Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Protein interaction partner”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources
PubMed2005

Identification of proteins interacting with the RNAPII FCP1 phosphatase: FCP1 forms a complex with arginine methyltransferase PRMT5 and it is a substrate for PRMT5-mediated methylation.

FCP1, a phosphatase specific of the carboxyl-terminal-domain of the large subunit of the RNA polymerase II (RNAPII), stimulates transcription elongation and it is required for general transcription and cell viability. To identify novel interacting proteins of FCP1, we used a human cell line expressing an epitope flagged FCP1 and proteins, which formed complexes with FCP1, were identified by mass spectrometry. We identified four proteins: RPB2 subunit of the RNAPII, the nuclear kinase, NDR1, the methyltransferase PRMT5 and the enhancer of rudimentary homologue (ERH) proteins. Intriguingly, both the PRMT5 and ERH proteins are interacting partners of the SPT5 elongation factor. Interactions of RPB2, ERH, NDR1 and PRMT5 with FCP1 were confirmed by co-immunoprecipitation or in vitro pull-down assays. Interaction between PRMT5 and FCP1 was further confirmed by co-immunoprecipitation of endogenous proteins. We found that FCP1 is a genuine substrate of PRMT5-methylation both in vivo and in vitro, and FCP1-associated PRMT5 can methylate histones H4 in vitro.

Amino Acid Sequence↗
PubMed2003

The physics and bioinformatics of binding and folding-an energy landscape perspective.

It has been recognized in the last few years that unstructured proteins play an important role in biological organisms, often participating in signal transduction, transcriptional regulation, and a variety of other regulatory activities. Various hypotheses have been put forward for the ubiquity of the unfolded state; rapid turnover, faster or more specific binding kinetics, multifunctionality may all possibly explain apparent ubiquitousness of unfolded proteins in eukaryotic cells. In this paper we extend the energy landscape theory of protein folding to construct an analytical model of how binding and folding are coupled thermodynamically when the energy landscape is partially rugged. To deduce the parameters that enter the theory, which is based on Generalized Random Energy Model, we have analyzed in a bioinformatic sense a large structural database of more than 500 protein complexes. We find that Miyazawa-Jernigan contact potential shows similar energy gaps for folding for both hydrophobic and hydrophilic proteins, but that for binding contacts hydrophobic interfaces turn out to be funneled while hydrophilic ones are antifunneled. This suggests evolution has found a mechanism for avoiding frustration between folding and binding by making use of indirect water-mediated interactions. By juxtaposing the monomeric protein folding free energy profile in the protein complex database with another database consisting of only well-folded monomers, we estimate that at least 15% of monomers in the former database are unfolded in the absence of partner protein interface interactions. When employing the parameters characteristic of these unfolded monomers to construct binding/folding phase diagrams, we find that these monomers would indeed fold if sufficiently stabilizing binding contacts, consistent with that fold, are formed.

Computational Biology↗
PubMed2001

Binding of neural cell adhesion molecules (N-CAMs) to the cellular prion protein.

To identify molecular interaction partners of the cellular prion protein (PrP(C)), we sought to apply an in situ crosslinking method that maintains the microenvironment of PrP(C). Mild formaldehyde crosslinking of mouse neuroblastoma cells (N2a) that are susceptible to prion infection revealed the presence of PrP(C) in high molecular mass (HMM) protein complexes of 200 to 225 kDa. LC/MS/MS analysis identified three murine splice-variants of the neural cell adhesion molecule (N-CAM) in the complexes, which isolate with caveolae-like domains (CLDs). Enzymatic removal of N-linked sugar moieties did not disrupt the complexes, arguing that the interaction of PrP with N-CAM occurs through amino acid side-chains. Additionally, similar levels of PrP/N-CAM complexes were found in N2a and prion-infected N2a (ScN2a) cells. With the use of an N-CAM-specific peptide library, the PrP-binding site was determined to comprise beta-strands C and C' within the two consecutive fibronectin type III (FNIII) modules found in proximity of the membrane-attachment site of N-CAM. As revealed by in situ crosslinking of PrP deletion mutants, the PrP face of the binding site is formed by the N terminus, helix A (residues 144-154) and the adjacent loop region of PrP. N-CAM-deficient (N-CAM(-/-)) mice that were intracerebrally challenged with scrapie prions succumbed to disease with a mean incubation period of 122 (+/-4.1, SEM) days, arguing that N-CAM is not involved in PrP(Sc) replication. Our findings raise the possibility that N-CAM may join with PrP(C) in carrying out some as yet unidentified physiologic cellular function.

