4597	17728244_MI:0096	c-Myc effectively bound to the wtcdk4 promoter sequences
4598	17728244_MI:0096	in vitro translated MM-1 bound strongly to the full-length GST-vIRF-3 fusion protein
4599	17728244_MI:0096	These data suggest that the interaction between vIRF-3 and MM-1 is direct and that the region between amino acids 31 and 62 of MM-1 protein is its primary interaction domain with vIRF-3.
4600	17728244_MI:0096	vIRF-3 associates with MM-1 in vitro
4601	17785451_MI:0096	The SOS2-NDPK2 interaction was confirmed in vitro by demonstrating that GST-fusion proteins of NDPK2
4602	17785451_MI:0096	The SOS2-NDPK2 interaction was confirmed in vitro by demonstrating that GST-fusion proteins of NDPK2 or the positive control SOS3
4603	17803915_MI:0096	SCRAPPER interacted with the C2B domain of RIM1.
4604	17825054_MI:0096	Interaction of CBL10 and CIPK24 in a pull-down assay
4605	17872410_MI:0096	FKF1-HA protein was co-purified with the glutathione S-transferase fused GI N-terminus (GSTGI- N) protein incubated under light
4606	17872410_MI:0096	Interaction between GI and CDF1 in yeast and in vitro.
4607	17875722_MI:0096	pDI also inhibited GST-p53 capture of in vitro translated MDM2 and MDMX with different efficiency
4608	17887956_MI:0096	Cdc45 did not bind to the third, the fourth and fifth and the seventh and eighth BRCT domains of TopBP1, neither to GST alone, whereas the first and second as well as the sixth BRCT domain were sufficient for Cdc45 binding.
4609	17887956_MI:0096	full-length TopBP1 bound specifically to the GST-Cdc45 matrix
4610	17893151_MI:0096	All GST-tagged constructs were expressed in tsA201 cells and effectively precipitated by glutathione-Sepharose beads (Figure 4, upper panel) as judged by staining with anti-GST antibodies. RINCK1 associated with all the PKC constructs that contained the C1A domain
4611	17893151_MI:0096	PKC bound to GST-RINCK1 (lane 2) but not to GST alone (lane 1), revealing that PKC binds to RINCK directly.
4612	17909037_MI:0096	we carried out pull-down experiments using purified Prx1 and in vitro-translated AR. The cell-free experiments showed a direct interaction between Prx1 and AR
4613	17928403_MI:0096	These results indicated the AGCCCU motif was the target site for nucleolin to bind with gastrin mRNA. Interestingly, the binding activity decreased with probe D-N.
4614	17928403_MI:0096	the UV cross-linking/biotin-labeled probe pull-down combined with Western-blot analysis using hnRNP K and PCBP1 antibodies were performed. The data revealed that both hnRNP K and PCBP bound with probe B and C, but not probe A
4615	17928403_MI:0096	This result indicated that nucleolin binds with gastrin mRNA not only dependent on the binding sequence but also regulated by hnRNP K/PCBP1 complex interacting with the C-rich region.
4616	17928403_MI:0096	To identify the trans-acting factors that may interact with the gastrin mRNA 3 UTR, the biotin pull-down assay was performed to analyze the potential proteins association with this region. Two major proteins were observed to interact with probe B and probe C (Figure 3A). Using mass spectrometry analysis, hnRNP K and PCBP1, belonging to the poly(C) binding protein family, were identified to be the target proteins interacted with the gastrin mRNA 3 UTR
4617	17928403_MI:0096	we also found the probe B bound with lower level nucleolin protein than probe C.
4618	17928403_MI:0096	We found nucleolin, a RNA-binding protein involved in many cellular processes, interacted with probes B and C, but not with probe A (Figure 4A, lanes 3-5). This result indicated that the nucleolin associates with gastrin mRNA 3 UTR in vitro.
4619	17934516_MI:0096	these results suggest that DNMT1 is a likely candidate to fulfil the requirements of an ICBP90 partner.
4620	17951432_MI:0096	AtRGS1(E320K) does not interact with AtGPA1. Direct interaction between AtGPA1 and wild-type or mutant forms of the extended RGS domain of AtRGS1 was measured by using a GST (glutatione S-transferase) pull-down (PD) assay as previously described (17).
4621	17956734_MI:0096	Actin bead assay with Cobl GST-WH2 domains.
4622	17956734_MI:0096	syndapin as well as Abp1 immobilized on beads were still able to induce F-actin halos around the beads (Figures 1B-1D and Figures S1A-S1F
4623	17965023_MI:0096	53BP2S Interacts with PTB Domain and a Central Region (Amino Acid Residues 750-861) of IRS-1
4624	17965023_MI:0096	Endogenous IRS-1 protein bound to GST-53BP2S was visualized by immunoblotting with anti-IRS-1 antibody.
4625	17981117_MI:0096	CS and deltaCS interacted strongly with importin alpha3 and weakly with importins alpha4
4626	17981117_MI:0096	deltaCS preferentially interacts with importin alpha3.
4627	17981117_MI:0096	Full-length CS also interacted weakly with alpha1, alpha5, and alpha7
4628	17981125_MI:0096	Indeed, Sepharose beads coupled to GST-Sig-1Rs 116-223 pulled down BiP in cell lysates from rat organs or CHO cells
4629	17991437_MI:0096	Angiogenin was pulled down by follistatin specifically.
4630	18001825_MI:0096	RNF8 interacts with MDC1 via its FHA domain
4631	18001825_MI:0096	We next generated a deletion mutant spanning residues 698-768 (Del) of MDC1 (Figure 3A) and showed that MDC1, but not Del, specifically bound to purified GST-RNF8 (Figures 3B and 3C). In addition, RNF8 coprecipitated with WT but not Del mutant of MDC1 in vivo (Figure 3D),
4632	18001825_MI:0096	WThe GST-RNF8 complex was separated by SDS-PAGE to evaluate the amount of endogenous MDC1 that bound specifically to RNF8.
4633	18022368_MI:0096	35S-labeled p31comet WT or Q83A/F191A proteins were incubated with beads bound to GST or GST-Mad2 L13A.
4634	18022368_MI:0096	Binding of different Mad2 proteins to p31comet
4635	18024891_MI:0096	GST pulldown experiments further revealed that in vitro-expressed [35S]methionine-labelled XPC protein can bind to both GST-BGLF4 and GST-BGLF4 KD
4636	18029035_MI:0096	An in vitro binding assay showed that Ymer interacts with RIP1, regardless of whether RIP1 is ubiquitinated or not
4637	18029035_MI:0096	An in vitro pull-down assay also verified that K63-linked polyubiquitin chains bound the wild type of Ymer
4638	18029035_MI:0096	The in vitro binding assay showed that A20 alone associates with the K63 polyubiquitin chain and that the association is enhanced in the presence of Ymer
4639	18045535_MI:0096	In a GST pull-down assay, we demonstrated that RPS3 binds to p65
4640	18056116_MI:0096	ACCA was pulled down by histidine-tagged recombinant AKR1B10 protein
4641	18056989_MI:0096	The GST-pull-down experiments showed that BCRP was associated with GST-Pim-1L
4642	18056989_MI:0096	The GST-pull-down experiments showed that BCRP was associated with GST-Pim-1L but not with GST, GST-Pim-1S, or GST-PR
4643	18064632_MI:0096	His6-GRP78 was constructed and expressed in E. coli BL21 (DE3) pLys for a pull-down assay. The purity of His6-GRP78 was confirmed by silver staining and verified by Western blot using anti-His or anti-GRP78 antibodies (Fig. 5A). From the pull-down assay, we found that GRP78 interacted with Raf-1 in both untreated and TG-treated cells
4644	18086875_MI:0096	we found that Wrch1 binds strongly to the FERM domain of Pyk2
4645	18093972_MI:0096	GST pull-down analysis showed that WSB-1 interacted physically with HIPK2
4646	18093972_MI:0096	GSTpulldown analysis with GST-HIPK2-(503-860) and Myc-tagged WSB-1 mutants showed that all of the deletion mutants of WSB-1 containing theWD40repeat interacted with HIPK2
4647	18160036_MI:0096	Tel2 binds to a HEAT-repeat segment of mTOR
4648	18160036_MI:0096	Tel2 binds to HEAT repeat and C-terminal regions of ATM
4649	18178112_MI:0096	These results indicate a specific, direct interaction of AtGIP1 with AtGCP3.
4650	18191226_MI:0096	GST pulldown showing interaction of recombinant phospho-Akt1 with a GST-&#946;Arr2 recombinant protein.
4651	18191611_MI:0096	Association of Oct-4 with PKM2 in vitro.
4652	18191611_MI:0096	PKM2 strongly bound to GSTOct-4 (POU)
4653	18191611_MI:0096	The interaction between Oct-4 and PKM2 is direct.
4654	18191611_MI:0096	we used affinity chromatography on immobilized Oct-4 (POU) together with MALDI-TOF (matrixassisted laser-desorption ionization-time-of-flight) MS (mass spectrometry) and isolated a novel Oct-4-interacting protein, pyruvate kinase type M2 (PKM2 or M2-PK).
4655	18250314_MI:0096	Direct interaction between TPD1 and EMS1 was further confirmed by GST pull-down experiments.
4656	18272596_MI:0096	AP-fused APP domains were tested for binding to Fc-fused contactin 3 or 4 domains
4657	18272596_MI:0096	APLP1 bound to contactins 3, 4 and 5.
4658	18272596_MI:0096	APP bound prominently to contactins 3 and 4.
4659	18286207_MI:0096	Both, VRK2A and VRK2B, were able to form a stable complex with JIP1
4660	18286207_MI:0096	In the absence of JIP1, TAK1 (Fig. 6A) [51], and MKK7 (Fig. 6B), but not JNK (Fig. 6C), were able to stably interact with VRK2A
4661	18286207_MI:0096	In the pulled-down proteins, as VRK2A protein (or its kinase-dead variant) increased, the level of phosphorylated JNK clearly decreased, a difference that was not detectable in the whole cell lysate, and thus is likely to represent a subpopulation of JNK bound to JIP1.
4662	18286207_MI:0096	JIP1 protein was also brought down by GST-VRK2A (Fig. 4I). These data supports the specificity of the interaction between VRK2A and JIP1.
4663	18286207_MI:0096	Since this cells expresses JIP1 is also possible that the interaction of TAK1 or MKK7 and VRK2A was mediated by endogenous JIP1
4664	18286207_MI:0096	The endogenous VRK2 protein was brought down in a pull-down assay with GST-JIP1 (Fig. 4H).
4665	18286207_MI:0096	VRK2A was in vitro translated and used for a pull-down-assay using different GSTJIP1 protein constructs expressed in bacteria. VRK2A was able to interact with the C-terminal region of JIP1 (Fig. 4G)
4666	18287201_MI:0096	GST pull-down assays performed with bacterially expressed GST fusion proteins and inflorescence protein extracts from 35S::UFO-Myc plants. Top panel, western blot probed with anti-Myc antibody. Bottom panel, Coomassie Blue stained gel showing GST fusion proteins used in the assays. LFYN2 does not pull down UFO as efficiently as does full-length LFY from plant extracts.
4667	18287201_MI:0096	Upper panel: GST pull-down assay showing interaction between a bacterially produced GST-LFY fusion protein and 35S-labeled UFO protein; GST alone does not show an interaction with UFO. Input lane represents 10% of total protein. Lower panel shows same blot probed with GST antibody, demonstrating equivalent loading of GST and GST-LFY lanes.
4668	18296627_MI:0096	As expected, COP1 bound to full-length CO and various lengths of CO containing the CCT motif (Figure 3B, lanes 3 to 7) but not to the fragments of CO lacking CCT or the control polypeptide LUC (Figure 3B, lanes 1, 2, and 8). None of these fragments bound to the control MBP protein (Figure 3C)
4669	18299245_MI:0096	The results of a GST pull-down assay demonstrated that hS14 protein does not directly physically interact with p53, but does directly interact with the p53 coactivator, Zac1
4670	18319262_MI:0096	Fhit complexes were purified through the His6-tag and co-purified proteins were detected with antisera against Hsp60, Hsp10 and Fdxr; Hsp60 and Fdxr were detected only in lysates of cells exposed to DSP (Fig. 2A,C), while Hsp10 was also detectable without cross-linking
4671	18358808_MI:0096	Recombinant pontin bound recombinant MBP-dyskerin and both MBP-TERT proteins, indicating that pontin interacts directly with both dyskerin and TERT (Figure 5E).
4672	18408765_MI:0096	Binding of 35S-labeled CDK1 proteins produced by in vitro transcription and translation to GST-FOXO1 recombinant proteins
4673	18420585_MI:0096	HIS-RACK1 and HIS-WD1-4 directly interacted with GST-DLC1
4674	18420585_MI:0096	RACK1 also interacted with BimEL directly in vitro
4675	18466309_MI:0096	To confirm the interaction observed in yeast, glutathione S-transferase (GST)-tagged BIF2 and 6 x HIS-tagged BA1 were expressed in bacteria and subjected to GST pull-down assays (Figure 2b). Bacterial lysate containing HIS-BA1 was incubated with glutathione sepharose resin bound to either GST alone or GST-BIF2. GST-BIF2 pulled down the BA1 protein from the bacterial lysate, as detected by western analysis
4676	18467490_MI:0096	Deletion of the N-terminal 41 amino acid of BES1 (BES1&#916;N) disrupted the interaction between BES1 and ELF6-C or REF6-C (Fig. 2  A). The fragment containing the first 41 residues of BES1 was sufficient for the interaction, although the binding was much weaker (BES1 1-41).
4677	18474220_MI:0096	Direct interaction between Apoptin and Ppil3 shown by GST Pull-down assay.
4678	18485870_MI:0096	As expected, 35S-labeled in vitro-translated Mdm2 bound the recombinant protein GST-p53 (aa 1-73) (lane 2, Figure 5D) but not GST (lane 5, Figure 5D). Surprisingly, both the core domain and the C terminus of p53 showed similar binding affinities for Mdm2 (lanes 3 and 4, Figure 5D),
4679	18485870_MI:0096	In vitro binding of p53 or p53-8KR to Mdm2
4680	18485870_MI:0096	More importantly, to examine the effect of acetylation in this interaction, we performed similar GST-pulldown assays with either purified unacetylated p53 or acetylated p53 proteins.
4681	18494853_MI:0096	The plant protein interactions were confirmed using a glutathione sepharose (GST) pulldown assay. GST-PCNA1 or GST-PCNA2 was bound to a GST affinity column, to which His6-AtPolg was then added. His6-AtPolg co-eluted from the column with GST-PCNA1 and GST-PCNA2, but not with GST alone (Figure 4b). The results demonstrate that AtPolg interacts with Arabidopsis and yeast PCNAs.
4682	18510931_MI:0096	a strong physical association was seen between in vitro-translated XFDL protein and recombinant GST-hp53 protein, indicating that the two proteins directly interact
4683	18518979_MI:0096	We found that GST-Vav3-DH+PH fusion protein, but GST protein, interacted with ER&#945;
4684	18550827_MI:0096	To further test this possibility, we performed pull-down assays with plant extracts by using a domain II peptide from IAA7, an SCFTIR1 substrate (8). Consistent with there being less assembled SCFTIR1, the axr6-2 mutation resulted in a reduction in the amount of CUL1 protein pulled down by the domain II bait peptide. However, CUL1 binding was partially restored in eta2-1 axr6-2 double mutants
4685	18571510_MI:0096	Mapping the NPR1 binding site of TGA2
4686	18585357_MI:0096	Netrin-1 specifically binds to DSCAM.
4687	18587275_MI:0096	n vitro pull down assays to confirm the OBF4 interaction with CO (left panel) and to identify the OBF4-binding region in CO
4688	18617507_MI:0096	As the amount of VRK1-His increased so did the amount bound to GST-Ran (Fig. 2E), indicating that this interaction is direct and does not require any additional protein.
4689	18617507_MI:0096	In the pull-down Ran was clearly detected in the corresponding immunoblot, in which RCC1 was also present in this complex (Fig. 3C, bottom).
4690	18617507_MI:0096	In VRK2 the overlapping region corresponds to residues 256-320 (Fig. 5C, D).
4691	18617507_MI:0096	The analysis of the MALDITOF spectrum in each case showed several tryptic peptide masses that matched to theoretical masses from the Ran GTPase sequence (Swissprot P62826) (Fig. 1C; Fig. S1B).
4692	18617507_MI:0096	The full length interacted very well, but there was a significant loss of binding with either the N or C-terminal region of VRK1, suggesting they are much less efficient (Fig. 5A). These two constructs have an overlapping region corresponding to residues 267 to 332 (Fig. 5B).
4693	18617507_MI:0096	The GST-VRK1 protein was unable to bring down the RCC1 protein by itself (Fig.6A) indicating that they do not appear to interact directly, even if VRK1 is in a molar excess over RCC1.
4694	18617507_MI:0096	The three GST-Ran proteins, wild-type and both mutants, but not the GST control, were able to stably interact with either VRK1 (Fig.2A), VRK2B (Fig.2B), VRK2A (Fig. 2C) and VRK3 (Fig. 2D). These results indicate that the three human VRK proteins are able to interact with human Ran protein.
4695	18617507_MI:0096	This was tested using VRK3 which was able to partially compete with VRK1 for the interaction with Ran (Fig. 5F).
4696	18617507_MI:0096	to determine if the conformation of Ran could significantly alter the interaction, a similar assay was performed using three different Ran proteins in the pull-down assay. The three Ran proteins, wild-type and L43E and T24N Ran mutants, were able to interact and brought down the endogenous VRK1 protein (Fig. 3B).
4697	18617507_MI:0096	VRK1 bound to Ran increased as the amount of RCC1 was raised (Fig.6B).
4698	18632581_MI:0096	Labeled pri-miR162b was added to the beads containing GST-DDL or GST. After washes and elution, the RNA was resolved on a polyacrylamide gel. Pri-miR162b was retained by GST-DDL but not GST alone
4699	18642946_MI:0096	To further estimate the reliability of our data set, we selected several novel interactions detected in our screens and attempted to confirm the interactions in vitro by affinity copurification. As the cytokinin receptors AHK2 and CRE1/AHK4 and the A-type ARRs ARR7 and ARR15 showed a high number of different interactors, 20 different interactions of those proteins were investigated. Using the affinity co-purification assay,11interactions,namely,AHK2withAT5G64070,AT5G62740, AT5G13120, AT5G42080, AT4g27160 and AT1G69840;
4700	18642946_MI:0096	To further estimate the reliability of our data set, we selected several novel interactions detected in our screens and attempted to confirm the interactions in vitro by affinity copurification. As the cytokinin receptors AHK2 and CRE1/AHK4 and the A-type ARRs ARR7 and ARR15 showed a high number of different interactors, 20 different interactions of those proteins were investigated. Using the affinity co-purification assay,11interactions,namely,AHK2withAT5G64070,AT5G62740, AT5G13120, AT5G42080, AT4g27160 and AT1G69840;AHK4 with AT3G51630, AT2G38280 and AT4G15630;
4701	18642946_MI:0096	To further estimate the reliability of our data set, we selected several novel interactions detected in our screens and attempted to confirm the interactions in vitro by affinity copurification. As the cytokinin receptors AHK2 and CRE1/AHK4 and the A-type ARRs ARR7 and ARR15 showed a high number of different interactors, 20 different interactions of those proteins were investigated. Using the affinity co-purification assay,11interactions,namely,AHK2withAT5G64070,AT5G62740, AT5G13120, AT5G42080, AT4g27160 and AT1G69840;AHK4 with AT3G51630, AT2G38280 and AT4G15630;and ARR15 with AT5G43170 could be verified.
4702	18642946_MI:0096	To further estimate the reliability of our data set, we selected several novel interactions detected in our screens and attempted to confirm the interactions in vitro by affinity copurification. As the cytokinin receptors AHK2 and CRE1/AHK4 and the A-type ARRs ARR7 and ARR15 showed a high number of different interactors, 20 different interactions of those proteins were investigated. Using the affinity co-purification assay,11interactions,namely,AHK2withAT5G64070,AT5G62740, AT5G13120, AT5G42080, AT4g27160 and AT1G69840;AHK4 with AT3G51630, AT2G38280 and AT4G15630;ARR7 with AT1G79690
4703	18649364_MI:0096	GST pulldown was performed as in (b) with the indicated GST-fusion proteins and 35S-labeledeEF1A1[305-462]
4704	18649364_MI:0096	GST-SET[74-223] (Fig. 2c, Lane 7) bound readily with eEF1A1[305-462].
4705	18649364_MI:0096	The results showed that eEF1A2[305-463] is capable of binding to TSPY
4706	18674533_MI:0096	Similarly, pull-down assays confirmed interactions of SCL28, SCL30 and SCL30a with RSZp21, SRp30, SRp34/SR1, SCL28, SCL30, and SCL30a
4707	18703495_MI:0096	These results indicate that AtRabD1 and AtRabC2a protein tagged with His6 interacted weakly with the MYA2 tails fused with GST in a GTP dependent manner.
4708	18769030_MI:0096	As seen in Figure 1, Panel C, only GST-KCC2-CT was able to pull-down RCC1/PAM (lane 2), whereas GST alone did not pull down RCC1/PAM.
4709	18775314_MI:0096	GST pull-down experiments indicate that VAMP7 longin domain but not Sec22b longin domain or GST alone binds full-length Hrb from A431 cell cytosol shown by immunoblotting with an anti-Hrb antibody.
4710	18775314_MI:0096	Interaction of GST Hrb(1-176) and GST control proteins with Wt and mutant versions of VAMP7 longin domain His6 as indicated by western blotting of 'GST pull down' experiments with anti His6 antibody.
4711	18775314_MI:0096	Interaction of GST VAMP7 longin domain and GST control proteins with Wt and mutant versions of Hrb(1-176)His6 as indicated by western blotting of 'GST pull down' experiments with anti His antibody.
4712	18775314_MI:0096	The binding of various C-terminally His6-tagged Hrb constructs to GST-VAMP7 longin domain demonstrates that the Hrb binding site for VAMP7 longin domain is located between residues 136 and 176.
4713	18775317_MI:0096	Chordin interacts with ONT1 via its CR2-4 domain
4714	18775317_MI:0096	In contrast, ONT1 protein was efficiently coimmunoprecipitated with Chordin in vitro
4715	18775317_MI:0096	ONT1 binds to B1TP via its CC domain.
4716	18775317_MI:0096	The interaction of Xlr and ONT1 was analyzed with an anti-myc antibody (C
4717	18805089_MI:0096	Similar experiments with purified poly-histidine-tagged ParB and PopZ (Figure S2) showed that His6-PopZ coimmunoprecipitated with His6-ParB (Figure 3J),
4718	18805096_MI:0096	CYFIP1 and FMRP still bound eIF4E (Figure 1G, lane 2),
4719	18805096_MI:0096	Human GST-eIF4E was applied to streptavidin beads containing wild-type or mutant CYFIP1 biotinylated peptides
4720	18805096_MI:0096	m7GTP-Sepharose beads were incubated with synaptic extracts; the recovered proteins were immunoblotted for CYFIP1, FMRP, and eIF4E
4721	18805096_MI:0096	When the beads were incubated with total brain cytoplasmic extracts, both FMRP and CYFIP1 were recovered from them but only after specific elution with m7GTP (Figure 1B, lane 3)
4722	18812496_MI:0096	To confirm the ARC6IMS-PDV2IMS interaction, we performed a coprecipitation assay (Figure 2B). A glutathione S-transferase (GST)-PDV2IMS fusion protein was precipitated from crude Escherichia coli extracts with Ni-Sepharose beads coated with His-ARC6IMS
4723	18845687_MI:0096	To corroborate the interactions observed in the yeast twohybrid assays, we performed an in vitro protein-protein interaction assay. CYP20-3 and SAT1 were co-expressed in Escherichia coli as a GST fusion protein and a 6xHis-tagged protein, respectively. For the interaction assay, the two proteins were coexpressed in the same E. coli strain, and both were immobilized on glutathione beads. Using anti-His antibody as a probe, we found that the SAT1 protein co-purified with the GSTCYP20- 3 fusion protein but not with GST (Fig. 3B, lanes 2 and 3 vs. lane 4), suggesting interaction between CYP20-3 and SAT1.
4724	18854162_MI:0096	Autoradiography of the 35S-labelled full-length TAF-4 pulled down by MBP::OMA-1 FL or MBP::OMA-1-N
4725	18930710_MI:0096	A double band of 200 kDa (p200) was observed in eluates from the GST-hTNIK1(279-1052) and -hTNIK1(753-1360) columns. LC-MS/MS analysis of p200 identified nine peptides matching rat TANC1 (rTANC1), the calculated molecular mass of which is 200,376 Da. (Fig. 2B).
4726	18930710_MI:0096	Both MINK and TNIK were found in the eluate from the GST-TPRcc column, but not in the eluates from the other columns (Fig. 2C).
4727	18930710_MI:0096	By the affinity chromatography/mass-spectrometry approach and the yeast two-hybrid screening, we identified Misshapen/NIKs-related kinase (MINK) as a novel Rap2-interacting protein
4728	18974936_MI:0096	Our data from the two independent approaches indicate that HIPP26 interacts with the zinc-finger homeodomain box transcription factor ATHB29. For this interaction an intact heavy metal associated domain including the two central cysteines is important.
4729	18976803_MI:0096	GST fused to the WW domains of Rsp5 (GST-3xWW) was purified and used to pull down in vitro-translated full-length Cvs7 containing either wild-type or mutated PY motifs.
4730	18976803_MI:0096	Members of the ART Family of Proteins in Yeast Are Adaptors for Rsp5
4731	19000167_MI:0096	IBR5 and MPK12 interact directly in vitro.
4732	19103756_MI:0096	First the endogenous VRK1 was brought down from cells transfected with either pCEFL-GST-Plk3 or pCEFL-GST-Plk3K52R . In the pulldown VRK1 was detected associated to Plk3 but not to GST (Fig. 3C)
4733	19103756_MI:0096	The common region of VRK1 that interacts with Plk3 is located in the region comprised between residues 1-267 (fig. 4C.
4734	19103756_MI:0096	the endogenous Plk3 was detected bound to VRK1, active or kinase dead, but not to GST, in the extracts of cells transfected with pCEFLGSTVRK1 or pCEFLGSTVRK1K179E (Fig. 3D).
4735	19103756_MI:0096	The full-length, but not the C-terminal region of VRK1 was able to interact with PLK3.
4736	19103756_MI:0096	This interaction between VRK1 and Plk3 was also detected by proteomic analysis of proteins associated with VRK1 in HEK293T cells (29). The proteomic identification by mass-spectrometry of Plk3 is shown in Fig. S2.
4737	19103756_MI:0096	VRK1 interacted with active and inactive Plk3; while the inactive VRK1K179E interacted more stably with inactive Plk3K52R . The interaction was lost if VRK1 has the S342A substitution, indicating that the intact target sequence in VRK1 was necessary in order to form a stable complex with Plk3 (Fig. 3B, top).
4738	7568034_MI:0096	To determine whether K35 and cyclin C interact in vivo, antibodies were raised against recombinant K35 and used for coimmunoprecipitation experiments.
4739	7724559_MI:0096	GST interaction assays show that TBP interacts independently with both p12 and p55 recombinant TFIIA subunits.
4740	7724559_MI:0096	N-terminal region of p55 interacts with p12.
4741	7759517_MI:0096	As shown in Fig. 3D, ERK5 binds to GST-MEK5 and the GST-MEK5 mutant K195M, but not to GST alone or to GST-MEK1
4742	7923370_MI:0096	GST-RB379-792 bound the 200 kDa mBRG1 efficiently
4743	7923370_MI:0096	In the oncoprotein free lines 3T3 (Figure 5B, lanes 1 and 2) and WI38 (lanes 5 and 6), mBRG1 efficiently bound the faster-migrating RB forms.
4744	7923370_MI:0096	The fusion protein, GST-mBRGla specifically bound the RB protein from the lysate
4745	8062390_MI:0096	Ste11M also copurifies specifically with Fus3-HA
4746	8062390_MI:0096	Ste11M also copurifies specifically with Ste5
4747	8062390_MI:0096	Ste11, Ste7, and Fus3 Copurify with Ste5
4748	8062390_MI:0096	Ste7 also copurifies with GST-Ste5
4749	8313896_MI:0096	Both p85a and p85,B were seen to bind p1 10 by Coomassie blue staining following SDS -PAGE
4750	8313896_MI:0096	Both p85a and p85,B were seen to bind p110 by Coomassie blue staining following SDS-PAGE
4751	8313896_MI:0096	Similar results were obtained when p110 was immobilized and the bound p85a protein was detected as a Coomassie blue-stained protein on SDS-PAGE following binding in vitro
4752	8552194_MI:0096	and was confirmed by finding that Cdc18 coprecipitated with GST-Orp2 in fission yeast lysates (Fig. 4c).
4753	8552194_MI:0096	To determine whether Cdc2 and Orp2 interact in S. pombe, functional GST-Orp2 fusion protein and a GST control were expressed in S. pombe and isolated by binding to GSH-Sepharose. Cdc2 was detected in association with the GST-Orp2 fusion but not with GST (Fig. 2a).
4754	8617797_MI:0096	An aliquot of the translation mixture containing B`alpha1 (panel B), B`alpha2 (panel C), and B`alpha3 (panel D) were assayed for binding to a GST-A subunit fusion protein
4755	8617797_MI:0096	An aliquot of the translation mixture containing B`alpha1 (panel B), B`alpha2 (panel C), and B`alpha3 (panel D) were assayed for binding to a GST-A subunit fusion protein.
4756	8626665_MI:0096	Homotypic interactions with GST-g were most severely affected by mutations of a pocket of hydrophobic amino acids at positions Tyr65, Phe67, Cys68, Trp72, Thr73, and Phe74 (Fig. 2B).
4757	8626665_MI:0096	Interactions with GST-a were most sensitive to mutations in g residues Asp41 and Lys42,
4758	8626665_MI:0096	We have previously demonstrated a direct protein-protein interaction between 35S-labeled g and a GST-TBP fusion protein (27) (Fig. 2C, right panel).
4759	8657141_MI:0096	As can be seen in Fig. 2A, E2F1 and truncated versions thereof retained Sp1 provided that the N-terminal 122 amino acids
4760	8657141_MI:0096	it is evident that, as expected, E2F1, E2F2, and E2F3 bound Sp1 whereas E2F4 and E2F5 failed to do so.
4761	8657141_MI:0096	Purified Sp1 could be used in this assay in place of the Sp1-containing cell extract and gave the same results, indicating that the binding of Sp1 to E2F1 is direct and not mediated by additional cellular proteins.
4762	8657141_MI:0096	This experiment (Fig. 2C) revealed that the binding domain for E2F within Sp1 lies within the C-terminal quarter of the protein
4763	8663349_MI:0096	HP1Hsalpha  and HP1Hsgamma  bound to the LBR fusion protein (lanes 3 and 6) but not to GST (lanes 2 and 5)
4764	8663349_MI:0096	The LBR amino-terminal domain GST fusion protein also bound to HP1 proteins in extracts of HeLa cells (Fig 3)
4765	8749394_MI:0096	GST-dRAM23 and GST-dNotch [1 769-2 109] interacted strongly with Su(H).
4766	8749394_MI:0096	RBP-J was specifically retained on beads coupled to GSTmRAM23,
4767	8749394_MI:0096	The anti-Myc antibody co-immunoprecipitated RBP-J&#954; and the mNotch1-RAMIC protein (Figure 3c). Conversely, the anti-T7 antibody co-immunoprecipitated mNotch1-RAMIC and RBP-J&#954;.
4768	8756677_MI:0096	Sst2 and Gpa1-GST physically interact.
4769	9096360_MI:0096	Yeast NC2 binds to TBP and can be purified as a two-subunit complex.
4770	9115279_MI:0096	The rescued strain was used to isolate either GST-Pch1-associated proteins using glutathione-Sepharose beads or Cdc2-associated proteins using p13Suc1-Sepharose. A wild-type strain expressing unfused GST served as a control. Western blot analysis was performed in duplicate with an affinity-purified polyclonal a-Pch1 antibody and with a polyclonal a-Cdc2 antibody (Fig. 3). A Cdc2 signal was detected in the lane containing proteins that associate with GST-Pch1. This signal was absent in the lane containing proteins that associate with GST, indicating that the association specifically involved Cdc2 and Pch1. The Cdc2 signal in the GST-Pch1 sample was much less than that detected with p13Suc1-Sepharose A, suggesting that the Pch1 co-precipitates with only a very small fraction of Cdc2.
4771	9125210_MI:0096	In vivo association of EF1a and rL3 with CAP
4772	9139733_MI:0096	Fig. 5A shows that both GST-PKC-delta -(1-298) and GST-PKC-delta -(1-121) co-immobilized with hisGAP-43 on Ni2+-NTA beads.
4773	9139733_MI:0096	To assess the potential interaction of PKC-delta  with GAP-43, the individual MonoQ fractions were incubated with hisGAP-43, after which hisGAP-43 was immobilized on Ni2+-NTA-agarose beads, washed, and eluted from the beads by imidazole
4774	9144171_MI:0096	The minimum RAS binding domain of RIN1, therefore, appears to lie within residues 294-727, and optimal binding requires some or all of the 62 aa that are missing in the internal splicing variant.
4775	9173976_MI:0096	Crude extracts infected with either XPB alone or in combination with his-tagged mSUG1 baculoviruses were loaded onto a nickel-chelate affinity column. After washing and elution with 100 and 500 mM imidazole, immunoblot analysis indicated that XPB is retained onto the affinity column only in the presence of His-tagged mSUG1
4776	9276444_MI:0096	As shown in Fig. 6C, Suc1-Sepharose (p13) bound Cdc2aAt but only weakly Cdc2bAt.
4777	9276444_MI:0096	CksHs1 beads (p9) associated with Cdc2aAt but not at all with Cdc2bAt,
4778	9276444_MI:0096	In vitro binding of Cks1At to Cdc2aAt and Cdc2bAt.
4779	9341137_MI:0096	We estimated a 20-fold difference in the binding of the full-length PRA1(1-185) to immobilized GST-VAMP2 when compared with the truncated PRA1(1-164) (Fig. 8B).
4780	9346235_MI:0096	antibody demonstrate that GST-MEIS1, but not GST, is able to directly bind EXD in vitro
4781	9346235_MI:0096	fusion protein between glutathione-S-transferase and MEIS1 (GST-MEIS1) is able to pull-down EXD from a Drosophila embryo extract.glutathione-agarose (Figure 8F).
4782	9395480_MI:0096	Analysis of the eluates by SDS-PAGE followed by Coomassie Blue staining and immunoblotting revealed that we purified Munc18-1 on both Mint columns as the major component and syntaxin 1 as a minor component
4783	9395480_MI:0096	Munc18-1 alone bound to Mint proteins. Syntaxin 1 bound only if Munc18-1 was also added, and SNAP-25 did not bind under any condition.
4784	9396801_MI:0096	Interaction of Rad51 and Pir51 proteins in vitro.
4785	9409784_MI:0096	HA-mUBC9 and HA-mE47del, but not HA-RCL protein copurify with immobilized H6-E47
4786	9418871_MI:0096	the p48DDB subunit quantitatively bound to E2F1, whereas only a trace of p125DDB bound to E2F1 under the assay conditions.
4787	9425043_MI:0096	Purification of the human EGFR by calmodulin-affinity chromatography
4788	9428767_MI:0096	coimmunoprecipitation experiments to analyse the in vivo association of Ste20 with an influenza haemagglutinin (HA)-epitope tagged version of G (HA-Ste4).
4789	9428767_MI:0096	mouse mPAK3 (ref. 9) bound 35S-Ste4
4790	9428767_MI:0096	The K55E and D62N mutants of Ste4 (ref. 11) were defective in binding to GST-Ste20,
4791	9428767_MI:0096	weak binding of Ste4 to Cla4
4792	9464541_MI:0096	Chx10 bound strongly to GST-p130 although weaker binding to GST-pRB was seen for this paired-like homeodomain protein in this assay
4793	9464541_MI:0096	Deletion of the helix III (Pax-3DH3) did not a&#128;ect the ability of Pax-3 to bind to p107
4794	9464541_MI:0096	Pax-3 bound strongly to GST-pRB
4795	9464541_MI:0096	pRB (Figure 1b), p107 (Figure 1c) and p130 (Figure 1d) specifically bound to Pax-3, B4 and Chx10 but did not bind to beads containing lysates from bacteria expressing GST alone or the empty His-tagged vector, pRSET.
4796	9464541_MI:0096	The resutls indicate that the association between Pax-3 and pRb involves multiple contacts.
4797	9464541_MI:0096	When lysates were passed over columns containing GST-Chx10, this fusion protein clearly bound to the unphosphorylated pRb present in the l-phosphatase treated (P) lysates. However, GST-Chx10 also bound exclusively to the unphosphorylated form of pRB in untreated lysates (L) and does not pull down the hyperphosphorylated species
4798	9488738_MI:0096	However, assembly of the 140-kDa subunit into the complex was observed to be dependent upon the 38- and 40-kDa subunits, because omission of the 38-kDa subunit from the complex resulted in complete loss of the 140-kDa subunit from the complex (Fig. 5A, lane 8, and Fig. 5B, alpha 140kDa immunoblot, lane 8),
4799	9488738_MI:0096	However, the 40-kDa subunit was discovered to interact with the 37-kDa subunit when the 36-kDa subunit was co-expressed with these two subunits (Fig. 6,
4800	9488738_MI:0096	omission of the 40-kDa subunit resulted in significantly reduced assembly of the 140-kDa subunit into the complex (Fig. 5A, lane 7, and Fig. 5B, alpha 140kDa immunoblot, lane 7).
4801	9488738_MI:0096	Purification of recombinant human RFC from Sf9 cells
4802	9488738_MI:0096	The 36- and 38-kDa subunits were found to interact directly with the 37-kDa subunit
4803	9488738_MI:0096	When either the 40- or 38-kDa subunit was omitted, only the 36- and 37-kDa subunits were found to co-immunoprecipitate with the HA-140kDa subunit (Fig. 7A
4804	9488738_MI:0096	When Sf9 cells were co-infected with all five RFC subunit viruses, bvHA-37kDa, bv140kDa, bv40kDa, bv38kDa, and bv36kDa, all of the untagged RFC subunits were observed to co-purify with the HA epitope-tagged 37-kDa subunit (Fig. 5A, silver-stained gels, lane 5; Fig. 5B, immunoblots of the samples in Fig. 5A probed with either an alpha -140kDa monoclonal antibody or alpha -40kDa rabbit antibody, lane 5).
4805	9488738_MI:0096	When the 140-kDa subunit was omitted from the co-infection, a quaternary complex consisting of the 40-, 38-, 37-, and 36-kDa subunits was observed (Fig. 5A, lane 6, and Fig. 5B, alpha 40kDa immunoblot, lane 6), indicating no dependence on the 140-kDa subunit for the small subunits to assemble into a complex.
4806	9488738_MI:0096	when the 36-kDa subunit was excluded from the co-infection, an interaction between the HA-140kDa subunit and the 38-, 37-, and 40-kDa subunits was observed
4807	9528852_MI:0096	Association of BRCA1 with BAP1 was tested in vitro by binding of full-length BRCA1 to hBAP1(483 +/- 729) fused to glutathione S-transferase (GST; Figure 4a).
4808	9556555_MI:0096	radiolabeled p65 readily interacted with GST/p50, GST/CBP-N, and GST/CBP-C but not with GST alone, whereas p50 interacted only with GST/p50
4809	9556555_MI:0096	The radiolabeled full-length SRC-1 interacted with GST/p50 but not with GST alone or GST/p65
4810	9560288_MI:0096	Additionally, we confirmed that both MBP-ETR1293-610 and MBP-ETR1293-729 could associate with one of the smaller AD-CTR1 fusions (CTR1 residues 171-521) (Fig. 4).
4811	9560288_MI:0096	In vitro association of purified MBP-CTR153-568 with yeast DB-ETR1 and DB-ERS fusions in yeast cell extracts.
4812	9560288_MI:0096	radiolabeled CTR1 amino-terminal domain (residues 53-568) could associate with MBP-ETR1293-610 and MBP- ETR1604-738 and only weakly with MBP-CKI1981-1122 and MBP alone
4813	9560288_MI:0096	We found that the purified MBP-CTR153-568 fusion could associate with DB-ETR1293-610,
4814	9659918_MI:0096	Since equal amounts HY5 or GST. The 74 kDa radioactive COP1 product is indicated by of GST-HY5 and GST were used in the binding experiment, our results indicate a specific and direct protein protein interaction between COP1 and HY5 in vitro.
4815	9660868_MI:0096	Direct binding study with syn-2 peptide and hCASK PDZ fusion protein.
4816	9671805_MI:0096	TRIP binds the LRR of FLI.
4817	9685490_MI:0096	Binding of Rsc6 to Swh3 in vitro.
4818	9724822_MI:0096	Autoradiograph of SDSyPAGE analysis showing in vitro interactions among CKB1, CKB3, CKA1, and CCA1.
4819	9741624_MI:0096	When Tup1 and Ssn6 are cotranslated, significantly more Tup1 (8% of total input) is bound by GST-Crt1, probably due to Tup1-s interaction with Ssn6 (lane 3). The Ssn6 to Tup1 molar ratio in lane 3 is 1 to 3.2 when the relative methionine contents are taken into account. T
4820	9742395_MI:0096	This analysis revealed that GST-Byr4-D8 only bound Spg1 (Table 2).
4821	9742395_MI:0096	To determine if the Byr4-Spg1 and Byr4-Cdc16 interactions found in the two-hybrid system resulted from direct binding, binding reactions were conducted using purified Byr4 and glutathione beads containing either GST, GST-Cdc16, GST-Spg1, or GST-Ras1. Western analysis of the bound material showed that GST-Cdc16 bound full-length Byr4, and that GST-Spg1 bound full-length Byr4 and Byr4 degradation products larger than 60 kDa (Figure 2b).
4822	9742395_MI:0096	Western analysis with anti-Byr4 antibodies revealed that Byr4 was precipitated when Spg1-HAH was isolated with either anti-HA agarose or Ni-agarose (Figure 2d) and when Cdc16-Myc was isolated with anti- Myc agarose (Figure 2e).
4823	9753775_MI:0096	Direct interaction of ICK1 with both Cdc2a
4824	9756887_MI:0096	As shown in Fig. 1B, the wild-type and N-terminal half of Hic-5 were precipitated with GST-FAK-CT, whereas the C-terminal half of Hic-5 was not precipitated with GST-FAK-CT.
4825	9756887_MI:0096	both Hic-5 and paxillin were precipitated with GST-FAK (903-1052) and its substitution mutants, K933E and Q1040G. However, neither protein were precipitated with GST and GST-FAK mutants, V928G and L1034S.
4826	9765207_MI:0096	Following stringent washes, immunoblotting of the matrix-bound proteins revealed that GST-PRL1-Delta B retained PKC-beta II, but not PKC-beta I,
4827	9765207_MI:0096	To support these data, [35S]methionine-labeled PRL1 was synthesized by coupled transcription and translation using the cDNA template, and equal aliquots of PRL1 protein were incubated with GST-ATHKAP2 and GST proteins immobilized on glutathione-S-Sepharose, as well as with the empty Sepharose matrix (see Materials and Methods). PRL1 was quantitatively removed from the control Sepharose and GST matrices by stringent washes, but remained tightly-bound to GST-ATHKAP2, confirming an interaction of ATHKAP2 with PRL1 in vitro
4828	9771897_MI:0096	In vitro binding assay showing a specific interaction between ARR4 and AtDBP1
4829	9774676_MI:0096	By using a GST fusion protein which contained a truncation mutant of hMSH6 containing aa 1302 to 1360 (similar to the GST-hMSH3 truncation system described above), the carboxyterminal interaction region of hMSH2 was localized to aa 875 to 934
4830	9774676_MI:0096	GST-hMSH3 (aa 1 to 297) interacted most strongly with aa 251 to 750 of hMSH2
4831	9774676_MI:0096	hMSH6 contained two interaction regions with hMSH2 (Fig. 5, pairs 1 to 6). The amino-terminal interaction region was mapped from aa 326 to 575 (Fig. 5, pairs 7 to 10). The carboxy-terminal interaction region lies between aa 953 and 1360
4832	9774676_MI:0096	one of these HNPCC mutant constructs, R524P (aa 499 to 650), appeared to show reduced interaction
4833	9774676_MI:0096	The aminoterminal region was resolved between aa 126 and 250 (Fig. 2, pairs 6 to 9). It is important to note that we found the level of IVTT expression to be insufficient with polypeptides that contained less than 100 aa (data not shown). Thus, in order to fully map the carboxy-terminal region we adopted an internal deletion strategy. Using this strategy, the carboxyl interaction region was localized between aa 1050 and 1128
4834	9774676_MI:0096	The GST-hMSH3 (aa 1025 to 1128) truncation also allowed us to further resolve the carboxy-terminal interaction region of hMSH2 to aa 875 to 934
4835	9774676_MI:0096	Using a GST-hMSH2 (aa 751 to 934) construct we found that this C-terminal region interacted with the carboxy terminus of hMSH2 (data not shown). This construct displayed specific interaction with the hMSH2 truncation mutants aa 751 to 934 and aa 700 to 934 (D800 to 875). However, it did not interact with either the hMSH2 truncation mutant aa 751 to 900 or aa 700 to 934 (D800 to 900). Thus, the hMSH2 homodimer appears to display the same C-terminal interaction pattern that we observed with hMSH2 binding to hMSH3 or hMSH6 (Fig. 4D and 7D, pairs 6 to 10), implicating aa 875 to 934 of hMSH2 in selfassociation
4836	9801140_MI:0096	Both AtTBP isoforms were able to bind to AtHSF1
4837	9807817_MI:0096	AtFIP37 binds to AtFKBP12 in vitro
4838	9864360_MI:0096	To achieve this, the COOH-terminal regions of Pex18p and Pex21p that interact with Pex7p in the two-hybrid system were overexpressed as polyhistidine (His6) tagged proteins in bacteria, and subsequently purified on polyhistidine affinity columns.
4839	9891085_MI:0096	Nip7p was present in IgG-Sepharose column eluates from whole-cell extracts containing either PrtA-Rrp43p or PrtA-Nop8p but not from control extract
4840	9989503_MI:0096	all STAT proteins except Stat2 bound to a GST-Nmi fusion protein
4841	9989503_MI:0096	Two regions of Nmi, corresponding to residues 57 to 99 and 143 to 202, could bind Stat5b (lanes 6 and 7 of upper panels), and simultaneous deletion of both regions markedly diminished the association of Nmi with Stat5b
4842	9990507_MI:0096	To address the sugeestion as to how Pop1 and Pop2 interact in the cell, a series of combinations of tagged pop1þ and pop2þ genes were constructed (they were all functional, see Experimental procedures), expressed in the fission yeast, and a physical interaction between Pop1 and Pop2 was examined. As shown in Fig. 4, the myc-Pop1 protein was specifically co-immunoprecipitated with anti-HA (haemagglutinin) antibody (lanes 3) but not upon mock treatment (lane 2). Likewise Pop1- HA and GST (glutathione S-transferase)-Pop2 were co-immunoprecipitated with anti-HA antibody (lane 5). Conversely pull-down experiments using GSH (glutathione)-coupled beads also precipitated both myc-Pop1 and GST-Pop2 (lane 6). These results strongly suggest that Pop1 and Pop2 act as heterodimers or hetero-multimers in the cell.
4843	imex:IM-11822_MI:0096	The C-terminal 60 aa of Prop1 interacted robustly with the full-length &#946;-catenin protein in a GST pull-down protein-protein interaction assay
4844	imex:IM-11854_MI:0096	tBID is displaced from BCL-w by sensitizer BH3 peptides in a pattern that replicates the pattern in Figure 2D.
4845	imex:IM-11865_MI:0096	Affinity isolation of GST-tagged COG subunits followed by immunoblot analysis for Hsp90 demonstrated that Hsp90 physically interacts with COG complex lobe B subunits Cog5p, Cog7p, and Cog8p
4846	imex:IM-11867_MI:0096	In competition experiments,RSUME enhanced SUMO-1 binding to Ubc9 (lower concentrations of SUMO-1 only interacted with Ubc9 when RSUME was present) (Figure 4C)
4847	imex:IM-11867_MI:0096	The interaction of RSUME to Ubc9 was confirmed in COS-7 cell extracts using GST-Ubc9
4848	imex:IM-11867_MI:0096	To address this hypothesis, we performed an in vitro pull-down experiment using recombinant GST-Ubc9 and RSUME, showing that RSUME interacts with Ubc9 (Figure 4A).
4849	imex:IM-11867_MI:0096	To further understand RSUME's action, we studied its effect on the interaction of Ubc9 with E1 and found that RSUME increased the binding of Ubc9 and E1
4850	imex:IM-11875_MI:0096	GST pull-down assay of rSlo-tail and rMBP.
4851	imex:IM-11877_MI:0096	Of the six human antiapoptotic Bcl-2-family proteins, only Bcl-2 and Bcl-XL associated with NALP1. In contrast, Mcl-1, Bcl-W, Bfl-1, and Bcl-B did not associate with NALP1 (Figures 1A and 1B), nor did various proapoptotic Bcl-2-family proteins, including Bax, Bak, Bid, and Bcl-G (Figure 1B). Similar conclusions were reached using in vitro protein-binding assays where NALP1-containing cell lysates were incubated with bacteria-produced GST-fusion proteins
4852	imex:IM-11882_MI:0096	As shown in Figure 3C, the PHD finger bound very efficiently to methylated H3K4, with a clear preference for H3K4me3,
4853	imex:IM-11882_MI:0096	As shown in Figure 3E, the ING2 and TAF3-PHD finger display similar binding affinities for H3K4me2, whereas the TAF3 PHD clearly has a much higher affinity for H3K4me3 compared to the ING2 PHD.
4854	imex:IM-11882_MI:0096	As shown in Figures 4B and 4C, immunoblotting with modification-specific antibodies revealed that the bound nucleosomes were enriched for H3K4me3 and contained only low levels of H3K4me2 or H3K4me1.
4855	imex:IM-11882_MI:0096	the TAF7 signal in the H3K4me3 pull-down of the TAF3&#916;PHD lysate most likely corresponds to TFIID complexes containing endogenous TAF3.
4856	imex:IM-11882_MI:0096	To further investigate this we assessed the ability of a GST fusion of the isolated TAF3-PHD finger to bind methylated histone peptides.
4857	imex:IM-11885_MI:0096	GST-Cdc20111-138 on GSH beads was incubated with the Mad2 species labeled in black on the upper part of the panel.
4858	imex:IM-11888_MI:0096	Isolation and Identification of LIMP-2 as a beta-Glucocerebrosidase-Interacting Protein
4859	imex:IM-11888_MI:0096	Recombinant fusion-tagged LIMP-2 lumenal domain protein (L2LD) encompassing residues 27-432 was expressed as a soluble protein, purified, and then used in an in vitro pull-down assay with &#946;GC (Figure 1D).
4860	imex:IM-11893_MI:0096	Direct interaction between PCNA and p16 was examined using affinity chromatography assays. Purified PCNA was loaded onto a p16-Sepharose 4B column and the binding analyzed by CBB staining. Results showed that PCNA was directly bound to the p16 column but not to the control column
4861	imex:IM-11893_MI:0096	Table 1. Mass spectrometric identified p16ink4-interacting proteins in MOLT-4 cells
4862	imex:IM-11893_MI:0096	Western blot validation of the association of p16 with PCNA and MCM6.
4863	imex:IM-11893_MI:0096	Western blot validation of the presence of CDK4 and CDK6 in the MOLT-4 eluates of the p16 chromatography columns.
4864	imex:IM-11905_MI:0096	In vitro transcribed/translated, 35S-labeled Cdh1 was assayed for in vitro binding to the indicated GST-tagged Claspin fragments.
4865	imex:IM-11905_MI:0096	tested for their binding to GST-tagged Cdh1 using in vitro pull-down assays.
4866	imex:IM-11909_MI:0096	In vitro-translated [35S]-labeled truncated CLOCK proteins were pulled down by GST-SIRT1.
4867	imex:IM-11920_MI:0096	To corroborate that Gsp1 and Gsm1 interact with one another via their C-terminal domains, glutathione-conjugated cellulose was used to trap GST (Glutathione-S-Transferase)-conjugated Gsm1, and its affinity for Gsp1 was assessed.
4868	imex:IM-11926_MI:0096	GST-tagged variants of Ronin, Ronin-C or Ronin-N, and with Myc-tagged variants of the putative interaction partners. Using this strategy, we confirmed the binding of Ronin to HCF-1 via the C terminus.
4869	imex:IM-11926_MI:0096	Other confirmed protein interaction partners (Figure 7D) were Ronin itself (via homodimerization through the C terminus); THAP7, another THAP domain protein (via heterodimerization through the N terminus); and Sin3A (C terminus) and HDAC3 (N terminus)
4870	imex:IM-11936_MI:0096	IpaB1-312 bound to MBP-Mad2L2 in the MBP pull-down assay
4871	imex:IM-11936_MI:0096	IpaB bound to Mad2L2 in the GST-pull down assay
4872	imex:IM-11936_MI:0096	When 35S-Cdc20 or 35S-Cdh1 was mixed with MBP-Mad2L2, Cdh1 and Cdc20 were precipitated by MBP-Mad2L2, but not by MBP alone
4873	imex:IM-11952_MI:0096	SDS-polyacrylamide gel electrophoresis of eluted proteins revealed two major bands (Figure 5A), with electrophoretic mobilities expected for SpRecA-His6 and DprA. Mass spectrometry of a trypsin digest of the purified two major bands unambiguously identified the proteins
4874	imex:IM-11958_MI:0096	the ability of fish Appl proteins to bind Rab5 was tested in a GST pull-down assay using recombinant GST-Rab5C preloaded with either GTPgS or GDP and in vitro translated Appl1 and Appl2. They strongly and specifically bound to the active form of Rab5C
4875	imex:IM-11961_MI:0096	GST-neurexin C-tail (GST-Nx-Ct) or GST alone were immobilized on glutathione beads, and incubated with full-length CASK,
4876	imex:IM-11979_MI:0096	In vitro GST pull-down analysis of purified p62 by recombinant GST or GST-LC3.
4877	imex:IM-11979_MI:0096	Subsequent binding assays with a series of recombinant p62 mutants indicated that p62 interacts with LC3 through a linker region that connects the N-terminal Zinc finger and the C-terminal ubiquitin-associated (UBA) domain of p62 (Figure S1).
4878	imex:IM-11980_MI:0096	LZAP interacted with full-length RelA, and RelA truncation mutants containing aa 195-313 and aa 195-350, but not with aa 250-350
4879	imex:IM-11988_MI:0096	Compared to a control assay with GST alone, significantly higher levels of purified Gle1 bound to GST-Sup45 (Figure 2C).
4880	imex:IM-11988_MI:0096	GST-Prt1 was coisolated with Gle1,
4881	imex:IM-11988_MI:0096	GST-Tif35, which is part of a subcomplex with Prt1, also bound Gle1.
4882	imex:IM-11999_MI:0096	GST-ATXN1 pulldowns of in vitro transcribed/translated RORa were used to assess whether ATXN1 and RORa might interact directly. As show in Figure 5B, the results of this analysis failed to demonstrate an interaction. None of the following were able to able to pull down RORa above background levels observed with GST alone: GST-Atx-30Q, 53Q, and 82Q.
4883	imex:IM-11999_MI:0096	GST-ATXN1 was able to pull down in vitro transcribed/translated Tip60. However, this analysis failed to provide evidence of a polyglutamine tract effect.
4884	imex:IM-11999_MI:0096	The ability of GSTATXN1 to pull down Tip60 from wild-type mouse cerebella extracts provided additional evidence that ATXN1 and Tip60 interact (Figure 5D). Furthermore, the GST-ATXN1 pull down results suggested that as the length of the polyglutamine tract increased from 30Q to 53Q to 82Q the amount of Tip60 pulled down increased.
4885	imex:IM-12002_MI:0096	(D) GST or GST-Cdc25 linked to glutathione-Sepharose was incubated in interphase extract, collected, and immunoblotted for B56 (top)
4886	imex:IM-12005_MI:0096	GST-bet5 fusion protein interacted with the bet3-trs33 heterodimer
4887	imex:IM-12005_MI:0096	GST-bet5 fusion protein interacted with the bet3-trs33 heterodimer and trs23
4888	imex:IM-12005_MI:0096	Quantitation of the bands on the gel indicates a 1:1:1 stoichiometry for the bet3-trs31-sedlin complex
4889	imex:IM-12041_MI:0096	amino acids 1-13 of H4 are bound by the NL domain,
4890	imex:IM-12041_MI:0096	Fpr4-s NL domain (GST-Fpr4[NL]) recovered histone H3 and H4 with comparable efficiency to fulllength Fpr4 (GST-Fpr4),
4891	imex:IM-12041_MI:0096	Only an affinity resin made of H3(1-16) peptide was able to recover the Fpr4(NL) domain
4892	imex:IM-12041_MI:0096	The binding of Fpr4 to H3 takes place via the H3 amino terminus, as recombinant histone H3 lacking the amino-terminal 21 amino acids (H3 D1-21), is not recovered by GST-Fpr4 (Figure 1B). The sequence of Fpr4 indicates the presence of two distinct domains: a carboxyl-terminal peptidyl-proline isomerase (PPI) domain (aa 280-411), which is common to all four members of the FKBP family and an amino terminal highly charged nucleolin-like (NL) domain (aa 1-280), which is present only in Fpr3 and Fpr4 (Figure 1C). To establish which one of these domains is responsible for interaction between Fpr4 and histones, the isomerase (PPI) and nucleolin-like (NL) domains were expressed separately and assayed for binding to recombinant histones (Figure 1D). Fpr4-s NL domain (GST-Fpr4[NL]) recovered histone H3 and H4 with comparable efficiency to fulllength Fpr4 (GST-Fpr4),
4893	imex:IM-12055_MI:0096	if that extract was first subjected to S5a pull-down, then virtually all of the immunoprecipitated Pax3 was monoubiquitinated
4894	imex:IM-12055_MI:0096	MEFs were transfected with Pax3 constructs, and extracts were subjected to S5a pulldown assays. Pax3 proteins could be pulled down only in cells expressing Rad23B
4895	imex:IM-12055_MI:0096	Pax3 bound weakly and Pax3-Ub bound strongly to the UBA2 domain of Rad23B
4896	imex:IM-12055_MI:0096	Pax3-Ub bound to Rad23B
4897	imex:IM-12055_MI:0096	The relative amount of Pax3 proteins pulled down using the Rad23B UBA2 domain was in the order Pax3 > Pax3SM> Pax3DM
4898	imex:IM-12055_MI:0096	we first tested for an association between S5a and Pax3 using a pull-down assay, again using p21CIP1 as a positive control
4899	imex:IM-12055_MI:0096	We were able to pull down Pax3 with S5a protein
4900	imex:IM-12065_MI:0096	In vitro binding assay with immobilized, recombinant Flag-CIP2A protein and recombinant GST protein or with GST-c-Myc 1-262 protein.
4901	imex:IM-12128_MI:0096	In purification experiments using H3K9me2 peptide, NML, SIRT1, and SUV39H1 were copurified (Figure 4I).
4902	imex:IM-12128_MI:0096	Nuclear extracts from HeLa S3 cells were used in the peptide pull-down assays and analyzed by immunoblotting with anti-NML and anti-MTA2 antibodies.
4903	imex:IM-12133_MI:0096	overlapping fragments of MRCK&#945; (Figure 2C) fused to a FLAG or glutathione S-transferase (GST) tag were used to coimmunoprecipitate HA-LRAP35a coexpressed in COS7 cells.
4904	imex:IM-12133_MI:0096	To determine the MRCK-interacting site in LRAP35a, overlapping fragments of LRAP35a (Figure 3A) fused to GST were used to pull down the coexpressed KIM-containing MRCK fragment.
4905	imex:IM-12135_MI:0096	directly incubated with GST or GST-PBD (PAK p21 binding domain) or GST-RBD (Rhotekin Rho binding domain) proteins bound to glutathione-coupled Sepharose beads to selectively pull down active Rac/Cdc42 or Rho.
4906	imex:IM-12136_MI:0096	In Drosophila, distinct Lgl/Par-6/aPKC
4907	imex:IM-12136_MI:0096	Phosphomimetic forms of Par-6 (S34D/E) and a control mutant (K23A) defective for binding to aPKC (Noda et al., 2003) were used in the pull-down assays
4908	imex:IM-12136_MI:0096	Recombinant Numb precipitated Baz, Par-6, and aPKC,
4909	imex:IM-12136_MI:0096	Recombinant NumbS52F failed to precipitate Baz and bound only minor amounts of Par-6 and aPKC, although its interaction with the downstream effector &#945;-adaptin was unimpaired
4910	imex:IM-12137_MI:0096	The PHD2 domain preferentially binds to H3K9me3, indicated by the peptide pull-down assay.
4911	imex:IM-12138_MI:0096	Consistent with this idea, cells expressing Lrp4 and MuSK bound more Cy5-Agrin than did cells expressing Lrp4 alone, but only at high concentrations of Agrin (Figure 3D).
4912	imex:IM-12138_MI:0096	Cy5-Agrin B8 bound selectively, in a saturable and dose-dependent manner, to BaF3 cells that expressed Lrp4 (Figure 3C).
4913	imex:IM-12138_MI:0096	Lrp4 Is a Receptor for Agrin
4914	imex:IM-12146_MI:0096	between RUNX3 and &#946;-catenin were also observed in a cell-free system (Figure 2E).
4915	imex:IM-12146_MI:0096	Interaction of in vitro-translated His-tagged RUNX3 with in vitro-translated Myc-TCF4 and/or HA-&#946;-catenin as revealed by pull-down assays with Ni-NTA agarose.
4916	imex:IM-12146_MI:0096	Interactions between RUNX3 and TCF4
4917	imex:IM-12147_MI:0096	As expected due to its known self-association properties, untagged DnaAIII-IV associated with MBP-DnaAIII-IV
4918	imex:IM-12149_MI:0096	Further analysis determined that a portion from aa 538 to 696 of PLEKHA7 was required for its binding to p120 (Figure S1 available online).
4919	imex:IM-12149_MI:0096	The results of this pull-down assay showed that PLEKHA7-Flag was precipitated only with the N-GST (Figure 1C).
4920	imex:IM-12149_MI:0096	To search for proteins interacting with the N-terminal region of p120-catenin (p120), we generated a GST fusion protein for this domain (N-GST) or an N-terminus-deleted p120 (&#916;N-GST; Figure 1A) and incubated them with lysates of human colon carcinoma Caco2 cells.
4921	imex:IM-12153_MI:0096	Both ankB and ankG bind directly to GST-dystrophin-Dp71 (Figure 5A).
4922	imex:IM-12153_MI:0096	GST-tagged &#946;-DG cytoplasmic domain binds ankG in a juxta-membrane region
4923	imex:IM-12153_MI:0096	In Figure 7C we show that ankB binds to GST-dyn4/p62 with high affinity with a dissociation constant (KD) of 50 nM.
4924	imex:IM-12153_MI:0096	Moreover, ankG also associates with the GST-tagged cytoplasmic tail of &#946;-DG
4925	imex:IM-12153_MI:0096	Therefore, dystrophin can form a ternary complex with &#946;-DG and either ankG or ankB.
4926	imex:IM-12154_MI:0096	His-pulldown using His-tagged human WDR23 (WDR23L: G88-Q546; WDR23S: R155-Q546) as bait with GST-DDB1 as prey.
4927	imex:IM-12156_MI:0096	In vitro translated SIRT6 binds purified recombinant GST-RELA (amino acids 1-431).
4928	imex:IM-12166_MI:0096	FLAG-tagged full-length HDAC6 or HDAC6(&#916;C) immunopurified as in (A) was subjected to a binding assay with in vitro translated 35S-Met-labeled Cdc20.
4929	17092313_MI:0097	Complementation of the yeast cdc25-2 mutant through interaction of CBL1 with CIPK1 at the plasma membrane.
4930	17293877_MI:0104	To confirm the histone H3-H4 tetramer-disrupting activity of CIA-I, the subunit rearrangement between the histone H3-H4 tetramer and human CIA-I(172) was analysed in solution using a static light-scattering technique
4931	17293877_MI:0104	To confirm the histone H3-H4 tetramer-disrupting activity of CIA-I, the subunit rearrangement between the histone H3-H4 tetramer and human CIA-I was analysed in solution using a static light-scattering technique
4932	10393905_MI:0107	Representative SPR sensorgrams of the binding between analytes, GST-KAPP mutants, and ligands, MBP-KIK1 and MBP-CLV1, from BIAcore 2000.
4933	10512628_MI:0107	Analysis of the Tube/Pelle Interaction Using Surface Plasmon Resonance (Biacore) Measurements.
4934	10521435_MI:0107	The binding affinity of DnaJ108-Bccp to DnaK in the presence of ATP is comparable to that of full-length DnaJ,whereas DnaJ76-Bccp binds with somewhat lower affinity.
4935	10521435_MI:0107	the J-domain alone neither stimulates ATP hydrolysis nor binds to DnaK in the reaction detected in the Biacore.
4936	11567028_MI:0107	BIAcore analysis of the interactions between sFcgamma RIIb and homogeneous Fc glycoforms.
4937	11567028_MI:0107	Thermodynamic parameters determined by surface plasmon resonance at 30 °C
4938	11567028_MI:0107	Thermodynamic parameters for the interactions between sFcgamma RIIb and homogeneous glycoforms of IgG1-Fc by ITC at 30 °C
4939	12756240_MI:0107	Purified Mge1 was immobilized on the sensor chip by random cross-linking, then purified Ssq1 was passed over the surface of the chip.
4940	12756240_MI:0107	SPR analysis of interactions among Jac, Isu1, and Ssq1 in the presence of ATP.
4941	12756240_MI:0107	When Ssq1 alone at 0.8 µM concentration was passed over the chip surface, only a weak signal (20 response units) was detected, indicating that in the presence of ATP Ssq1 was not able to strongly interact with Isu1 (Fig. 2B).
4942	12820899_MI:0107	Kinetic parameters for the interaction of &#945;II-&#946;II2 at different temperatures
4943	12820899_MI:0107	SPR assay for &#945;-&#946; spectrin interaction
4944	14691232_MI:0107	Binding kinetics for thrombin binding to thrombomodulin and mAb
4945	15171681_MI:0107	In the presence of Ca2+, the association rate constant for the interaction between rhS100P and rhS100A1 [kass =(2.2+&#8722; 0.3)× 105 M&#8722;1 · s&#8722;1] (Table 1) was similar to that previously determined for the self-association of rhS100P [kass =(1.5+&#8722; 0.1)×105 M&#8722;1 · s&#8722;1] [29]. In the absence of Ca2+, the association rate constant for the interaction between rhS100P and rhS100A1 was 30&#8722;50-fold slower [kass =(4.7+&#8722; 0.1)×103 M&#8722;1 · s&#8722;1; Table 1] than that observed in the presence of Ca2+.
4946	15171681_MI:0107	These results suggest that rhS100A1 has an inhibitory effect on the binding of rhS100P to the immobilized rhC-MHC-IIA, particularly at lowmolar excesses of S100A1 over S100P.
4947	15890360_MI:0107	Association (ka) and dissociation (kd) rate constants for the binding of CKIs to components of Cdk/cyclin complexes derived from the analysis of SPR data at 25C
4948	15933069_MI:0107	Histone methyltransferase assay of Pr-Set7 incubated with increasing concentration of H4 30-mer peptide substrate.
4949	16221672_MI:0107	we performed SPR analysis. Monoclonal antibody-mediated orientation-specific coupling of either VWF115 or ADAMTS13 to the sensor chip was not possible due to the relatively fast off-rates of these molecules with the available antibodies to each ligand (not shown). Consequently, we covalently bound either VWF115 or ADAMTS13 to the sensor chip by amine coupling. With VWF115 bound to the chip and ADAMTS13 injected over the sensor, we monitored a concentration-dependent binding response indicative of a high affinity interaction (KD, 20 nM) for this interaction (Fig. 6, inset). Determination of both the association and dissociation rates for the ADAMTS13-VWF115 interaction (n 3) demonstrated a slow off-rate (1.72  103 s1), which would appear to   be the major determinant for the high affinity binding. A second approach, in which ADAMTS13 was coupled to the sensor chip and varying concentrations of VWF115 injected, gave a similar high affinity binding component (KD 
 15 nM, not shown). These data demonstrate that the affinity of ADAMTS13 for VWF115 is significantly higher than is suggested by the Km for VWF115 proteolysis. SPR analysis of VWF115 mutants (D1587A, D1614A, E1615A, and DEK1614/5/7AAA) using both binding approaches revealed a markedly reduced affinity of ADAMTS13 for each of the mutants when compared with wild-type VWF115 (Fig. 6). Because of the low binding response measured, an accurate KD could not be derived from the VWF115 mutant data. Despite the poor fitting the estimate for the KD for the DEK1614/5/7AAA mutant was 
1.3 M. It was clear that for each variant the binding with ADAMTS13 was appreciably compromised and thus the likely cause of their reduced specificity constants.
4950	16257968_MI:0107	Surface plasmon resonance analysis of the 42-amino-acid C-terminal FGF-BP1 fragment (BP1 C-term) binding to immobilized FGF-2
4951	16267044_MI:0107	binding of CaM to recombinant N termini of ACA8 was further analysed by surface palsmon resonance.
4952	16267044_MI:0107	binding of CaM to recombinant N termini of ACA8 was further analysed by surface plasmon resonance
4953	16284400_MI:0107	A similar construction linking the sushi domain of IL-15R
 to human IL-2 also bound IL-15 (Fig. 1B) but with a 10-fold lower affinity, mainly due to a more rapid off rate (kon 
 3.1  105 M1 s1; koff 
 1.3  104 s1; Kd 
 420 pM).
4954	16284400_MI:0107	A soluble sushi domain was also produced in E. coli. This sIL-15R
-sushi also bound IL-15 with a lower affinity (kon 
 2.5  105 M1 s1; koff 
 3.8  104  s1; Kd
1.5 nM) (Fig. 1C).
4955	16284400_MI:0107	As shown in Fig. 1A, a sIL-15R

IL-2 fusion protein produced in Chinese hamster ovary cells and consisting of the entire IL-15R
 extracellular domain linked to a molecule of human IL-2 (used as a tag for purification) bound IL-15 with high affinity (kon 
 3.7  105 M1 s1;koff 
 1.4  105 s1; Kd 
 38 pM).
4956	16286452_MI:0107	Binding to this empty cell is much lower than to the PrP82-146-coated cell and tends to zero after 15-20 min of dissociation. This indicates that the injected peptide does not bind to the chip matrix and that the binding measured in Fc2 is due to binding to immobilized PrP82-146 (i.e. no new seeds are generated).
4957	16286452_MI:0107	Much lower binding levels were also found when PrP82-146 was injected on flow cells in which PrP82-146scr or A42 prefibrillar aggregates had been immobilized (Fig. 4); furthermore PrP82-146 binding to PrP82-146scr and A42 dissociated rapidly and completely
4958	16286452_MI:0107	This shape was seen in the peptide-coated flow cell and in the empty cell, suggesting that the PrP82-146 prefibrillar aggregates, unlike PrP82-146 small oligomers, concentrate on the chip matrix, quite likely by weak electrostatic forces. Despite this -preconcentration- on the sensor surface, the specific binding of these aggregates to immobilized structures (obtained by subtracting the signal in the empty cell) was much smaller than the signal obtained after injection of 20 M of the  small PrP82-146 oligomers (Fig. 6B).
4959	16293618_MI:0107	His-tagged Shank2 PDZ domain was captured with an nitrilotriacetic acid chip, and various concentrations of peptides containing the C-terminal 32 aa of NHE3 were perfused at a flow rate of 30 l/min. of Shank2.
4960	16293619_MI:0107	Fitting of surface plasmon resonance data for Ecyto and phosphoEcyto binding to 
-catenin
4961	16293625_MI:0107	The binding to this immobilized IgA2 of SSL7 at different concentrations was recorded (Fig. 1B) after 3000 s when equilibrium was being approached. Plotting the equilibrium binding responses fitted best to a single binding site with an apparent affinity of 5.01.5 nM(n   5, Fig. 1C, one representative experiment KD  6.8  0.8 nM).
4962	16317005_MI:0107	As a comparison we immobilized S.cerevisiae Sml1p to a sensor chip (Fig. 4B). Injection of S. cerevisiae Rnr1p resulted in an efficient binding
4963	16317005_MI:0107	sensorgram showing the interaction between immobilized Spd1 (200RU) and increasing concentrations of mobile phase Cdc22p
4964	16339310_MI:0107	Using surface plasmon resonance (SPR), we found that RHL1 binds to DNA in a concentration- and salt-dependent manner
4965	16446437_MI:0107	We used surface plasmon resonance to determine the binding affinity of A
 for tau
4966	16518399_MI:0107	The Lif-LipA complex has a notable 5,400 A ° 2 of buried solventaccessible surface area at the interface (Fig. 2a) consistent with the high affinity (Kd ¼ 5 nM) between the two partner molecules as measured by surface plasmon resonance.
4967	16601153_MI:0107	Changing Tyr973 to an alanine (Y973A) or Trp967 to a histidine (W967H) abolishes the binding of H3K4Me3, whereas the wild-type double tudor domain binds the peptide with an apparent equilibrium dissociation constant (Kd) of 10.4 µM. The binding constants were determined using surface plasmon resonance (SPR) (Fig. 3, A and B).
4968	16855233_MI:0107	Surface plasmon resonance analyses of the interaction between YeeI and Mlc
4969	17254966_MI:0107	Surface Plasmon Resonance (SPR) Analysis of p27 Species Binding to Cyclin A, Cdk2, and Cyclin A/Cdk2
4970	17347412_MI:0107	We first used surface plasmon resonance spectroscopy to investigate the interaction between GCR2 and GPA1. For this purpose, we expressed and purified recombinant GCR2 and GPA1 proteins in bacteria (fig. S2). This in vitro assay clearly indicated that GPA1 is capable of binding to GCR2, whereas no binding activity was detected between GPA1 and bovine serum albumin (BSA) (fig. S3, A and B). The dissociation binding constant (Kd) for GCR2 and GPA1 is 2.1 x 10-9 M (fig. S3C).
4971	17350572_MI:0107	mutation of the final proline in the 717PSAP720 motif (Pro720Leu) eliminated TSG101 UEV binding entirely
4972	17350572_MI:0107	the immobilized ALIX V domain bound both HIV-1 p6Gag and EIAV p9Ga
4973	17525340_MI:0107	Purified GST-Brca1-BRCT fragments bind specifically to phosphorylated Abraxas peptides conjugated on BIAcore chip surfaces.
4974	17567753_MI:0107	We used surface plasmon resonance to further analyze the binding of c-JMJD2A to H3K9me3 and H3K36me3.
4975	17951432_MI:0107	we measured the AtGPA1-AtRGS1 interaction by using surface plasmon resonance spectroscopy. Consistent with published data (12), AtRGS1(wild-type) bound AtGPA1 in the transition state for GTP hydrolysis
4976	18243098_MI:0107	BIAcore analysis of the interaction between GCN5 and H3 peptides.
4977	18267072_MI:0107	We observed a direct, calcium-dependent high-affinity interaction between purified Ad5 hexon and human FX (Figure 2D).
4978	18805088_MI:0107	The direct interaction between PopZ and ParB was demonstrated in vitro using Surface Plasmon Resonance (Figure 3D).
4979	imex:IM-11848_MI:0107	A glutathionylated SPR biosensor chip detected specific interactions of GST-E6AP, E6, and p53.
4980	imex:IM-12063_MI:0107	the binding of WT CskFL (10 mM) to mutants of c-SrcKD
4981	imex:IM-12063_MI:0107	The effects of mutations on the binding of Csk to c-Src as measured by surface plasmon resonance.
4982	imex:IM-12063_MI:0107	We used surface plasmon resonance to measure the binding of Csk to c-Src.
4983	16257968_MI:0108	Binding of FGF-BP1-expressing phage to immobilized FGF-2.
4984	16844784_MI:0111	Cfp-10-interacting Mtb proteins identified in an M-PFC screen
4985	16844784_MI:0111	Fusion of F[1,2] and F[3] to the N or C Terminus of Esat-6 and Cfp-10 Does Not Significantly Influence Association.
4986	16844784_MI:0111	To assess whether M-PFC is capable of detecting interactions between Mtb cytosolic and membrane signaling proteins, we studied the interaction between the Mtb membrane-spanning sensor histidine kinase, DevS (Rv3132c), and its corresponding response regulator DevR (Rv3133c; Fig. 4A).
4987	16844784_MI:0111	We generated these bait and prey plasmids as C-terminal fusions with the complementary fragments of mDHFR to generate the interacting protein pairs GCN4[F1,2]/GCN4[F3], KdpD[F1,2]/KdpE[F3], and Esat-6[F1,2]/Cfp-10[F3].
4988	12057192_MI:0112	Comparable results were obtained when using the orthologous protein from tomato, LeSUT1 (Figures 1 and 3B). Interestingly, the N-terminal half of LeSUT1 not only interacted with the C-terminal half of StSUT1, but also with a C-terminal fragment encompassing membrane spans V-XII (LeSUT1-IIV-XII)
4989	12057192_MI:0112	the N-terminal half of LeSUT2 was fused to CubPLV. LeSUT2-I-CubPLV interacted with the second half of StSUT1
4990	12057192_MI:0112	The results indicate a physical interaction between StSUT1-I and StSUT1-II
4991	12119375_MI:0112	To test this, LeSUT1-CubPLV and LeSUT2-CubPLV were used as bait and NubG fusions of LeSUT1, LeSUT2, and LeSUT4 were used as prey (Figure 3). Yeast cells expressing LeSUT1 or LeSUT2 in combination with either of the two other Suc transporters as prey, growth on His-free medium (data not shown), and  -galactosidase filter assays demonstrated the potential for both Suc transporters to interact with their paralogs, indicating the potential of Suc transporters to form heterooligomeric complexes (Figure 4).
4992	12689351_MI:0112	Both AtSUT2 as well as AtSUC2 were able to interact with themselves and with NubG-fusions of sucrose transporters AtSUT2, AtSUC2, and AtSUT4, but not with soluble NubG alone
4993	15155892_MI:0112	GPA1-Cub protein interacts with NubG-GCR1 but not with GCR1-NubG (Figure 1C, plate 1, I and II). GCR1-Cub, however, does not show interaction with GPA1-Nub constructs (Figure 1C, plate 2, I and II), illustrating that a free GCR1 C terminus is required for interaction.
4994	15299147_MI:0112	Growth of diploid cells under selective conditions revealed interaction of KAT1-CubPLV with NubG-KAT1
4995	15299147_MI:0112	Interaction of AKT1-CubPLV with NubG-KAT1 was observed after 6 days of incubation
4996	15299147_MI:0112	KAT1-CubPLV and AKT2-CubPLV interacted with NubG fusions of KAT1, AKT1, and AKT2
4997	15299147_MI:0112	The NubG-X screen revealed interactions of KAT1-CubPLV with NubG-KAT1 and NubG-AKT1, and of AKT1-CubPLV with NubG-AKT1 after 2 days of incubation
4998	15456723_MI:0112	To verify the interaction between CLF and EMF2 in an independent system, we first used the yeast split-ubiquitin assay, which differs from the two-hybrid assay in that candidate proteins are fused to portions of the ubiquitin protein and the fusions are expressed in the cytoplasm rather than the nucleus (Johnsson and Varshavsky, 1994; Kim et al., 2002; Stagljar et al., 1998). Again, we observed an interaction of CLF with the VEFS box domain of EMF2
4999	15988575_MI:0112	Activation of HIS3 and lacZ was also present in cells co-expressing cpSecY-Cub-TF and the Alg5-NubI construct. The latter is a fusion of the resident yeast ER protein Alg5 with wild-type Nub and served as a positive control.
5000	15988575_MI:0112	Combining Alb3-Cub-TF and NubG-D1 resulted in strong activation of HIS3 and LacZ as shown in Table 3.
5001	15988575_MI:0112	The construct cpSecE122-177 interacted as strongly with cpSecY as full-length cpSecE, whereas no interaction occurred with cpSecE41-133
5002	15988575_MI:0112	To test whether the split-ubiquitin system can be used to characterise the nature of this interaction in more detail, the interaction of cpSecY-Cub-TF with NubG-Alb3 was analysed. As shown in Table 2 and Fig. 1a, strong binding between these proteins was observed. Interestingly, removal of the C-terminus of Alb3 (construct Alb357-350) led to a complete loss of binding to cpSecY, suggesting that this region of Alb3 is crucial for its interaction with cpSecY.
5003	15988575_MI:0112	We were also able to demonstrate that Alb3 interacts with other choloroplast-encoded subunits of PSII like D2 and CP43.
5004	16766674_MI:0112	In contrast, CYCD3;1 interacts with all three ICK1/KRP1 variants, full-length ICK1/KRP1, ICK1/KRP11-152, and ICK1/KRP11-108.
5005	16766674_MI:0112	we also observed in this yeast assay that the full-length ICK1/KRP1 protein interacted with CDKA;1, whereas ICK1/KRP11-152 did not bind to CDKA;1 (Wang et al., 1998); inaddition,wefoundthat ICK1/KRP11-108 didnot interact withCDKA;1.
5006	17012411_MI:0112	Growth of diploid cells under selective conditions revealed interaction of AtNAR2.1-CubPLV with NubG-AtNRT2.1 and NubG-AtNRT2.3, but not with NubG-CrNRT2.1
5007	17012411_MI:0112	The activity detected when AtNAR2.1-CubPLV was in combination with NubG-AtRNT2.1was 2 and 16 times higher than in combination with NubG-AtNRT2.3 and NubG-CrNRT2.1, respectively.
5008	17142482_MI:0112	AtBI-1 interacts with CaM in yeast.
5009	17347412_MI:0112	The interaction was abolished when the C terminus of the receptor was blocked by fusing the ubiquitin fragment (CubPLV) to the C terminus of GCR2 (fig. S4A). We also found that the C terminus of GCR2 (C290-401, containing the free C terminus and the predicted third cytoplasmic loop) interacted with GPA1, whereas the N terminus (N1-289) of GCR2 did not (fig. S4, B and C), indicating that the C terminus of GCR2 is necessary and sufficient for its interaction with GPA1.
5010	17347412_MI:0112	This assay confirmed the reported interaction of the full-length GCR1 with GPA1 (19), and the full-length GCR2 also interacted with GPA1
5011	17612295_MI:0112	As shown in Figure 1E, full-length Uri1p bait interacted strongly with two of its known binding partners, Rf6p and Rpb5p, demonstrating that interactions between cytosolic proteins can also be detected using the cytoY2H system.
5012	17612295_MI:0112	The fact that dimerization of full-length p53 is detectable in the cytoY2H system
5013	17612295_MI:0112	To reconstruct the interaction between p53 and the large T antigen, the latter was fused to Ost4p and Cub-LexA-VP16 as bait, and deltap53 was fused to NubG for use as prey.
5014	17612295_MI:0112	Upon co-expression, an IkappaB-alpha bait interacted with full-length p65 prey.
5015	18644794_MI:0112	First, split ubiquitin assays showed that CCMH Cub fusion proteins could interact with both CcmFN1 and CcmFN2 Nub fusions, but not with the CcmFC fusion
5016	18644794_MI:0112	FN2 Cub growth was observed with both apocytocrome c and apocytochrome c1 constructs.
5017	18644794_MI:0112	For FN1 Cub, we observed growth with FN2 constructs,
5018	18644794_MI:0112	for FN2 Cub, growth was observed with both FN1 and FC constructs
5019	18644794_MI:0112	This shows that CcmFN2 can interact with CcmFN1 and CcmFC whereas CcmFN1 cannot interact with CcmFC.