Alternative Splicing↗
PubMed2000

Transcriptional repression by Pax5 (BSAP) through interaction with corepressors of the Groucho family.

Pax5 (BSAP) functions as both a transcriptional activator and repressor during midbrain patterning, B-cell development and lymphomagenesis. Here we demonstrate that Pax5 exerts its repression function by recruiting members of the Groucho corepressor family. In a yeast two-hybrid screen, the groucho-related gene product Grg4 was identified as a Pax5 partner protein. Both proteins interact cooperatively via two separate domains: the N-terminal Q and central SP regions of Grg4, and the octapeptide motif and C-terminal transactivation domain of Pax5. The phosphorylation state of Grg4 is altered in vivo upon Pax5 binding. Moreover, Grg4 efficiently represses the transcriptional activity of Pax5 in an octapeptide-dependent manner. Similar protein interactions resulting in transcriptional repression were also observed between distantly related members of both the Pax2/5/8 and Groucho protein families. In agreement with this evolutionary conservation, the octapeptide motif of Pax proteins functions as a Groucho-dependent repression domain in Drosophila embryos. These data indicate that Pax proteins can be converted from transcriptional activators to repressors through interaction with corepressors of the Groucho protein family.

3T3 Cells↗
PubMed2004

Molecular evolution in large genetic networks: does connectivity equal constraint?

Genetic networks show a broad-tailed distribution of the number of interaction partners per protein, which is consistent with a power-law. It has been proposed that such broad-tailed distributions are observed because they confer robustness against mutations to the network. We evaluate this hypothesis for two genetic networks, that of the E. coli core intermediary metabolism and that of the yeast protein-interaction network. Specifically, we test the hypothesis through one of its key predictions: highly connected proteins should be more important to the cell and, thus, subject to more severe selective and evolutionary constraints. We find, however, that no correlation between highly connected proteins and evolutionary rate exists in the E. coli metabolic network and that there is only a weak correlation in the yeast protein-interaction network. Furthermore, we show that the observed correlation is function-specific within the protein-interaction network: only genes involved in the cell cycle and transcription show significant correlations. Our work sheds light on conflicting results by previous researchers by comparing data from multiple types of protein-interaction datasets and by using a closely related species as a reference taxon. The finding that highly connected proteins can tolerate just as many amino acid substitutions as other proteins leads us to conclude that power-laws in cellular networks do not reflect selection for mutational robustness.

Energy Metabolism↗
PubMed2000

An essential phosphorylation-site domain of human cdc25C interacts with both 14-3-3 and cyclins.

Human cdc25C is a dual-specificity phosphatase involved in the regulation of cell cycle progression in both unperturbed cells and in cells subject to DNA damage or replication checkpoints. In this study, we describe the structure-function relationship of an essential domain of human cdc25C that interacts with 14-3-3 proteins. We show that this domain is a bi-functional interactive motif that interacts with cyclins primarily through their P-box motif in addition to 14-3-3 proteins. Characterization of the structural features of this domain by NMR and circular dichroism reveals two distinct alpha helical moieties interconnected by a loop carrying the 14-3-3 binding site. Moreover, the helical folding is induced upon binding to 14-3-3, suggestive of a conformational regulation of this domain of cdc25C through interactions with partner proteins in vivo. Combining our structural and biochemical data, we propose a detailed model of the molecular mechanism of cdc25C regulation by differential association with 14-3-3 and cdc2-cyclin B.

14-3-3 Proteins↗
PubMed2002

Matching SOX: partner proteins and co-factors of the SOX family of transcriptional regulators.

SOX transcription factors perform a remarkable variety of important roles in vertebrate development, either activating or repressing specific target genes through interaction with different partner proteins. Surprisingly, these interactions are often mediated by the conserved, DNA-binding HMG domain, raising questions as to how each factor's specificity is generated. We propose a model whereby non-HMG domains may influence partner protein selection and/or binding stability.