5020	18671868_MI:0112	As shown in sector 2 of Figure 3d, the candidate GPCR Cand5 interacts with GPA1 as shown by the presence of yeast growth; however, this interaction does not occur when the Cand5 protein has a carboxy-terminal NubG or Cub fusion protein
5021	18671868_MI:0112	Fusion proteins made using Cand1, 2, 3, 5, 7, 8 and HHP2 in the NubG-candidate orientation interacted with the GPA1-Cub-PLV fusion protein as indicated by yeast growth
5022	imex:IM-11906_MI:0112	PGRL1 protein interacts in the split-ubiquitin assay with Fd, PSI-D, Cyt b6, FNR1, and FNR2
5023	imex:IM-11906_MI:0112	Whereas PGR5 interacts in yeast two-hybrid assays with Fd and in the split-ubiquitin assay with Cyt b6,
5024	imex:IM-11923_MI:0112	Utilizing BAP31 as bait in the split-ubiquitin yeast 2-hybrid screen to detect interactions between membrane-associated proteins, two constituents of the Sec61 preprotein translocon, Sec61&#946; and TRAM, exhibited the highest hit rate.
5025	10600387_MI:0114	We solved the structure of the Hpa2-AcCoA complex using multiple wavelength anomalous diffraction (MAD) on a single crystal of selenomethionyl protein (Table 1 and Materials and Methods). Hpa2 crystallizes in the orthorhombic space group C2221 with four Hpa2 molecules in the asymmetric unit.
5026	11880631_MI:0114	Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c
5027	12079350_MI:0114	Structure of the 147 bp nucleosome core particle (NCP147) at 1.9  resolution.
5028	12079350_MI:0114	We generated these bait and prey plasmids as C-terminal fusions with the complementary fragments of mDHFR to generate the interacting protein pairs GCN4[F1,2]/GCN4[F3], KdpD[F1,2]/KdpE[F3], and Esat-6[F1,2]/Cfp-10[F3].
5029	12876341_MI:0114	the chick erythrocyte histone octamer, described herein, crystallized in space group P65, with one octamer in the asymmetric unit.
5030	12887903_MI:0114	For cocrystallization, an H3 peptide residues 1 to 15 was added at a final concentration of 2 mM to purified DIM-5 protein
5031	15084729_MI:0114	The asymmetric unit of the Z. mays HPPD crystals of space group P212121 contains two dimers of 44.8-kD subunits (Fig. 2A )
5032	15201901_MI:0114	Here we report the crystal structure of the five-protein clamp loader complex (replication factor-C, RFC) of the yeast Saccharomyces cerevisiae, bound to the sliding clamp (proliferating cell nuclear antigen, PCNA).
5033	15301540_MI:0114	the HPPD from rat (RnHPPD) was cloned, overexpressed in E. coli, purified,and cocrystallized with DAS869
5034	15301540_MI:0114	The structure of DAS645 in complex with AtHPPD (AtHPPD- 645) was solved and refined to 1.9 Å resolution.
5035	15301540_MI:0114	The truncated AtHPPD was overexpressed in E. coli and purified to homogeneity. The structure of the purified enzyme was solved by multiple isomorphous replacement and refined to 1.8 A(Table 1). The enzyme forms a homodimer
5036	15525938_MI:0114	We next determined the structure of Set9 in complex with a mono-methylated p53 peptide and cofactor product AdoHcy.
5037	15526038_MI:0114	The crystal structure of the WAT/PRAD complex
5038	15916958_MI:0114	To visualize the interaction between LuxP and LuxQp, we determined the crystal structure of the apoLuxP:LuxQp complex by using multiwavelength anomalous diffraction (MAD) phasing and refined the structure to 1.9 Å resolution
5039	15933069_MI:0114	Crystals of the ternary complex of Pr-Set7 175-352 with 10 mer peptide
5040	16001076_MI:0114	We have determined, at low resolution, the first structure of an oligonucleosome using a tetranucleosome assembled in vitro
5041	16230338_MI:0114	Crystal structure of the SC-(1-325)
bovine
-thrombin complex.
5042	16249186_MI:0114	The recombinant HPV 1AE7 CR3 region (residues 44-93; Fig. 1A) was prepared from bacteria andcrystallized in space group P21212. The crystal structure was determined usingM ADfrom the two bound zinc atoms per asymmetric unit. and refined to a resolution of 1.6 Å,
5043	16263718_MI:0114	In this study, we characterized binding of human E3 to the E3-binding domain of E3BP by x-ray crystallography at 2.6-A&#730; resolution, and we used this structural information to interpret the specificity for selective binding. Two subunits of E3 form a single recognition site for the E3-binding domain of E3BP through their hydrophobic interface.
5044	16321984_MI:0114	We report here the x-ray structure of a covalent serpin-proteinase complex, 1-proteinase inhibitor (1PI) with porcine pancreatic elastase (PPE)
5045	16474402_MI:0114	Crystals of the USP7 NTD bound to peptide 4 (acetyl-141-ELQEEKPSSS-150-amide) were obtained, the structure of the complex was determined using molecular replacement and the model was refined to 2.1-Å resolution
5046	16474402_MI:0114	To further investigate the nature of the interaction of the mutant p53 peptide (acetyl-358-EAGGARAHSS-367-amide) with USP7, this peptide was cocrystallized with the USP7 NTD. The structure of the complex was determined using molecular replacement and the model refined to 1.60-Å resolution
5047	16518399_MI:0114	The crystal structure of the Lif-LipA complex reveals that Lif adopts a previously unobserved fold, featuring an extended a-helical structure consisting of 11 a-helices, which engulfs the lipase
5048	16601153_MI:0114	crystal structure of the double tudor domain of JMJD2A both in the presence and absence of a trimethylated H3-K4 peptide (H3K4Me3).
5049	16615894_MI:0114	The crystal structures of a Vps23:Vps28 core subcomplex and the Vps23:Vps28:Vps37 core were solved at 2.1 and 2.8 Å resolution.
5050	16885027_MI:0114	The crystal structure of LSD1-CoREST was determined by single-wavelength anomalous dispersion and molecular replacement
5051	16923391_MI:0114	Crystals that diffract to 3.2A° resolution were obtained with the complex of Mago (full length), Y14 (residues 66-174, referred to as Y14DN), eIF4AIII (full length), Btz (the SELOR domain, residues 137-286, Degot et al., 2004), a nonhydrolyzable ATP analog (AMPPNP), and U15 RNA. A crystal form that diffracts to 2.2A° resolution was obtained by reconstituting the EJC with a Y14 construct that also lacks the low-complexity C terminal region (Y14DCDN, residues 66-154)
5052	16923391_MI:0114	To determine the structure of the eIF4AIII-Btz subcomplex, we used an eIF4AIII construct (residues 38-411) lacking the N-terminal sequence that flanks the helicase domains and a Btz construct trimmed to residues 137-250. The structure is refined at 3.0 A ° resolution to an Rfree of 32.5% and R factor of 27.1%.
5053	16990134_MI:0114	we crystallized AI-2 bound LuxPQp, after first deleting five residues from the N terminus of LuxP (see above). Crystals were improved by deleting, from the termini of LuxQp, those residues that were poorly ordered in the previously determined AI-2-free LuxPQp crystal structure (Neiditch et al., 2005). The 2.3A° resolution structure (Figures 3A-3C) was determined using phases obtained by molecular replacement (see Experimental Procedures, as well as Table S1 in the Supplemental Data available with this article online). The structure indeed contains two similar LuxPQp complexes,
5054	16990139_MI:0114	The crystal was of space group C2221 with unit-cell dimensions of a = 174.1A° , b = 181.0A° , c = 252.7A° , a = b = g = 90 and contained eight RCK subunits in one asymmetric unit.
5055	17055435_MI:0114	The PP2A core enzyme was separately incubated with 1.2 molar equivalence of OA or MCLR for crystallization. After extensive trials, we succeeded in obtaining crystals of the 100 kDa PP2A core enzyme separately bound to OA and MCLR under similar conditions. The structures were determined by molecular replacement and refined to 2.6 and 2.8 A resolution, respectively, for the OA- and MCLR-bound PP2A core enzyme
5056	17081977_MI:0114	Within our crystals, three dimers are crystallographically related to one another to form an intact, closed-ring Rho hexamer that is 3-fold symmetric
5057	17110337_MI:0114	we determined the crystal structure of the DsbB-DsbA complex at 3.7 Å resolution.
5058	17293877_MI:0114	In the crystal, CIA I forms a complex with one histone H3 H4 dimer
5059	17418792_MI:0114	Using these smaller, more stable versions of the TCR and pMHC, we were able to crystallize and solve the structure of the 2C H-2Ld-QL9 complex at 2.35 A resolution
5060	17442384_MI:0114	The structure of a heterotetrameric core complex of ESCRT-I was determined at a nominal resolution of 2.7 Figure 2A Table S1.
5061	17537733_MI:0114	Crystal structure of LSD1-CoREST in complex with pLys4Met H3 peptide.
5062	17540173_MI:0114	We present the crystal structure of E. coli RF3.GDP, which has a three-domain architecture strikingly similar to the structure of EF-Tu.GTP.
5063	17567753_MI:0114	crystals of the complex of c-JMJD2A with a trimethylated H3K36 peptide were obtained
5064	17567753_MI:0114	The overall complex structure of c-JMJD2A with the H3K36me3 peptide
5065	17626883_MI:0114	We determined the crystal structure of a complex between the bovine p110a ABD (residues 1 to 108) and the human p85a iSH2 domain (residues 431 to 600) at 2.4 A resolution
5066	17662939_MI:0114	We present the crystal structure of the complex between a large fragment of the human Met ectodomain and the Met-binding domain of InlB.
5067	17662946_MI:0114	The observed SCF-KIT 2:2 complex in the crystal lattice is consistent with experiments demonstrating that KIT dimerization is driven by the dimeric SCF ligand ([Philo et al., 1996] and [Lemmon et al., 1997]).
5068	17803912_MI:0114	Among the hybrids, MD-2-bound TV3 was successfully crystallized with Eritoran and their complex structure was solved
5069	17803912_MI:0114	the full-length ectodomains of mouse TLR4 and MD-2 were expressed in cultured insect cells using recombinant baculoviruses. The mouse TLR4 and MD-2 proteins form a stable 1:1 complex and are not separated during purification. In the crystal structure, one molecule of MD-2 binds to each TLR4
5070	17889648_MI:0114	We report here the structure of a complex between the PKA catalytic subunit and a mutant RI regulatory subunit, alpha(91-379:R333K), containing both cAMP-binding domains.
5071	17889651_MI:0114	Here we present the crystal structures of the human TLR1-TLR2-lipopeptide complex
5072	17981120_MI:0114	we generated cocrystals and solved the structures of Scr and Exd bound to 20 bp overhanging nucleotides containing either the fkh250 and fkh250con binding sites.
5073	18001825_MI:0114	and solved the high-resolution structure of the RNF8 FHA:optimal phosphopeptide complex by X-ray crystallography at 1.35 A (Table S1; the PDB code for the RNF8 FHA domain is 2PIE)
5074	18022368_MI:0114	To further eliminate conformational heterogeneity of Mad2, MBP1 was also added to yield a 1:1:1 Mad2 L13A-MBP1-p31comet&#916;N35 ternary complex (referred to as Mad2-p31comet for simplicity), for which we were able to produce diffracting crystals.
5075	18160037_MI:0114	An A14/43 variant lacking the mobile regions crystallized and enabled structure determination at 3.1 A resolution
5076	18243101_MI:0114	Here we present the crystal structures of the complete set of type I (IL-4Ra/gc/IL-4) and type II (IL-4Ra/IL-13Ra1/ IL-4, IL-4Ra/IL-13Ra1/IL-13) ternary signaling complexes.
5077	18243101_MI:0114	Here we present the crystal structures of the complete set of type I (IL-4Ra/gc/IL-4) and type II (IL-4Ra/IL-13Ra1/IL-4, IL-4Ra/IL-13Ra1/IL-13) ternary signaling complexes.
5078	18510924_MI:0114	we therefore crystallized SaXPD and solved crystal structures with and without the bound 4Fe-4S cluster.
5079	18555782_MI:0114	Crystals were obtained for a complex of Hsp70N and a truncated variant of Sse1p, Sse1-&#916;loop, in which the poorly conserved and presumably flexible insertion (residues 503-524) found in all Hsp110/Hsp170 homologs is replaced by the peptide linker sequence AGSD.
5080	18585358_MI:0114	Therefore,we solved the X-ray crystal structure of LUSH bound to cVA pheromone
5081	18805092_MI:0114	Thus, we determined NEDD8not, vert, similarCul5ctd-Rbx1 and Cul5ctd-Rbx1 structures to directly compare modified and unmodified complexes for insight into the CRL family (Table S1).
5082	18957204_MI:0114	We have determined a crystal structure of Thermus thermophilus RNAP holoenzyme in complex with Myx.
5083	19135891_MI:0114	In the crystal, two MukE molecules interacted with one molecule of MukF.
5084	19135891_MI:0114	In the Form I crystal, the symmetric dimer of hMukBhdEQ complexed with hMukF C-WHD and ATP&#947;S was clearly visible,
5085	19135891_MI:0114	One finally crystallized complex was composed of full-length hMukE, a hMukF fragment (residue 292-443) spanning the middle region and the C-WHD, designated as hMukF(M+C), and the head domain of a hMukB mutant containing an E1435Q substitution (Figure 2A). T
5086	8524402_MI:0114	CaN is a heterodimer composed of an A subunit (CaNA; relative molecular mass 59K) and a B subunit (CaNB; Mr 19K).
5087	9469799_MI:0114	The 2C TCR and H-2Kb-dEV8 were expressed and purified from Drosophila melanogaster cells and cocrystallized
5088	imex:IM-11859_MI:0114	A second, rhombohedral, crystal form of apoMRP1/MRP2 was obtained (Table 1), solved by Molecular Replacement using EPMR (Kissinger et al., 1999), and was minimally refined to an Rfree of 29.9% to 3.35 A ° resolution. The model contains two tetramers that are identical to the P21 tetramer structure and consists of residues 28-173 of each of the four MRP1 subunits, 60-175 and 188-221 of one MRP2 subunit and 59-175 and 188-221 of three of the MRP2 subunits and 56 solvent molecules.
5089	imex:IM-11859_MI:0114	Crystals of this complex were grown under low salt conditions using a gRNA fragment encompassing gND7-506 stem/loops I and II (gND7- 506(I-II)), corresponding to nucleotides 1-44 in Figure 3A (Experimental Procedures). The structure was solved by Molecular Replacement and the ASU contains one MRP1, one MRP2, and one gND7-506(I-II).
5090	imex:IM-11859_MI:0114	MRP1 and MRP2 combine to form a heterotetramer
5091	imex:IM-11885_MI:0114	We crystallized Mad2LL-Mad2w-MBP1 and collected X-ray diffraction data to 2.9 A resolution.
5092	imex:IM-11908_MI:0114	The S. cerevisiae Uba1-Ub complex was crystallized,
5093	imex:IM-11911_MI:0114	We have determined the structure of the GM-CSF ternary complex revealing a 2:2:2 hexamer consisting of two Bc chains, two GMRa chains, and two GM-CSF molecules
5094	imex:IM-11961_MI:0114	Ribbon diagrams depicting the overall fold of the CASK CaM-kinase domain in a complex with 3'-AMP
5095	imex:IM-11961_MI:0114	Stereo plots of  the nucleotide-binding pockets of the CASK (B, in complex with AMPPNP; triclinic form)
5096	imex:IM-11984_MI:0114	The Sec13-Nup145C hetero-octamer forms a slightly bent rod
5097	imex:IM-11992_MI:0114	A single Asf1-H3/H4 complex formed the asymmetric unit in the crystals, which belong to space group P3121
5098	imex:IM-12005_MI:0114	The structure of the bet3-trs31-sedlin subcomplex was determined at 2.1 Å resolution.
5099	imex:IM-12005_MI:0114	The structure of the bet3-trs33-bet5-trs23 subcomplex was determined at 2.4 Å resolution.
5100	imex:IM-12018_MI:0114	The Survivin-Borealin10-109-INCENP1-58 complex was crystallized and its structure determined by single-wavelength anomalous dispersion (SAD).
5101	imex:IM-12024_MI:0114	The complex of human GCC185 (residues 1547-1612) and the constitutively active mutant of Rab6 (Q72L) was crystallized in the presence of GTP and Mg2+
5102	imex:IM-12058_MI:0114	The crystal structure of a TRAPPI subassembly (Figures 1A-1C) consisting of one copy each of Bet5p, Trs23p, and Trs31p and two copies of Bet3p (named Bet3p-A and Bet3p-B) was determined in complex with a C-terminally truncated Ypt1p (residues 1-180).
5103	imex:IM-12063_MI:0114	In the case of the CskKD:c-SrcKD crystals, the protein mixture was concentrated in the presence of a 2-fold molar excess of staurosporine (Sigma) prior to crystallization.
5104	imex:IM-12132_MI:0114	Mre11 X-Ray Structures for Synaptic and Branched DNA Complexes
5105	imex:IM-12147_MI:0114	soaked crystals of ADP-DnaCAAA+ overnight in a solution of 2 mM BeF3, a widely used substitute for the &#947;-phosphate of ATP
5106	imex:IM-12147_MI:0114	To better understand this process, we determined the structure of the ATPase region of the bacterial helicase loader DnaC from Aquifex aeolicus to 2.7 Å resolution.
5107	imex:IM-12154_MI:0114	The Overall Structure of the DDB1-DDB2 Complex
5108	11278694_MI:0115	Retransformation assay showed that GAL4-AD-UBC9 fusion protein interacted with pSTRA13 specifically, since no binding of ADUBC9 was detected with either the pAS2-1 vector alone (BD domain) or with pAS2-1-ARNT1 that produces the BD-ARNT1 fusion protein
5109	10490601_MI:0226	As demonstrated in Fig. 5, partially purified ADA prepared from the wild-type strain was eluted in fractions 18 to 22 (identified by H3-H2B HAT activity and Ada2 and Gcn5 Western blotting). In addition, the other previously identified HATs, NuA4, NuA3, and SAGA, were eluted as predicted.
5110	10490601_MI:0226	Similarly, Ada2, Ada3, Gcn5, and Ahc1 coeluted with ADA complex HAT activity on the Mini Q column, the ninth column.
5111	10809665_MI:0226	The anti-OSA antibody efficiently recognized p300 as well as a number of bands migrating between 200 and 300 kD, which might be alternatively processed forms (Fig. 3C, lanes 1,2). The BRM and MOR subunits were readily detected by Western blot analysis (Fig. 3C, lanes 3-6),
5112	10869553_MI:0226	An attempt was made to demonstrate homo- and heterodimerization of S100A4 and S100A1 by anion-exchange chromatography. Purified preparations of S100A4 and S100A1 were mixed and incubated without denaturation, then concentrated and fractionated on a Resource Q column. Several distinct peaks were detected (Fig. 1A). Two of them eluting at 50 mM NaCl and 180 mM NaCl were shown to be the S100A4 and S100A1 homodimers, respectively.
5113	10869553_MI:0226	An attempt was made to demonstrate homo- and heterodimerization of S100A4 and S100A1 by anion-exchange chromatography. Purified preparations of S100A4 and S100A1 were mixed and incubated without denaturation, then concentrated and fractionated on a Resource Q column. Several distinct peaks were detected (Fig. 1A). Two of them eluting at 50 mM NaCl and 180 mM NaCl were shown to be the S100A4 and S100A1 homodimers, respectively. The intermediate peak was very small and contained both S100A4 and S100A1 proteins.
5114	11124122_MI:0226	On a DEAESepharose column, p55 elutes in multiple peaks and cofractionates with FLAG-ESC and E(Z) in fractions 18-25
5115	12482963_MI:0226	Identification of the proteins associated with Isw1p: Ioc2p, Ioc3p, and Ioc4p.
5116	14555658_MI:0226	Edman degradation of each of the enzyme preparations reveals the presence of only the sequences of the {alpha}, {beta}, and {gamma} subunits of human NAD-dependent isocitrate dehydrogenase
5117	8805366_MI:0226	MSH2 and MSH2-MSH3 were purified to near homogeneity from extracts prepared from yeast strain LY2 harboring plasmids pPM608, and pMMR8 and pMMR20, respectively (Figure 1).
5118	9096360_MI:0226	These data confirm that the yeast NC2a and NC2b proteins are stoichiometric subunits of a complex that can bind specifically to TBP.
5119	imex:IM-12052_MI:0226	Mass spectrometric data for the identified &#945; and &#946; 20S proteasome subunits from S.mansoni.
5120	14555658_MI:0227	Determination of Subunit Composition of Enzymes by Reverse Phase Chromatography
5121	1961752_MI:0227	Identity of the soluble monomeric form with the complexed 25-kDa protein from chromatin is indicated by immunological crossreaction, apparent molecular mass in gel electrophoresis, the elution pattern of CNBr fragments from a reversedphase column (Fig. 5), the amino acid sequences (see below), and the isoelectric points (Fig. 6).
5122	11739376_MI:0232	Atx1 Interacts with the Amino-terminal Region of CtaA in a Bacterial Two-hybrid Assay
5123	11739376_MI:0232	Atx1 Interacts with the Amino-terminal Region of PacS in a Bacterial Two-hybrid Assay.
5124	14711369_MI:0232	The present experiments (Figure 4A) show that although the electrostatic properties of Synechocystis Atx1 are expected to be similar to B. subtilis CopZ, the interaction of the chaperone with its ATPase is highly specific, with no detectable cross-interactions between Atx1 and B. subtilis CopAN, or between CopZ and PacS.
5125	10648604_MI:0276	With mitochondria from the strain expressing HA-tagged Tim18p, the tagged Tim18p comigrated with Tim54p and Tim22p (Tim18pHA in Fig. 4A).
5126	11483513_MI:0276	BN-PAGE was performed on the recombinant TIM10 complex (Figure 1C) and we found that the recombinant TIM10 complex migrated as the endogenous, authentic complex from mitochondria
5127	12198123_MI:0276	35S-Tom7 and 35S-Tom22 precursors were incubated with mitochondria from HeLa cells for 30 min and subjected to BN-PAGE and PhosphorImager analysis and immuno-decoration using antibodies specific for Tom22 and Tom40
5128	12198123_MI:0276	radiolabeled Tom7 was incubated with mitochondria for 30 min, solubilized in digitonin-containing buffer, and incubated with increasing concentrations of antibodies specific for Tom40, Tom22, Tom20, and VDAC and subjected to BN-PAGE.
5129	12198123_MI:0276	To determine whether in vitro imported 35S-Tom7 had assembled into a complex, we used Blue Native-PAGE (BN-PAGE) of digitonin-lysed mitochondria, which allows separation and visualization of mitochondrial translocase complexes
5130	12198123_MI:0276	Western analysis of mitochondrial extracts using antibodies against the IMS domain of Tom22 (26) revealed that both radiolabeled Tom7 and Tom22 precursors assembled into a complex indistinguishable in molecular weight from the endogenous TOM complex (Fig. 2B, lanes 13 and 14).
5131	12217076_MI:0276	Thylakoid membrane proteins were solubilized in digitonin and subjected to blue native gel electrophoresis, and the distributions of ALB3 and cpSecY within the gel were detected by Western blot analysis. The two proteins showed a very similar fractionation pattern (
5132	12869544_MI:0276	In contrast to Toc33-wt, the putative 70-kDa dimer band of Toc33-R130A was much weaker (Fig. 4A, lanes 6-9, dimer), suggesting reduced dimerization when compared with Toc33-wt
5133	12869544_MI:0276	The result suggests that the upper bands also largely consist of Toc33-wt and Toc33-R130A, respectively, most likely as dimers. However, the upper band of Toc33-R130A gave a much weaker signal than that of Toc33-wt, likely due to reduced dimer formation and/or streaking of the protein across the length of the gel (Fig. 4A, lanes 6-9).
5134	15250827_MI:0276	The identity of the 900 kDa ND complex as a fully assembled complex I was confirmed by immunodetection with antibodies against the 24, 39 and 49 kDa complex I subunits.
5135	15797382_MI:0276	Upon separation of digitonin-lysed mitochondria by BN-PAGE, Tim23 and Tim17 are found in a 90 kDa core complex (TIM23core) and additionally in larger TIM23* complexes (Dekker et al., 1997 and Chacinska et al., 2003) (Figure 3A, lanes 1 and 5).
5136	16079137_MI:0276	A 404-kDa subcomplex contained the NuoCD protein and a 135-kDa complex contained the 90-kDa NuoG subunit
5137	16079137_MI:0276	Both the 54-kDa sodium/proline symporter (PutP) and the 59-kDa acetate permease (YjcG/ActP) are major facilitator superfamily transporters. For neither protein are we aware of any reports alluding to their existence in an oligomeric complex. However, both proteins seemed to be dimeric
5138	16079137_MI:0276	From the SDS gel, we could identify the 66-kDa flavoprotein subunit (SdhA) and the 26-kDa iron-sulfur protein (SdhB) (Fig. 3A).
5139	16079137_MI:0276	MdtE and MdtF were identified in two separate complexes of 343 and 114 kDa, corresponding to homotrimers
5140	16079137_MI:0276	Since the LepB complex is not abundant, we could not identify interacting partners but the size of the complex in the BN gel suggests that LepB may form a dimer in the inner membrane.
5141	16079137_MI:0276	Since we could not find any interacting proteins in this complex, we conclude that YajC is present as a homo-oligomer in excess to the other components of the translocon.
5142	16079137_MI:0276	This complex is reported to be a heterodimer, CydAB, with a molecular mass of 100kDa (38). Unexpectedly, be identified CydA (58 kDa) and CydB (42 kDa) along with  third proteibn, YhcB (15 kDa)
5143	16079137_MI:0276	Using soluble molecular mass markers to estimate molecular mass, we observed that SecA resolved at 200 kDa in the BN gel (Fig. 4C), corresponding exactly to a dimer.
5144	16079137_MI:0276	We detected the 8-kDa MulI in a complex with an estimated molecular mass of 87 kDa (Fig. 2B). Other less abundant, higher molecular mass complexes were also detected.
5145	16079137_MI:0276	We identified AcrB (113 kDa) in a complex of 342kDa and AcrA (42 kDa) in a separate complex of 115 kDa, both corresponding to homotrimeric complexes
5146	16079137_MI:0276	We identified OmpA and FadL (Fig. 2B) at the anticipated molecular masses of 30 and 33 kDa in the SDS gel; however, in contrast to the literature, both were estimated to be dimers from their molecular mass in the BN gel (OmpA at 74 kDa, FadL at 77 kDa).
5147	16079137_MI:0276	We identified Slp as a smeared band in the SDS gel (Fig. 2B), indicating that it forms higher order oligomers.
5148	16079137_MI:0276	We identified the 37-kDaOmpFin a predominant complex that corresponds in molecular mass to a trimer in the BN gel (relative to the soluble markers), and we conclude that (OmpF)3 is intact.
5149	16079137_MI:0276	We identified the 47-kDa LamB protein in a complex that corresponds in molecular mass to a trimer (again relative to soluble markers) (Fig. 2B), and we conclude that LamB3 is intact.
5150	16079137_MI:0276	We identified the 50-kDa TolC in a complex that corresponded in molecular mass to the trimer (again relative to soluble markers) (Fig. 2B), and we conclude that(TolC)3 is intact.
5151	16079137_MI:0276	We identified ZipA in a channel with two other proteins (Fig. 4A). Although the 24-kDa interacting partner could not be identified, wE could identify YjdB (61 kDa) as an interacting partner to ZipA.
5152	16079137_MI:0276	We were able to identify subunit c (11 kDa), subunit b (18 kDa), the subunit (54 kDa), the subunit (51 kDa), and the subunit (29 kDa) (Fig. 3A).
5153	16079137_MI:0276	YaeT (85 kDa), NlpB (34 kDa), and YfiO (26 kDa), along with a fourth protein of 40 kDa, in a complex, corresponding to exactly 178 kDa was identified.
5154	16079137_MI:0276	YagU has three predicted TMHs and no known biochemical function. We identified YagU (22 kDa) at 47 kDa in the BN (Fig. 2A and supplemental Fig. 2) and conclude that it is present as a dimer.
5155	16079137_MI:0276	YdgA resolved at 106 kDa in the BN gel (Fig. 2A and supplemental Fig. 2), and we conclude that it is present as a dimer.
5156	16260785_MI:0276	We further tested this result by blue native gel electrophoresis (Fig. 6C), where recombinant Arr4p purified from E. coli migrated in two species, presumably representing the monomer (lower band) and the homodimer (upper band), which was absent for the C285T/C288T and not the C240T/C242T double mutant.
5157	16286465_MI:0276	The PSII complex in Synechocystis assembles in a stepwise fashion through a number of distinct intermediates, including the PSII reaction center (comprising D1, D2, and cytochrome b559), a PSII core complex lacking CP43 (RC47), and the monomeric core complex reaction center core (RCC).
5158	16473966_MI:0276	In contrast with SERK1, most of the BRI1 protein was found as probably a homodimeric form of &#8764;250 kD
5159	16473966_MI:0276	Therefore, a microsomal fraction prepared from SERK1-CFP transgenic plants was examined for the presence of BRI1 proteins. BRI1 was found in complex with the same size range of 400 to 500 kD
5160	16619302_MI:0276	We identified the previously known GR interacting proteins hsp70 and hsp90 and others listed in Table 3.
5161	16641999_MI:0276	On 2D-gel electrophoresis in wild type cells expressing endogenous proteins, TMP21 is distributed into a series of peaks, some of which overlap those of the mature, functional ~660 kDa PS1 complex, the ~440 kDa immature non-functional complex, and the ~150 kDa nicastrin-aph-1 complex. About 25% of the TMP21 signal resides in the ~660 kDa complex. In contrast, in both PS1/PS2 double knockout cells and in pen-2 knock-down cells, TMP21 is destabilized from the ~660 kDa complex (<5% of signal intensity), and instead, TMP21 is predominantly localized with the ~150 kDa nicastrin:aph-1 complex and in a 30 kDa complex.
5162	17092930_MI:0276	Description of the protein complexes identified in H. pylori reference strain J99 using 2D BN/SDS-PAGE
5163	17205597_MI:0276	A summary of identified proteins is shown in Table 1.
5164	18492870_MI:0276	After the solubilization with the mild detergent dodecyl-b-D-maltoside (DDM) in concentrations of total protein to DDM ratio of 1.33 and low NaCl concentrations (10 and 30 mM), a range of high molecular mass complexes was detected for four of the five exocyst complex components tested: SEC3, SEC6, SEC8, and EXO70A1
5165	18492870_MI:0276	Notably, we observed a well defined complex detected only by anti-SEC6 that could represent SEC6 dimers.
5166	18492870_MI:0276	Under the conditions of higher detergent concentrations (total protein:DDM ratio of 0.67) and no additional salt, SEC6 and EXO70A1 were predominantly present in small, rather than in high, molecular complexes
5167	18644794_MI:0276	This does not prove a direct interaction between the 3 Arabidopsis CcmF proteins but strongly suggests that they are, together with other proteins, in particular CCMH that was also found in a 500 kDa complex
5168	8120006_MI:0276	subunits. We purified succinate dehydrogenase by blue native gel electrophoresis, determined the amino-terminal sequence of the Sdh4p subunit and used this information to clone the SDH4 gene.
5169	9774667_MI:0276	Upon overexposure of the immunoblot, a small amount of Tom20(~5 to 10%) was found in the higher-molecular-weight range, slightly above the peak of the 400K position (small amounts of Tom40 and other components of the GIP complex were also observed at this slightly higher position)
5170	9774667_MI:0276	We conclude that Tom40, Tom22, and the three small Tom proteins comigrate at the 400K position in blue native gel electrophoresis.
5171	11259609_MI:0397	coexpression of pRb fails to support cell growth of cells containing the mutated AhR constructs implying that the AhR-pRb interaction requires each of the conserved amino acids within the LXCXE motif.
5172	11259609_MI:0397	Growth of cells 666 Elferink et al. containing the C-terminal truncated AhR constructs required cotransformation with pB42ADpRb
5173	17825065_MI:0397	Cac1p can also interact with Orc5p and Orc6p.
5174	17825065_MI:0397	Coexpression of a BD fusion of ORC5 (BD-ORC5) and an AD fusion of ORC4 (AD-ORC4) resulted in higher bgalactosidase activity than the vector-alone control
5175	17825065_MI:0397	Coexpression of a BD fusion of ORC5 (BD-ORC5) and an AD fusion of ORC4 (AD-ORC4) resulted in higher bgalactosidase activity than the vector-alone control (Fig. 1a). Expression of the opposite combination (BD-ORC4 and AD-ORC5) also resulted in higher b-galactosidase activity
5176	17825065_MI:0397	Mih1p can also interact with Orc2p, Orc3p and Orc5p.
5177	17825065_MI:0397	Orc5p also interacts with itself, as does Orc6p.
5178	17825065_MI:0397	We confirmed that full length Mih1p interacts with Orc6p.
5179	17825065_MI:0397	we finally selected Sir4p and Mad1p as Orc2p-interacting proteins
5180	17825065_MI:0397	we finally selected Sir4p and Mad1p as Orc2p-interacting proteins, Cac1p and Ykr077wp as Orc3p-interacting proteins
5181	17825065_MI:0397	we finally selected Sir4p and Mad1p as Orc2p-interacting proteins, Cac1p and Ykr077wp as Orc3p-interacting proteins, Rrm3p and Swi6p as Orc5p-interacting proteins,
5182	17825065_MI:0397	we finally selected Sir4p and Mad1p as Orc2p-interacting proteins, Cac1p and Ykr077wp as Orc3p-interacting proteins, Rrm3p and Swi6p as Orc5p-interacting proteins, and Mih1p as an Orc6p-interacting protein.
5183	17825065_MI:0397	we revealed strong interactions between Orc2p and Ord3p (2p-3p), Orc2p and Ord5p (2p-5p), Orc2p and Ord6p (2p-6p) and Orc3p and Ord6p (3p-6p) and weaker interactions between Orc1p and Ord4p (1p-4p), Orc3p and Ord4p (3p-4p)
5184	17825065_MI:0397	we used yeast two-hybrid analysis to examine the interaction between ORC subunits and to search for ORC-binding proteins. As well as the known Orc4p-Orc5p interaction, we revealed strong interactions between Orc2p and Ord3p (2p-3p)
5185	17825065_MI:0397	we used yeast two-hybrid analysis to examine the interaction between ORC subunits and to search for ORC-binding proteins. As well as the known Orc4p-Orc5p interaction, we revealed strong interactions between Orc2p and Ord3p (2p-3p), Orc2p and Ord5p (2p-5p)
5186	17825065_MI:0397	we used yeast two-hybrid analysis to examine the interaction between ORC subunits and to search for ORC-binding proteins. As well as the known Orc4p-Orc5p interaction, we revealed strong interactions between Orc2p and Ord3p (2p-3p), Orc2p and Ord5p (2p-5p),
5187	17825065_MI:0397	we used yeast two-hybrid analysis to examine the interaction between ORC subunits and to search for ORC-binding proteins. As well as the known Orc4p-Orc5p interaction, we revealed strong interactions between Orc2p and Ord3p (2p-3p), Orc2p and Ord5p (2p-5p), Orc2p and Ord6p (2p-6p)
5188	17825065_MI:0397	we used yeast two-hybrid analysis to examine the interaction between ORC subunits and to search for ORC-binding proteins. As well as the known Orc4p-Orc5p interaction, we revealed strong interactions between Orc2p and Ord3p (2p-3p), Orc2p and Ord5p (2p-5p), Orc2p and Ord6p (2p-6p) and Orc3p and Ord6p (3p-6p)
5189	17825065_MI:0397	Yeast two-hybrid analysis confirmed that full length Cac1p interacts with Orc3p
5190	8596950_MI:0397	Using quantitative yeast interaction trap system, We foundA evidence for direct physical interaction between Dsh and a fragment of N (Fig. 4) (44).
5191	14627543_MI:0398	The specificity of the interaction between VCY2IP-1 and VCY2 was further confirmed by testing interactions between specific proteins during yeast mating using two different yeast strains.
5192	15809031_MI:0399	Tea4-YFP colocalizes precisely with tea1-CFP both at cell tips and at MT plus ends (Figure 2B).
5193	15936270_MI:0399	Wsh3 is colocalized with Tea1. Furthermore, significant overlaps of cellular localization of Wsh3 and Tea1 were confirmed with a tea1:GFP strain in which the chromosomal wsh3+ gene was tagged with the RFP sequence (Figure 4C).
5194	11106648_MI:0400	Optimal binding of PTP1B to immobilized N-cadherin depends on phosphorylated tyrosine residues.
5195	11168407_MI:0400	Interaction of cysteine synthase complexes after coexpression of SAT and OAS-TL in E. coli.
5196	12620624_MI:0400	FliS bound comparably to full length FliC and N terminally truncated derivatives up to and including FliC&#916;1 400, but did not bind to any of the C terminally truncated derivatives (Fig. 2). Of the internally deleted variants only C&#916;408 425, C&#916;426 444 and less so C&#916;444 454 were bound by FliS ( Fig. 2 and Fig. 3).
5197	14732713_MI:0400	Interaction of Rapostlin-splicing variants with Rnd2 in a dot-blot assay.
5198	15316289_MI:0400	These binding tests demonstrated that the CaMBD of the AtBT1 protein binds to three conserved CaM isoforms
5199	18191225_MI:0400	PTRF binding to phosphatidylserine (PS) in a solid-phase assay.
5200	10531384_MI:0401	KCBP peptide retarded the mobility of AtCaM isoforms and bovine CaM compared with the free CaMs. These results show that all isoforms of Arabidopsis CaM bind to the KCBP peptide.
5201	10998188_MI:0401	This shows that pSSU binds strongly to atToc33&#916;C in the presence of GTP and therefore is sequestered from the assay. However, atToc34&#916;C binds only weakly to pSSU in the presence of GTP, as both proteins do without GTP. From our data we cannot exclude that the presence of GTP even disturbs the interaction of atToc34&#916;C with the pSSU precursor.
5202	12379796_MI:0401	As shown in Fig. 1, mixing of increasing molar amounts of the AtCstF-64 N-terminal domain with the octopine synthetase 3 terminator RNA resulted in progressively slower migration of the 32[P]-radiolabelled band in a native polyacrylamide gel. This could result either from interaction of the N-terminal domain of AtCstF-64 with several different regions of the octopine synthetase 3 terminator RNA or from multimerization of the protein, in a concentration-dependent manner.
5203	16275649_MI:0401	Inhibition of WNV Entry by Soluble WNV E DIII Protein
5204	17681130_MI:0401	unphosphorylated, but not the phosphorylated MBP-BZR1 showed DNA binding,
5205	9263453_MI:0401	Characterization of KI domain interacting kinase 1 (KIK1).
5206	9263453_MI:0401	To isolate maize kinase interaction domain-containing genes, we screened a maize leaf cDNA library at reduced stringency using the Arabidopsis KI domain as a hybridization probe. Approximately 3.2 x 105 plaques were screened and five positive clones identified. All positive clones corresponded to the maize homolog of KAPP; no other genes containing a KI domain were identified. The longestlength cDNA insert was sequenced and encodes the complete protein as shown by comparison to the Arabidopsis protein
5207	16280327_MI:0402	The results of the p65 ChIP assay indicated that TNFalpha induced a strong but shorter binding of p65 to the Bcl10 genomic fragment; in contrast, p65 bound to the IkappaBalpha genomic fragment for a longer period (Fig. 3A).
5208	16809346_MI:0402	both the anti-FoxM1 and anti-FoxO3a antibodies, but not the control antibodies (IgGs), precipitated the ER promoter regions containing the S1/S2, S4, and S6/S7 FHREs.
5209	17138694_MI:0402	SUF4 Binding to the FLC Promoter Region.
5210	17157259_MI:0402	This experiment confirmed that recruitment of both SNIP1 and p300 to the Cad promoter is c-Myc dependent (Figure 6D). Significantly, recruitment of p300 and SNIP1 was found to be interdependent: depletion of either protein resulted in reduced recruitment of the other, without a significant reduction in c-Myc promoter binding.
5211	17157259_MI:0402	Two antibodies raised against different domains of SNIP1 and a c-Myc antibody each immunoprecipitated the cyclin B1 and Cad promoter E box domains (Figure 3F) in control cells, but in c-Myc siRNA cells, promoter binding by both c-Myc and SNIP1 was greatly reduced.
5212	17202144_MI:0402	Interaction of Foxo1 and AR within the human PSA promoter.
5213	17704303_MI:0402	To address this possibility, we analyzed the recruitment of these two transcription factors to the endogenous Myogenin promoter by chromatin immunoprecipitation (ChIP) using specific antibodies to TAF3 and TRF3.
5214	17719542_MI:0402	ChIP analysis showed p53 association with p21 and HDM2 promoters in both intermediately and rapidly sedimenting gradient fractions, while p53 at PIG3 and p53AIP1 promoters was exclusively in the most rapidly sedimenting fractions (Figure 1C).
5215	17719542_MI:0402	Thus, there was a striking correlation between binding of hCAS/CSE1L uniquely to those promoters of p53 target genes (PIG3, p53AIP1, and p53R2) whose induction was reduced after hCAS/CSE1L downregulation.
5216	17719542_MI:0402	When anti-FLAG antibody (M2) was used to measure association of ectopic wild-type hCAS/CSE1L with the p53 binding site at &#8722;318 within the PIG3 promoter, there was a strong signal over the vector control (Figure 4C, lower panels).
5217	18022365_MI:0402	CHiP analysis of histone H3K18 acetylation (H3K18Ac) over the PHO84 locus
5218	18045535_MI:0402	those in the CD25 and CD69 genes are occupied by p65
5219	18045535_MI:0402	We found that precipitation of either p65 or RPS3 gave the same signal for the 200-300 bp region containing kappaB sites of two well-studied NF-kappaB target genes, IkappaBalpha and IL-8 (Figures 5A and S5).
5220	18045535_MI:0402	We found that the p65 occupancy of kappaB sites in the promoters of IkappaBalpha, IL-8, and IL-2 was markedly reduced in RPS3-knockdown cells
5221	18167341_MI:0402	BMPR1B promoter DNA from 0308 cells, but not from 0822 cells, was coimmunoprecipitated by both anti-EZH2 and anti-DNMT1 antibodies,
5222	18242510_MI:0402	identified a putative ETS2-binding site in the c-RAF promoter (Figure 7E). We demonstrated using chromatin IP (ChIP) that ETS2 and CDK10 bind to this site
5223	18267069_MI:0402	ChIP experiments revealed that following addition of rIGFBP7, SMARCB1 as well as BRG1, an essential subunit of the SWI/SNF complex (Bultman et al., 2000), were recruited to the BNIP3L promoter near the transcription start site (Figure 3G). Following knockdown of SMARCB1, BRG1 (and, as expected, SMARCB1) failed to associate with the BNIP3L promoter.
5224	18267069_MI:0402	ChIP experiments revealed that following addition of rIGFBP7 to SK-MEL-28 cells, STAT1 was recruited to the SMARCB1 promoter
5225	18267069_MI:0402	Chromatin immunoprecipitation (ChIP) analysis verified that JUN bound to the IGFBP7 promoter in response to BRAFV600E expression
5226	18287201_MI:0402	ChIP was carried out using inflorescence tissues obtained from genotypes as indicated. Chromatin immunoprecipitations carried out using anti-Myc antibody or normal mouse IgG serum. UFO specifically associates with both AP3 promoter regions, DEE and PEE; however, the presence of the lfy-26 mutation abolished these interactions, indicating that LFY is required for UFO to associate with AP3 promoter sequences.
5227	18287201_MI:0402	Chromatin immunoprecipitation (ChIP) was performed with anti-FLAG antibody or mouse normal IgG serum from inflorescence tissue of plants of the indicated genotypes. Promoter regions from AP1 and AP3 were amplified using PCR as indicated. A region of the Mu transposon was used as a positive control for amplification. LFY specifically associates with both the DEE and PEE elements of the AP3 promoter, as well as with the AP1 promoter fragment. The ufo-2 mutation does not compromise the ability of LFY to bind to target sequences. (Right) DEE and PEE levels were normalized to Mu and the fold change of experimental IP over IgG control IP is indicated. The values are mean±s.e.m. from three PCR experiments
5228	18316612_MI:0402	both p65 and AEG-1 associated with the IL-8 promoter.
5229	18394558_MI:0402	the activating E2F1 transcription factor was indeed bound physically to the p18INK4C promoter
5230	18408765_MI:0402	chromatin immunoprecipitation (ChIP) assays demonstrated that the binding of FOXO1-A3 but not FOXO1-A3/S249A to the promoter of the Bim gene was largely inhibited in cells transfected with CDK1-AF and cyclin B1
5231	18485870_MI:0402	As expected, immunoprecipitation with the p53 antibody showed that an increasing amount of p53 associated with the p21 promoter (Figure 6B); conversely, although the levels of Mdm2 were elevated (Figure 6A), the recruitment of Mdm2 to the p21 promoter by p53 was severely inhibited when p53 was acetylated (Figure 6B).
5232	18485870_MI:0402	nterestingly, coexpression of the CBP and Tip60 acetylases with wild-type p53, which led to increasing levels of p53 acetylation (lane 4, Figure 4B)
5233	18485870_MI:0402	Pirh2 as another p53 target (Leng et al., 2003), whose induction by p53 is independent of the acetylation status (Figure S10).
5234	18485870_MI:0402	The occupancy of p53, Mdm2, Mdmx, CBP, and Tip60 of the p21, Pig3, and Mdm2 promoters was detected by PCR-agarose gel electrophoresis.
5235	18485870_MI:0402	To elucidate the mechanism of p53 acetylation in p21 activation in cells, we performed chromatin immunoprecipitation (ChIP) assays with cells expressing either wild-type or acetylation-defective p53 proteins.
5236	18510931_MI:0402	in chromatin immunoprecipitation (ChIP) assays of genomic DNA using the endogenous Mix.2 promoter (Figure 5E), the specific binding of p53 to this site was augmented by coinjection of XFDL-MO (compare lanes 3 and 4) and suppressed by XFDL overexpression
5237	18598942_MI:0402	Chromatin immunoprecipitation (ChIP) analyses demonstrated that LEDGF colocalizes with MLL/menin complexes at target sites within HOXA, MEIS1, and CDKI genes
5238	18614011_MI:0402	we were able to detect physical association of p53 with the CD44 promoter sequence in BPEC-T cells.
5239	imex:IM-11846_MI:0402	the mouse Rad51 promoter was PCR-amplified from ChIP products of Pten+/+ MEFs
5240	imex:IM-11846_MI:0402	the PTEN-bound Rad51 promoter was detected from chromatin of PC-3 cells
5241	imex:IM-11846_MI:0402	the Rad51 promoter was amplified from the anti- E2F-1 antibody immunoprecipitates from E2F-1+/+ MEFs
5242	imex:IM-11909_MI:0402	CLOCK and BMAL1 are recruited to E-box elements in the Dbp gene in a time-dependent manner (Figure 4D).
5243	imex:IM-11909_MI:0402	Importantly, we found that SIRT1 is jointly recruited to the same E-box elements in the Dbp gene.
5244	imex:IM-11926_MI:0402	Ronin binds to the 3x sequence present in the promoter regions of GATA4 and GATA6.
5245	imex:IM-11926_MI:0402	we also identified a putative DNA-binding sequence for Ronin in the promoter region of Oct4, and indeed Ronin did bind to this region, but only in differentiated ES cells;
5246	imex:IM-12146_MI:0402	However, when RUNX3 was stably expressed in DLD1 cells, &#946;-catenin/TCF4 binding to either promoter was greatly reduced (Figure 3A, lanes 3 and 6, and Figure 3D
5247	imex:IM-12156_MI:0402	Endogenous SIRT6 is recruited to the promoters of NF-&#954;B target genes.
5248	imex:IM-12156_MI:0402	In response to TNF-&#945;, FLAG-SIRT6 was detected at the promoters of several NF-&#954;B target genes, including IAP2, MnSOD, ICAM, and NFKBIA
5249	imex:IM-12156_MI:0402	Shown is Sirt6 occupancy (mean +/- s.e) at the Birc3 (murine homologue to IAP2) and Il1rl1 promoters relative to untreated control samples.
5250	11248038_MI:0404	In contrast, when HSP17 was incubated at 47°C in the presence of increasing amounts of denaturing MDH, the two proteins formed increasing and saturating amounts of gel-electrophoresis-resistant oligomers, which were larger than 800 kDa at the expense of the initial low molecular mass species (Fig. 1).
5251	16230339_MI:0404	complex of SC-(1-325) and FPR-CH2Cl-substituted thrombin was band-shifted in the presence of both human (Fig. 4B) and bovine Fbg
5252	16303767_MI:0404	In vitro formation of E1-substrate intermediates between Atg7 and the three human Atg8 homologs.
5253	16303767_MI:0404	In vitro formation of E2-substrate intermediates between Atg3 and the three human Atg8 homologs.
5254	16321984_MI:0404	Lanes 2, 5, and 8 are 1PI complexes of trypsin, PPE, and HNE, respectively, before incubation.
5255	17137328_MI:0404	In line 3 complex, RL1 and RL9 disappeared.
5256	17137328_MI:0404	Line 1 complex included seven proteins, in which OmpW, Slp, and YbjP are OMPs; YdgA is an IMP and may function in the periplasmic space as a dimer;18 and Frd flavoprotein subunit (FrdA), Frd iron-sulfur protein (FrdB), and pyruvate dehydrogenase (Odp1) are not membrane proteins annotated from the Swiss-Prot database.
5257	17137328_MI:0404	Line 2 complex included D-methionine-binding lipoprotein (MetQ), and aerobic glycerol-3-phosphate dehydrogenase (GlpD) and glutamate decarboxylase alpha (DceA), respectively,
5258	17137328_MI:0404	Line 3 complex consisted of four IMPs or peripheral membrane proteins, ATP synthase alpha chain (AtpA), ATP synthase beta chain (AtpB), D-amino acid dehydrogenase small subunit (DadA), and dehydroorotate dehydrogenase (PyrD), and two cytoplasimic proteins ribosomal proteins, 50S ribosomal protein L1 (RL1) and 50S ribosomal protein L9 (RL9).
5259	17137328_MI:0404	Out of the seven proteins in line 1 complex, Slp and YbjP moved to line 2; Odp1, FrdA, FrdB, and OmpW disappeared from the gel; and only YdgA kept at the same location.
5260	17314099_MI:0404	As shown in Fig. 2D, a shift in the mobility of autophosphorylated NM23-H1 was clearly evident upon incubation in the presence of wild-type STRAP
5261	19135891_MI:0404	As a result of the separation of MukF C-WHD from MukBhdEQ, this reaction generated five new complexes as shown on a native gel (Figure 6A; bands 1,2,3,5,6), which were subsequently identified as 1:4, 1:3, 1:2, 1:1 and 1:0 complexes between MukEF and MukBhd
5262	19135891_MI:0404	Detachment of hMukE-hMukF(M+C) from dimerized MukB heads in solution.
5263	imex:IM-11908_MI:0404	Fluorescence intensities of bands corresponding to Ubc1~Ub product were quantified using the Odyssey program.
5264	imex:IM-11908_MI:0404	Uba1 (1.0 &#956;M) was incubated with Ub (4
5265	imex:IM-12140_MI:0404	spontaneous formation of the Sm subcore was observed upon incubation of D1/D2 and E/F/G with U1snRNA
5266	imex:IM-12140_MI:0404	spontaneous formation of the Sm subcore was observed upon incubation of D1/D2 and E/F/G with U1snRNA, which is matured into the snRNP core upon addition of D3/B (Figure 2E, lanes 2 and 3).
5267	10077571_MI:0405	Displacement en passant of labeled GroES7 by unlabeled GroES7 added after initiation of electrophoresis.
5268	12869544_MI:0405	At 100 nM [{alpha}-32P]GTP both Toc33-wt and Toc33-R130A bound [{alpha}-32P]GTP with similar efficiency (Fig. 2A). The binding appeared to be specific as a bovine serum albumin control failed to retain [{alpha}-32P]GTP. These results suggest that both Toc33-wt and Toc33-R130A bind GTP with high affinity.
5269	15525938_MI:0405	The affinity of Set9 for putative peptide substrates derived from the sequences of either the H3 tail or p53 was determined by competition binding studies against an N-terminal dansyl-labelled H3 10-mer peptide
5270	16230338_MI:0405	Competitive binding of SC-(1-325) to native bovine ProT and human [OG]FPR-ProT.
5271	16230340_MI:0405	Competitive binding of SC-(1-325) to native ProT and [OG]FPR-ProT.
5272	16257968_MI:0405	competition of Malt-BP1 for binding of radiolabeled FGF-2 to immobilized full-length recombinant FGF-BP1
5273	16275649_MI:0405	Recombinant WNV E DIII Protein Interacts with 
V3 Integrin
5274	16293613_MI:0405	The total cellular expression of transfected receptors was compared with wild type using radioligand binding analyses.
5275	16319056_MI:0405	Saturation binding analysis of biotinylated Glu-plasminogen to immobilized recombinant PAM variant proteins.
5276	16525503_MI:0405	Competition assays with the peptides BP-E4B (SADEIRRRRLARLAG, aa 5-19) and BP43 (Figure 4A) were performed and the association between VCP and E4B was analyzed by immunoblotting (IB). As shown in Figure 4F, both peptides prevented the interaction between E4B and VCP in vitro
5277	16525503_MI:0405	To test whether BP43 can specifically inhibit the VCP-Atx-3 interaction, competition assays were performed (Figure 4B). Indeed, the addition of soluble BP43 to binding reactions completely abolished the interaction between His-VCP and GST-Atx22Q (Figure 4B, lane 3)
5278	17662946_MI:0405	Displacement assay of cell-bound 125I-SCF using native SCF. 3T3 cells expressing WT (), R381A (down triangle, filled), R381A/E386A (), or a kinase-negative KIT (up triangle, filled) were treated with 125I-SCF in the presence of increasing concentrations of native SCF.
5279	17951432_MI:0405	indicating that AtGPA1 is selective toward guanine nucleotides and is a bona fide GTPbinding protein.
5280	18555774_MI:0405	To confirm competition, we incubated mEphA4Ex-V5His and hVAPMSP-His proteins together with EphrinB2 protein.
5281	18617507_MI:0405	RCC1 increased the amount of GTP bound to Ran, in both a time and a RCC1 dose dependent way, but neither of them was affected by incubation in the presence of VRK1 (Fig. 8B).
5282	18617507_MI:0405	RCC1 induced a dose dependent release of GDP that was not affected by VRK1 (Fig. 8A).
5283	10220385_MI:0406	The gel then was exposed to autoradiography to determine the relative amount of acetylated histones remaining in each case. HDAC1, HDAC4, HDAC5, and HDAC6 deacetylate all four core histones equally well, though again deacetylation by HDAC4 and HDAC5 is incomplete
5284	imex:IM-11909_MI:0406	SIRT1 deacetylates BMAL1(K537) in vitro.
5285	16275649_MI:0410	Binding force between WNV E DIII protein interactions with the 
V3 integrin molecule.
5286	10383400_MI:0411	B, the V1 variable domains of theta PKC and delta PKC were compared for ability to bind MBP-p59fyn.
5287	10383400_MI:0411	To further establish that theta PKC can bind to p59fyn, purified recombinant constructs were used in a 96-well microplate binding assay (Fig. 2)
5288	10393905_MI:0411	Representative binding results between GST fusion proteins (GST, KID119, and KID239) and MBP fusion proteins [MBP (&#9679;), RLK5 (&#9675;), CLV1 (&#9632;), KIK1 (&#9652;), and K558E (&#9662;)] by ELISA
5289	11919189_MI:0411	To confirm the direct interaction of nm23-H2 with ICAP-1alpha , we carried out an ELISA-based solid phase binding assay
5290	14507921_MI:0411	PA-ATR binding requires specific divalent cations and the MIDAS of the receptor.
5291	15377662_MI:0411	The p85 protein bound directly to Rab5 in a concentration-dependent manner
5292	16272158_MI:0411	E. shows interaction of different PAI-1 forms with AGP analyzed by a solid phase binding assay.
5293	16288713_MI:0411	Consistent with this observation, the &#946;-subunit specifically interacts with the purified eIF2B in ELISA studies
5294	16288713_MI:0411	Interaction between and among the recombinant subunits of human eIF2 in vitro
5295	16288713_MI:0411	Interaction between reconstituted eIF2 trimeric complex and purified eIF2B.
5296	16446437_MI:0411	ELISA detection of recombinant Tau-A&#946;1-42
5297	17222790_MI:0411	Anti-NRP1B strongly blocked VEGF binding to NRP1 and ECs, whereas anti-NRP1A did not
5298	17662939_MI:0411	In contrast, InlB321 bound with high- and virtually identical affinity to longer variants of the Met ectodomain (Met741, Met838, and Met928) that contain two, three, or four immunoglobulin (Ig)-like domains, respectively (Figure 1F).
5299	17662939_MI:0411	InlB241 and InlB321 bind to Met928 with identical apparent affinity in a solid phase binding assay.
5300	17875722_MI:0411	In an ELISA assay, pDI inhibited MDM2-p53 and MDMX-p53 interactions with IC50 of 10 and 100 nmol/L respectively,
5301	17981115_MI:0411	anti-PlGF inhibited the binding of PlGF to VEGFR-1 (IC50: 27 pM)
5302	17981115_MI:0411	As measured in ELISA blocking assays, antiPlGF did not inhibit binding of PDGF-BB to PDGFR-beta
5303	17981115_MI:0411	FGF2 binding to FGFR2(IIIc)
5304	17981115_MI:0411	HGF binding to Met
5305	17981115_MI:0411	Using a blocking ELISA assay, anti-PlGF did not inhibit the binding of VEGF to VEGFR-2
5306	imex:IM-12129_MI:0411	We tested the ability of DscamR496W mutant proteins to engage in homophilic binding in vitro using an enzyme-linked immunosorbent assay (ELISA)-based binding assay (Wojtowicz et al., 2007).
5307	11891322_MI:0412	anti-GFP antibody supershifts the dimer/DNA complex
5308	12674497_MI:0412	(B)Binding of 6xHis-NSAP-1 to the AU-rich RNA oligonucleotide.
5309	12674497_MI:0412	Binding of 6His-AUF1 to the AU-rich RNA oligonucleotide.
5310	12674497_MI:0412	Binding of GST-IMP-2 to the AU-rich RNA oligonucleotide.
5311	12674497_MI:0412	Binding of GST-NSEP-1 to the AU-rich RNA oligonucleotide.
5312	12674497_MI:0412	Binding of GST-UBCE2I to the AU-rich RNA oligonucleotide.
5313	18287201_MI:0412	LFY and UFO physically interact. (A) UFO induces a supershift of a LFY-DNA complex. Electrophoretic mobility shift assay (EMSA) using an AP3 promoter sequence. BMV, non-specific brome mosaic virus control; LFY, in vitro transcribed and translated LFY protein; UFO, in vitro transcribed and translated UFO protein; LFY+UFO lane shows a supershift of the LFY-DNA complex, while UFO alone does not bind to the AP3 promoter sequence, indicating that UFO binds to the LFY-DNA complex.
5314	18485870_MI:0412	this complex was either supershifted by the p53-specific antibody or blocked by the Mdm2-specific antibody
5315	18614011_MI:0412	we demonstrated direct binding of p53 protein to the CD44 promoter sequence
5316	imex:IM-12048_MI:0412	Nuclear NF-B DNA binding activities (arrows and arrowhead) induced by 1 ng/ml of TNF, 10 g/ml or 0.3 g/ml of LT R agonistic antibody were resolved by EMSA with a B-site containing probe.
5317	imex:IM-12048_MI:0412	Nuclear NF-B DNA binding activities (arrows and arrowhead) induced by 1 ng/ml of TNF, 10 g/ml or 0.3 g/ml of LTR agonistic antibody were resolved by EMSA with a B-site containing probe.
5318	10490612_MI:0413	Incubation of the probe with crude insect cell lysates from cells coinfected with baculovirus vectors expressing Swi4 and Swi6 led to the formation of a major complex that comigrated with SBF from yeast extracts (Fig. 2, lane 6).
5319	10490612_MI:0413	Swi4Delta 144 formed a specific complex with DNA that was efficiently competed by wild-type but not by mutated SCB-containing DNA (Fig. 4B, lanes 4, 6, and 7)
5320	10659709_MI:0413	Binding of TGA2 and TGA3 to the TGACG-containing fragment of the PR-1 promoter.
5321	11275986_MI:0413	we performed electrophoretic mobility shift assays and found that DNA binding activity of p53 was abolished by adding increasing amounts of in vitro translated HPV-16 E6, whereas that of p73 was not affected by E6
5322	11431700_MI:0413	incubation of both Tbx5 and Nkx2-5 with the DNA fragment produced a larger shifted band
5323	11431700_MI:0413	Nkx2-5, as well as Tbx5 binds to the DNA fragment of bp -254 to -236
5324	11431700_MI:0413	Tbx5 bound to the fragment of bp -254 to -227, and the DNA fragment corresponding to the sequence of bp -254 to -236
5325	11891322_MI:0413	Under the assay conditions, Myc/Max dimers, but not Max/Max homodimers efficiently bound DNA, resulting in a single retarded band in electrophoresis
5326	12072504_MI:0413	In this approach, the REMSA was performed on the 32P-labeled viral transcript following incubation with rabbit reticulocyte lysate. A parallel sample containing proteinase K was run as a control. Figure 2C, lane 2, shows the presence of an mRNA-protein complex that could be detected following 5% PAGE. No gel shift signal was evident when the reaction mixture was supplemented with proteinase K (Fig. 2C, lane 3), documenting the protein nature of the complex. No protein complex was evident when c-myc or eIF-4E mRNA was used (Fig. 2A and B, respectively, lane 2).
5327	12072504_MI:0413	The peptide binding sequence was further investigated by synthesizing three biotinylated 6-mer peptides changed at the three invariant positions S52, Q54, and K56, i.e., GEQIKA, SELIKA, and SEQILA, with the changed residues in italics. The three substituted 6-mer peptides were then used in the PEMSAs reported in Fig. 7C. It can be seen that the K amino acid residue was essential for peptide binding to HPV16 E7 mRNA.
5328	12072504_MI:0413	To gain some preliminary insights into the mode of rabbit {alpha}1-globin52-57/human CK791-96 SEQIKA action, I tested the mRNA-binding ability of hemoglobins having double and triple amino acid substitutions inside the {alpha}1-globin52-57 motif. Table 2 describes the hemoglobins that were assayed. It can be seen that the common {alpha}1-globin52-57 motif is the sequence SXQXKX, where S52, Q54, and K56 are invariant amino acid residues in the hemoglobins analyzed. Then, the hemoglobins described in Table 1 were tested by REMSA performed on the 32P-labeled viral transcript. Figure 7A illustrates that all of the hemoglobins listed in Table 1 were able to bind HPV16 E7 mRNA, indicating that the conserved globin motif S52-Q54-K56 was sufficient for the interaction with the transcript. Anti-p32 PAbs suppressed hemoglobin binding to HPV16 E7 mRNA (Fig. 7B).
5329	12084833_MI:0413	The TGA2CT mutant could no longer bind to the as-1 element, as demonstrated by a gel mobility shift assay
5330	12124176_MI:0413	Compared to the wild-type protein, the hMSH2(P622L)- hMSH6 and hMSH2(R524P)-hMSH6 proteins failed to elicit a spethe cific gel shift of the labeled G/T mispair (Figure 2A). These results suggest that the hMSH2(P622L)-hMSH6 and hMSH2(R524P)- hMSH6 proteins confer a fundamental defect in mismatch rec- ognition.
5331	12657652_MI:0413	EMSA experiments shown in Fig. 4C, display the binding behavior of different amounts of AtbZIP10 or O2 proteins incubated with target DNA sequences. A clear increase in the binding of both proteins to their target sites was obtained in the presence of ABI3
5332	12657652_MI:0413	In Fig. 4B the results of EMSA demonstrate that the AtbZIP10 and AtbZIP25 binding to these sequences occurs specifically through the ACGT boxes, since mutations (AaGg) introduced at this core abolished the interaction in the context of both At21S and CRU3 promoters.
5333	16002617_MI:0413	CDF1 protein binds to both fragments but exhibited a 10-fold greater preference for the -173/-135 fragment over the -397/-358 fragment (Fig. 4F).
5334	16280327_MI:0413	EMSA was used to verify that the core sequence responsible for NF-kappaB binding resides in the BCL10 or I-kappa-Balpha gene.
5335	16319058_MI:0413	To test whether the defect in nuclear translocation of NF-B was associated with impaired formation of NF-B-DNA complexes, nuclear extracts from CHO-IR cells were subjected to EMSA to detect NF-B complexes bound to a consensus B probe.
5336	16339759_MI:0413	Sp3 and Sp1 independently bind to the KCS element. A, EMSA supershift analysis of constitutive protein binding to the KCS element of the PKR promoter.
5337	16428600_MI:0413	The ZF-HD ATHB33 protein binds to a core consensus sequence of ATTA
5338	16429262_MI:0413	Electrophoretic mobility shifts indicate specific interaction of a complex with the GCC box.
5339	16603654_MI:0413	As shown in Figure 6B, combining WRKY18 and WRKY40 in the binding reactions generally produced much higher intensities of the retarded bands than the single WRKY18 or WRKY40 protein.
5340	16603654_MI:0413	By contrast, when WRKY40 was mixed with WRKY60, less DNA binding of WRKY40 was observed
5341	16603654_MI:0413	To test the DNA binding activities of WRKY40 and WRKY60, we generated recombinant proteins in Escherichia coli and tested each for in vitro binding activity to a DNA molecule with a W-box sequence (Figure 5A). When the same amount of WRKY18 and WRKY40 was used in these binding assays, the intensities of the retarded bands were substantially higher with WRKY40 than with WRKY18
5342	17234752_MI:0413	Binding of Topo to NKX3.1 is of sufficiently high affinity to compete NKX3.1 from its cognate DNA sequence at a Topo I/NKX3.1 molar ratio as low as 2:1
5343	17234752_MI:0413	This interaction was suggested by an EMSA using the 50-mer Tetrahymena sequence as a probe and purified proteins. The amount of NKX3.1 used in this assay alone did not bind to the Tetrahymena 50-mer probe (data not shown). However, NKX3.1 enhanced Topo I binding as shown by the increasing intensity of the two species formed by Topo I and the DNA probe and the depletion of the probe-alone band. Moreover, a supershifted complex can be seen, suggesting the formation of a complex of probe, Topo I, and NKX3.1
5344	17482134_MI:0413	Gel-shift analysis demonstrated the ability of c-Jun to bind to an oligonucleotide containing the AP-1 site
5345	17513757_MI:0413	To test whether the phosphorylation of KLF13 by PRP4 affects its interaction with the CCL5 promoter, EMSA was performed using a {gamma}-32P-end-labeled oligonucleotide derived from the A/B region of the CCL5 promoter.
5346	17587183_MI:0413	Again, MEKK1 was able to form a DNAprotein complex with the WRKY53 promoter fragment which could be competed with an excess of specific unlabelled competitor DNA but not with an excess of unspecific competitor indicating the specificity of the DNA-protein interaction
5347	17623278_MI:0413	After cleavage with TEV protease, the Prep1-CBP (Prep1CBP) eluate formed DNA-binding complexes with endogenous Pbx1b or Pbx2 (Fig. 1E) which were inhibited by Prep1, Pbx1b, or Pbx2 antibodies (Fig. 1E).
5348	17637675_MI:0413	It is noteworthy that these two boxes are the target binding sites of MYC2. This transcription factor specifically recognizes the G-box (and T/Gbox) sequence in the promoter of JAI3 (and also present in the promoters of other JAZ genes; Supplementary Table 2), but does not recognize the mutant versions lacking the G- or T/G-boxes
5349	17644729_MI:0413	Previously, it has been shown by gel mobility shift experiments that WER binds to the GL2 MYB binding site (GL2MBS1 [GACTAACGGTAAG])
5350	17960875_MI:0413	Moreover, we found that the HIPK2-phosphorylated HMGA1a reduced the binding affinity of HMGA1a to human germ line epsilon promoter
5351	17981120_MI:0413	Binding of SCR and SCR mutants to fkh250 and fkh250con DNAs
5352	18083099_MI:0413	Both Cps35p and Cps60p are recruited to the coding sequence of the active GAL1 gene
5353	18083099_MI:0413	Histone H3K4-dimethylation at the GAL1 coding sequence is lost in deltaset1.
5354	18083099_MI:0413	we performed similar ChIP studies on two constitutively active genes, ADH1 and PHO84 (Figure 5D and 5E)
5355	18485870_MI:0413	An EMSA was then used to examine whether Mdm2 can form a protein complex with DNAbound p53.
5356	18485870_MI:0413	As shown in Figure 2D, p53/DNA complexes were obtained by incubation of highly purified, recombinant full-length human wild-type p53 with a radiolabeled probe containing the p53-binding site from the p21 promoter.
5357	18571510_MI:0413	Subsequently, the DNA-binding activity of the two fractions was assessed by electrophoretic mobility shift assay (Fig. 1C), which shows that 10ng of either input or eluted TGA2 protein bound the LS7 DNA probe (lanes 3 and 5), whereas TGA2 from the flowthrough fraction failed to bind probe
5358	18587275_MI:0413	OBF4 binds to the FT promoter.
5359	18599455_MI:0413	Using the same conditions, ARF2 could bind to the SAUR-15 promoter, and preincubation with BIN2 greatly reduced DNA binding activity (Fig. 3A). The addition of BES1 did not alter ARF2 interaction with DNA (Fig. 3A). BIN2-dependent inhibition of ARF2 DNA binding required ATP and functional kinase activity as shown by the kinase-dead [K69R] BIN2 control (32). This finding suggests that BIN2 effects on ARF2 occurred via phosphorylation.
5360	18805088_MI:0413	When ParB was mixed with two labeled DNA probes, a 614 base pair sequence containing two tandem parS sites and a 435 base pair sequence with no parS sites, only the parS-containing sequence was shifted to a higher molecular weight form
5361	18805088_MI:0413	When PopZ was added to the reaction, the band corresponding to the parS-ParB complex was shifted to a higher molecular weight form indicative of a ternary parS-ParB-PopZ complex (Figure 3E, lane 3).
5362	19135891_MI:0413	The triple complex of hMukE-hMukF(M+C)-hMukBhdEQ and its variants containing the indicated mutations on hMukBhdEQ were reacted with ATP and mixed with the pBR322 plasmid.
5363	8372350_MI:0413	Cotranslation of Mbpl and Swi6 not only decreased the amount of binary Mbp1-DNA complexes but also generated new protein-DNA complexes which comigrate with MBF from yeast (Fig. 4B, lane 6).
5364	8372350_MI:0413	The NH2-terminal 124 residues of MBP1 were translated in vitro and tested for binding to the TIMP1 promoter.
5365	8805366_MI:0413	We carried out mobility-shift experiments to examine binding of purified MSH2 and MSH2-MSH3 to 32P-labeled DNA duplexes containing a loop that was 2, 4, 8 or 14 nucleotides in length (designated +2, +4, +8 and +14, respectively) and located in the middle of the duplexes (Figure 2a).
5366	9396801_MI:0413	A gel mobility shift assay was used for this purpose. First, two types of DNA substrates were utilized: (i) a single-stranded 83mer oligonucleotide, and (ii) linearized 6.4 kb double-stranded DNA of M13 phage. Indeed, we found that both 23.3 and 31.4 kDa forms of Pir51 protein bound both types of DNA in our assay (Figs 6 and 7B).
5367	9659918_MI:0413	HY5 Binds Specifically to the Light-Responsive Unit 1 Region (U1) of a CHS1 Promoter
5368	9724822_MI:0413	CKB1 also enhanced DNA binding activity of CCA1 in the same way
5369	9764821_MI:0413	A control of mouse MYC with mouse MAX was included to demonstrate the MAX homodimer and MYC/MAX heterodimer shifts
5370	9764821_MI:0413	MDL-1 could dimerize with mouse MAX and bind to the CACGTG sequence in an EMSA (Figure 2b), although the DNA binding activity of this interspecies heterodimer was much weaker than the intraspecies MDL-1/MXL-1 heterodimer
5371	9764821_MI:0413	When the MDL-1 binding reaction was supplemented with full length MXL-1 protein, a complex formed that bound tightly to the vertebrate MYC/MAX consensus sequence oligonucleotide
5372	9801140_MI:0413	In EMSA analyses, we exploited the capacity of AtHSF1 to bind to consensus HSE and not to mutated HSE, leading to specic AtHSF1:HSE complexes
5373	imex:IM-11882_MI:0413	Analysis of chromatin immunoprecipitation (ChIP) samples by quantitative PCR showed that the WDR5 siRNA reduced TBP association to the HMG-CoA reductase but not to the fibronectin core promoter (Figure 2C).
5374	imex:IM-11882_MI:0413	An extensive ChIP analysis of TBP and TAF1 binding was performed for the RPL34, RPL31, and RPS10 genes by scanning their 5&#8242; regions using different PCR primer pairs (Figures 2D, 2E and S6).
5375	imex:IM-11952_MI:0413	The ability of DprA to bind oligonucleotides of various size and sequence was tested by electro mobility shift assay (EMSA). DprA interacted with a 90-mer poly-dT (dT90)
5376	imex:IM-11952_MI:0413	The ability of DprA to bind oligonucleotides of various size and sequence was tested by electro mobility shift assay (EMSA). DprA interacted with a 90-mer poly-dT (dT90) (Figure 2B) as well as with an 80-mer of random sequence
5377	imex:IM-11952_MI:0413	To determine whether DprA and its B. subtilis counterpart, Smf, require a free end for binding, we investigated their interaction with circular FX174 (FX) ssDNA. When increasing concentrations of the proteins were added to FX ssDNA, the mobility of ssDNA in native agarose gels decreased progressively
5378	imex:IM-11998_MI:0413	the CG-1 domain of dCAMTA bound specifically to a DNA fragment that contains a CGCG box
5379	imex:IM-12004_MI:0413	The C/EBPa-DNA binding activity was markedly reduced by Trib2 (Figure 5E, lanes 1 and 3), with the specificity of the observed gel shift being confirmed by production of a supershift upon addition of an antibody against C/EBPa
5380	imex:IM-12132_MI:0413	EMSA DNA-binding analysis of pfMre11 dimerization variants.
5381	10428848_MI:0415	The instructive finding was that Cet1(276-549)p also retained full triphosphatase function in vitro (Fig. 4B).
5382	10805743_MI:0415	Rai1p stabilizes the exoribonuclease activity of Rat1p in vitro.
5383	10982829_MI:0415	mutant Stat3 which lacks the N-domain and helix a1 (b-ST3-DN1H) and full-length Stat3 (b-ST3-FL) were expressed and purified in the baculovirus expression system. The recombinant proteins were phosphorylated with Src kinase in vitro, and tyrosine phosphorylation and DNA-binding activity were examined. As shown in Fig. 6, strong Tyr phosphorylation by Src was detected in both the wild type and the deletion mutant.
5384	12482963_MI:0415	Approximately equimolar amounts of Isw1p monomer and Isw1a or Isw1b complex (as determined by normalizing the Isw1p subunit in silver-stained SDS-PAGE gels) were assayed for ATPase activity in the presence or absence of nucleosomes.
5385	12876288_MI:0415	Stimulation of sufS cysteine desulfurase activity by sufE
5386	12876288_MI:0415	SufS cysteine desulfurase activity.
5387	12878161_MI:0415	TRIM5delta exhibited E3 activity toward itself in vitro in a reaction that was RING dependent and required UbcH5B
5388	12887903_MI:0415	For cocrystallization, an H3 peptide residues 1 to 15 was added at a final concentration of 2 mM to purified DIM-5 protein
5389	14871493_MI:0415	Unlike the results obtained previously, using these same ferredoxins as electron donors to spinach glutamate synthase [41], E94K and E95K charge-reversal variants of Anabaena ferredoxin were both much impaired in their ability to serve as electron donors to Synechococcus nitrate reductase (Table 1), even though the effect with the E94K variant (with a relative activity of 19% of the wild-type control) was somewhat greater than that observed with the E95K variant (with a relative activity of 38% of the wildtype control).
5390	15138274_MI:0415	Surprisingly, Elongator retained in vitro HAT activity directed against H3 even in the absence of Elp2.
5391	15525938_MI:0415	Set9 methylated the tumour suppressor protein p53 in vitro
5392	15525938_MI:0415	We found that Set9 methylated lysine 372
5393	15665379_MI:0415	Mal3 strikingly stimulates the rate of ATP hydrolysis for T2NM and T2NMC1at subsaturating levels of MTs but has little effect on the kcat value at saturation as indicated in Fig. 3. The magnitude and rate of onset of the activation are illustrated in Fig. 4.
5394	15741320_MI:0415	Figure 3 shows that HFR1 was polyubiquitinated by COP1 E3 ligase in a reaction dependent on E1 and E2 activities.
5395	15901727_MI:0415	Activation of CsdA cysteine desulfurase activity by CsdE
5396	15935327_MI:0415	Incubation with -calpain rapidly cleaved GST-DSCR1.4 fusion protein into multiple fragments of a molecular mass that ranged from 40 to 12 kDa (Fig. 3A, lane 2) within 5min.
5397	16230340_MI:0415	Proteolytic cleavage of ProT in the presence of SC
5398	16272578_MI:0415	His6-tagged HDAC-6 proteins could be purified as single protein and equal amount of wild type and mutant proteins were used for activity assays (Fig. 1C, left panel). As shown in Fig. 1C, right panel, the HDAC and TDAC activity of HDAC-6 is intrinsic and requires both intact catalytic cores.
5399	16272578_MI:0415	point mutations in the catalytic core of both hdac domains (HD1/2m) completely abolished the HDAC and the TDAC activities of HDAC-6. Surprisingly, mutating either of the hdac catalytic cores (HD1m or HD2m) also destroyed the whole activity on both substrates. This suggests that the cooperation between the two hdac catalytic cores is critical for the deacetylation reaction mediated by HDAC-6. Interestingly, the mutations in the presumed substrate recognition region (7) led to somewhat different effects on enzymatic activities. The mutation in the second substrate recognition site (L798A) completely inactivated the catalytic activity on both peptides, whereas the mutation of the corresponding region in the first hdac domain (L402A) retained partial activity
5400	16275660_MI:0415	CHIP efficiently stimulated the ubiquitination of caytaxin, indicating that the protein is a substrate for the E3 ligase activity of CHIP and that the interaction between both proteins could be important for regulation of caytaxin turnover in vivo.
5401	16286470_MI:0415	We next performed an in vitro assay to verify that the E3 activity of SCFSkp2 directs MKP-1 ubiquitination.
5402	16362057_MI:0415	We analysed its site specificity using histone substrates radiolabelled at all known methylated sites in histones H3 (K4, K9, K27, K36, K79) and H4 (K20, R3). Of the seven substrates, only H3-K36 methylated by Set2 was a substrate for JHDM1A
5403	16368681_MI:0415	We found that both AAxxAA
CxxC and ACxxCA
AxxA   have large defects in promoting RNase A folding when compared with wild-type PDI under conditions in which the number of active sites are matched (Fig. 2B).
5404	16368681_MI:0415	We matched the rate of RNase A oxidation by ERp57 and Ero1p to the rate with PDI and Ero1p by either altering ERp57 levels (data not shown) or using more Ero1p (Fig. 6D).
5405	16374505_MI:0415	Trf5-TAP reproducibly showed poly(A) polymerase activity.
5406	16603259_MI:0415	The effect of ADA2b on acetylation of histones by gcn5 is accessed.
5407	17081977_MI:0415	Although Rho411 is down ~6-fold in overall activity, its ATPase is activated by long RNAs.
5408	17098746_MI:0415	The FBXO11 complex was able to promote the neddylation of p53 under these conditions (lane 2).
5409	17314099_MI:0415	NDP kinase activity was assayed in the presence of purified wild-type and mutant NM23-H1 proteins
5410	17719543_MI:0415	As for Smurf2, wild-type Nedd4-1 and WWP2 enzymes showed low ubiquitination levels that were significantly enhanced upon deletion of their C2 domains
5411	17719543_MI:0415	Deletion of the Smurf2 C2 domain enables Smurf2 Ub thioester formation.
5412	17719543_MI:0415	In total, we generated six mutants and tested their autoubiquitination efficiency by comparing protein levels of unmodified and ubiquitinated Smurf2 (Figure 4B). Smurf2 variants in which the C2 domain hydrophobic residues involved in HECT domain binding were mutated (F29A/F30A and T56A/L57A) displayed the highest ubiquitination levels.
5413	17719543_MI:0415	RhoA was efficiently ubiquitinated by the F29/30A Smurf2 mutant
5414	17719543_MI:0415	we detected almost no difference in the autoubiquitination efficiency for Rsp5p and AIP4 in the absence or presence of their C2 domains
5415	18191223_MI:0415	Autoradiograms of radiolabelled Xbp1mini cleavage products generated by wild-type and the indicated single-site dimer interface mutants of Ire1cyto
5416	18313049_MI:0415	Autoubiquitylation of RNF43
5417	18455986_MI:0415	To explore the regulatory link between PleD, PleC, and DivK, activation of PleD diguanylate cyclase activity was assayed in vitro in the presence of PleC and DivK.
5418	18485870_MI:0415	In vitro acetylation of p53 by p300/CBP
5419	18510924_MI:0415	Helicase assays were performed on a 5&#8242;-overhang substrate and yielded a wild-type rate of 2.22 base pairs per min per XPD molecule.
5420	18510925_MI:0415	Helicase activities of wild-type and mutant proteins of S. acidocaldarius XPD showing the time course of unwinding of a partial DNA duplex with a 25 nt 5&#8242; overhang.
5421	18796637_MI:0415	Using these fusion proteins, we performed in vitro ubiquitination assays in the presence of different ubiquitin versions: free ubiquitin, HA-ubiquitin, or flagellin (Flag)-tagged ubiquitin. As a result, we found upshifted bands (usually two bands) when MBP-COP1 and HA-STH3 were incubated in the presence of both E1 ubiquitin-activating and E2 ubiquitin-conjugating enzymes, most likely indicating that MBP-COP1 polyubiquitinates HA-STH3
5422	18805092_MI:0415	NEDD8ylation of Cul5ctd-Rbx1 on Lys724
5423	18805092_MI:0415	NEDD8ylation time course for wild-type (WT) Cul1-Rbx1, nonNEDD8ylatable (K720R) control,
5424	18805092_MI:0415	SCF&#946;TRCP-mediated polyubiquitination of a biotin-labeled &#946;-catenin phosphopeptide.
5425	18805092_MI:0415	SCFSkp2/CksHs1-mediated polyubiquitination of phospho-p27
5426	8313896_MI:0415	Both p85a and p85,B were seen to bind p110 by Coomassie blue staining following SDS-PAGE (Figure lBi, lanes 1 and 2) or upon assay for associated PI 3-kinase activity
5427	9235916_MI:0415	To test whether p110d has PI 3-kinase activity, immunoprecipitates from COS cells transfected with epitope-tagged p110d were incubated with [32P]ATP and phosphatidylinositol, and the radiolabeled phospholipids were resolved by chromatography. A product was detected that migrates slightly slower than the PI 4-phosphate (PIP) standard, consistent with the generation of PI3-phosphate
5428	imex:IM-11809_MI:0415	The increased catalytic activity of the mutants, as compared with the wild-type enzyme, likely results from a shift of the equilibrium toward the active conformation of the enzyme
5429	imex:IM-11868_MI:0415	recombinant SRP-6 inhibited papain-like lysosomal cysteine peptidases (clan CA, family C1) such as catL
5430	imex:IM-11868_MI:0415	recombinant SRP-6 inhibited papain-like lysosomal cysteine peptidases (clan CA, family C1) such as catL and catK,
5431	imex:IM-11868_MI:0415	The stoichiometry of inhibition (SI) for the interaction of SRP-6 with catL (A) or calpain-2 (B). Inhibitor:enzyme ratio of 1:1 and 1:1.5 completely inhibited catL and calpain-2 activity, respectively.