DNA-Binding Proteins↗
PubMed2006

Critical residues and novel effects of overexpression of the Streptomyces coelicolor developmental protein BldB: evidence for a critical interacting partner.

The bldB gene of Streptomyces coelicolor encodes the best-characterized member of a family of small proteins that have low isoelectric points but that lack any previously characterized sequence motifs. BldB is dimeric and is required for the efficient production of antibiotics and spore-forming cells, called aerial hyphae, by growing colonies. The mechanism of action of BldB and its relatives is unknown. Here, we have explored amino acids in BldB that either are highly conserved or have been implicated in function genetically. We show that five amino acids are important for its function at physiological expression levels. Mutations in three of these amino acids gave rise to proteins that were either monomeric or unstable in vivo, while two others are not. We find that overexpression of bldB in S. coelicolor blocks sporulation prior to sporulation-specific septation but permits the formation of aerial hyphae. Vegetative septation was apparently normal in both the bldB null mutant and the bldB overexpression strain. To our surprise, overexpression of the dimerization-competent but functionally defective alleles caused a dramatic acceleration of sporulation. Our results suggest that BldB makes at least one important contact with another subcellular constituent and that a loss or alteration of this interaction impairs the phenotypic properties of the organism.

Alleles↗
PubMed2004

Bipolar orientation of chromosomes in Saccharomyces cerevisiae is monitored by Mad1 and Mad2, but not by Mad3.

The spindle checkpoint governs the timing of anaphase separation of sister chromatids. In budding yeast, Mad1, Mad2, and Mad3 proteins are equally required for arrest in the presence of damage induced by antimicrotubule drugs or catastrophic loss of spindle structure. We find that the MAD genes are not equally required for robust growth in the presence of more subtle kinetochore and microtubule damage. A mad1Delta synthetic lethal screen identified 16 genes whose deletion in cells lacking MAD1 results in death or slow growth. Eleven of these mad1Delta genetic interaction partners encode proteins at the kinetochore-microtubule interface. Analysis of the entire panel revealed similar phenotypes in combination with mad2Delta. In contrast, 13 panel mutants exhibited a less severe phenotype in combination with mad3Delta. Checkpoint arrest in the absence of bipolar orientation and tension (induced by replication block in a cdc6 mutant) was lacking in cells without MAD1 or MAD2. Cells without MAD3 were checkpoint-proficient. We conclude that Mad1 and Mad2 are required to detect bipolar orientation and/or tension at kinetochores, whereas Mad3 is not.

Antineoplastic Agents↗
PubMed2004

Conserved network motifs allow protein-protein interaction prediction.

MOTIVATION: High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions but it is often difficult to decide which proteins to probe as interaction partners. Developing reliable computational methods assisting this decision process is a pressing need in bioinformatics. RESULTS: We show that we can use the conserved properties of the protein network to identify and validate interaction candidates. We apply a number of machine learning algorithms to the protein connectivity information and achieve a surprisingly good overall performance in predicting interacting proteins. Using a 'leave-one-out' approach we find average success rates between 20 and 40% for predicting the correct interaction partner of a protein. We demonstrate that the success of these methods is based on the presence of conserved interaction motifs within the network. AVAILABILITY: A reference implementation and a table with candidate interacting partners for each yeast protein are available at http://www.protsuggest.org.

Algorithms↗
PubMed2005

Proteomic study of Galectin-1 expression in human mesenchymal stem cells.

Bone marrow-derived mesenchymal stem cells (MSCs) are known to interact with hematopoietic stem cells (HSCs) and immune cells, and are of potential interest to be used as therapeutic agents for enhancing allogenic hematopoietic engraftment and preventing graft-versus-host disease (GVHD). Galectin 1 (Gal1) belongs to a family of structurally related molecules expressed in many vertebrate tissues that exert their functions both by binding to glycoconjugates, and by interaction with protein partners. In this work using a proteomic approach, we looked for the presence and the localization of Gal1 in short- and long-term culture of human (h) hMSC. We first determined, that Gal1 is one of the major proteins expressed in hMSC. We futher demonstrated that its expression is maintained when hMSC are expanded through a subculturing process up to five passages. Moreover, Gal1 is secreted and found at the cell surface of MSC, participating in extra cellular matrix (ECM)-cell interactions. Given the immunomodulatory properties of Gal1, its potential involvement in immunological functions of hMSC could be suggested.