5432	imex:IM-11902_MI:0415	PER2 was acetylated (Figure S6) and that the acetyl groups were removed in vitro by recombinant SIRT1 in an NAD+-dependent manner (Figure 6B).
5433	imex:IM-11952_MI:0415	We first monitored the effect of DprA on the ssDNA-dependent ATPase activity of EcRecA. We observed that at low concentration DprA, which itself exhibits no detectable ATPase activity (either in the presence or absence of ssDNA, data not shown), stimulates ssDNAdependent EcRecA ATPase
5434	imex:IM-12006_MI:0415	in Figure 4E demonstrate that demethylation of a dimethyl-K9 peptide depends on the presence of JHDM2A and generated products with masses that correlate with both monomethyl and unmethylated forms of the peptide, indicating that both mono- and dimethyl-K9 can serve as substrates.
5435	imex:IM-12008_MI:0415	a known Cas kinase, Abl (Mayer et al., 1995) and another SFK, FynT, phosphorylated CasSD in an extension-dependent manner
5436	imex:IM-12008_MI:0415	we examined the effect of extension on tyrosine phosphorylation of CasSD by recombinant active c-Src. While the level of phosphorylation was low without stretching (Figure 4A, lane 1), CasSD phosphorylation increased in proportion to the magnitude of latex membrane stretching (25%, 50%, 75%, 100%, and 150%)
5437	imex:IM-12009_MI:0415	Ipl1/Aurora B phosphorylated the NDC-80 subunit of the intact NDC-80 complex as well as the head dimer (Figure 7B). No significant phosphorylation of other complex subunits was observed (Figure 7B). Importantly, mutation of the four putative Aurora B phosphorylation sites in the N terminus of NDC-80 (T8, S18, S44, S51; Figure 7A) to alanine virtually eliminated Ipl1-directed phosphorylation
5438	imex:IM-12041_MI:0415	methylation of unmodified peptide occurs rapidly in vitro as labeled peptide is detected as early as 2 min after Set2 addition
5439	imex:IM-12041_MI:0415	Using this assay, Fpr4 was seen to have cis to trans isomerase activity on P30 and P38 of H3 but minimal activity toward H3P16 or H4P32
5440	10801826_MI:0416	Stable PECAM-1 expression elicits a partial co-localization with desmoplakin in HEK 293 cells.
5441	10801826_MI:0416	The merged staining of PECAM-1 and vimentin is shown in panels c and f, and that of PECAM-1 and desmoplakin is shown in panel i. Note partial PECAM-1/vimentin co-localization in migrating but not confluent HUVECs and partial PECAM-1/desmoplakin co-localization at the cell edges.
5442	10801826_MI:0416	upon PECAM-1 expression, gamma -catenin was found mainly at cell-cell junctions (Fig. 4A, b), co-localizing with PECAM-1
5443	11029466_MI:0416	The localization of eIF3e overlapped that of the CSN7 protein, which was found in both nucleus and cytoplasm of root and leaf protoplasts
5444	11090136_MI:0416	cl-8 cells transfected with both GFPNLS-CORD and Cos2 expressing constructs retain Ci in the cytoplasm
5445	11397012_MI:0416	Colocalization of endogenous ASX (D; red) and TAN (E; green) on a section of salivary gland polytene chromosome from a third instar larva.
5446	11397085_MI:0416	In case of FRET, the CFP ¯uorescence will be quenched and the YFP ¯uorescence would be increased (sensitized). Assuming approximately equal expression levels of both AtSERK1-CFP (Figure 1(c)) and -YFP (Figure 1(d)), we consider a ratio of ¯uorescence intensity at 525 nm over 475 nm (designated as the YFP/CFP emission ratio) of 1.3 or higher as evidence of FRET and hence of AtSERK1-AtSERK1 interactions such as oligomerization or homodimerization.
5447	11684708_MI:0416	In attempts to characterize the K18-TRADD association in vivo, we first determined the subcellular localization of overexpressed myc-tagged TRADD in various epithelial cells. We transfected HeLa cells, T24 cells, MDCK cells, and immortalized human mammary epithelial cells (HMEC) with a myc-tagged vector encoding the full-length TRADD. 16 h later, the cells were fixed and doubly stained with anti-myc polyclonal antibody and anti-K18 monoclonal antibody (Fig. 3A). In various cells, overexpressed myc-TRADD exhibited a filamentous pattern, and these myc-TRADD filaments markedly colocalized with K8/18 filaments (Fig. 3 A).
5448	11684708_MI:0416	In untransfected SW13 cells, which are devoid of keratins, native TRADD was diffusely present in the cytoplasm (Fig. 7 C, a). In K8/ 18-transfected SW13 cells, TRADD was recruited to overexpressed K8/18 filaments (Fig. 7 C, d-f). In cells overexpressing the NH2 terminus of K18, TRADD markedly colocalized with the overexpressed NH2 terminus (Fig. 7 C, g-i). These results indicate that overexpressed K8/18 or K18 NH2 terminus could sequester endogenous TRADD, leading to the inhibition of TNF-induced apoptosis in SW13 cells.
5449	11684708_MI:0416	To search for the role of K18-TRADD interaction in cellular responses to various apoptotic stimuli, we treated HMEC with 1microM aclarubicin (ACR), a topoisomerase inhibitor, 10microg/ml neocarzinostatin (NCS), a chemical that directly causes DNA breaks, 1microM taxol, a microtubule stabilizer, and UV irradiation (100 J/m2). 20 min after treatment with these stimuli, we examined the distribution of TRADD using immunostaining techniques (Fig. 6 A).
5450	11751918_MI:0416	When Bis1-YFP and Ish1-GFP are co-overexpressed in wild type cells, they display partial overlap in their localization at the nuclear envelope (Fig. 6, D and E).
5451	11903063_MI:0416	Indirect immuno¯uorescence microscopy using the TACC1 antibody revealed a similar staining pattern to the EGGAS41 fusion protein,
5452	11909965_MI:0416	Mad3-GFP (green in the merged image) colocalizes with Cnp1/CENP-A (red in the merged image).
5453	11988016_MI:0416	In some cotransfected cells, BFP-tagged MRG X was localized mainly in the nucleus and partially in the cytoplasm (A), and GFP-tagged PCD17 was expressed in the cytoplasm (B). In other cotransfected cells, BFP-tagged MRG X was expressed in the nucleus (C) , and GFP-tagged PCD17 was expressed mainly in the nucleus and partially in the cytoplasm (D).
5454	12007189_MI:0416	Subcellular localization of SSX2IP and SSX2 protein fragments in transfected HeLa cells.
5455	12007189_MI:0416	Subcellular localization of the EGFP-RAB3IP and SSX2 proteins in transfected HeLa cells.
5456	12015115_MI:0416	Detail of body-wall muscle from a rescued pat-4(st551) adult hermaphrodite coexpressing (D) pat-4::yfp and (E) pat-3::cfp.
5457	12015115_MI:0416	PAT-4/ILK and betaPAT-3 Integrin Colocalize at Muscle Attachments(
5458	12082530_MI:0416	H1299 cells were assayed for endogenous JAB1 and fibrillarin localization by immunofluorescence
5459	12082530_MI:0416	PGP9.5 and JAB1 were detected both in the cytoplasm and in the nucleoli, whereas p27Kip1 was detected primarily in the nucleus with strong staining to the nucleoli
5460	12082530_MI:0416	PGP9.5 colocalizes with JAB1 both to the nucleus and cytoplasm of H1299 cell
5461	12417715_MI:0416	Transiently expressed hDcp1a and hDcp2 localize primarily to the cytoplasm.
5462	12493754_MI:0416	Chk2 and Plk1 Co-localize to Centrosomes and the Midbody
5463	12740913_MI:0416	Expression of GFPp14ARF induces the relocalization of EBNA-5 from homogeneous nucleoplasmic distribution into nuclear inclusions in MCF7 cells double transfected with pBABE EBNA-5
5464	12740913_MI:0416	p14ARF positive nuclear inclusions (hollow arrowheads) but not nucleoli (full arrowheads) accumulate PML bodies
5465	12740913_MI:0416	transfection of GFP-p14ARF or pBabe-p14ARF into MCF7 that constitutively expressed EBNA-5 (M1 cells) led to the relocation of EBNA-5 into the p14ARF-positive nuclear inclusions
5466	12740913_MI:0416	where p14ARF was present both in the nucleoli and in the inclusions, EBNA-5, p53 and HDM2 accumulated exclusively in the inclusions.The expansion of nuclear inclusions was paralleled by the complete relocation of EBNA-5 (Fig. 4c), p53 (Fig. 5d) and HDM2 (Fig. 5c) to these sites.
5467	12757932_MI:0416	ataxin-1 interacts and co-localizes with p80 coilin in the nucleoplasm
5468	12805220_MI:0416	Flag-tagged STRAD and myc-tagged LKB1 could be co-immunoprecipitated following co-transfection of HEK- 293T cells (Figure 3A).
5469	12874278_MI:0416	These results suggest that 
-catenin and TIP-1 interact in vivo and that complex formation probably takes place in the nucleus.
5470	12878161_MI:0416	BTBD2(149-525)-myc, was co-expressed with either DsRed-BTBD1, GFP-BTBD2, or GFP-TRIM5delta;, instead of localizing to nuclear speckles, it localized together with DsRed-BTBD1, GFP-BTBD2, or GFP-TRIM5delta; to cytoplasmic bodies. Other fragments having an intact BTB/POZ domain localized diffusely when expressed alone, but, when expressed with full-length DsRed-BTBD1 or myc-BTBD2, also co-localized to cytoplasmic bodies (Fig. 5, 1-217, 103-217, and 103- 525).
5471	12878161_MI:0416	DsRed-BTBD1 ( Fig. 3G) and endogenous BTBD2 immunostaining ( Fig. 3H) colocalize
5472	12878161_MI:0416	Endogenous BTBD1 immunostaining ( Fig. 3A) and transfected GFP-BTBD2 ( Fig. 3B) colocalize in transfected cells
5473	12878161_MI:0416	GFP-TRIM5delta; [2] co-localized with endogenous BTBD2
5474	12878161_MI:0416	myc-BTBD2 (410-525), did co-localize to cytoplasmic bodies when coexpressed with GFP-TRIM5&#948;
5475	12878161_MI:0416	Requirement of the RING domain and the coiled-coil region of TRIM5&#948; for colocalization with BTBD1/2
5476	14508515_MI:0416	Menin and NMHC II-A colocalize in the cleavage furrow by indirect immunofluoresence microscopy.
5477	14517282_MI:0416	Daxx colocalized with PML at 10 to 20 nuclear dots in control cells
5478	14557665_MI:0416	Daxx was present in the anti-E1B immunocomplexes
5479	14557665_MI:0416	In addition, simultaneous staining of the transfected 293 cells with goat anti-p53 antibody and 2A6 indicated that Daxx, p53, and the E1B 55-kDa protein were present in the same complex in the nuclear dots (Fig. 3C).
5480	14715275_MI:0416	We found that in most HeLa cells both SMN and 3×Flag-Rpp20 accumulated and co-localized in punctuated cytoplasmic granules.
5481	14742702_MI:0416	As shown in Figure 2D, the central dots of Alp7-YFP colocalized with Nuf2-CFP
5482	14742702_MI:0416	Figure 2A shows that Alp7 colocalized with Cut12 during mitosis.
5483	14742702_MI:0416	From this it was evident that Alp7 and Alp14 colocalize during mitosis (Figure 3A).
5484	14998928_MI:0416	Myc-tagged Ttv proteins were present in both endoplasmic reticulum (ER) and Golgi (Fig. 7D-E'').
5485	14998928_MI:0416	we found that Ttv and Sotv protein staining were virtually identical, and that they were concentrated in certain compartment(s).
5486	15016378_MI:0416	APPL1 largely colocalized with myc-APPL2 in the same structures (Figure 2A), which were also positive for GFP-Rab5 (Figure 2B).
5487	15016378_MI:0416	At 15 min, Rh-EGF appeared in EEA1-containing early endosomes (Figure 5A) that expanded in size
5488	15016378_MI:0416	Endogenous APPL1 localizes to Rab5Q79L-enlarged endosomes in vivo.
5489	15016378_MI:0416	myc epitope-tagged APPL1 and APPL2 colocalized with the endogenous proteins in the peripheral structures
5490	15016378_MI:0416	The response of APPL1 to EGF indeed correlated with the accessibility of APPL1-positive membranes to this growth factor (Figure 4C). After 5 min of internalization, a fraction of Rh-EGF (between 5% 28%) localized to fine punctate structures harboring APPL1 (the extent of colocalization varied depending on the degree of APPL1 solubilization). At this point, the majority of Rh-EGF (70% 90%) was present in EEA1-positive early endosomes and, presumably, EEA1-negative clathrin-coated vesicles
5491	15044383_MI:0416	Co-localization of aprataxin and XRCC1 charged particle tracks in chromatin.
5492	15044383_MI:0416	we looked for co-localization of aprataxin with the nucleolus-specific marker protein, nucleolin, in stably transfected HeLa cells using anti nucleolin antibody staining (Fig. 2C). When this fluorescence pattern was merged with the EGFP aprataxin signal, co localization of these proteins was observed.
5493	15063184_MI:0416	N-terminal region of Ci from aa 346 to aa 440, which we named CDN (Cos2 Responsive Domain in the N-terminal region of Ci), and CDN can mediate cytoplasmic retention by Cos2.
5494	15105425_MI:0416	Colocalization and interaction of VRK1 and ATF2 in the cell nucleus.
5495	15147888_MI:0416	Furthermore, co-expressed hNinein and CGI-99 in HeLa cells also show tht they are partially co-localized in the centrosome during interphase ( Fig. 4D).
5496	15155879_MI:0416	Overlay of the microscopic images indicates that the PHYA:YFP and PIF3:CFP fusion proteins are colocalized in the nucleus
5497	15155879_MI:0416	Overlay pictures of the speckles indicate that PIF3:CFP colocalizes transiently with both PHYB:YFP (Figure 8, insert) and PHYD:YFP (data not shown).
5498	15159385_MI:0416	HAX-1 and BSEP-EYFP co-localize in the apical domain of MDCK II cells.
5499	15177031_MI:0416	we performed immunostaining on cells expressing myc-tagged tea2p and GFP-tagged tubulin. Tea2p-myc and tip1p showed a mostly overlapping staining pattern
5500	15364927_MI:0416	Codistribution of Daxx, MDM2, and p53 in DKO MEF
5501	15467741_MI:0416	Colocalization of magician with merlin and actin
5502	15520167_MI:0416	we determined whether in nuclei, MGC5306 colocalizes with pol. The top right panel in Fig. 2B shows Texas Red-stained MGC5306 in nuclei of 293 cells and green fluorescence emitted from nuclei demonstrates distinct nuclear localization of pol (Fig. 2B, top left panel). Upon overlapping of both, the yellow stain (Fig. 2B, bottom left panel) in the nuclei is clearly visualized, indicating both proteins reside in nuclei and in close physical distance.
5503	15696166_MI:0416	we used immunofluorescence to investigate the localization of Brm and MeCP2 in NIH3T3 cells. Staining for the protein determinants showed considerable, but not precise, overlap for Brm and HDAC2 and colocalization of Brm and MeCP2 (Fig. 1d).
5504	15917470_MI:0416	the colocalization of the endogenously expressed Oct-4 and EWS proteins was also determined by indirect immunofluorescence studies using &#945;-Oct-4 (C-10, Santa Cruz Biotechnology) or &#945;-EWS (C-19, Santa Cruz Biotechnology) antibodies. As shown in Figure 6B, both proteins are exclusively localized to the nucleus in P19 cells,
5505	15917470_MI:0416	The overlay image indicated that Oct-4 and EWS in the nucleoplasm partially overlapped
5506	15983381_MI:0416	DJ-1 interacts with Daxx.
5507	16229834_MI:0416	GFPAmida was no longer diffusely distributed in the cytoplasm but clearly colocalized with Par-4 at actin filaments in the coexpressing cells
5508	16234233_MI:0416	ASIC3 co-localizes with endogenous ezrin in the presence of NHERF-1.
5509	16234233_MI:0416	Co-localization of ASIC3 and NHERF-1
5510	16234233_MI:0416	NHERF-1 co-localizes with ASIC3 in COS-7 cells and alters its cellular distribution.
5511	16253999_MI:0416	SPIN90 binds to and colocalizes with the Arp2/3 complex.
5512	16257957_MI:0416	XAP2 retains the nonactivated AhR in the cell cytoplasm
5513	16257958_MI:0416	Kv4.2 colocalizes with Kif17
5514	16275660_MI:0416	Co-localization of VCP, labeled with CY3 (red) and AMFR, labeled with Alexa 488 (green), is indicated by the yellow color when the cell is observed under a triple filter. Both proteins co-localized in the cytoplasm as well as in membranous structures in the perinuclear region of COS-1 cells (Fig. 2D)
5515	16284401_MI:0416	Co-localization of ARMS and EEA1 using indirect immunofluorescence (Fig. 4A) also confirms these results.
5516	16298995_MI:0416	The double immunolabeling also showed co-localization of EphB puncta and Tyr(P)397FAK clusters as a result of the ephrinB2-mediated activation of EphB2
5517	16298995_MI:0416	the immunolabeling of hippocampal neurons with an antibody specifically recognizing phosphorylated/activated paxillin (Tyr(P)31pax) showed a significant increase in clustering of phosphorylated paxillin at the sites of EphB clustering following treatment with ephrinB2-Fc
5518	16298995_MI:0416	the phosphorylation of Src on tyrosine 418 significantly increased (Fig. 3, D and G), specifically at the sites of EphB clustering
5519	16316992_MI:0416	Cellular association of full-length MAGI-3 and full-length beta1AR.
5520	16332538_MI:0416	FHY1 but also FHL colocalises with phyA in the nucleus.
5521	16332688_MI:0416	the co-localization of RanBP2 and GFP-Parkin was observed (Fig. 1C).
5522	16339760_MI:0416	KHC and HAP1-A were clearly colocalized in the same neurite tips
5523	16364915_MI:0416	At low tetracycline concentrations, FLAGhDcp1a and FLAG-hDcp1b primarily colocalize with endogenous hDcp1a in cytoplasmic PBs (Figure S1 available in the Supplemental Data online, and data not shown)
5524	16364915_MI:0416	endogenous Hedls colocalize in PBs with exogenous Myc-hDcp1a (Figure 3B)
5525	16364915_MI:0416	Myc-tagged hDcp1b colocalize with endogenous hDcp1a in PBs when expressed at low levels.
5526	16364915_MI:0416	Myc-tagged hEDc3 colocalize with endogenous hDcp1a in PBs when expressed at low levels.
5527	16364915_MI:0416	Myc-tagged Hedls, colocalize with endogenous hDcp1a in PBs when expressed at low levels.
5528	16364915_MI:0416	Myc-tagged hRck/p54 colocalize with endogenous hDcp1a in PBs when expressed at low levels.
5529	16364915_MI:0416	overexpression of Hedls leads to the formation of multiple enlarged PB-like structures, which contain Hedls, hDcp1, and hXrn1 (Figure 3C, 13-16)
5530	16369483_MI:0416	Interaction of CgA and CgB with mutant SOD in cultured cell lines.
5531	16369483_MI:0416	We also detected partial colocalisation of mutant SOD1 with CgA and CgB in irregular and large vesicular struuctures of spinal neurons from G37R transgenic mice.
5532	16438971_MI:0416	Finally, the common localization pattern of both proteinfusions (Fig. 3C) is also consistent with interactions occurring between AtCPK11 and AtDi19 in the nucleus, where both AtCPK11 and AtDi19 are present.
5533	16473966_MI:0416	SERK1-YFP also formed heterodimers with SERK3-CFP in the plasma membrane, as shown by the green plasma membrane in Figure 3D
5534	16473966_MI:0416	The results presented in Figure 3D (panel V) show that SERK1 and BRI1 heterodimerize in small patches in the plasma membrane,
5535	16476580_MI:0416	Colocalization of Pin1 and Nek6 in Hep 3B cells
5536	16522632_MI:0416	Fet3p·Ftr1p Interaction Motifs Are Required for Protein Trafficking to the Yeast Plasma Membrane.
5537	16525419_MI:0416	Nck recruitment to phosphorylated nephrin facilitates localised actin reorganisation.
5538	16525474_MI:0416	a, b, Immunofluorescence of cerebellar Purkinje cells. a, Ostm1 co-localized with ClC-7 in late endosomes/lysosomes4 of wild-type cells.
5539	16525474_MI:0416	Co-transfection with ClC-7 restored a punctate Ostm1 staining pattern that largely co-stained with Lamp-1 (Fig. 2c) and ClC-7 (Fig. 2d).
5540	16525474_MI:0416	Immunofluorescence of osteoclasts in situ. Ostm1 and ClC-7 co-localized in the ruffled border (c), as did ClC-7 and the a3 proton-pump subunit (d).
5541	16525474_MI:0416	In cultured primary fibroblasts, Ostm1 co-localized with Lamp-1, a marker for late endosomes and lysosomes (Fig. 2a).
5542	16525503_MI:0416	Immunohistochemical studies of brain sections prepared from SCA3 patients revealed that Atx-3, VCP and ubiquitin colocalize in neuronal nuclear inclusions
5543	16648843_MI:0416	In embryonic neuroblasts, we found that Mud and Pins were both enriched at the cortex over the apical centrosome/spindle pole from late interphase and up to the end of metaphase (Fig. 2a, b, d, e; Fig. 3a).
5544	16652156_MI:0416	Colocalisation of PIDD, RAIDD and caspase-2 in HCT116p53 and p53 cells.
5545	16682412_MI:0416	partial co-localization between endogenous SETDB1 and exogenous DNMTs
5546	16702408_MI:0416	In mouse keratinocytes transfected with GFP fusion constructs, both full-length TRADD (residues 1-312)(Fig. 3B-B") and its C-terminal moiety (residues 105-312)(Fig. 3C-C") partially colocalize with K17 in the cytoplasm.
5547	16710422_MI:0416	We find that 14-3-3-sigma colocalizes with K17 in the cytoplasm of skin keratinocytes, where their interaction is phosphorylation-dependant (Supplementary Fig. 3b-d).
5548	16760425_MI:0416	Because CP110 is a centrosomal protein, we examined whether these proteins colocalize during mitosis. We found that CP110 and a portion of CaM colocalized, substantially overlapping during metaphase, anaphase, and telophase (Figure 2A).
5549	16847100_MI:0416	We found that HP-1{alpha} was associated with condensed DNA in all three types of chromatin condensation that we studied (mitotic, apoptotic, and UCC), whereas SMC2 was loaded onto DNA in mitosis and upon UCC but not upon apoptotic chromatin condensation
5550	16857966_MI:0416	B, Immunocytochemistry analyses of murine cardiomyocytes labeled with antibodies against Rpn2 (A) or estrogen receptor 
 (ER
) (B), and an overlay of Rpn2 and ER
 (C).
5551	16861711_MI:0416	FHL colocalises with phyA
5552	16861711_MI:0416	FHY1 but also FHL colocalises with phyA
5553	16862148_MI:0416	Colocalisation of FilGAP and FLNa in lamellae of A7 cells is indicated in the merged image (yellow).
5554	16888242_MI:0416	Immunofluorescent microscopy showed that FHL2 and SK1 are colocalized in the cytoplasm
5555	16892067_MI:0416	RAPL and Mst1 localized together in unstimulated T cells and also at the leading edge in CCL21-stimulated T cells
5556	16905657_MI:0416	Colocalisation of ESPIN1 with clathrin.
5557	16905657_MI:0416	EPSIN1-positive punctate stains largely colocalised with those of VTI11:HA
5558	16949368_MI:0416	Immunofluorescent analysis further revealed that both CTCF and CHD8 had a similar distribution pattern in HeLa cell nuclei. Especially, they were colocalized at a part of multiple small foci in the nucleus
5559	16949368_MI:0416	The overlap between the two proteins was estimated to be about 25.0% of the CTCF foci and 30.0% of the CHD8 foci in HeLa cells, and to be about 20.9% of the CTCF foci and 15.3% of the CHD8 foci in Hep3B cells.
5560	16962094_MI:0416	Interestingly, redistribution of ank1.5 and ank1.9 signal to stress fiber-like assemblies, where GFP-A7/obscurin is located and/or a relocation of GFP-A7/obscurin signals towards endoplasmic reticulum structures was observed in the transfected cells.
5561	16982639_MI:0416	Interaction of XE7 with ZNF265
5562	17016471_MI:0416	As reported for the budding yeast homologue of Erg9 (Kumar et al, 2002), SpErg9 associated with vesicle-like and ER (including a nuclear rim) structures (Figure 2D, left panel), consistent with the presence of a conserved transmembrane domain in Erg9 (Figure 2B; Robinson et al, 1993). Pof14 displayed a very similar localisation (Figure 2D, central panel), and colocalisation was confirmed (Figure 2D, right panel).
5563	17137291_MI:0416	MAGE-C1 and NY-ESO-1 appear to co-localize to the cytoplasm of these cells.
5564	17216128_MI:0416	Furthermore, the immunofluorescent signals for LKB1 and WDR6 were interwoven, indicating that LKB1, at least partly, co-localizes with WDR6 in the cytoplasm.
5565	17276458_MI:0416	PLD2 colocalizes with Grb2 in the perinuclear Golgi region of COS7shGrb2 cells.
5566	17276458_MI:0416	PLD2 colocalizes with Grb2 in the perinuclear region, and this colocalization becomes more pronounced upon stimulation by EGF
5567	17289665_MI:0416	During prometaphase, DYNLT3 was observed at kinetochores and co-localized with Bub3
5568	17324924_MI:0416	Colocalization of HA-Int6-wt with Myc-HIF-2-wt was detected in MCF-7 cells by immunofluorescence analysis under normoxia as described previously (55). Cytoplasmic localization of HA-Int6-wt changed to nuclear following coexpression with Myc-HIF-2; both proteins were expressed in the nucleus
5569	17353262_MI:0416	More significantly, APLF colocalized and accumulated with XRCC1 at these sites, confirming that APLF is a component of the response to UVA-induced cellular damage.
5570	17353262_MI:0416	The fraction of cells with largely nuclear YFP-APLF transiently increased after H2O2 treatment in an RFP-XRCC1-dependent manner (Fig. 4C, middle and right panels).
5571	17395368_MI:0416	When RFP-ELL was co-transfected with GFP-FB1, co-localization was observed between these two tagged proteins, suggesting that ELL and FB1 coexist in the same nuclear structure,
5572	17403664_MI:0416	Cells in D and E were stained for Def-6 (D, panel a and E, panel a) and the {alpha}7 integrin chain
5573	17470967_MI:0416	By contrast, when AtSWC6:RFP proteins were expressed with SUF3:GFP, most of the AtSWC6:RFP proteins moved to where SUF3:GFP proteins were localized, such that the fluorescence overlapped
5574	17535814_MI:0416	Exogenously expressed GFP-D5 codistributed with CENP-E at the kinetochore (Fig. 3D, middle GFP-Nuf2-D5 panel), indicating that the HsNUF2 C terminus is sufficient for the kinetochore localization of HsNUF2.
5575	17535814_MI:0416	HsNUF2 and HEC1 localized with CENP-E at the prometaphase kinetochores
5576	17577629_MI:0416	Akt1 and SETDB1 were co-resided in the nucleus (Fig. 3A, right panel, yellow). The result also implied that a proportion of Akt1 proteins were recruited or retained in the nucleus, since Akt1 alone is mainly in the cytoplasm. Similar results were also observed in mouse fibroblast NIH3T3 cells
5577	17577629_MI:0416	In HeLa cells, overexpressed Akt1 was localized both in the cytoplasm and the nucleus (Fig. 3A, left panel), whereas SETDB1 was absolutely in the nucleus (middle panel). Akt1 and SETDB1 were co-resided in the nucleus
5578	17662947_MI:0416	Colocalization of YFP-UgtP and a CFP fusion to the cell division protein EzrA (which functions as a proxy for FtsZ localization [Levin et al., 1999; Wu and Errington, 2004]) confirmed that 84% (42/50) of UgtP foci colocalize with FtsZ at midcell in wild-type cells. In contrast, the majority of UgtP puncta in pgcA::Tn10 cells (67.2%, 45/ 67) are not associated with FtsZ (Figure 4D).
5579	17681274_MI:0416	Aurora B (Fig. 3B i and ii) and survivin (Fig. 3B iii) were again localised to the centromeres on chromosomes. Cdk1 co-localised with Aurora B and survivin at centromeres.
5580	17681274_MI:0416	In control K562 cells, Cdk1 was seen to co-localise with Aurora B (Fig. 3A) and survivin (Supplementary data) to the chromosomal centromeres during prophase (Fig. 3A i) and metaphase (Fig. 3A ii), to the midzone in anaphase (Fig. 3A iii) and to midbodies in telophase (Fig. 3A iv).
5581	17690294_MI:0416	In the course of our experiments, we noted that the subcellular distribution of klotho and Wnt proteins within transfected cells overlapped (fig. S2).
5582	17693538_MI:0416	In Figure 2, images of the nucleus of CDC48A are shown in the focal plane. CDC48A colocalizes with CDC48C in the nucleus (Fig. 2, A-C) and also localizes to the PM and the cytoplasm. The PM is not in the focal plane and can therefore not be seen. The merge shows an overlay of the cells containing chloroplasts in red, CDC48A in yellow, and the nucleus in cyan. The CDC48AN-D1 protein (Fig. 2, D-F) is found in the cytoplasm but not in the nucleus
5583	17803915_MI:0416	Immunofluorescence analysis revealed a punctate distribution of SCRAPPER (Figure 1F) that predominantly colocalized with synaptophysin, a known synaptic vesicle protein and presynapse marker.
5584	17803915_MI:0416	SCRAPPER partially colocalized with RIM1 in cultured neurons (Figure 2D)
5585	17855368_MI:0416	fluorescent immunostaining also showed that both Id-1 and Cav-1 were co-localized in the cytoplasm of Hpr-1 cells
5586	17891176_MI:0416	Further analyses revealed centrosomal S5A staining throughout the cell division cycle (Figure 3 and Supplementary Figures 2 and 3), similar to that reported for ID1
5587	17891176_MI:0416	S5A was substantiated by colocalization of the S5Asignal with the centrosome markers g-tubulin (Figure 3a) and pericentrin
5588	17937504_MI:0416	An antibody directed against a synthetic peptide specific for the AtDMC1 protein [46] was used in immunolocalization experiments, together with an antibody against ASY1 [35]. We analyzed the number of AtDMC1 foci on wild-type chromosomes during meiotic progression and obtained results similar to those reported by [46], with the number of AtDMC1 foci maximal during zygotene
5589	17937504_MI:0416	As meiosis progressed and the ASY1 signal extended all along the axial element, AtMND1 was detected along the entire length of the chromosome, in both unsynapsed and synapsed chromosome regions
5590	17981125_MI:0416	Images represent colocalization of IP3R3 and endogenous Sig-1Rs at MAM in a CHO cell.
5591	17983804_MI:0416	-catenin accumulated in the nucleus as well as the cell membrane (Figure 1B, green), whereas Topo II was present exclusively in the nucleus (red). The merged images revealed that the 2 proteins were colocalized in the nucleus (yellow).
5592	17983804_MI:0416	Immunofluorescence microscopy of specimens from colorectal cancer patients revealed that Topo II was colocalized with -catenin in the nuclei of cancer cells(Figure 7D-I), but not in the nuclei of normal intestinal epithelial cells
5593	18001825_MI:0416	As expected, RNF8 colocalizes with MDC1, NBS1, 53BP1, BRCA1, pATM, and MCPH1, further lending credence to the potential role of RNF8 in the DNA-damage response (Figure S1C).
5594	18001825_MI:0416	Interestingly and surprisingly, RNF8 foci can be readily observed after DNA damage, and these foci colocalized with the DNA-damage marker gamma-H2AX.
5595	18024891_MI:0416	colocalization of BGLF4 and XPC was observed in the nucleus by using an indirect immunofluorescence assay
5596	18024891_MI:0416	XPC partially colocalized with BGLF4
5597	18029035_MI:0416	Immunofluorescence staining showed that both A20 and Ymer partially localized in the cytosol
5598	18056989_MI:0416	We also observed the co-localization of BCRP and Pim-1L on the plasma membrane
5599	18191225_MI:0416	For FLIM studies, mGFP-PTRF was transfected into BHK cells or cotransfected with mRFP-Cav3, and its fluorescence lifetime measured.
5600	18296627_MI:0416	Colocalization of CO with COP1 in vivo.
5601	18329369_MI:0416	BRUCE-C co-localizes with MKLP1.
5602	18329369_MI:0416	BRUCE colocalizes with the exocyst component Sec8 in a perinuclear compartment.
5603	18329369_MI:0416	BRUCE localizes to Rab8 tubular endosomes in interphase cells.
5604	18329369_MI:0416	Immunofluorescence (IF) of HeLa cells stained with anti-Plk-1 (red) and anti-BRUCE (green) and DAPI to visualize DNA.
5605	18329369_MI:0416	On the midbody, BRUCE localizes in a characteristic ring-like arrangement that is embraced by Aurora B and microtubules
5606	18329369_MI:0416	U2OS cells were stained with anti-BRUCE (green) and anti-golgin p230 (red), and DAPI (blue).
5607	18339839_MI:0416	we did immunocytochemical analyses of PC3 cells and showed a high degree of spatial concordance between ILK and rictor, particularly at the leading edge of cells and at membrane ruffles
5608	18358808_MI:0416	HA-TERT is expressed in a nuclear distribution overlapping with pontin and reptin,
5609	18466309_MI:0416	BIF2 and BA1 colocalize in the nucleus
5610	18585357_MI:0416	As shown in Figure 3A, cells expressing DSCAM showed significant binding to netrin-1-Fc.
5611	18585357_MI:0416	Netrin-1-Fc bound to these cells to an apparently similar extent as to cells expressing DCC
5612	18617507_MI:0416	Both proteins presented some overlap of their signals both in nucleus and cytosol in interphase (Fig. 4A). In cells that have finished cell division, Ran is mostly located on, or near, the nuclear membrane, but its overlap with VRK1 is intranuclear (Fig. 4B).
5613	18617507_MI:0416	In HEK293T cells there was a strong overlap between the cytosolic signal of VRK2 and Ran (Fig. 4E),
5614	18724936_MI:0416	Red fluorescent protein (RFP) fused to Get3 (Get3-tdRFP) and GFP-Sed5 colocalized in these punctate structures (Figure 2C)
5615	18805088_MI:0416	When CFP-ParB was expressed in combination with PopZ-YFP, the CFP-ParB protein colocalized with the PopZ-YFP foci (Figure 3B, left panels).
5616	18805089_MI:0416	Covisualization of PopZ-YFP and CFPParB ori (both present at native levels) revealed that the ParB signal is often found overlapping with the pole-distal tip of the PopZ signal (Figure 6K)
5617	18805096_MI:0416	CYFIP1-eIF4E colocalization in dendrites
5618	18854156_MI:0416	SojD40A colocalizes with Spo0J.
5619	18854156_MI:0416	SojG12V colocalizes with oriC.
5620	19135897_MI:0416	KHC-mCit is diffusely cytoplasmic when only Miro has been expressed but colocalizes in puncta with MitoTracker and Miro when milton is also expressed.
5621	imex:IM-11875_MI:0416	Co-localization of rMBP and BKCa channels
5622	imex:IM-11875_MI:0416	Merged image shows co-localization of rMBP and CaM in a punctate pattern along the axons
5623	imex:IM-11888_MI:0416	A triple staining with LIMP-2, BetaGC, and LAMP-2 (Figures 3D-3G) confirmed the correct lysosomal sorting of BetaGC after LIMP-2 re-expression
5624	imex:IM-11888_MI:0416	Merged image showing an almost complete colocalization of LIMP-2 and GC.
5625	imex:IM-11893_MI:0416	To further confirm that PCNA and p16 interact in vivo, we examined the intracellular distribution of PCNA and p16 proteins in order to analyze whether they colocalize within the cell. Thus, immunocytochemical experiments were performed in NP-18 andHeLa cells using antibodies against PCNA and p16 proteins (Fig. 5A). In these experiments, cells showed both proteins located in the nucleus, being the nucleoli excluded, and colocalizing in some nuclear regions.
5626	imex:IM-11923_MI:0416	A significant fraction of CFTR colocalizes with BAP31 in the ER.
5627	imex:IM-11923_MI:0416	BAP31 colocalizes with TRAM
5628	imex:IM-11923_MI:0416	BAP31 colocalizes with TRAM and Sec61&#946;.
5629	imex:IM-11936_MI:0416	lthough GFP-IpaB1-312 was detected in the cytoplasm by 3 hr after DTB, IpaB and Mad2L2 were detected in the nucleus between 6 and 12 hr (Figure 2), suggesting that IpaB interacts with Mad2L2 in the G2/M phase.
5630	imex:IM-11941_MI:0416	Confocal images of spindles immunostained with anti-xCep57, anti-Ndc80, and anti-tubulin antibodies
5631	imex:IM-11941_MI:0416	Immunofluorescent images localize xCep57 to the spindle poles and to punctuate double dots on metaphase chromatin (Merge: xCep57, red; tubulin, green; DNA, blue; scale bar = 5 &#956;M).
5632	imex:IM-11942_MI:0416	Closer examination by immunolocalization revealed colocalization of a fraction of PP2AA1:GFP with PIN1 and PIN2 at the plasma membrane
5633	imex:IM-11942_MI:0416	Quantitative analysis demonstrated that about 7% of the detected PP2AA1 signal colocalizes with PIN1,whereas 80% of PIN1 overlaps with PP2AA1.
5634	imex:IM-11942_MI:0416	Quantitative analysis of colocalization revealed that 23% of PID:YFP colocalizes with PIN2, whereas 89% of PIN2 colocalizes with PID:YFP.
5635	imex:IM-11943_MI:0416	In hybrid seedlings, we detected a strong colocalization between VPS29-GFP and mRFP-RABF2b (Figures 4I-4K) or SNX1-mRFP
5636	imex:IM-11955_MI:0416	As shown in Figure 3A, SKAR significantly colocalizes with SC35,
5637	imex:IM-11973_MI:0416	pSmad1GSK3-A (green) colocalizes with the centrosome marker gamma-Tubulin (red).
5638	imex:IM-11979_MI:0416	Double-immunofluorescence microscopy revealed extensive colocalization of p62 and LC3 (Figure 3C, left panels), or p62 and ubiquitin (Figure 3C, right panels), in numerous inclusions in the cerebral cortex
5639	imex:IM-11979_MI:0416	Immunofluorescence analysis of the liver of GFP-LC3 Tg mice. Mice were fasted for 1 day, and then the liver sections were immunostained with anti-p62 antibody.
5640	imex:IM-11979_MI:0416	Immunofluorescence microscopy using hepatocytes isolated from GFP-LC3 Tg mice showed colocalization of large numbers of punctate signal for GFP-LC3 (84.7% ± 10.9%, ± SD, n = 21) with that for p62 (Figure 1E).
5641	imex:IM-12030_MI:0416	Immunofluorescence microscopic analysis of colocalization of Btk and BLNK
5642	imex:IM-12031_MI:0416	namely CIP4/Toca-3 and FBP17/Toca-2, were coexpressed, they colocalized on the same tubules (Figure 1B).
5643	imex:IM-12034_MI:0416	The colocalization of Cyld and Bcl-3 in the perinuclear region of TPA- or UV-B-treated keratinocytes suggested that Cyld may associate with Bcl-3 and regulate its activity.
5644	imex:IM-12133_MI:0416	Double staining of HeLa cells with anti-MRCK&#945; and anti-MYO18A antibodies showed endogenous MYO18A colocalized with MRCK (Figure 5A).
5645	imex:IM-12133_MI:0416	GFP-LRAP35a and FLAG-MYO18A colocalized extensively when coexpressed in HeLa cells (Figure 5A),
5646	imex:IM-12142_MI:0416	Colocalization of transferrin receptors (TfR) and Rab11-FIP2 in neuronal cell bodies
5647	imex:IM-12142_MI:0416	Cultured hippocampal neurons (DIV19) were fixed and immunolabeled for endogenous MyoVb and PSD-95 (left).
5648	imex:IM-12142_MI:0416	TfR-mCh labeled REs in spines colocalized with GFP-MyoVb clusters and both showed correlated movement into and out of spines (Figures 1C and 1E; Movies S1 and S2).
5649	imex:IM-12142_MI:0416	whereas MyoVb-WT (wild-type) showed only partial overlap with Rab11-FIP2 and TfR-positive REs, the constitutively extended MyoVb-CCtr mutant strongly colocalized with Rab11-FIP2
5650	imex:IM-12152_MI:0416	CUG2-GFP colocalized with CENP-C throughout the cell cycle (Figure 1D), demonstrating that CUG2 localizes constitutively to centromeres.
5651	imex:IM-12152_MI:0416	Simultaneous detection of CENP-A and CENP-C
5652	imex:IM-12152_MI:0416	Simultaneous detection of CENP-A and CENP-C or CENP-A and CENP-T
5653	10409688_MI:0417	The protection of these residues from digestion in the presence but not the absence of eIF4E indicated that they become inaccessible upon the formation of the eIF4G-eIF4E complex.
5654	15236960_MI:0417	The native-CTD-enolase complex is very sensitive to partial proteolysis by protease K. It is less sensitive to partial digestion by chymotrypsin (Figure 7B), and this enabled identification of the minimal binding fragment of native-CTD to enolase by native PAGE and N-terminal sequencing analysis.
5655	15890360_MI:0417	Trypsin cleavage patterns based on analysis by MALDI-TOF mass spectrometry for (a) free p27-KID, and (b) p27-KID in the presence of cyclin A, (c) Cdk2, (d) Cdk5, (e) Cdk5/p25 and (f) Cdk2/cyclin A.
5656	imex:IM-12018_MI:0417	Upon trypsin treatment, Survivin remained intact while Borealin was digested to a stable fragment encompassing residues 10-109 (mass spectrometry and N-terminal sequencing; results not shown).
5657	10209756_MI:0419	FtsZ has GTPase activity that is associated with polymerization
5658	11058119_MI:0419	GTPase activity was detected in the fractions containing His-XAB1
5659	12869544_MI:0419	The results suggest that both Toc33-wt (Fig. 3A, lanes 1-4) and Toc33-R130A (Fig. 3A, lanes 5-8) hydrolyze GTP, at a low concentration, with similar efficiencies.
5660	15377662_MI:0419	The addition of p85 to the assay did substantially accelerate the Rab5-mediated hydrolysis of the bound [-32P]GTP to [-32P]GDP,
5661	15377662_MI:0419	The GTPase activity of Rab6 was also stimulated by p85
5662	15377662_MI:0419	The p85 protein displayed similar GAP activity toward Rab5 and Rab4, and of the Rab proteins tested, these were the GTPases most stimulated by p85
5663	15377662_MI:0419	We observed that p85 did have GAP activity toward both Rac1 and Cdc42
5664	16862148_MI:0419	A GST fusion fragment of FilGAP encompassing amino acids 96-395 stimulates the intrinsic GTPase activity of both Cdc42 and Rac1
5665	17951432_MI:0419	AtGPA1 GTPase activity was accelerated by substoichiometric amounts of AtRGS1(wild type), whereas AtRGS1(E320K) was ineffective over a wide range of concentrations. The E320K substitution reduced AtRGS1 GAP activity by at least three orders of magnitude (
5666	17951432_MI:0419	We also directly measured GDP release by using [-32P]GDP-bound AtGPA1 (Fig. 2D). The rate of GDP dissociation from AtGPA1 (koff  12.6 min1) was highly concordant with the measured GTPS-binding rate.
5667	17951432_MI:0419	We tested these two predictions by performing steady-state GTPase assays by using [-32P]GTP. The rate of GTP hydrolysis at steady state (ks) at 20°C was 0.063 min1 (0.015 min1; n  4) (Fig. 2F).
5668	18250306_MI:0419	Bcl-xL, which had little GTPase activity itself, increased Drp1 GTPase activity by 60%, relative to a control protein BSA
5669	19135895_MI:0419	GTG1 has GTPase activity.
5670	19135895_MI:0419	GTG2 has GTPase activity.
5671	19135895_MI:0419	Purified GTG1, GTG2, GPA1 as well as the enzyme standard PNP (purine nucleoside phosphorylase) hydrolyze GTP as measured by enzymatic conversion of MESG (2-amino-6- mercapto-7-methylpurine riboside) to ribose-1-phosphate and 2-amino-6-mercapto-7- methylpurine upon production of free Pi.
5672	9742395_MI:0419	Byr4 inhibited GTP dissociation and hydrolysis in a dose-dependent manner that was in reasonable agreement with a model in which the Byr4-Spg1-GTP complex had negligible GTP dissociation and hydrolysis rates (Figure 3c).
5673	9742395_MI:0419	In contrast, when these reactions were performed with GST-Cdc16 in combination with Byr4, a dramatic decrease in Spg1-[g-32P]GTP was observed (Figure 3d).
5674	9742395_MI:0419	Second, GTPases were labeled with [g-32P]GTP and release of the radiolabel bound to the GTPase was measured with or without Byr4 and Cdc16. Whereas Byr4 and Cdc16 had the expected effects on Spg1, neither Byr4 nor Cdc16 had a measurable effect on the seven other GTPases tested (Table 2).
5675	9742395_MI:0419	Using Spg1-[3H]GDP and Spg1-[g-35S]GTP, the GDP and GTP dissociation rates for Spg1 were measured as 0.7 min-1 and 0.07 min-1, respectively (Figure 3a). Using Spg1-[g-32P]GTP, an apparent first-order rate constant of 0.3 min-1 was found (Figure 3a).
5676	14625560_MI:0420	In vitro kinase assays directly demonstrated that recombinant Swi6 is a substrate for wild-type Hsk1&#8722;Dfp1
5677	12857841_MI:0423	GST:PID phosphorylates MBP,
5678	12857841_MI:0423	PID protein is also active as a protein kinase (Fig. 6). Next, we determined whether PID phosphorylates TCH3 and PBP1 by coincubating GST:PID with the His-tagged versions of TCH3 or PBP1 in the presence of calcium. GST:PID did not phosphorylate TCH3 or PBP1, whereas autophosphorylation of GST:PID was still detectable.
5679	16601102_MI:0423	The interaction between PID and PDK1 results in a dramatic increase in PID phosphorylation (Fig. 3B). PID showed a 6.5-fold increase in measured phosphate incorporation as compared with MPID. This difference must represent increased PID autocatalysis in response to activation by PDK1, suggesting that transphosphorylation by PDK1 activates PID through up-regulation of autophosphorylation activity
5680	16601102_MI:0423	These results demonstrate that At- PDK1 is a potent upstream activator of PID in vivo.
5681	16857903_MI:0423	MBP-BKI1 can be phosphorylated by BRI1 kinase in vitro.
5682	17693538_MI:0423	Only in the sample containing the SERK1 kinase, one phosphorylated Ser residue was found at position 41 of CDC48A, which is located in the N domain
5683	17785451_MI:0423	SOS2 inhibits NDPK2 autophosphorylation
5684	17785451_MI:0423	We also note that SnRK3.22 itself had a much higher autophosphorylation activity (Figure 3C) than that of SOS2
5685	10069336_MI:0424	The phosphorylation of GST fusion proteins by purified d-Abl is shown following a kinase assay with gamma32P-ATP
5686	10329624_MI:0424	Immunopurified Tor2 phosphorylates recombinant Tap42 in vitro.
5687	10383400_MI:0424	In vitro phosphorylation of theta PKC-V1 by p59fyn.
5688	10535927_MI:0424	Phosphorylation of LHY by CK2
5689	10535927_MI:0424	Phosphorylation of LHY by CK2 in vitro
5690	10590166_MI:0424	As shown in Figure 7A, both the GST fusion form and the cleaved form of CIPK1 autophosphorylated themselves in the presence of Mg21 or Mn21. Interestingly, Mn21 seemed to be a much more effective cofactor than Mg21.
5691	10593939_MI:0424	To test if the Arabidopsis U1-70K-interacting proteins (SR33, SR45, and recently reported SRZ21 and SRZ22 (62)) are the substrates for AFC1 or AFC2, in vitro phosphorylation assays were performed. Each plant SR protein was incubated with [g-32P]ATP either in the presence or absence of protein kinase. Duplicate blots were made exposed to x-ray film and then probed with either T7.Ab or S protein. As shown in Fig. 5B, SR proteins are phosphorylated by AFC2, and the phosphorylation resulted in slower migration of proteins.
5692	10733566_MI:0424	TNF-a stimulation of HEK293 cells transfected with each IKKa isoform resulted in an increase in immunoprecipitable kinase activity towards GST-IkBa(1-62)
5693	10801826_MI:0424	purified GST-PECAM-1 fusion protein was phosphorylated ex vivo with Src enzyme
5694	10801826_MI:0424	Taken together, our in vitro model systems support the concept of an inverse correlation between PECAM-1 serine/threonine phosphorylation and its ability to associate with gamma -catenin and, moreover, may indicate that PECAM-1 is an in vivo PKC substrate.
5695	10951572_MI:0424	p53 as target of VRK1 activity
5696	11030144_MI:0424	In vitro kinase assays using purified recombinant proteins showed (Figure 5a) that His6-BUBR1 (lane 3), but not His6-BUBR1K795M (lane 4), strongly phosphorylated GST-p55CDC.
5697	11154276_MI:0424	Recombinant Akt phosphorylated a GST fusion protein containing a 99-amino-acid fragment of human ASK1 (aa 20 to 118) (GST-ASK1), which contains the putative Akt phosphorylation
5698	11402167_MI:0424	In agreement with previous findings (Halfter et al., 2000Go), SOS3 was necessary for SOS2 phosphorylation of p3 but not for SOS2 autophosphorylation
5699	11577348_MI:0424	we assayed the enzyme activity of Btk on a peptide, KKVVALYDYMPMN, that corresponds to aa 217-229 of human Btk and includes the principal tyrosine autophosphorylation site28. This peptide functions as a good substrate of Btk kinase activity29. First, we tested the activity of GST-IBtk on the kinase activity of purified GST-Btk (Fig. 4a,b); in these experiments, IBtk inhibited Btk tyrosine activity in a dose-dependent manner
5700	11577348_MI:0424	we recovered endogenous Btk from MC3 B cells by immunoprecipitation and tested it for tyrosine kinase activity in the presence of either full-length or truncated IBtk. IBtk efficiently downregulated Btk tyrosine kinase activity
5701	11683500_MI:0424	To determine whether Bob1 is Byr1 substrate, kinase assays were performed in which purified GST and GSTByr1 proteins were incubated with CM-Spk1 (positive control) and CM-Bob1 immune complexes. GST-Byr1 phosphorylated CM-Spk1 in these assays, but did not phosphorylate CM-Bob1 (Fig. 4A), suggesting that Bob1 is not a direct substrate for Byr1.
5702	11883897_MI:0424	Use of nucleotide donor by the GST VRK1 kinase in an autophosphorylation assay.
5703	12393858_MI:0424	Thus, KPI-2 phosphorylated Thr320 in PP1C,
5704	12493754_MI:0424	Immune complexes containing FLAG-Plk1 transiently expressed in 293T cells phosphorylated recombinant His-FLAG-Chk2-KD and GST-Chk2-(1-221) in vitro
5705	12529400_MI:0424	Daxx was also phosphorylated by HIPK1 in vitro
5706	12612082_MI:0424	Purified bacterially expressed GST-HEI10 was incubated with purified active cyclin B-cdc2 complex in the presence of [-32P]ATP. The presence of an 65-kDa band corresponding to autophosphorylated cyclin B indicates that the cyclin B-cdc2 complex is active (Fig. 7A, lanes 1 to 4). When HEI10-GST was added to the reaction as a substrate, an additional phosphorylated band (60 kDa) that comigrates with HEI10-GST was observed
5707	12727879_MI:0424	KaiB interacts with a KaiA-KaiC complex during the late subjective night. KaiB-KaiC binding is accompanied by a dramatic reduction in KaiC phosphorylation and followed by dissociation of the clock protein complex(es).
5708	12727879_MI:0424	KaiC rhythmically associated with KaiA prior to binding with KaiB
5709	12730857_MI:0424	In vitro phosphorylation experiment on glutathione S-transferase-I-B showing that recombinant ROCK, in the absence or presence of Y-27632, did not phosphorylate I-B (upper panel), whereas it induced S6 kinase substrate peptide phosphorylation that was inhibited by Y-27632
5710	12730857_MI:0424	ROCK associates with and activates IKK. The IKK immune complex was assayed for I-B kinase activity
5711	12805220_MI:0424	An in vitro kinase analysis of the purified proteins showed that LKB1-WT directly phosphorylated STRAD, whereas LKB1-KD did not (Figure 3D).
5712	12805220_MI:0424	Remarkably, when the isolated complexes were analysed in an in vitro kinase assay in the presence of [&#947;-32P]ATP, STRAD became phosphorylated and LKB1 autophosphorylation was strongly enhanced (Figure 3A and B).
5713	14521924_MI:0424	hAATYKs and KIAA0641 were phosphorylated by Cdk5/p35 in vitro
5714	14978263_MI:0424	We identified the sites in CCA1 that are phosphorylated by CK2 in vitro.
5715	15105425_MI:0424	293T cells were transfected with a construct expressing HA-VRK1, and the exogenous VRK1 was immunoprecipitated with an anti-HA antibody (Fig. 2B, right lane).
5716	15105425_MI:0424	endogenous human VRK1 also can phosphorylate ATF2 in its amino-terminal region.
5717	15105425_MI:0424	phosphorylation of GSTATF2 by GST-VRK1 in vitro.
5718	15147888_MI:0424	CGI-99 interaction with hNinein blocks hNinein phosphorylation by GSK3&#946;
5719	15169888_MI:0424	The MEK kinase activity of immunoprecipitated Myc-TPL-2 was determined using GST-MEK1(K207A) protein as a substrate.
5720	15319482_MI:0424	However, TTL was phosphorylated when the two fusion proteins were mixed together in the kinase assay solution.
5721	15378002_MI:0424	VRK1 phosphorylates c-Jun
5722	15380617_MI:0424	As shown in Fig. 4A, B'gamma3 was identified as a potent Chk2 substrate
5723	15380617_MI:0424	B'gamma1 was also phosphorylated by Chk2
5724	15542844_MI:0424	Phosphorylation of p53 in Thr18 in vitro by using GST-VRK1 fusion.
5725	15592873_MI:0424	AtSERK1kinase is able to transphosphorylate AtCDC48 and GF14
5726	15592873_MI:0424	Transphosphorylation of GF14 and GF1439-248 by GST-AtSERK1
5727	15695390_MI:0424	Analysis of phosphorylation by autoradiography (Fig. 2B) showed strong incorporation of radioactivity in the E-cadherin immunoprecipitate at 120 kDa, demonstrating phosphorylation of E-cadherin by PKD1
5728	15695390_MI:0424	a strong band in lane 3 below 6 kDa [Fig. 2B(1) lane 3)] indicates Syntide-2 phosphorylation by PKD1.
5729	15886098_MI:0424	Kinase assays with purified His6-ABL2 (1.5 nM), GST-CRK or GST-CRKY222F (chicken) (17 nM), and RIN1-ABD-His6 (5 nM or 10 nM).
5730	15886098_MI:0424	Kinase assays with purified His6-ABL2 (1 nM), His6-CRKII (human) (1 &#956;M), and RIN1-ABD-His6 (± STI571 [10 &#956;M]).
5731	15935775_MI:0424	BRI1 Phosphorylation Can Be Intermolecular
5732	15964553_MI:0424	TSSK5 phosphorylated CREB at Ser-133.
5733	15990873_MI:0424	HA-tagged MPK4 from plants phosphorylated recombinant His-tagged MKS1
5734	15990873_MI:0424	Kinase assays with MPK6 or MPK4 immunoprecipitated from plant cells showed that fulllength W25 was preferentially phosphorylated by MPK4
5735	16278681_MI:0424	Inhibition of Pak1 activity by CRIPak in vitro and in vivo
5736	16280327_MI:0424	Akt1 Phosphorylates the cl10 C-terminal Ser218 and Ser231 Residues
5737	16282323_MI:0424	in vitro kinase assays were performed using equal units of activity of either pure ERK, Akt, Rsk, or Gsk-3
 using GSTBimEL (top left panel) or GST (bottom left panel) as substrate. As positive controls, the kinase activity of each pure enzyme was tested using its model substrate protein (right panel).
5738	16286467_MI:0424	IL-1beta or H2O2 treatment of MCF-7 cells induces IKKalpha and IKKbeta kinase activity.
5739	16286467_MI:0424	Immunoprecipitated FLAG-tagged WT-NIK demonstrated a significant increase in its ability to phosphorylate GST-IKKalpha following H2O2 treatment)
5740	16286467_MI:0424	Results from these studies demonstrated that H2O2 and IL-1beta treatments stimulated immunoprecipitated NIK to phosphorylate GST-IKKalpha but not GST-IKK beta(Fig 5C).
5741	16286467_MI:0424	the ability of MEKK1 to phosphorylate GST-IKKbeta following TNFalpha treatment.
5742	16286470_MI:0424	Furthermore, active ERK2 could phosphorylate 
N-MKP-1 but not 
N-MKP-1(ANAP) (Fig. 2B).
5743	16291755_MI:0424	Anti-ERK2 immunoprecipitates (I.P.) of total cell lysates were subjected to in vitro kinase assay using GST-Elk1 as substrate.
5744	16291755_MI:0424	Lysates were immunoprecipitates with an anti-IKKbeta mAb and analyzed for catalytic activity by in vitro kinase assays (IVK) using GST-IkappaBalpha as a substrate.
5745	16291755_MI:0424	Similarly, the TNF-mediated activation of ERK, as measured by in vitro kinase assays using GST-Elk1 as substrate
5746	16291755_MI:0424	the same cell lysates were immunoprecipitated using anti-JNK1 antibody prior to eamination of JNK kinase in vitro kinase assay using GST-c-jun as substrate.
5747	16293614_MI:0424	N-WASP Phosphorylation Is Enhanced 40-fold upon Binding to Activated Cdc42
5748	16293614_MI:0424	We measured the rate of phosphate incorporation from ATP by the Lck kinase domain into a series of N-WASP constructs.
5749	16293623_MI:0424	Differential phosphorylation of p53 and CREB in response to UV light.
5750	16299177_MI:0424	Ser-110 of ABF4 May Be Phosphorylated by AtCPK32
5751	16306228_MI:0424	We assayed QSK and SIK kinase activity using the CREB co-activator protein TORC2, a recently identified substrate for QIK (Screaton et al., 2004Go), which is also phosphorylated by QSK and SIK
5752	16316999_MI:0424	Whereas SLK and ASK1 independently autophosphorylated to a minor extent, cotransfection of SLK with ASK1 resulted in marked phosphorylation of ASK1 but not SLK
5753	16319058_MI:0424	By using IKK immunocomplex kinase assays with GST-IB as a substrate, we found that TNF evoked increases in IKK activity measured in either anti-IKK or anti-IKK immunoprecipitates of HepG2 cells (Fig. 5A). However, pretreatment with manumycin A blocked both the constitutive and TNFstimulated responses.
5754	16330544_MI:0424	In vitro transcription/translation reactions were programmed with empty vector or a vector that expresses HA-tagged full-length Chk1 and immunoprecipitated with anti-HA antibody conjugated to agarose beads. Following washing, the precipitates were subjected to kinase assays by incubating with [-32P]ATP and the GST-Cdc25C substrate.
5755	16365431_MI:0424	IKK--mediated incorporation of 32P into GST-IB as a substrate was also stimulated in the presence of STAP-2.
5756	16438971_MI:0424	AtDi19 bipartite NLS is phosphorylated by AtCPK11. (A) in vitro phosphorylation of the S100GTNSTLSLLR110 peptide and effect of mutation of specific amino acids on the phosphorylation of the peptide by AtCPK11.
5757	16438971_MI:0424	Recombinant AtCPK11 phosphorylates AtDi19 in vitro
5758	16446437_MI:0424	tau enhance its phosphorylation by GSK-3
5759	16446437_MI:0424	We have also shown by Western blotting that both A40 and A42 when complexed with tau enhance its phosphorylation by GSK-3, and that A42 has a greater capacity to do so than A40.
5760	16461343_MI:0424	After activation of Zap70 by recombinant Lck, both sites became phosphorylated (Fig. 2D).
5761	16461343_MI:0424	To confirm that the interaction between PTPN22cd and TCR{zeta} was direct, recombinant cytoplasmic domain TCR{zeta} (cyto-TCR{zeta}) containing all three ITAMs was phosphorylated in vitro with purified Lck and tested as a potential substrate for PTPN22cd.
5762	16472779_MI:0424	Phosphorylation assays indicated that both AtCRK3 and AtCPK3P1 proteins were able to phosphorylate full length AtGLN1;1 protein and the truncated form AtGLNP2 (Fig. 4, lanes 1-4), which is consistent with the protein interaction results.
5763	16533805_MI:0424	Also, as shown in Fig. 8F, the MEK2-derived D-site peptide was a more effective ERK2 inhibitor than any of the three MKK7-derived peptides.
5764	16533805_MI:0424	Compared with their potency in inhibiting JNK1, the ability of the MKK7-derived D-site peptides to inhibit JNK2 phosphorylation of c-Jun or ATF2 was about 5-fold lower (Fig. 7, F,
5765	16533805_MI:0424	D-site Peptides from MKK7 Inhibit JNK1/2 Phosphorylation of c-Jun and ATF2
5766	16533805_MI:0424	Inhibition of JNK phosphorylation of transcription factors c-Jun and ATF2 with D-site peptides from MKK7.
5767	16533805_MI:0424	To assess the ability of the D1/D2 double mutant to phosphorylate and activate JNK1, wild-type or mutant MKK7 was expressed in HEK293 cells, immunoprecipitated, and mixed with purified JNK1 and c-Jun proteins in a coupled kinase assay (Fig. 5C).
5768	16713564_MI:0424	Clb2 was immunoprecipitated, and associated kinase activity was measured using Histone H1 and the Net1(1-600) fragement as substrates.
5769	16814720_MI:0424	The results showed that CIPK23 phosphorylated cAKT1
5770	16837009_MI:0424	The determination of KM values for (a) LIMKtide and (b) RAFtide. Initial velocities were measured with 40nM full length PAK2 using a coupled kinase assay
5771	16837009_MI:0424	To test this, we performed kinase assays to measure the rate of incorporation of 32P-labeled phosphate onto the inactive kinase domain (PAK2Inact) by full length wild-type PAK2.
5772	16843263_MI:0424	Myc-tagged wild-type and mutant HER2 were precipitated from MCF10A/HER2WT and MCF10A/HER2YVMA cells, respectively, and the pull-downs were tested in an in vitro kinase reaction. When ATP was added, HER2YVMA showed markedly higher tyrosine phosphorylation than HER2WT
5773	16843263_MI:0424	we performed an in vitro kinase assay using GFP-fused K721R (kinase-dead) EGFR (Ewald et al., 2003) (EGFRKD) as substrate. Myc-tagged wild-type and mutant HER2 receptors were precipitated from transfected MCF10A cells and incubated with EGFRKD-GFP in the presence or absence of ATP. In the absence of ATP, no phosphorylation of EGFRKD-GFP was detected. Both HER2WT and HER2YVMA phosphorylated EGFRKD-GFP in vitro, but this effect was at least 5-fold higher with the insertion mutant
5774	16862148_MI:0424	To determine whether or not ROCK phosphorylates FilGAP in vitro, recombinant ROCK was incubatd with purified full-length FilGAP protein.
5775	16887178_MI:0424	We also observed that NAK phosphorylated XIAP in vitro
5776	16887178_MI:0424	Wildtype DmIKK3 was autophosphorylated and induced the phosphorylation of DIAP1 in S2 cells, whereas none of the four mutant DmIKK3s generated from the alleles DmIKK3G19R, DmIKK3D160N,DmIKK3G250D, or DmIKK3DUbl did so
5777	16899217_MI:0424	Magicin is phosphorylated by Fyn kinase in vitro.
5778	16899217_MI:0424	We mutated these residues (Y64F or Y163F) in His-tagged magicin by site-directed mutagenesis and performed in vitro kinase assays in the presence of Lck.
5779	16930133_MI:0424	As seen in Fig. 1B, both Mst1 and Mst2 were efficiently coimmunoprecipitated with flag-Sav.
5780	16938345_MI:0424	Substantial phosphorylation of the recombinant LAT protein by Fyn or Lck was observed (Fig. 1c).
5781	16963448_MI:0424	To confirm this phosphorylation of Claspin by Chk1, we isolated both proteins separately and performed in vitro kinase assays.
5782	17045206_MI:0424	Kinase activity of CDK2 and CDK4 immunoprecipitates was determined with histone H1 and GST-RB as substrates.
5783	17088250_MI:0424	Phosphorylation of BII2-Spectrin C-terminal by PKA and CK2
5784	17157788_MI:0424	A kinase assay was performed with immunoprecipitated Flag-Chk1 from transfected 293 cells. GST-Che-1 was strongly phosphorylated by Chk1
5785	17157788_MI:0424	Che-1 was phosphorylated by Chk2 as efficiently as p53.
5786	17157788_MI:0424	substitution of Che-1 Ser187 with an alanine (Che-1S187A) prevented Che-1 phosphorylation by ATM
5787	17157788_MI:0424	the phosphorylation of Che-1 with double Ser-to-Ala mutations at residues 141 and 474 (Myc-Che-1S141A/S474A) or 141 and 508 (Myc-Che-1S141A/S508A) was markedly attenuated, whereas the phosphorylation of Che-1 with a triple mutation (Myc-Che-1S3A) was abrogated
5788	17157788_MI:0424	The presence of a specific phosphorylation signal on GST-Che-1 and His-p53 positive control, but not on GST alone
5789	17157788_MI:0424	The presence of a specific phosphorylation signal on GST-Che-1 and His-p53 positive control, but not on GST alone (Figure 2E), indicated that Che-1 can be phosphorylated by ATM in vitro.
5790	17157788_MI:0424	The presence of a specific phosphorylation signal on GST-Che-1 and His-p53 positive control, but not on GST alone (Figure 2E), indicated that Che-1 can be phosphorylated by ATM in vitro. Similar results were obtained by performing the kinase assay with ATR
5791	17254966_MI:0424	Lyn and Abl phosphorylate Y88 of p27 in vitro.
5792	17254966_MI:0424	While monomeric p27 was a better substrate for Abl phosphorylation, tyrosine phosphorylation of cyclin A/Cdk2-bound p27 was clearly detected (Figure 1G)
5793	17254967_MI:0424	As for Src, Yes kinase assays showed that phosphorylation of p27 by Yes was reduced by mutational loss of Y74 and Y88 phosphorylation, while Y89F only modestly attenuated phosphorylation by Yes (Figures 1D and 1E).
5794	17254967_MI:0424	Src Preferentially Phosphorylates p27 at Y74 and Y88 In Vitro
5795	17254968_MI:0424	HA-tagged PRAK immunoprecipitated from BJ cells transduced with Ha-RasV12, MKK3E, or MKK6E readily phosphorylated human p53 in vitro
5796	17254968_MI:0424	mutation of Ser37 to Asp essentially abolished phosphorylation by recombinant PRAK or PRAK immunoprecipitated from senescent cells, while mutations of Ser15 or Ser33 had no effect on p53 phosphorylation
5797	17254968_MI:0424	p38 immunoprecipitated from BJ cells at PD29 on day 7 post transduction with Ha-RasV12 or vector control was assayed for kinase activity toward ATF2, wild type p53(1-61) or indicated mutants of p53(1-61).
5798	17254968_MI:0424	PRAK and p38 immunoprecipitated from the DMBA-induced papilloma in the wild-type mouse also showed increased kinase activity toward their substrates, HSP27 and ATF2 respectively, in comparison to the proteins isolated from normal skin in the same mouse
5799	17254968_MI:0424	PRAK immunoprecipitated from the wild-type papilloma had an increased kinase activity toward Ser37 of mp53 when compared to PRAK from the adjacent normal skin
5800	17254968_MI:0424	The S37D protein was accessible to kinases since it was readily phosphorylated by recombinant and immunoprecipitated p38 at Ser33
5801	17280616_MI:0424	we also confirmed that WT-MELK could phosphorylate GST-Bcl-GL but D150A-MELK could not
5802	17289571_MI:0424	Purified Cln2/Cdc28 phosphorylated the WT Ste5 fragment, and this was severely reduced by the 8A or 8E mutations
5803	17292828_MI:0424	Cdc25A may be a direct target of MK2 in vivo, since bothMK2 and Chk1 phosphorylate Cdc25A equivalently in vitro
5804	17314099_MI:0424	PDK1 was immunoprecipitated from the transfected cells, and its activity was measured in an in vitro kinase assay using serum- and glucocorticoid-inducible kinase as a substrate (31).
5805	17349581_MI:0424	Elevated resting levels of p15 and p16 do not restrict the growth of KP#3 cells, which also unexpectedly show stimulation of Cdk4 and Cdk2 kinase activities in response to TGF&#946
5806	17486070_MI:0424	Stearic acid-modified Fus1 peptide inhibits GST-Crk phosphorylation by a bacterially purified, constitutively active, Abl kinase
5807	17486070_MI:0424	Stearic acid-modified Fus1 peptide inhibits target peptide phosphorylation by full-length human Abl kinase
5808	17513757_MI:0424	Under these conditions, immunoprecipitated PRP4 phosphorylated both itself and KLF13 (Fig. 3A, lane 4).
5809	17535800_MI:0424	It can be seen that full-length GST-POSH is indeed directly phosphorylated by both Akt1 and Akt2 in vitro, whereas GST alone is unmodified (Fig. 2B, compare lanes 5 and 6 with 2 and 3).
5810	17587183_MI:0424	In vitro, MEKK1 was able to transfer the radioactive phosphor to WRKY53
5811	17588663_MI:0424	The regulatory domain (RD) of PKCzeta is selectively phosphorylated by PKCtheta
5812	17657516_MI:0424	STK25 phosphorylates CCM3
5813	17681130_MI:0424	Mass spectrometric analysis of BIN2-phosphorylated BZR1 protein showed that serine-173 in the putative 14-3-3 binding site of BZR1 is phosphorylated by BIN2
5814	17693255_MI:0424	In vitro kinase assays demonstrated that the TSC1 domain 301-600 was strongly phosphorylated by IKK&#946;, whereas other domains of TSC1 were not phosphorylated by IKK&#946; under the same conditions (Figure S7A, lanes 1-4).
5815	17693538_MI:0424	SERK1 Phosphorylates Ser-41 in the N Domain of CDC48A
5816	17721511_MI:0424	Finally, we confirmed DDR1 as a potent imatinib target by measuring inhibition of the purified catalytic domain by means of autophosphorylation (IC50  22 nM) and the phosphorylation of a peptide substrate (IC50 31 nM, Fig. 4c).
5817	17889654_MI:0424	Wts phosphorylates Yki at S168 in vitro
5818	17960875_MI:0424	Here, we found that HIPK2 phosphorylates HMGA1a at Ser-35, Thr-52, and Thr-77, and HMGA1b at Thr-41 and Thr-66.
5819	17960875_MI:0424	In addition, we demonstrated that cdc2, which is known to phosphorylate HMGA1 proteins, could induce the phosphorylation of HMGA1 proteins at the same Ser/Thr sites.
5820	18191223_MI:0424	Autophosphorylation of &#955;PPase treated Ire1cyto occurs in trans
5821	18243099_MI:0424	Phosphorylation of Borealin by TTK/Mps1
5822	18358814_MI:0424	In contrast, SKN-1A(1-90) was phosphorylated by AKT-1 and AKT-2
5823	18358814_MI:0424	SKN-1C is phosphorylated by AKT-1
5824	18358814_MI:0424	SKN-1C is phosphorylated by AKT-1, -2, and SGK-1
5825	18358814_MI:0424	SKN-1C is phosphorylated by AKT-1, AKT-2
5826	18384742_MI:0424	Autokinase activity of purified recombinant ETR1
5827	18408765_MI:0424	CDK1 immunoprecipitated from LNCaP prostate cancer (PCa) cells phosphorylates the FO1-2 and FO1-3 GST-FOXO1 recombinant proteins.
5828	18449195_MI:0424	In vitro kinase assays5 showed that hSSB1 was a substrate of ATM (Fig. 1d)
5829	18455986_MI:0424	Activation of DivJ by DivKD53N led to increased phosphotransfer to the response regulators DivK
5830	18455986_MI:0424	Activation of DivJ by DivKD53N led to increased phosphotransfer to the response regulators DivK and PleD
5831	18455986_MI:0424	Although DivJnot, vert, similarP readily served as phosphodonor for PleD
5832	18455986_MI:0424	As a consequence of this stimulation, phosphotransfer from PleC to PleD (Figure 2B)
5833	18455986_MI:0424	DivK stimulates DivJ autophosphorylation
5834	18455986_MI:0424	n vitro phosphotransfer between DivJ (2.5 &#956;M) and the response regulators DivK (2.5 &#956;M)
5835	18455986_MI:0424	Phosphotransfer reactions with PleC (10 &#956;M), DivKD53N (10 &#956;M), and PleD (10 &#956;M).
5836	18455986_MI:0424	PleC-mediated phosphorylation of DivK.
5837	18455986_MI:0424	To test this, PleC autophosphorylation activity was monitored in the presence and absence of DivK
5838	18466301_MI:0424	In vitro phosphorylation of AtHSFA1a by AtCBK3.
5839	18466309_MI:0424	BIF2 autophosphorylates and transphosphorylates BA1 in vitro
5840	18599455_MI:0424	B) In vitro kinase assays using GST-BIN2 and MBP or MBP-ARF2. The autophosphorylation of GST-BIN2 serves as a loading control.
5841	18599455_MI:0424	In vitro kinase assay demonstrated that BIN2 is able to bind to and phosphorylate ARF2
5842	18653891_MI:0424	In vitro kinase assays demonstrated that BRI1, but not BAK1, phosphorylates BSK1
5843	18653891_MI:0424	Similar to BSK1, the BSK3 protein is also regulated by BR (fig. S8), is phosphorylated by BRI1 kinase in vitro
5844	18692471_MI:0424	IKK2 Phosphorylates SNAP-23 on Ser120 and Ser95
5845	19000167_MI:0424	eight Arabidopsis MAPKKs that are thought to represent functional MKK enzymes (Hamel et al., 2006). When the incubation products were resolved by SDS-PAGE and probed on a western blot using an anti-pERK antibody that recognizes only the dually phosphorylated form of MAPK, we observed that several upstream MAPKKs, including MKK6, possess the ability to phosphorylate MPK12 in vitro
5846	19103756_MI:0424	Both kinases, Plk3 and VRK1, have autophosphorylation activity, as detected by the strong phosphorylation of the corresponding bands (Fig.1B, lanes 1 and 2).
5847	19103756_MI:0424	Inactive VRK1K179E was phosphorylated when Plk3 was present (Fig.1D, lane 2), but not in the control
5848	19103756_MI:0424	When GSTVRK1 K179E/S342A 28 was used as substrate of Plk3 activity there was no phosphorylation signal of kinase-dead VRK1K179E/S342A (Fig. 1B, lane 5), suggesting that Ser342 is the target residue.
5849	8521818_MI:0424	The second half of the immunoprecipitate was assayed for CAK activity on the GST-CDK2 fusion protein (CAK activity).
5850	9139733_MI:0424	Phosphorylation of GAP-43 by PKC-delta
5851	9144171_MI:0424	RIN1N is a substrate and binding partner for c-ABL
5852	9294234_MI:0424	The ability of the CLV1 kinase domain to phosphorylate KAPP was also tested. The GST-CKD protein was able to phosphorylate the full-length KAPP protein fused to GST (Fig. 4B). Consistent with their abilities to autophosphorylate, GST-CKD1-1 could phosphorylate GST-KAPP at reduced levels and the GST-CKDK720E protein could not phosphorylate GST-KAPP at any detectable level (
5853	9294234_MI:0424	We therefore tested the ability of CLV1 to transphosphorylate. The inactive CKDK720E protein, when removed from the GST-moiety by thrombin cleavage, could be phosphorylated in the presence of the active GST-CKD protein
5854	9303310_MI:0424	p25rum1 kinase activity was detected with both the anti-p34cdc2 and anti-cig1p antibodies, but not with the other two (Figure 8). This result indicates that p25rum1 can be phosphorylated in vitro by the p34cdc2 protein kinase activity associated with the cig1-encoded B-cyclin, but not with the other two B-cyclins.
5855	9482949_MI:0424	Based on this example, we determined whether the purified ARR polypeptides (designated as ARR-H6) can acquire the phosphoryl group from a labeled phospho-HPt domain in a purified system
5856	9520446_MI:0424	At equivalent levels of expression, IKK-a(S176E) had significantly greater kinase activity than IKK-a, as measured by either autophosphorylation or phosphorylation of IkB-a
5857	9520446_MI:0424	mutation of the equivalent serine in IKK-b results in a kinase, IKK-b(S177A), that is fully active in autophosphorylation and in phosphorylation of IkB-a
5858	9520446_MI:0424	To examine its ability to phosphorylate IKK-a and IKK-b, we coexpressed NIK with the catalytically inactive IKK mutants. We found that NIK can phosphorylate IKK-a(KA), but only weakly phosphorylates IKK-b(KA)
5859	9724822_MI:0424	Phosphorylation of CCA1 by CK2 in vitro.
5860	imex:IM-11852_MI:0424	A quantitative assay showed that an additional 4 moles of phosphate were incorporated per mole of Pep-2P substrate and an additional 3 moles of phosphate were incorporated per mole of APC peptide
5861	imex:IM-11852_MI:0424	In vitro kinase assays showed that the PER2 peptide with a phosphate covalently linked to the first serine is phosphorylated at other residues by CKI.
5862	imex:IM-11935_MI:0424	Phosphorylation of SET by CK2
5863	imex:IM-11935_MI:0424	With the aim of studying the functional implication of CK2-SET interaction we performed in vitro phosphorylation assays in the presence of SET using the monomeric (CK2a) or the tetrameric and more active form of the enzyme (CK2ab).
5864	imex:IM-11942_MI:0424	GST:PID or HIS:PID autophosphorylates and efficiently phosphorylates the large hydrophilic loop of PIN1 (HIS:PIN1HL) and Myelin Basic Protein (MBP) (B) or the loop of PIN2 (HIS:PIN2HL) (C) in vitro.
5865	imex:IM-11973_MI:0424	GSK3 radioactively phosphorylates Smad1 in vitro, but only when primed by MAPK
5866	imex:IM-12002_MI:0424	we phosphorylated GST-Cdc25 with Cdk2 in vitro (Figure 1E),
5867	imex:IM-12043_MI:0424	We found that GSK3 phosphorylated TSC2 only when TSC2 had been previously phosphorylated by AMPK
5868	imex:IM-12063_MI:0424	The effects of mutations in the Csk:c-Src interface on the ability of Csk to phosphorylate c-Src, measured by phosphorimaging,
5869	imex:IM-12136_MI:0424	Although the immunoprecipitates contained comparable amounts of aPKC, only the Baz complex phosphorylated Numb
5870	imex:IM-12155_MI:0424	Autoradiograph showing the specific phosphorylation of wild-type Cdc13 by Cdk1-as1/cyclin complexes in vitro
5871	15293782_MI:0426	This was visualized by conventional (Figure 2e-h) and confocal microscopy (Figure 2g-l). Actin bundles (Figure 2h, l) were proximal to caveolae and triggered their accumulation (Figure 2g,k) at or within these cortical areas.
5872	16959611_MI:0428	Immunostaining analysis revealed that mutant p53 and NF-YA localize in the nucleus of SKBR3 cells. RNAi knockdown of mutant p53His175 did not affect the localization of NF-YA
5873	17513757_MI:0428	In contrast, overexpressed KLF13 resides exclusively in the nuclei of the other cells in the same field that is coexpressing both KLF13 and PRP4, supporting the role of PRP4 in KLF13 nuclear translocation.
5874	11489176_MI:0432	Neither the ABI3 nor the ABI4 fusion had any effect on expression, but addition of the ABI5 fusion produced a threefold increase in b-galactosidase activity, re¯ecting binding of ABI5 to this promoter fragment
5875	16428600_MI:0432	The noncanonical Met residue is essential for binding to DNA. Various mutations in an ATHB33-GAL4AD fusion protein were assayed for their ability to bind to target DNA sequences using yeast one-hybrid assays
5876	17202144_MI:0432	pACT-Foxo1 (with a viral VP16 activation domain fused to the Foxo1 N terminus) enhanced the liganded AR function
5877	17587183_MI:0432	The transformation resulted in growth of the yeast on selection medium indicating DNAbinding activity to the WRKY53 promoter of MEKK1 and WRKY53
5878	17587183_MI:0432	To our surprise, a MAP kinase kinase kinase, MEKK1 (At4g08500), was identified as a DNA-binding protein.
5879	18467490_MI:0432	ELF6 and REF6 interact with BES1 at the C termini in yeast.
5880	18467490_MI:0432	Whereas ELF6-C alone had little effect on reporter gene expression, BES1 by itself can activate reporter gene expression.
5881	10069336_MI:0434	Abl and Ena Are Substrates for the Dlar Phosphatase In Vitro
5882	15896299_MI:0434	we assayed PTP1B activity using PNPP as a substrate to determine if phosphatase activity was lost or altered under the experimental conditions. The results presented in Fig. 4A indicate that PTP1B was active in a concentration-dependent manner in the buffers used above. Moreover, under these conditions, PTP1B exhibited its normal range of regulation: stimulation by millimolar concentrations of DTT and EDTA, and inhibition by micromolar concentrations of ZnCl2
5883	16291744_MI:0434	Purified PTP 1B dephosphorylated alpha-actinin in vitro.
5884	16293614_MI:0434	Here we examined the effects of the autoinhibited fold on the ability of the T cell phosphatase to dephosphorylate p-Tyr256-N-WASP proteins.
5885	16293614_MI:0434	N-WASP Dephosphorylation Is Enhanced 30-fold upon Binding to Activated Cdc42
5886	16461343_MI:0434	Interestingly, PTPN22cd dephosphorylated phosphotyrosine 493 (Fig. 3C, lanes 1-5) but not phosphotyrosine 319 (Fig. 3C, lanes 6-10).
5887	16461343_MI:0434	Wild type PTPN22cd clearly dephosphorylated phosphotyrosine 394 of Lck, but did not dephosphorylate phosphotyrosine 505 of Lck (Fig. 3A).
5888	16959610_MI:0434	the wild-type but not the C265S mutant laforin dephosphorylated the p-Ser9 peptide. The same laforin preparation, however, failed to dephosphorylate Bad
5889	17159996_MI:0434	Activity was also tested against a physiological substrate, the insulin receptor. Again, although wild-type PTP1B exhibited robust activity toward this substrate
5890	17350576_MI:0434	Recombinant Coronin 1B phosphorylated in vitro with purified PKCa was efficiently dephosphorylated by SSH1L
5891	17657516_MI:0434	cdFAP-1 of 0.005 U were sufficient to dephosphorylate GST-CCM3
5892	17657516_MI:0434	cdFAP-1 of 0.005 U were sufficient to dephosphorylate GST-CCM3 as well as the kinase GST-STK25 (Fig. 3c).
5893	17936559_MI:0434	The Mdm2 phosphopeptide was dephosphorylated by Wip1 in a dose-dependent manner at serine 395
5894	17936559_MI:0434	Wip1 dephosphorylates intact Mdm2 protein.
5895	18455986_MI:0434	In contrast to PleC mediated phosphorylation of DivK, dephosphorylation of DivK was not increased in the presence of DivKD53N (Figures 3A-3C). Rather, the rate of DivKnot, vert, similarP dephosphorylation was reduced in the presence of DivKD53N.
5896	18455986_MI:0434	PleC-mediated dephosphorylation of DivK.
5897	19000167_MI:0434	The ability of IBR5 to dephosphorylate the -pTEpY- motif of phospho-MPK12 in vitro was then tested by incubating different concentrations of recombinant GST-IBR5 with equal amounts of purified phospho-MPK12 and monitoring the disappearance of the -pTXpY- immuno-signal by western blot analysis. The abundance of the dually phosphorylated form of MPK12 decreased in an IBR5-dose-dependent manner, whereas incubation of phospho-MPK12 with GST alone had no effect (Figure 3c). The efficiency with which IBR5 dephosphorylated MPK12 was markedly increased after cleavage of the GST tag from GST-IBR5 (Figure 3d).
5898	19000167_MI:0434	we used the synthetic phosphatase substrate 3-O-methylfluorescein phosphate (OMFP), and found that the GST-IBR5 could dephosphorylate OMFP in a time-dependent manner
5899	9294234_MI:0434	The CKD protein is dephosphorylated by KAPP, and like other type 2C protein phosphatases, KAPP activity is dependent on Mg2+ and/or Mn2+
5900	16221672_MI:0435	ADAMTS13 was incubated at 37 °C with either VWF76, VWF115, or VWF115-A3 in the presence of physiological concentrations of Ca2 and NaCl. Sub-samples were stopped between 0 and 6 h and analyzed by SDS-PAGE and Coomassie staining to give a qualitative assessment of each reaction (Fig. 2, A-C). In each case, only the full-length substrate band was visible at 0 h. Thereafter, the intensity of this band diminished and two smaller cleavage product bands appeared. In each case, these bands corresponded to the predicted molecular masses of fragments generated following cleavage at the Tyr1605-Met1606 bond. N-terminal sequencing was performed upon the smallest cleavage product and confirmed that proteolysis had occurred between the Tyr1605-Met1606 bond. Visually, VWF76, VWF115, and VWF115-A3 appeared to be proteolyzed by ADAMTS13 at similar rates. Parallel samples were also analyzed by HPLC. The resolution of the full-length substrate from the two cleavage fragments (peaks 1 and 2) arising from proteolysis (Fig. 2) of each different substrate allowed precise quantification of the extent of cleavage at each time point
5901	16221672_MI:0435	For separate determination of the catalytic efficiency of VWF115, repeated time course experiments were performed using low substrate concentrations (250 -500 nM). Repeated time course experiments (n 8) gave a mean value of 7.83  104 M1 s1 for kcat/Km (Table 1). Confirmation of the pseudo-first order conditions was obtained by deriving the same kcat/Km value for VWF115 proteolysis at both 250 and 500 nM. Determination of kcat/Km for VWF76 and VWF115-A3 gave values of 6.39  104 M1 s1 and 6.70  104 M1 s1, respectively (Table 1). These kinetic data confirmed that the VWFA3 domain does not significantly contribute to the rate of A2 domain proteolysis, despite containing an ADAMTS13 binding site (18). The contribution of each selected charged amino acid to VWF proteolysis was assessed by determination of the catalytic efficiency of all the mutant VWF115 substrates at 500 nM(Fig. 4Cand Table 1). The rate of proteolysis of the R1583A mutant was not significantly different from that of VWF115, suggesting that this residue is not important for cleavage. Mutation of Glu1638 and Glu1640 induced a mild (2-3-fold) reduction in catalytic efficiency. The most affected (12-fold reduction) single mutant was D1587A, the kcat/Km of which was 0.640.10104M1   s1. The kcat/Km for K1617A, D1614A, and E1615A, which are predicted to lie on the same surface-exposed loop, were 1.90, 1.36, and 1.13104  M1 s1, respectively. These results implied that this loop might play an important role in the cleavage reaction. Consequently, we generated a triple mutant DEK1614/5/7AAA) containing all 3 residues substituted for alanine. Whereas individually these mutations caused a 4-7-fold reduction in kcat/Km, in combination the catalytic efficiency was 13- fold less than wild-type VWF115, implying that the amino acids in this charged loop may act in synergy
5902	16221672_MI:0435	this approach also served to ascertain whether the most affected charged residue mutants (D1587A, D1614A, E1615A) induced gross structural changes. Despite using increased concentrations of ADAMTS13 (16.5 nM) in the absence of a denaturant, the intact wildtype A2 domain was proteolyzed very slowly, as visualized by gel staining (Fig. 5A), when compared with the A2 domain fragments VWF115, VWF76, and VWF115-A3. When samples containing 500 nM VWFA2 were analyzed by HPLC (Fig. 5C), it was clear that the cleavage reaction did not proceed toward completion (
28% after 5 h), as previously reported (13). The D1587A, D1614A, and E1615A VWFA2 mutants were proteolyzed either at a similar or slower rate (Fig. 5, A and C), suggesting that these mutations do not alter the A2 domain structure markedly. Under denaturing conditions (1 M urea), the wild-type VWFA2 was proteolyzed faster, although it still did not reach completion (
50% after 5 h) (Fig. 5, B and D). Although all the mutants were cleaved at a higher rate under denaturing conditions, they were cleaved appreciably slower than VWFA2, corroborating the direct influence of these mutations upon VWF115 proteolysis.
5903	17981123_MI:0435	In the absence of OMP peptide, a DegS variant lacking the PDZ domain (DegSdeltaPDZ) cleaved RseA
5904	17981123_MI:0435	this variant (called DegS for simplicity) cleaved the periplasmic domain of RseA (residues 121-216; Rseperi) at a single site when OMP peptide was present
5905	17981123_MI:0435	To determine steady-state kinetic parameters, we assayed initial rates of DegS cleavage of different concentrations of RseAperi in the presence of saturating YYF-OMP peptide.
5906	18083098_MI:0435	Synthetic peptides based on predicted SERA4 and SERA6 cleavage sites are correctly cleaved by rPfSUB1.
5907	18083098_MI:0435	They were then compared in kinetic assays with pepF1-6R (6-IATR-labeled Ac-CLVSADNIDIC), a substrate based on the PfSUB1 autocatalytic processing site (Blackman et al., 2002).
5908	18083098_MI:0435	To explore this, peptides incorporating SERA5 processing sites 1, 2, and 3 were assessed for susceptibility to PfSUB1 cleavage.
5909	18083098_MI:0435	To test directly whether SERA5 can be correctly processed by PfSUB1, SERA5 P126 was purified from schizont extracts (Figure S4) and incubated with recombinant PfSUB1 (rPfSUB1).
5910	18083098_MI:0435	To test this, full-length SERA4 and SERA6 were isolated from schizont extracts (Figure S4) then incubated with rPfSUB1 as described above for SERA5.
5911	imex:IM-11918_MI:0435	rhNDUFS3 was specifically and directly cleaved by human GzmA,
5912	imex:IM-11926_MI:0435	The reduction of the molecular size of the full length Ronin and the appearance of an additional smaller band are indicative for Caspase-3 mediated cleavage of Ronin
5913	16330538_MI:0440	In further investigations, the linking sequences between CCPs 1, 2, 3, and 4 of the 
-chain were engineered by insertions of Ala residues (Fig. 1B). Addition of residues between CCP2 and CCP3, or between CCP3 and CCP4, had no effect on binding, whereas insertions between CCP1 and CCP2 caused a loss of M4 binding.
5914	16330538_MI:0440	To define the C4BP region involved in M protein binding, deletion mutants of the 
-chain were tested for binding to theMprotein,
5915	17347412_MI:0440	Binding of ABA to GCR2. (A) ABA binds to the purified GCR2 protein (mean ± SD; n = 3).
5916	18585357_MI:0440	The affinity of DSCAM for netrin-1 was estimated in equilibrium binding experiments using netrin-1(VI.V)-Fc
5917	imex:IM-11911_MI:0440	Summary of Scatchard analysis of 125I-labelled GM-CSF or IL-3 binding to CTLEN/IL3R&#945;/GMR&#945; cells expressing wild type or mutant &#946;c.
5918	12540855_MI:0515	SET7/9 catalyses the addition of a single methyl group to its target lysine.
5919	15933069_MI:0515	Histone methyltransferase assay of Pr-Set7 incubated with increasing concentration of H4 30-mer peptide substrate.
5920	15933069_MI:0515	Pr-Set7 is, indeed, responsible for the addition of a single methyl group to H4-K20 presented either as a peptide or nucleosomal substrate.
5921	16321977_MI:0515	Mtq1p Is Sufficient to Methylate Mrf1p in Vitro.
5922	16321977_MI:0515	Mtq1p Is Sufficient to Methylate Mrf1p in Vivo.
5923	16415881_MI:0515	Mutational analysis of the P-2 position in TAF10 reveals that either a lysine or arginine is required for methylation by SET7/9.
5924	16603186_MI:0515	vSET catalyzes consecutive mono, di and tri-methylation of a H3-K27 peptide (residues 15-33) with rate constants of 0.047 min&#8722;1, 0.015 min&#8722;1 and 0.005 min&#8722;1, respectively (Figure 5(b)). Our steady-state kinetics study showed that the apparent Km and kcat for the overall H3-K27 methylation by vSET are 276.2(±20.7) &#956;M and 1.32(±0.03) s&#8722;1,
5925	17666011_MI:0515	As shown in Fig.6B, both AtFib2 and its N terminal region AtFib2N1-150 were methylated by AtPRMT1a and AtPRMT1b in vitro,
5926	17666011_MI:0515	Fluorography results showed that GST-H4R3N1-54 was methylated by GST-AtPRMT1a
5927	17666011_MI:0515	Fluorography results showed that GST-H4R3N1-54 was methylated by GST-AtPRMT1a and GST-AtPRMT1b
5928	11117257_MI:0588	Figure 4 shows that expression of wheat eIF(iso)4G does interfere with the eIF(iso)4E-LOX2 interaction since no histidine prototrophs could be recovered when methionine was omitted from the growth medium. In contrast, in the presence of methionine that represses wheat eIF(iso)4G expression, growth of the colonies indicates that the interaction between Lex-4E2 and ACTLOX2 can occur.
5929	11117257_MI:0588	In a control experiment, the interaction between Lex-4E2 and wheat eIF(iso)4G expressed from pGAD-Wp86 can be displaced by co-expression of wheat eIF(iso)4G protein as the third partner. This result implies that eIF(iso)4G is able to compete effectively with itself for eIF(iso)4E, and that, despite a strong binding, there is a turnover of eIF(iso)4G bound to eIF4E.
5930	12649160_MI:0588	Analysis of beta-galactosidase reporter activity revealed elevated levels for cotransformants of BrFG and AD-FANCA(Figure 4), implying the ability of HA-FANCG to mediate an interaction between BD-FANCF and AD-FANCA.
5931	12649160_MI:0588	elevated beta-galactosidase activity on conditional expression of HA-FANCG in the presence of AD-FANCA revealed the ability of HA-FANCG to mediate an interaction between monomers of BD-FANCA and AD-FANCA
5932	15047801_MI:0588	When NSP3:88-313 was expressed as the bridging protein in combination with DBD-eIF4G I:120-330 and AD-RoXaN I:1-387, the transformed yeast colonies were able to grow in the absence of histidine (Fig. 5, lane 3), demonstrating that NSP3, eIF4G I, and RoXaN I can form a multiprotein complex. Deletion of the NSP3/PABP-binding domain of eIF4G I (eIF4G I:142-548) impaired the formation of this complex, and yeast colonies were unable to grow on selective medium (Fig. 5, lane 6).
5933	15604664_MI:0588	Mutations in K2 and the amino-terminal portion of K3 are defective in forming AP3/PI/SEP1 ternary complexes
5934	16925602_MI:0588	Higher-order complex formation for the petunia and Arabidopsis Bs proteins.
5935	17644729_MI:0588	CPC and CPC Chimera Proteins Compete with WER for Binding Sites on GL3 or EGL3
5936	18055606_MI:0588	As we observed that PRR3 binds TOC1 in vitro and in vivo and that increased levels of PRR3 resulted in higher levels of TOC1 interact, while in the presence of PRR3, the formation of the TOC1-ZTL complex was disturbed, as indicated by a 50% decrease in b-gal activity
5937	10498867_MI:0663	GFP-53BP2 as well as endogenous p65 were located in the cytoplasm. The colocalization of GFP-53BP2 and p65 was shown by the overlay as yellow in Figure 5h.
5938	10669747_MI:0663	SCHIP-1 colocalizes partially with schwannomin.
5939	10727209_MI:0663	We were able to use immunofluorescent staining in A431 cells to show that 12-LOX co-localized with keratin in the cytoplasm, mostly around the cell nucleus forming a ring-like structure
5940	11259404_MI:0663	Most notably, cells expressing both p19ARF-myc and GFP-Pex19p showed p19ARF in the cytoplasm in more than 90% of cells (Fig. 2A, d) where it colocalized with Pex19p (Fig. 2A, d-f)
5941	11274188_MI:0663	Within certain populations of spines, there was nearly complete colocalization of the PMCA2b and SAP90 fluorescence
5942	11356864_MI:0663	Neurofibromin also codistributed with syndecan-2 in synapses in the mossy fiber tract of the hippocampus
5943	11356864_MI:0663	neurofibromin colocalized with syndecan-3 in axonal pathways such as the corpus callosum
5944	11477570_MI:0663	Cotransfection of the 2 genes changed the distribution pattern of SART3 from diffuse nucleoplasmic spreading to nuclear speckled regions in which DsRed-RNPS1 was colocalized as seen via double-label fluorescence, suggesting a complex formation of the 2 proteins in the nuclear speckled regions.
5945	11577348_MI:0663	In unstimulated cells, confocal analysis revealed a diffuse localization of IBtk and Btk at discrete cytoplasmic regions (Fig. 3f, A,B); an overlay of the two images together with the differential interference contrast (DIC) image showed some colocalization of the two proteins (Fig. 3f, C). Upon BCR cross-linking, the cells showed a predominant submembrane localization of both Btk and IBtk
5946	11786550_MI:0663	GFP-PMCA2b and NHERF2 demonstrated a significant amount of co-localization at the apical plasma membrane of transfected MDCK cells
5947	11919189_MI:0663	ICAP-1alpha  co-localizes with nm23-H2 in peripheral ruffles in spreading Hs68 cells.
5948	11973299_MI:0663	Both Ady3p-CFP and Don1p-YFP formed  rings around the spindles during meiosis II, and these  structures were coincident throughout the second mei-otic division
5949	12011449_MI:0663	The two patterns are highly superimposable (yellow) with punctate distribution around the nucleus characteristic of mitochondrial expression, favoring Siva-1/BCL-XL interaction in the cell.
5950	12050667_MI:0663	The merged picture shows co-expression of p11 and NaV1.8 in the plasma membrane
5951	12065423_MI:0663	Figure 2J shows that ScpA and ScpB foci were coincident in all cells (53/53 cells), suggesting that they might form a complex in vivo.
5952	12080051_MI:0663	Cellular localization of SKIP
5953	12223483_MI:0663	In HeLa cells cotransfected with FLAG-AAT-1alpha  and AMY-1-HA, AAT-1alpha  was found to be still localized in the cytoplasm and colocalized with AMY-1-HA
5954	12421915_MI:0663	We found a clear-cut colocalization pattern of NMMHCIIA and F-actin (Fig. 3A), and also with CXCR4 (Fig. 3B) at the leading edge of migrating T lymphocytes.
5955	12441357_MI:0663	Co-localization by confocal microscopy of Pax8 and TTF-1 in PC cells.
5956	12646258_MI:0663	ECRG2-null EC109 cells were transiently co-transfected with plasmids encoding GFP-tagged ECRG2, HA-tagged MT2A, or both of the two plasmids. Immunofluorescence and confocal laser microscopy showed that these two proteins were all localized mostly to nuclei and slightly to cytoplasm
5957	12651155_MI:0663	CD44 similarly colocalised with transfected PACE-1 and PACE-1-myc proteins in the lamellar ruffles
5958	12651155_MI:0663	When MCF-7 cells were cotransfected with PACE-1 and ezrin-GFP and examined with anti-PACE-1 antibody staining and GFP fluorescence, transfected proteins were also demonstrated to colocalise
5959	12651155_MI:0663	When the MDA-MB-231 cells were transfected with PACE-1-myc and costained with 9E10 anti-myc and anti-ezrin antibodies, the PACE-1 protein was found to colocalise with ezrin but only in the most distal part of the lamellipodia
5960	12711603_MI:0663	multiple foci formation in the interphase nuclei and colocalized with both Suv39h1 and HP1{alpha}.
5961	12827204_MI:0663	Similar experiments showed that SPA1 was distributed in the nucleus and the cytosol but it could be relocalized by COP1 to the same LAF1/COP1 nuclear bodies, which is consistent with an interaction between SPA1 and COP1 in vitro
5962	12827204_MI:0663	To this end, we transiently expressed LAF1 tagged with yellow fluorescent protein (YFP) and COP1 tagged with cyan fluorescent protein (CFP) in onion epidermal cells. Figure 1a shows that the two proteins were indeed localized in the same nuclear bodies, although COP1 was also found in cytoplasmic regions not containing LAF1, which is strictly localized in the nucleus.
5963	14531730_MI:0663	Localization of WBP-2 and tWBP-2 in PC Cl3 thyroid cells
5964	14550308_MI:0663	Both PKCl and MT 2A co-localized in the cytoplasm, particularly to the perinuclear areas as shown by yellow areas in the merged images
5965	14561633_MI:0663	These results place TRY, GL3 and GL1 proteins in the trichome nuclei, where they could interact as observed in the yeast system.
5966	14627983_MI:0663	CASK was also accumulated at cell contacts and colocalized with GFP-Carom (Figure 7Bb-2, arrows).
5967	14627983_MI:0663	Then, cells started to contact with each other and GFP-Carom and MAGI-1 were accumulated at the cell contacts (Ca2+, 15 min).
5968	14653779_MI:0663	However, when ABIN-2 was co-expressed with IKKg, ABIN-2 was redistributed completely to the punctate structures of IKKg (Figure 2B).
5969	14657239_MI:0663	Subcellular localization of p140Cap and colocalization with p130Cas.
5970	14685242_MI:0663	suggesting that Murr1 interacted preferentially with the NF-kappaB-IkappaB-alpha complex. This association was confirmed in vivo by confocal microscopy with fluorescent fusion proteins
5971	14718544_MI:0663	MTCBP-1 expressed in cells formed a complex with MT1-MMP and co-localized at the membrane.
5972	14739298_MI:0663	Furthermore, in the HeLa cells expressing FLAG-MAGE-A4{Delta}N1 and HA-Miz-1, double immunofluorescence staining showed that expression of MAGE-A4{Delta}N1 did not affect the localization of Miz-1 and that both proteins were co-localized in the nucleus
5973	15107855_MI:0663	BBS4 is a pericentriolar protein colocalizing with PCM1
5974	15171681_MI:0663	MCF-7 cells were co-transfected with vectors encoding ECFPS100A1 and S100P-EYFP fusion proteins, and the transfected cells were examined by confocal microscopy. Although there was some variability in the nuclear/cytoplasmic location of the fluorescent fusion proteins, the EGFP and EYFP fluorescence is distributed in the same regions in the transfected cells observed
5975	15182174_MI:0663	In hepatoma cells, the colocalized SCP-2/caveolin-1 (yellow pixels) were distributed primarily in distinct punctuate structures (Figure 1D) but less so at the plasma membrane
5976	15182174_MI:0663	in L-cells the colocalized SCP-2/caveolin-1 was significantly more concentrated at the plasma membrane
5977	15280210_MI:0663	after BMP4 treatment OLIG2 was localized predominantly in the cytoplasm in association with ID4 and ID2.
5978	15280210_MI:0663	Both OLIG1 and OLIG2 colocalized with ID2 and ID4 in the cultured cells.
5979	15293782_MI:0663	Consistently, confocal sections demonstrated a punctate distribution of caveolin-1 in calf pulmonary artery, large vessel endothelial (CPAE) cells (Figure 1i, k) coinciding with ESA/reggie-1/flotillin- 2 positive structures (Figure 1j, l).
5980	15293782_MI:0663	This was visualized by conventional (Figure 2e-h) and confocal microscopy (Figure 2g-l). Actin bundles (Figure 2h, l) were proximal to caveolae and triggered their accumulation (Figure 2g,k) at or within these cortical areas.
5981	15293782_MI:0663	We find that actin localized at caveolae in microvascular SVEC4-10 mouse endothelial cells as analyzed by confocal immunofluorescence microscopy (Figure 2a-d).
5982	15350535_MI:0663	Colocalizatation of NCKbeta and Wrch1 in fibroblasts.
5983	15378002_MI:0663	both VRK1 and c-Jun are located in the nuclei, but outside the nucleolus.
5984	15542844_MI:0663	Accumulation and stabilization of nuclear p53 induced by overexpression of VRK1 detected by confocal microscopy.
5985	15548744_MI:0663	An interesting observation in the BRI1/AtSERK3 coexpression experiments was the lack of complete colocalization between the two fluorescently tagged proteins in the endosomes
5986	15592873_MI:0663	Co-localisation and interaction of AtSERK1 and GF14 in plant protoplasts
5987	15695390_MI:0663	Figure 5 shows the merging of images taken in green (1, PKD1-GFP), red (2, E-cadherin), and DIC (3, DIC) channels indicating that PKD1 colocalizes with E-cadherin at cell junctions
5988	15695390_MI:0663	Merging of images 1 and 2 show that PKD1 and E-cadherin colocalized at the cell junctions of prostatic glandular epithelial cells
5989	15695390_MI:0663	Serial Z-sections of the LNCaP cells were taken at every micrometer using the LSM version 399 software and a gallery of serial Z-sections was constructed confirming the junctional localization and colocalization of PKD1 with E-cadherin in LNCaP prostate cancer cells.
5990	15741320_MI:0663	Colocalization of HFR1 or HFR1(
N) with COP1 in nuclear bodies
5991	15743878_MI:0663	However, VAN3-Venus-positive compartments overlapped with those of the TGN marker, SYP41-GFP
5992	15781858_MI:0663	AtOFP1 controls subcellular localization of TALE protein BLH1.
5993	15781858_MI:0663	KNAT1-GFP is relocated to the cytoplasmic space and colocalizes with AtOFP1 in punctate structures at the cytoskeleton and in the cell periphery.
5994	15827353_MI:0663	whereas the PF6 C terminus-GFP when expressed alone was localized to perinuclear vesicles (Fig. 6C, panels a and b), but it was co-localized with SPAG6-DsRed in co-transfected cells (Fig. 6C, panels c-f).
5995	15855171_MI:0663	Endogenous FAK and p53 clearly co-localized in both cytoplasmic and nuclear areas in BT-474 cells
5996	15855171_MI:0663	GFP-FAK co-localized with p53 in the nuclear, perinuclear, and cytoplasmic speckles
5997	15887118_MI:0663	the intracellular localization of HHM (Figure 6A and 6E) and Jab1 proteins (Figure 6B and 6F) were analyzed in each cell line (KMC-1 and HepG2 cells) by immunofluorescent staining, and the results showed that these 2 proteins were bound in the nucleus
5998	16204054_MI:0663	Double immunofluorescence cytochemistry (Fig. 2E-G) showed that the h-catenin (Fig. 2F) and actinin-4 (Fig. 2E) proteins were colocalized in bleb-like protrusions formed on the free surfaces of SW480 cell clusters
5999	16204054_MI:0663	Immunofluorescence microscopy revealed that the h-catenin and actinin-4 proteins were colocalized at the leading edges of these wavy protrusions
6000	16204054_MI:0663	The expression level of h-catenin was significantly elevated by the inhibition of E-cadherin expression (Fig. 3I and L), and h-catenin and actinin-4 proteins jointly distributed in the bleb-like protrusions formed at the free cell surfaces (Fig. 3J, arrowheads), the same as in SW480 cells lacking expression of E-cadherin (Fig. 2G). In the control transfection, h-catenin and actinin-4 proteins overlapped mainly in the nucleus, and hardly any association between h-catenin and actinin-4 was detected in the cell membranes
6001	16205631_MI:0663	Most cells in the neoplastic urothelium showedcytopl asmic colocalization of E5 andPDGF b receptor, as judged by the yellow fluorescence of the mergedimages
6002	16214168_MI:0663	70% of all Sox10-positive C6 cells contain nuclear Nmi
6003	16272158_MI:0663	Binding of active PAI-1 to the AGP expressed on endothelial cells.
6004	16278681_MI:0663	To further examine the association of CRIPak with PAK1 in vivo, we localized transiently expressed PAK1 and CRIPak by confocal microscopy
6005	16293613_MI:0663	When HA-CLR was co-expressed with RAMP1, fluorescence was seen both inside the cell and on the plasma membrane
6006	16293632_MI:0663	As shown in Fig. 6Aplasmamembrane overlapping was only observed in cells expressing TRPV4-A and TRPV4-D (with almost identical localization),
6007	16293632_MI:0663	To determine whether B, C, and E variants were trapped in the ER, we analyzed their glycosylation profile and carried out colocalization studies with calnexin (an ER resident protein) in transfected HeLa cells.
6008	16301118_MI:0663	AKAP13 colocalizes with transglutaminase in vivo
6009	16314420_MI:0663	confocal microscopy demonstrated that polyclonal antibody to lysosomal Neu1 and monoclonal antibody raised against EBP co-localized on the surface of nonfixed ASMCs.
6010	16316996_MI:0663	upon coexpression with GFP-H-RasLeu-61 (Fig. 4, C and D), the GEF was predominantly redistributed to the plasma membrane (Fig. 4D) where it colocalized with Ras (Fig. 4C).
6011	16319068_MI:0663	Camptothecin treatment does not induce migration of prohibitin and p53 to cytoplasm in untransformed cell lines.
6012	16319068_MI:0663	Prohibitin and p53 co-localize in the nuclei of untreated breast cancer cells and migrate to the cytoplasm upon camptothecin treatment.
6013	16331268_MI:0663	STAT3 translocated into the nucleus and co-localized with Daxx in the nucleus after IL-6 stimulation (Figure 3d). Moreover, we could observe co-localization of endogenous Daxx and STAT3 in the nucleus
6014	16354655_MI:0663	NaTrxh colocalization with the secreted SC10-RNase in the ECM of TT in N. alata SC10SC10.
6015	16403913_MI:0663	nucleolin colocalized with MyH9 during tubule formation
6016	16446437_MI:0663	Coexpression of A
 and tau in neurofibrillary tangles
6017	16449236_MI:0663	colocalization between HA-PITX2A and R127H or S131L FOXC1-GFP is largely disrupted.
6018	16449236_MI:0663	FOXC1-GFP and WT PITX2A were indeed highly colocalized within the cell nucleus
6019	16449236_MI:0663	PITX2 and FOXC1 colocalize in the developing mouse eye
6020	16497658_MI:0663	In cells coexpressing SRp30-RFP or SRp34-RFP and AtCyp59-GFP only low levels of colocalization were observed.
6021	16497658_MI:0663	In cells coexpressing SRp34-RFP and AtCyp59-GFP only low levels of colocalization were observed.
6022	16541025_MI:0663	Here we find a specific subtype of serine/threonine protein phosphatase 2A (PP2A) associating with human shugoshin.
6023	16541025_MI:0663	Meiotic shugoshin of fission yeast also associates with PP2A, with both proteins collaboratively protecting Rec8-containing cohesin at centromeres.
6024	16555005_MI:0663	In cells cosynthesising Tre-GAP and Myl2 or LOC91526, the cosynthesised proteins were found to colocalise to the cell membrane
6025	16621602_MI:0663	Co-localization of CDC48A-CrFP (I) and SERK1-YFP (J) and the merged image (K)
6026	16621602_MI:0663	The SERK1-CrFP containing vesicles all colocalized with Ara6-YFP at the PM and in the cytoplasmic area
6027	16672379_MI:0663	As seen in confocal and deconvolution images in Figure 2, there was significant colocalization of cytLEK1 with SNAP-25 in NIH 3T3 fibroblast and C2C12 myoblast cells.
6028	16672379_MI:0663	Interestingly, when COS-7 cells were cotransfected with 5'LSD and GFP-SNAP-25, a dramatic redistribution of transiently expressed protein localization was observed.
6029	16672379_MI:0663	To determine whether components of the endosomal recycling pathway were also present in the 5'LSD/GFP-SNAP-25 complex, we assesed the distribution of Rab11a in cotransfected cells (Ullrich et al., 1996; Green et al., 1997).
6030	16672379_MI:0663	We next examined  whether these proteins were also in the perinuclear focus in  cotransfected cells. We examined and detected both VAMP2  and syntaxin 4 at the perinuclear focus in cells coexpressing  5'LSD and GFP-SNAP-25 (Figure 4, C and D).
6031	16672379_MI:0663	We next examined whether these proteins were also in the perinuclear focus in cotransfected cells. We examined and detected both VAMP2  and syntaxin 4 at the perinuclear focus in cells coexpressing  5' LSD and GFP-SNAP-25 (Figure 4, C and D).
6032	16845383_MI:0663	Immunofluorescence microscopy analysis revealed that Hausp and Daxx colocalized in nucleoplasma with accumulation in speckled structures
6033	16854975_MI:0663	Co-localization of CFP-SPA1 and YFP-CO in transiently transfected Arabidopsis leaf
6034	16951195_MI:0663	confocal microscopy data supported the colocalization of TG2 with p65 in the cytoplasm (Fig. 4B). The association between TG2 and p65 further increased in response to treatment with A23187, which led to increased translocation of the p65/TG2 complex in the nucleus
6035	16963744_MI:0663	HA-tagged VRK2 appeared to have a pattern of cytoplasmic staining in the transfected cells that was virtually identical to that of BHRF1.
6036	16990133_MI:0663	As observed for Ste2 (Figure 5B), preventing ubiquitylation and endocytosis of Ste3 with 3K-to-R mutations greatly increased the amount of Sst2 recruited to the plasma membrane
6037	16990133_MI:0663	In cells lacking native Ste2, GAL1-promoter-expressed Ste2(297-431)-mCherry, tethered to the plasma membrane via its fusion to Gpa1(1-10), recruited endogenously expressed Sst2-GFP to the cell membrane, especially in the bud
6038	16990133_MI:0663	Ste2(7K-to-R)-mCherry displayed prominent decoration of the plasma membrane (Figure 5B, lower panels). Most strikingly, the Sst2-GFP signal now was also most pronounced at the plasma membrane (Figure 5B, lower panels). Thus, localization of Sst2- GFP tracked with localization of Ste2-mCherry (Figure S3), as expected for two proteins that associate rather stably and with high affinity. When identical experiments were conducted using Sst2(Q304N)-GFP (Figure 5C), green fluorescence remained exclusively in the cytosol, even in the cells expressing Ste2(7K-to-R)-mCherry
6039	17196169_MI:0663	Among several mAbs against marker proteins, including calnexin and GM130 (Fig. 1C and Supplementary Fig. 1), p125, which is known to localize principally to ER exit sites (or transitional ERs) [10], showed remarkably good colocalization with ALG-2 in the juxtanuclear area
6040	17196169_MI:0663	HeLa cells, Sec31A-1 signals in the perinuclear region colabeled with ALG-2 ones
6041	17196169_MI:0663	the Ca2+-dependent colocalization of ALG-2 with p125 in HeLa cells
6042	17196169_MI:0663	To confirm the interaction between ALG-2 and Sec31A in mammalian cells, we examined subcellular distributions of exogenously expressed FLAG-tagged proteins and endogenous ones by double immunostaining analysis.
6043	17196367_MI:0663	PKD3 partially colocalized with VAMP2, and translocated with RFP-PKD3 in response to 1uM PMA.
6044	17202144_MI:0663	These observations suggest that liganded AR sequestered part of the Foxo1 in the nucleus, even in the presence of IGF1.
6045	17210637_MI:0663	NGB and merlin predominantly colocalized in the perinuclear cytoplasm
6046	17220200_MI:0663	Confocal microscopic analysis showed that PIP5K9 was localized mainly in cellular membranes, the nucleus, and the cytosol, and CINV1 was found mainly in the cytosol but was also detected in the nucleus and membranes
6047	17220200_MI:0663	When the two proteins were coexpressed in tobacco mesophyll and onion epidermal cells, colocalization of PIP5K9-green fluorescent protein (GFP) and CINV1-red fluorescent protein (RFP) was found mainly in membranes and the nucleus (Figure 4D).
6048	17234752_MI:0663	NKX3.1 and Topo I were localized by antibody staining to aggregates in the nucleus as shown on Fig. 9A
6049	17234752_MI:0663	We also transfected LNCaP cells with a fusion construct of Topo I and EGFP. The EGFP-Topo I fusion protein localized similarly to Topo I. NKX3.1 was detected by antibody staining. The two proteins were seen to colocalize in the nuclei
6050	17237354_MI:0663	PGP19 and ProPIN1:PIN1-GFP signals overlapped in the stele, endodermis, and pericycle of roots
6051	17237354_MI:0663	PGP1, PIN1, and PIN2 were also coimmunolocalized in roots. ProPGP1:PGP1-cmyc signal overlapped with PIN1 in stelar tissues between the lateral root cap and the distal elongation zone of the root (Figure 3E) and with PIN2 signal in cortical and epidermal cells in the same region (Figure 3F).
6052	17237354_MI:0663	ProPGP19:PGP19-HA and PIN2 signals overlapped in cortical cells in the root
6053	17237354_MI:0663	ProPGP1:PGP1-cmyc signal overlapped with PIN1 in stelar tissues between the lateral root cap and the distal elongation zone of the root (Figure 3E)
6054	17255092_MI:0663	Confocal microscopic analysis revealed that BRG1 was localized in the nucleus when expressed alone or co-expressed with wild-type SRG3
6055	17255092_MI:0663	SRG3 and SNF5 produced a strong fluorescence signal in the nucleus of cells co-expressing wildtype SRG3 and SNF5.
6056	17314099_MI:0663	Both STRAP and NM23-H1 were distributed mainly in the cytoplasm and colocalized with each other, as seen in the merged image in Fig. 1C.
6057	17329248_MI:0663	Co-localization ofPDE2AandXAP2in HeLa cells
6058	17334399_MI:0663	Asynchronous MCF-7 cells, hydroxyurea (HU; early S phase blocker) and nocodazole (G2/M blocker)-treated cells were fixed and fluorescently stained for both cyclin D1 and BRCA1 proteins (Figure 2). BRCA1 was detected in both the nucleus and cytoplasm of untreated cells, previously reported for MCF-7 cells (Fabbro et al., 2002). Cyclin D1 staining was also found in both the cytoplasm and nucleus (Figure 2, untreated cells). However, both cyclin D1 and BRCA1 were present mostly in the nucleus after HU treatment, indicating that they most likely migrate between the cytoplasm and nucleus at various stages of cell cycle. When red and green channels were merged, colocalization could be observed
6059	17342744_MI:0663	Confocal microscopy showed co-localization/aggregation of HSP27 and CD10 at several locations throughout the C4-2 cells
6060	17347654_MI:0663	In 293T cells cotransfected with PRB and CUEDC2, we found that PRB and CUEDC2 colocalize in the cytoplasm in the absence of progesterone, but colocalized in the nucleus in the presence of progesterone
6061	17355907_MI:0663	Overexpressed GFP-tagged hamartin predominantly localized to cytoplasm, which co-localized with myc-NADE distribution
6062	17373842_MI:0663	Results of this experiment (Figure 4) show that although the HDM2 (detected by green fluorescence) is predominantly localized in the nucleus and EF1R (red fluorescence) in the cytoplasm, co-localization of HDM2 and EF1R can be detected (yellow fluorescence) in the cytoplasm.
6063	17374643_MI:0663	In OVCAR-3 cells, PR65alpha and HRSL3 were preferably localized in the cytoplasm where both proteins are co-distributed
6064	17419841_MI:0663	When BY-2 cells were cotransformed with QQT1-GFP and QQT2-RFP fusions, the signal of QQT2-RFP fusion was much lower compared with QQT2-GFP (Figure 7g,j), but was still higher than the cell autofluorescence level (verified in non-transformed BY-2 cells). Both proteins were colocalized on spindle microtubules (Figure 6i-k), whereas colocalization observed at interphase did not reveal labelling at the cortical microtubule array
6065	17468262_MI:0663	Partial colocalization of ARA6/RabF1-mRFP and GFP-SKD1 in Arabidopsis root epidermal cells.
6066	17468262_MI:0663	Partial colocalization of EYFP-RHA1/RabF2a and GFP-SKD1 in Arabidopsis root epidermal cells.
6067	17468262_MI:0663	Partial colocalization of mRFP-ARA7/RabF2b and GFP-SKD1 in Arabidopsis root epidermal cells.
6068	17510388_MI:0663	Yellow pixels from the LNCaP images in Fig. 3C were displayed alone and indicate that DJ-1-AR colocalization increased during hormonal treatment
6069	17553790_MI:0663	Co-localization of ILK and kAE1
6070	17657516_MI:0663	Furthermore, immunofluorescence analyses demonstrated colocalization of Myc-CCM2 and Flag-CCM3 (Fig. 4c).
6071	17693260_MI:0663	both endogenous SARA (data not shown) and transfected Flag-SARA (Figure 1G) extensively colocalized with EEA1 on early endosomes in HEK cells. Cotransfected rhodopsin was also frequently found on EEA1+/SARA+ early endosomes (Figure 1G)
6072	17693260_MI:0663	The intracellular vesicular myc-syntaxin 3 also colocalized with FLAG-SARA in double transfected HEK cells (Figure 6B).
6073	17699755_MI:0663	Co-localization of HFR1 and LAF1 in nuclear bodies.
6074	17702749_MI:0663	Co-localization of UT-A1 and snapin in UT-A1-MDCK cells.
6075	17785436_MI:0663	colocalization between caveolin-1 and catenin was evident in HT29(ATCC) but not in HT29(US) cells
6076	17785436_MI:0663	ectopically expressed caveolin-1 accumulated near the cell surface in a manner similar to that of -catenin, and an appreciable degree of colocalization was apparent in cells expressing high levels of caveolin-1, as was also the case for MDCK cells
6077	17825054_MI:0663	The GFP::CBL10 fusion protein exhibited a localization overlapping with, but not identical to, ARA6 (Figure 7A:a-c) or ARA7 (Figure 7A:d-f),
6078	17875708_MI:0663	we confirmed that PARP-14-PGI/AMF are indeed colocalized in vivo in HT-1080 cells by immunofluorescence analysis (Fig. 3) using confocal microscopy. PARP-14 was found to predominantly localize at the perinuclear region and slightly at the peripheral region of the cells (Fig. 3A), whereas PGI/AMF was distributed throughout the cytoplasm (Fig. 3B) and colocalization was readily observed mainly in the perinuclear region
6079	17922164_MI:0663	Overexpressed Flag-SEPT9 and GFP-SEPT14 colocalize to stress fibers in CHO cells
6080	17934516_MI:0663	In HVTs-SM1 cells, ICBP90 (Figure 6a) and DNMT1 (Figure 6b) were also co-localized in the entire nucleoplasm
6081	17934516_MI:0663	The merged picture (Figure 5c) showed that ICBP90 and DNMT1 were in general colocalized in discrete regions in the nucleus, and that the interaction between ICBP90 and DNMT1 is a highly frequent event.
6082	17965270_MI:0663	Since STH2 by itself gives a uniform fluorescence, the detection of nuclear speckles when coexpressed with untagged COP1 suggests the recruitment of STH2 into COP1 speckles. Coexpression of CFPCOP1 also resulted in the localization of YFP-STH2 into nuclear speckles; however, we did not detect any FRET in these experiments
6083	17965270_MI:0663	Since STH2 showed a similar localization pattern to HY5, we wanted to determine whether STH2 interacts with COP1 in vivo. To this end, we coexpressed unfused COP1 (35S:COP1) with CFP-STH2 in onion epidermal cells. A weak uniform fluorescence with consistent nuclear speckles was seen
6084	17967441_MI:0663	Transfection of 293T cells with hMLH1 wt (Fig. 2, third panel) or restoration of endogenous hMLH1 expression by promoter demethylation using 5-aza-2-deoxycytidine (Fig. 2, bottom panel) prompted strong expression of endogenous Tb4 and colocalization with hMLH1 mainly in the nucleus.
6085	17967441_MI:0663	Transfection of 293T cells with hMLH1 wt (Fig. 2, third panel) or restoration of endogenous hMLH1 expression by promoter demethylation using 5-aza-2-deoxycytidine (Fig. 2, bottom panel) prompted strong expression of endogenous Tb4 and colocalization with hMLH1 mainly in the nucleus. This finding was confirmed in HCT-116 mlh 1-2 cells (data
6086	17991437_MI:0663	FS co-localizes with ANG in the nucleus
6087	18000879_MI:0663	Additionally, HeLa cells were cotransfected with BBS1, BBS2, BBS4, and BBS7 inserted into pDsRed and ALDOB-/EXOC7-/FLOT1-/KRT18-/PAX2-pEGFP. Colocalization of BBS proteins and their interactions partners was detectable at punctuate subcellular structures, suggesting partially overlapping protein expression at the microtubule-organizing center (Fig. 4).
6088	18001824_MI:0663	Figure S5. Accumulation of 53BP1 and BRCA1 at the DSB sites is independent of each other
6089	18001824_MI:0663	Strikingly, although MDC1-WT and MDC1-3A were expressed to similar levels (Figure S3A) and formed readily discernible IR-induced foci (Figure 2G, bottom), only the WT protein was able to restore GFP-RNF8 accumulation at the DSB sites (Figure 2G, bottom).
6090	18001824_MI:0663	the same MDC1-3A mutant remained fully proficient to interact with NBS1 (Figure S3B) and support NBS1 focus formation (Figure S3C).
6091	18001824_MI:0663	Thus, GFP-RNF8 spanned the entire chromatin regions marked by &#947;-H2AX (Figure 1C, left).
6092	18001824_MI:0663	U-2-OS/shRNF8 cells were induced or not with Dox for 48 hr, exposed to laser microirradiation, and 1 hr later coimmunostained with antibodies to RAP80 and gamma-H2AX.
6093	18056116_MI:0663	intracellular fluorescent studies showed that ectopic AKR1B10-EGFP co-localizes with cellular ACCA protein in the cytoplasm of RAO-3 cells
6094	18056989_MI:0663	We also observed the co-localization of BCRP and Pim-1L on the plasma membrane
6095	18065690_MI:0663	Subpools of SGT1b and HSC70 Localize to the Nucleus
6096	18165900_MI:0663	In untreated cells transfected DR4 was localized at the membrane and in the ER/Golgi compartment surrounding the nuclei. ARAP1 was positioned in the ER/Golgi compartment in agreement with previously published data, but a significant fraction of ARAP1 was also localized at the cellular membrane. At both sites ARAP1 apparently co-localized with DR4
6097	18191225_MI:0663	Cav1&#8722;/&#8722; MEF cotransfected with PTRF-Flag and Cav1-HA
6098	18191225_MI:0663	Cav3 (Figure 3C) in Cav1-/- MEFs also caused the recruitment of PTRF to the plasma membrane,
6099	18191225_MI:0663	In contrast, zebrafish caveolin generated caveolae and recruited PTRF to the plasma membran
6100	18191225_MI:0663	WT MEF (A) and NIH 3T3 (B) fibroblasts grown on coverslips were labeled for endogenous Cav1 and PTRF, then examined by confocal microscopy.
6101	18191611_MI:0663	Overlay images indicated that Oct-4 and PKM2 in the nucleoplasm partially overlapped
6102	18286207_MI:0663	endogenous JIP1 proteinm overlapped in part with the VRK2A signal that has been reported to be bound to the endoplasmic reticulum by its C-terminal region (Fig. 5C, left column). In the case of VRK2B the pattern detected is much more diffuse in the cytosol (Fig. 5C, right column)
6103	18286207_MI:0663	JIP1 signal colocalized, in both cell lines, indicating close proximity with both ER
6104	18326491_MI:0663	We infer that G&#947;1 is required for plasma membrane localization of G&#946;,
6105	18329370_MI:0663	Analysis of naive CD4+ T cells revealed that Crtam, Talin, and CD3 coaccumulated
6106	18329370_MI:0663	coaccumulation of Scrib and Crtam in naive T cells activated for 14 hr with plate-bound anti-CD3/28 mAbs (Figure 4B, panels 1-3) and with OVA-pulsed dendritic cells (DCs) (Figure S10A, top).
6107	18329370_MI:0663	Scrib and Cdc42 polarization and coaccumulation
6108	18329370_MI:0663	The biochemical interaction was further supported by analysis with confocal microscopy demonstrating coaccumulation of Scrib and Crtam in naive T cells activated for 14 hr with plate-bound anti-CD3/28 mAbs
6109	18332111_MI:0663	JRAB/MICAL-L2 and actinin-4 primarily colocalized at cell-cell junctions
6110	18492870_MI:0663	We took advantage of the distinct sources for anti-SEC8 (rabbit) versus anti-EXO70A1 and anti-SEC6 (mouse) and demonstrated colocalization of SEC8 and EXO70 proteins and SEC8 and SEC6 proteins, respectively, by double labeling
6111	18505803_MI:0663	The YFP-tagged MTA proteins clearly colocalize to the same discrete spots within the nucleus when coexpressed with FIP37-CFP (Figure 7C), further supporting their in vivo interaction.
6112	18510929_MI:0663	&#916;ECN-HA (red) expressed using MARCM colocalizes with Hrs (aqua) in endosomes
6113	18510929_MI:0663	Colocalization of endogenous Bib and Hrs in WT wing disc endosomes
6114	18510929_MI:0663	Subcellular distribution of HA-Bib-E71N expressed using patched (ptc)-GAL4 (C) in a wing imaginal disc also labeled for Hrs (C') showing colocalization in some intracellular puncta
6115	18585357_MI:0663	DSCAM (red) and DCC (green) proteins colocalize in precrossing commissural axons in transverse sections of the E12 rat spinal cord.
6116	18624398_MI:0663	CLEC4G was colocalized with EIF3S2 in MCF-7 cells.
6117	18624398_MI:0663	CLEC4G was colocalized with IFI35 in the cytoplasm
6118	18624398_MI:0663	RBBP6 localized to the nuclear region, where it colocalized well with SFRS7 (Figure 6c).
6119	18649364_MI:0663	Immunofluorescence analysis showed that FLAG-NLS-TSPY was indeed preferentially localized in the nuclei of transfected COS7 cells, while FLAG-TSPY was distributed in both nuclei and cytoplasm similarly with non-tagged TSPY
6120	18649364_MI:0663	To confirm the interaction between TSPY and eEF1A in mammalian cells, immunofluorescence was performed on COS7 cells transfected with TSPY and FLAG-eEF1A1 or eEF1A2-V5 expression vectors.
6121	18674533_MI:0663	Coexpression of atSC35 with SCL proteins resulted in nearly complete co-localisation
6122	18674533_MI:0663	Co-expression of protein pairs indicated in Fig. 5A clearly revealed that SCL proteins do co-localise with each other.
6123	18674533_MI:0663	co-expression of RSp31-GFP with SCL30a-RFP and with SRp30-RFP (another ortholog of the human SF2/ASF) also resulted in complete co-localisation of these fusion proteins
6124	18674533_MI:0663	Co-expression of RSZ33-GFP with SCL28, SCL30, and SCL30a fused to RFP resulted in their partial co-localisation
6125	18674533_MI:0663	Co-expression of RSZp21 and RSZp22 fused to GFP with RSZ33-RFP resulted in co-localisation of each protein pair
6126	18674533_MI:0663	Co-expression of RSZp21-GFP and RSZp22-RFP also resulted in their complete co-localisation
6127	18674533_MI:0663	In contrast, cells co-expressing atSC35 and SRp34/SR1 showed only partial co-localisation which is also evident from quantification of fluorescence intensities along the three lines
6128	18674533_MI:0663	In line with the above results cells coexpressing RSZ33-RFP and U1-70K-GFP showed only partial co-localisation
6129	18674533_MI:0663	Therefore, co-localisation of atSC35 with RSZ33 was analysed. As evident from Fig. 6 the two proteins showed precise co-localisation in maximum intensity projections as well as in single confocal images
6130	18796637_MI:0663	Interestingly, upon coexpression of COP1, we found consistent nuclear speckles in addition to a weak uniform fluorescence
6131	18812496_MI:0663	Colocalization of ARC6-CFP and YFP-PDV2 in the cells of young Arabidopsis leaves. Both proteins are expressed under the control otheir native promoters.
6132	18854162_MI:0663	Coexpression of GFP::TAF-4 and HA::TAF-12 resulted in nuclear localization of GFP::TAF-4 in almost all cells that exhibited nuclear HA::TAF-12
6133	18930710_MI:0663	Strikingly, in coexpression experiments, MINK colocalized with most of the vesicular structures containing Rap2 or Rap2(G12V).
6134	19103756_MI:0663	Both VRK1 and Plk3 also colocalized in cytosolic granules in A549 cells (Fig. 2D)
6135	19103756_MI:0663	In interphase and late telophase cells, VRK1 and giantin colocalized in a compacted body, but in intermediate steps along the progression of mitosis they retained their colocalization into smaller vesicles (Fig. 5).
6136	19103756_MI:0663	In the HEK293T cell line VRK1 has a particulate perinuclear, nuclear and fine granular cytosolic aspect and colocalizes with Plk3 in the perinuclear granules. ( 1 Fig.2C).
6137	7954795_MI:0663	Double staining of S2 cells expressing both Su(H)-Myc and N proteins with anti-Myc and anti-N antibodies revealed that Su(H)-Myc is detected primarily in the cytoplasm
6138	8334998_MI:0663	Immunolocalization of Sec2Op and Tip20p.
6139	8596950_MI:0663	Figure 5A shows colocalisation between Dsh and the capped N, consistent with binding of DSH to N.
6140	9580671_MI:0663	Colocalization of hamartin and tuberin in the cytoplasm of COS cells
6141	9614144_MI:0663	Intranuclear sites of CAF-1 were first analyzed by confocal immunofluorescence microscopy (Fig. 6). The p60 subunit (Fig. 6A) directly co-localized with p150 (Fig. 6B),
6142	imex:IM-11867_MI:0663	To explore whether this interaction was supported by the intracellular localization of RSUME and Ubc9, COS-7 and HeLa cells were cotransfected with EGFP-RSUME and RFP-Ubc9 constructs.
6143	imex:IM-11877_MI:0663	These experiments demonstrated that the LRRs (but not the CARD or FIIND domains)of NALP1 are necessary, but insufficient, for binding Bcl-XL (Figures 4D, 4E, S7C, and S7D). These protein-interaction studies were performed by coIP using cell lysates and were independently confirmed by immunofluorescence confocal microscopy analysis of intact cells, where fulllength NALP1 but not NALP1DLRR was shown to redistribute from a diffuse cytosolic to an organellar location when coexpressed with Bcl-2
6144	imex:IM-11902_MI:0663	coimmunostaining experiments for SIRT1 and CLOCK in NIH 3T3 cells showed that at least a fraction of these proteins colocalized in the nucleus (Figure 5C).
6145	imex:IM-11920_MI:0663	Transient expression of C-terminal-truncated Gsm1 or Gsp1 conjugated to Citrine (CIT-GSM1512-934, CIT-GSP1559-1037) monitored in moss cells by confocal microscopy
6146	imex:IM-11931_MI:0663	EphA5 and ephrin-As colocalized in regions where MIN6 cells were in contact with each other
6147	imex:IM-11958_MI:0663	In coexpressing cells, Appl1- and Appl2-Venus colocalized with CFP-Rab5C in a characteristic endosomal pattern
6148	imex:IM-11999_MI:0663	ATXN1[30Q] and RORa proteins colocalized within the nuclei of Purkinje cells by confocal microscopy
6149	imex:IM-12065_MI:0663	Confocal microscopy of endogenous PR65 and CIP2A in HeLa cells
6150	imex:IM-12149_MI:0663	Caco2 cells were doubly immunostained for KIFC3 and E-cadherin.
6151	imex:IM-12149_MI:0663	Caco2 cells were transiently transfected with p120 siRNA, and then double-immunostained for p120 and PLEKHA7
6152	imex:IM-12149_MI:0663	Double-immunostaining for endogenous PLEKHA7 and E-cadherin in Caco2 cells.
6153	imex:IM-12149_MI:0663	Endogenous KIFC3 is increased at the sites where PLEKHA7 or Nezha is overexpressed.
6154	imex:IM-12149_MI:0663	Endogenous Nezha and PLEKHA7 are colocalized at the ZA
6155	imex:IM-12149_MI:0663	Intriguingly, the overexpressed PLEKHA7 molecules upregulated the level of E-cadherin accumulating at the ZA while concomitantly downregulating its level at the lower portions of the junction (Figure 1F).
6156	imex:IM-12153_MI:0663	AnkG colocalizes with &#947;-actin in costameres of isolated muscle fibers.
6157	imex:IM-12153_MI:0663	In control fibers dyn4 demonstrates a punctate distribution along costameres, marked by ankB
6158	imex:IM-12153_MI:0663	In isolated adult tibialis anterior (TA) fibers, ankB colocalizes with &#947;-actin in costameres.
6159	11689709_MI:0676	Using the tandem affinity purification (TAP) procedure, we have purified a six-subunit yeast Holo-Elongator complex containing three additional polypeptides, which we have named Elp4, Elp5, and Elp6.
6160	11742990_MI:0676	In the absence of Set1, we observed that (i) Bre2-TAP and Sdc1 remain associated and no other Set1C members were found;
6161	11742990_MI:0676	Sdc1-TAP and Bre2 remain associated and no other Set1C members were found;
6162	11742990_MI:0676	Swd1-TAP and Swd3 remain associated and no other Set1C members were found
6163	12242279_MI:0676	Conversely, tagging and purification of Iws1 resulted in the isolation of Spt6, further confirming that this interaction occurs in vivo (Fig. 1C).
6164	12242279_MI:0676	Copurifying with the tagged Spt5 were Spt4, a substoichiometric amount of RNAPII, and, surprisingly, a truncated form of Spt6. The small untagged Spt4 polypeptide ran off the gel shown in Fig. 1A, but the presence of Spt4 in the sample applied to the gel was confirmed by tandem mass spectrometry.
6165	12242279_MI:0676	Purification of tagged Spt4 from yeast extracts in the presence of 100 mM NaCl resulted in copurification of three forms of Spt5 as well as a substoichiometric amount of RNAPII (Fig. 1A).
6166	12242279_MI:0676	Tagging and purification of Ctr9 resulted in the coisolation of Rtf1, Leo1, Paf1, and Cdc73, as well as Spt16 and Pob3, but neither the histones nor CKII and Chd1 (Fig. 3F).
6167	12242279_MI:0676	Tagging and purification of yeast Spt6 resulted in copurification of substoichiometric amounts of a previously uncharacterized protein, encoded by the essential open reading frame (ORF) YPR133c, which we have called Iws1 (interacts with Spt6) (Fig. 1B).
6168	12242279_MI:0676	Tagging of Chd1 resulted in copurification of approximately stoichiometric amounts of the four subunits of CKII (CkaI, CkaII, CkbI, and CkbII), as well as substoichiometric amounts of Spt16 and Pob3 (Fig. 3E)
6169	12242279_MI:0676	Tandem and MALDI-TOF mass spectrometry were used to identify the following proteins that copurified with Spt16 and Pob3: Chd1, Ctr9, Paf1, Cdc73, Rtf1, CkaI, CkaII, CkbI, CkbII, histones, and proteins encoded by two uncharacterized ORFs, YOL054w and YOR123c (also known as LEO1)
6170	12242279_MI:0676	These results indicated that there are at least three separable complexes that associate with Spt16 and Pob3: histones and nucleosomes, Chd1/CKII, and the complex containing Ctr9, Paf1, Cdc73, Rtf1, and Leo1. Confirmation came from experiments in which we labeled and purified Leo1 and Rtf1 (Fig. 3F),
6171	12242279_MI:0676	These results indicated that there are at least three separable complexes that associate with Spt16 and Pob3: histones and nucleosomes, Chd1/CKII, and the complex containing Ctr9, Paf1, Cdc73, Rtf1, and Leo1. Confirmation came from experiments in which we labeled and purified Leo1 and Rtf1 (Fig. 3F), Paf1 (Fig. 3G)
6172	12242279_MI:0676	These results indicated that there are at least three separable complexes that associate with Spt16 and Pob3: histones and nucleosomes, Chd1/CKII, and the complex containing Ctr9, Paf1, Cdc73, Rtf1, and Leo1. Confirmation came from experiments in which we labeled and purified Leo1 and Rtf1 (Fig. 3F), Paf1 (Fig. 3G), and Cdc73(Fig. 3H).
6173	12242279_MI:0676	When the yeast counterparts of FACT, Spt16 and Pob3, were tagged and subsequently purified from yeast extracts in buffers containing 150 mM NaCl, large and approximately stoichiometric amounts of Spt16 and Pob3 were isolated and no other proteins were detected by silver staining (Fig. 3A).
6174	12482963_MI:0676	Ioc2p copurified two other proteins in approximately stoichiometric amounts (Fig. 2C). These proteins were subsequently identified by mass spectrometry as Isw1p and Ioc4p (data not shown).
6175	12482963_MI:0676	Ioc3p copurified one other protein in near-stoichiometric amounts, which was subsequently identified by mass spectrometry as Isw1p (data not shown).
6176	14508515_MI:0676	Two bands were unambiguously identified from the eluates obtained from TAP purification as follows: the band migrating at about 72 kDa was identified as menin, while that migrating at about 200 kDa was identified as NMHC II-A.
6177	14508515_MI:0676	While endogenous NMHC II-A was present in both crude extracts, it copurified with menin-tap but not with tap alone.
6178	14565975_MI:0676	Purification of Spc105p coupled to protein A also copurified Ydr532p, a protein of unknown function
6179	14565975_MI:0676	purification of Ydr532p-protein A also copurified Spc105p
6180	14565975_MI:0676	The Mtw1p protein A isolations always showed Dsn1p,Nnf1p, and Nsl1p but some preparations also showed all of the components of the Spc105p and Ndc80p complexes. The reason for this variability was not clear, because Dsn1p-protein A isolations always showed all three complexes. These results suggest that the Mtw1p, Spc105p, and Ndc80p complexes are closely associated.
6181	14565975_MI:0676	The result of the Nnf1p-protein A isolation was consistent with the results shown in Figure 1A; i.e., only Dsn1p, Mtw1p, and Nsl1p were found
6182	14565975_MI:0676	When Mtw1p was coupled to protein A and purified, three other proteins copurified (Figure 1A) and were identified by mass spectrometry as Dsn1p, Nnf1p, and Nsl1p.
6183	14690608_MI:0676	Isolation of the SWR Protein Complex(A) Tandem affinity purifications of the SWR-C were carried out on strains containing either no tagged protein or TAP-tagged versions of Swr1, Swc2, Swc3, Swc5, and Swc6.
6184	15485833_MI:0676	Here we first showed by mass spectrometry and gel filtration that Arc40 is indeed a component of purified yeast Arp2/3 complex but has a strong tendency to form high molecular weight species when analyzed by SDS-PAGE.
6185	15637077_MI:0676	Identification of protein components in purified nuclear RNase MRP
6186	15703063_MI:0676	CSN1 and CSN8 identification by mass spectrometry analysis. Amino acid sequences in boxes correspond to Arabidopsis CSN1 or CSN8 peptides identified by MS/MS mass spectrometry analysis of TAPa-purified protein samples.
6187	15703063_MI:0676	Immunoblotting using antibodies listed in the left panel was performed to recognize six of seven other COP9 signalosome subunits tested.
6188	15761952_MI:0676	When the beads were incubated with total brain cytoplasmic extracts, both FMRP and CYFIP1 were recovered from them but only after specific elution with m7GTP (Figure 1B, lane 3)
6189	15799966_MI:0676	COMMD3, -4, and -6 were identified as COMMD1-associated factors in our TAP screen
6190	15800064_MI:0676	To validate our TAP results, we performed a reciprocal purification from a strain expressing Mto2p-TAP and found Mto1p in the protein complex reproducibly, albeit at a low sequence coverage (4.8, 7.2, and 7% by mass).
6191	15935758_MI:0676	Finally, Trf4p, Trf5p, and Air2p coprecipitated with Mtr4p-TAP; however, in this case, the recovery of Mtr4p was clearly greater than the other proteins.
6192	15935758_MI:0676	Mtr4p and Air2p coprecipitated with Trf4p-TAP, again with apparent stoichiometry
6193	15935758_MI:0676	Mtr4p coprecipitated with Trf5p-TAP,
6194	16301313_MI:0676	pull-down of endogenous, C-terminally TAP-tagged RavA. Identification of the bands by mass spectrometry reveals that RavA interacts with the inducible lysine decarboxylase enzyme, LdcI
6195	16306228_MI:0676	Identification of proteins associated with AMPK-related kinases
6196	16374505_MI:0676	Both Mtr4p and Air1p were identified by mass spectrometry as bands that showed approximate stoichiometry with Trf5-TAP.
6197	16407405_MI:0676	We found two novel proteins that coprecipitated with Csx1-TAP, which we termed Cip1 and Cip2. Cip1 (Csx1-interacting protein 1) was identified by peptides covering 18.4% of its 490 amino acid primary sequence (Figure 1A).
6198	16829593_MI:0676	The database searches identified 13 unique proteins, which were either exosome core proteins (Rrp41, Rrp42, Mtr3, Rrp43, Rrp46, Rrp45, Rrp4, Rrp40, and Csl4) or proteins known to be associated with the exosome (Rrp6, Dis3, Lrp1, and Ski7)
6199	16829593_MI:0676	The subsequent on-line analysis of the eluted proteins using an electrospray ionization time-of-flight mass spectrometer allowed us to identify eight exosome proteins (Dis3, Rrp45, Csl4, Rrp42, Mtr3, Rrp41, Rrp40, and Rrp46)
6200	17101441_MI:0676	Among these specific proteins, Rpd3, Sin3, Ume1, Rco1, and Eaf3 were recovered in all 6 runs, while Sds3, Dep1, Sap30, Cti6, Rxt2, Pho23, Rxt3, and Ash1 were not found in the Rpd3S preparations
6201	17101441_MI:0676	Among these specific proteins, Rpd3, Sin3, Ume1, Rco1, and Eaf3 were recovered in all 6 runs, while Sds3, Dep1, Sap30, Cti6, Rxt2, Pho23, Rxt3, and Ash1 were not found in the Rpd3S preparations (
6202	17215244_MI:0676	Mit1-associated proteins.
6203	17215244_MI:0676	Mit2-associated proteins.
6204	17314511_MI:0676	MudPIT identifications of c&#8209;MYC&#8209;associated proteins were confirmed by Western blot analysis of tandem affinity purified proteins from cells expressing c&#8209;MYC&#8209;TAP (MT) or TAP (T).
6205	17426018_MI:0676	Proteins identified by MALDI-TOF-TOF-MS after a TAP procedure from cultures producing CDKA;1 and CDKF;1 under control of their endogenous promoter, and CDKA;1, CDKB1;1, CKS1, CDKD;2, CDKF;1, and CYCD3;1 under control of the 35S-CaMV promoter
6206	17525340_MI:0676	A search for additional BRCA1-BRCT-binding proteins that bound to tandem affinity purification (TAP)-tagged BRCA1-BRCT domains (15) identified RAP80
6207	17623278_MI:0676	Summary of proteins found to copurify with Prep1-TAP
6208	17704763_MI:0676	The amount of ZTL associated with the TOC1 immune complex was determined from N. benthamiana plants incubated in darkness, red or blue light. In strong contrast to the ZTL-GI interaction, there was no effect of light on the association of TOC1 and ZTL
6209	17704763_MI:0676	We determined the relative proportion of wild-type or mutant ZTL in GI immunoprecipitates from N. benthamiana extracts when expressed together under dark, white, red or blue light. The GI-ZTL interaction was enhanced fourfold in blue light, relative to dark or red light, and similar to results in white light
6210	17704763_MI:0676	We next tested immunoprecipitates from GI-GI-TAP extracts8 for the presence of ZTL. During the light and dark periods, ZTL levels closely correlated with the increasing and decreasing steady-state level of GI (Fig. 3a; light/dark), showing that ZTL and GI exist in a complex together in proportion to their total abundances.
6211	17785451_MI:0676	SOS2 interacts with CAT2 and CAT3
6212	17875927_MI:0676	SOS2 interaction with and regulation of V-ATPase. NTAP-SOS2 purification identified five subunits (A, B1/2/3, C, E1, and G1) of the V-ATPase peripheral (cytoplasmic) sector as being components of a SOS2-containing protein complex.
6213	17979178_MI:0676	Bands corresponding to B-Raf (bait), MEK1 and 14-3-3 are indicated.
6214	17979178_MI:0676	Copurification of Raf isoforms with MEK1 (lane 1) and 14-3-3e (lane 3) baits was confirmed by Western blotting. HEK293 lysates (lane 2) served as negative control. Upper panel: Western blot probed with anti-B-Raf (H145, Santa Cruz). Lower panel: Western blot probed with anti-C-Raf (C12, Santa Cruz).
6215	18045535_MI:0676	p65 Interacts with RPS3
6216	18298670_MI:0676	Arabidopsis Pcf11p-similar protein 4 (PCFS4) forms a protein complex with FY and CLP1p-similar protein 3 (CLPS3)
6217	18577522_MI:0676	The pull-down experiments demonstrated that ETR1 co-purified with TAP-tagged ERS1, ETR2, ERS2, and EIN4
6218	18591351_MI:0676	Silver-stained gel of tandemaffinity purification from TAP-WPP2-expressing 14-d-old Arabidopsis seedlings. Peptides corresponding to WIT1 andWIT2 were identified using tandem mass spectrometry in-gel slices excised fromthe regionsmarkedwith arrowheads.
6219	18835996_MI:0676	Cul1 proteins were detected in the pull-down product of DOR-TAPs transgenic plants
6220	imex:IM-11971_MI:0676	These experiments suggest that the Doa10p complex is relatively simple, consisting of ubiquitin-conjugating and -ligating enzymes and the Cdc48p ATPase complex, including its membrane-recruiting factor Ubx2p
6221	imex:IM-11983_MI:0676	TAP-tagged complexes were purified, and polypeptides shared between RRP4-TAP and RRP41-TAP samples but absent from the wild-type (WT) sample were subjected to MALDI and MS/MS analyses. Nine polypeptides corresponding to known subunits of the exosome core were identified: S1 and/or KH domain-containing subunits RRP4, RRP40A, and CSL4 as well as the RNase PH-type subunits RRP41, RRP42, RRP43, RRP45B, RRP46, and MTR3 (Figure 1 and Table S1 available online).
6222	imex:IM-11988_MI:0676	Although substantially lower, Gle1 also coimmunoprecipitated with Sup35-TAP
6223	imex:IM-11988_MI:0676	Endogenous Gle1 was coimmunoprecipitated with Prt1-TAP (eIF3b)
6224	imex:IM-11988_MI:0676	Substantial levels of endogenous Gle1 were coimmunoprecipitated with Sup45-TAP
6225	imex:IM-12048_MI:0676	LC-MS/MS analysis revealed that indicated gel slices contained p100, p65, and p50 proteins respectively.
6226	imex:IM-12137_MI:0676	Mass spectrometry analysis revealed that the purified fraction included Clr8 and Cul4, consistent with previous findings ([Hong et al., 2005] and [Thon et al., 2005]), as well as a 170 kDa JmjC-domain protein, Lid2 (Figure 1B).
6227	16501604_MI:0678	WNK3 interacts with proteins involved in the regulation of apoptosis
6228	17274640_MI:0678	In murine FLECs, 10 of the 14 remaining PIPs were recognized, including ATM and eIF-2R, two proteins that so far have not been demonstrated to interact stably with PP1.
6229	17274640_MI:0678	In murine FLECs, 10 of the 14 remaining PIPs were recognized, including ATM and eIF-2R, two proteins that so far have not been demonstrated to interact stably with PP1. In addition, this assay identified 27 novel potential PIPs. Remarkably, individual PP1 isoforms were apparently interacting with overlapping but distinct subsets of proteins
6230	17274640_MI:0678	PP1R interactions were markedly different in A549 lung cancer cells. First, the PP1R antibody reacted only with 6 known PIPs including Aurora, while 22 novel PIPs were recognized. It is noteworthy that, in A549 cells, some interactions (protein kinase B or Akt, E-cadherin, PTEN, and survivin) were uniquely present, while others (e.g., ATR, Bax, cyclin E, EGFR, GSK-3R, hamartin, histone deacetylase 1, Id2, MAP ô, Nek2, PP2B, and TSG101) were absent. Altogether, 5 of the tentatively identified novel PIPs bound to only one PP1 isozyme, whereas 13 other novel PIPs appeared to be specific for one isozyme and one of the two cell types
6231	11545742_MI:0697	To assess the functional significance of Pol&#951; interaction with PCNA, we examined whether PCNA could stimulate DNA synthesis by Pol&#951; in the presence of RFC and RPA
6232	12864730_MI:0726	Approx. 3x106 transformants were screened with all three AR NTD baits and the positive clones were sequenced and compared with known sequences available in GenBankTM. A total of 40 unique in-frame positive clones were detected from the LNCaP cDNA library, some of which were picked up multiple times. These included: a steroid receptor chaperone Hsp (only detected with the DBD-containing AR1&#8722;646 bait); the cyclin G-associated Ser/Thr kinase
6233	12864730_MI:0726	DDC (L-dopa decarboxylase) was detected multiple times as a novel AR-interacting protein,
6234	15604664_MI:0726	PI mutants isolated in the PI/SEP3 reverse two-hybrid screen.
6235	11259404_MI:0728	Pex19p and p19ARF interacted strongly in a mammalian two-hybrid assay (Fig. 1B).
6236	16600381_MI:0728	In contrast, we found that the VP-LRR fusion protein activated the reporter plasmid when co-expressed with Gal4-ZXDC.
6237	18430226_MI:0728	For GAL4-BMAL1/PER2-VP16, a 1000-fold increase in luciferase activity was observed (Fig. 1A).
6238	18430226_MI:0728	For GAL4-BMAL1/PER2-VP16, a 1000-fold increase in luciferase activity was observed (Fig. 1A). Similar values were obtained for GAL4-BMAL1/CRY1-VP16 and GAL4-BMAL1/CRY2-VP16 (750- and 950-fold, respectively; Fig. 1C).
6239	18430226_MI:0728	When repeating the same experiments using Gal4-Clock instead of Gal4-Bmal1, we still found a 75-fold transactivation of the reporter in the case of co-transfection with Per2 (Fig. 2A).
6240	18577522_MI:0807	a new band at a size of 180 kDa was detected between the homodimer bands of ETR1-TAP and ERS2(1- 356)-GST, consistent with a predicted heterodimer molecular mass of 167 KD
6241	1961752_MI:0807	Two-dimensional gel electrophoresis of the 25-kDa Ran protein nucleoplasmic monomer (a) or complexed with 47-kDa RCC1 (b).
6242	imex:IM-11868_MI:0808	Autoradiogram after SDS-PAGE revealed native or cleaved SRP-6 (*) and a higher molecular mass complex with catL or calpain-2
6243	imex:IM-11919_MI:0808	The purified FimD:tip complexes were incubated in SDS sample buffer at 25° or 95°C, separated by gel electrophoresis, and immunoblotted with anti-FimC:F, anti-FimC:G, or anti-FimC:H polyclonal antibodies
6244	15469499_MI:0809	Interaction between FTA and FTB fused to either YN or YC resulted in similar fluorescence intensity as long as they were fused downstream of the YFP domain (Figure 2a,b). YFP fluorescence was substantially weaker when FTA and FTB were fused to YN and YC at opposite orientations, upstream and downstream of the split YFP domains (Figure 2c). No fluorescence was detected when FTA and FTB were fused at the same orientation, upstream of YN and YC
6245	15469499_MI:0809	The fluorescence intensity obtained from the interaction between FIE and MEA
6246	16014621_MI:0809	tobacco co-bombarded with pWEN-NY/AtMinD1 and pWEN-CY/AtMinD1 showed clear fluorescence (Fig. 5B). Tobacco co-bombarded with pWEN-NY/AtMinD1(K72A) and pWEN-CY/AtMinD1 also showed clear fluorescence (Fig. 5B), demonstrating that AtMinD1(K72A) is able to dimerize in planta and showing that AtMinD1(K72A) mislocalization is not because of loss of dimerization as observed for ARC11/AtMinD1 (A296G). Tobacco cells bombarded with single vectors (negative controls) showed no fluorescence, as expected.
6247	16489121_MI:0809	These two constructs were cobombarded into onion (Allium cepa) epidermal cells. If they interact physically, YFP fluorescence would be restored, and YFP fluorescence was indeed observed in the nucleus of onion epidermal cells when cobombarded with GRP23-YFPN and RBP36B-YFP
6248	16766674_MI:0809	Subcellular interaction of ICK1/KRP1 with CDKA;1
6249	16814720_MI:0809	The in vivo interaction between CIPK23 and CBL1 or CBL9 was confirmed using BiFC assays
6250	16957774_MI:0809	Characterisation of the AtBARD1 and AtBRCA1 interaction by yeast two-hybrid assay and by BiFC in transiently transfected mustard seedlings.
6251	17092313_MI:0809	To directly establish the physical interaction of CBL1 and CBL9 with CIPK1 in planta, we used bimolecular fluorescence complementation (BiFC) in N. benthamiana protoplasts (Walter et al., 2004). In these assays, both CBL1/CIPK1 and CBL9/CIPK1 complexes were observed exclusively at the plasma membrane
6252	17142482_MI:0809	When the AtBI-1 fused to the N-terminal yellow fluorescent protein (YFP) fragment and AtCaM7 fused with the C-terminal YFP were coexpressed in tobacco leaves, a strong BiFC signal was detected in the epidermal cells
6253	17347412_MI:0809	This indicated that the interaction between GCR2 and GPA1 is specific and that the C terminus of GCR2 is necessary for its interaction with GPA1
6254	17369373_MI:0809	Therefore, we used a technique designated as bimolecular fluorescence complementation. Protoplasts prepared from leaves of 35Spro:GFPc155-HA-ESR transgenic Arabidopsis plants were transiently transformed with plasmids encoding a 35Spro:GFPn173-c-myc-WRKY53 fusion protein. If the WRKY53 and ESR proteins are able to interact directly in plant cells, green fluorescent protein (GFP) should be reconstituted and should then be able to emit green fluorescence. Whereas cells transformed with empty vectors produced no or only background fluorescence, a strong signal was observed in the nucleus when GFPc155-HA-ESR was coexpressed with GFPn173-cmyc-WRKY53
6255	17369373_MI:0809	To show direct interaction between WRKY53 and ESR in plant tissue, we also transformed the constructs into leaf epidermal cells of Arabidopsis by Agrobacterium tumefaciens infiltration. A strong GFP fluorescence was observed in the nuclei of the epidermal cells when GFPn173-c-myc-WRKY53 and GFPc155-HA-ESR were coexpressed
6256	17376809_MI:0809	in leek epidermal cells to verify the observed biochemical interaction between DRN or DRNL and PHV, in vivo, using fulllength DRN and PHVs as the C-terminal part of PHV was sufficient to sustain interaction with DRN in the two-hybrid screen.
6257	17397508_MI:0809	GRX480 interacts with TGA2 in planta
6258	17535810_MI:0809	These data nicely corroborate previous findings based on biochemical analysis (which showed that Tic110 and Tic40 are envelope proteins) and indicated that BiFC fluorescence associated with an atTic110-atTic40 interaction should localize to the envelope.
6259	17535810_MI:0809	The Tic110-Tic40 BiFC signal was also stronger than that mediated by AtFtsZ2-1 homodimerization
6260	17587183_MI:0809	In protoplasts or leaf cells which were transformed with GFPc155-MEKK1/ GFPn173-WRKY53 green fluorescence could clearly be detected indicating that MEKK1 and WRKY53 also interact in living plant cells
6261	17681130_MI:0809	The in vivo interactions of wild type and mutant BZR1s with 14-3-3&#955; were studied using a Bi-Molecular Fluorescence Complementation system (BiFC). BiFC is based on the principle that a functional fluorescence complex is observed when two proteins of interest fused to the N- and C- terminal halves of YFP interact in vivo. Co-transformed BZR1-cYFP and 14-3-3&#955;-nYFP produced strong YFP fluorescence
6262	17712600_MI:0809	BiFC analysis showing interaction of AtCBF5-NYFP and AtNAF1-CYFP within nuclei of transiently transformed N. benthamiana leaves
6263	17825054_MI:0809	CBL10 interacts with CIPK24 at the tonoplast.
6264	17951446_MI:0809	we cotransformed plasmids encoding BiFC fusion constructs of the two proteins with the N- or C-terminal part of YFP into Arabidopsis protoplasts. A restored YFP fluorescence was localized in the nuclei of transfected protoplasts, suggesting that MID and RHL1 can interact in planta
6265	18267075_MI:0809	Reconstituted fluorescence was detected in the cytoplasm, nuclei and chloroplasts
6266	18267075_MI:0809	These results confirm that N and NRIP1 associate only in the presence of p50 in intact, living tissue.
6267	18268542_MI:0809	These results clearly illustrate that FIT interacts with AtbHLH38 or AtbHLH39 in plant cells, while no interaction was observed between AtbHLH38 and AtbHLH39.
6268	18429938_MI:0809	BiFC assays indicate that the coiled-coil region mediates MYA1 dimerization in tobacco leaf epidermis.
6269	18429938_MI:0809	However, the combination of YN-CCGT and YC-CCGT clearly generated reconstituted YFP signal targeted to organelles (Figure 4d), in this case peroxisomes due to co-localization of YFP signal with CFP-labeled peroxisomes
6270	18467490_MI:0809	ELF6 interacts with BES1 in Arabidopsis mesophyll protoplasts, as shown by BiFC.
6271	18653891_MI:0809	cells coexpressing BRI1-nYFP and BSK1-cYFP showed strong BiFC fluorescence at the plasma membrane
6272	18713402_MI:0809	ACI1 interacts with ALC in nuclei of onion cells demonstrated by bimolecular fluorescent complementation assay.
6273	18776063_MI:0809	Indeed, whenWRKY38 was fused to the terminal YFP fragment and coexpressed with HDA19-C-YFP in tobacco leaves, a BiFC signal was also observed predominantly in the nuclear compartment
6274	18776063_MI:0809	when WRKY40 was fused to the C-terminal YFP fragment and coexpressed with WRKY18-NYFP in tobacco leaves, a strong BiFC signal was observed predominantly in the nuclear compartment
6275	18776063_MI:0809	WhenWRKY62-N-YFP was coexpressed with HDA19-C-YFP, a strong BiFC signal was observed predominantly in the nuclear compartment, based on staining with 4,6-diamidino-2-phenylindole (DAPI)
6276	18830673_MI:0809	Additionally, BiFC using full-length DRN and BIM1 proteins reproducibly demonstrated a functional in planta interaction between BIM1 and DRN in multiple independent experiments when co-bombarded into leek cells
6277	18849490_MI:0809	This result was confirmed in Arabidopsis protoplasts using a bimolecular fluorescence complementation (BiFC) assay. HUB1 and HUB2 interacted with both HUB1 and HUB2, whereas neither HUB1 (YFPN-HUB1 or YFPC-HUB1) nor HUB2 (YFPNHUB2 or YFPC-HUB2) was able to interact with YFPC or YFPN (Figure 2B), suggesting that the observed interactions were specific.
6278	18948957_MI:0809	Further support for the hypothesis that KRP6 and KRP7 may be in vivo substrates of FBL17 is provided by binding of N-terminal yellow fluorescent protein (YFP)-FBL17 to C-terminal YFP-KRP6 and KRP7 in bimolecular fluorescence complementation (BiFC) assays in transfected protoplasts
6279	imex:IM-11920_MI:0809	In vivo interaction and nuclear localization (arrows) of Gsm1 and Gsp1 C-terminal domains demonstrated by bi-fluorescent complementation (CITNt + CITCt)
6280	imex:IM-9153_MI:0809	affirmation of the protein interaction through fluorescent microscopy with the pFer-YcADIPOR1-YnADIPOR1 expression vector
6281	imex:IM-9153_MI:0809	Consecutive confirmation with fluroscent microscopy demonstrated interactions among pFer-YcVIM-ynVIM, pFer-YcAPPL1-YnADIPOR1 protein partners (Fig.3B)
6282	imex:IM-9153_MI:0809	Expression vector pFer-YcVIM-YnVIM transfected cells generated substantial EYFP emission above the negligible pFer-YcVIM-YnTUBA1B background in all analyzers.
6283	imex:IM-9153_MI:0809	Flow cytometry further validated positive interactions by detecting EYFP fluorescent cell populations in pFer-YcAPPL1-YnADIPOR1 transfected HeLa cells
6284	imex:IM-9153_MI:0809	Investigation of pFER-YcADIPOR1-YnADIPOR1 with a 96-well plate reader and flow cytometer confirmed results identified with FRET procaryotic construct (Fig.5b)
6285	18805092_MI:0826	First, we performed small-angle X-ray scattering (SAXS) analyses of NEDD8not, vert, similarCul1ctd-Rbx1 and Cul1ctd-Rbx1 (Figures 3 and S7).
6286	17314099_MI:0841	Phosphotransferase assays were performed with the indicated wild type (WT) and NM23-H1 mutants
6287	17981125_MI:0858	Association of Sig-1RS with BiP
6288	17567753_MI:0870	The detailed interaction between c-JMJD2A and the methylated peptides.
6289	imex:IM-11878_MI:0870	when bulk histones were used as substrates, western blot analysis also showed SMCX-mediated demethylation of both H3K4me3 and H3K4me2 but not mono-, di-, or trimethylated H3K9 and H3K27 (Figure 2A).
6290	imex:IM-11878_MI:0870	while SMCY demethylated H3K4me3 and H3K4me2, PLU-1 mediated demethylation of all three methylation states of H3K4.
6291	12756240_MI:0880	As expected, the presence of unlabeled ATP strongly inhibited  ATP hydrolysis by the Hsc66·[{alpha}-32P]ATP complex, because the unlabeled ATP replaced the radioactive nucleotide bound to Hsc66 prior to its hydrolysis (Fig. 4).
6292	12756240_MI:0880	In this assay, a complex of purified Ssq1 protein with radioactive ATP was preformed and subjected to sizing chromatography to separate it away from free nucleotides.
6293	16014621_MI:0880	Characterization of AtMinD1 ATP hydrolysis. A, increasing amounts of AtMinD1 lead to a linear increase in ATP hydrolysis.
6294	17468262_MI:0880	In vitro ATPase activity of recombinant SKD1,
6295	18510924_MI:0880	Wild-type SaXPD had an ATP-hydrolysis rate of 0.55 mol ATP per second per mol XPD with ssDNA.
6296	18510925_MI:0880	Plot of the ssDNA-stimulated ATPase activities of the indicated wild-type and mutant proteins of S. acidocaldarius XPD.
6297	19135891_MI:0880	It hydrolyzed ATP slowly but appreciably at a rate of 0.8 ATP/min/MukB dimer, and this ATPase activity was considerably enhanced (not, vert, similar7 folds) by MukE-MukF(M+C) or MukEF (Figure 5A).
6298	imex:IM-12135_MI:0880	Autoradiography and quantification revealed significant ATP hydrolysis for full-length ACF7 in comparison to ACF7-NC or GST (Figure6C)
6299	18296487_MI:0892	A prey activity threshold was selected which was able to detect the 8 &#956;M CD244-CD48 interaction (Brown et al. 1998) in both bait-prey orientations
6300	18984158_MI:0920	Functional reconstitution of mtRNase P activity from MRPP1, MRPP2, and MRPP3.