Amino Acid Sequence↗
PubMed1999

The tetratricopeptide repeat: a structural motif mediating protein-protein interactions.

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s). Three-dimensional structural data have shown that a TPR motif contains two antiparallel alpha-helices such that tandem arrays of TPR motifs generate a right-handed helical structure with an amphipathic channel that might accommodate the complementary region of a target protein. Most TPR-containing proteins are associated with multiprotein complexes, and there is extensive evidence indicating that TPR motifs are important to the functioning of chaperone, cell-cycle, transcription, and protein transport complexes. The TPR motif may represent an ancient protein-protein interaction module that has been recruited by different proteins and adapted for specific functions. BioEssays 1999;21:932-939.

Amino Acid Sequence↗
PubMed2002

Doing (F/L)PPPPs: EVH1 domains and their proline-rich partners in cell polarity and migration.

Actin filament assembly is a tightly regulated process that functions in many aspects of cell physiology. Members of the Ena/VASP (Drosophila Enabled/vasodilator-stimulated phosphoprotein) family are key players in regulating actin filament assembly, in many cases through their association with binding partners that display a particular proline-rich motif, FPPPP. Ena/VASP proteins interact with these partners via the highly conserved Ena/VASP homology 1 (EVH1) domain. The diverse array of binding partners for EVH1 domains, including cytoskeletal proteins such as zyxin, transmembrane guidance receptors such as Roundabout, and the T-cell signaling protein Fyb/SLAP, shows that these interactions are likely to be important in a number of cellular processes that require regulated actin filament assembly.

Amino Acid Motifs↗
PubMed2006

A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration.

Many human inherited neurodegenerative disorders are characterized by loss of balance due to cerebellar Purkinje cell (PC) degeneration. Although the disease-causing mutations have been identified for a number of these disorders, the normal functions of the proteins involved remain, in many cases, unknown. To gain insight into the function of proteins involved in PC degeneration, we developed an interaction network for 54 proteins involved in 23 inherited ataxias and expanded the network by incorporating literature-curated and evolutionarily conserved interactions. We identified 770 mostly novel protein-protein interactions using a stringent yeast two-hybrid screen; of 75 pairs tested, 83% of the interactions were verified in mammalian cells. Many ataxia-causing proteins share interacting partners, a subset of which have been found to modify neurodegeneration in animal models. This interactome thus provides a tool for understanding pathogenic mechanisms common for this class of neurodegenerative disorders and for identifying candidate genes for inherited ataxias.

Animals↗
PubMed2004

Phytochrome A: functional diversity and polymorphism.

Phytochrome (phy), a 124 kDa biliprotein, mediates plants' perception of environmental light conditions including quantity, quality and duration of light. The complex phenomenology of phy function is connected with its polymorphism, the major phys being phyA and phyB. PhyA mediates irreversible photoresponses in the very low and high fluence ranges (VLFR and HIR) primarily in the far-red (FR) spectral region, whereas phyB mediates the 'classical' R/FR reversible responses in the low fluence range (LFR). This phyA specificity is determined at the level of (i) intramolecular events, (ii) turnover, phyA being light-labile, and (iii) nuclear-cytoplasmic partitioning and interaction with partner proteins. A unique feature of phyA is that two native isoforms, phyA' and phyA'', comprise it, distinguished by spectroscopic and photochemical properties, localization and abundance in plant tissues, light stability, and other properties. They differ by the post-translational modification at the 6 kDa N-terminus, possibly phosphorylation, phyA' being phosphorylated and phyA'' dephosphorylated. Both species participate in the light-induced nuclear-cytoplasmic partitioning. The light-labile phyA' is responsible for de-etiolation (VLFR and HIR modes), whereas the relatively more light-stable phyA'' could be active throughout the whole life cycle. PhyA'' interferes with the action of phyA' and this interaction may be part of the fine tuning mechanism of the phyA function. Finally, within the phyA' pool there are different conformers in thermal equilibrium, that differ by the activation and kinetic parameters of the Pr-->lumi-R photoreaction. This heterogeneity of phyA may account, at least partially, for the complex dynamics of its photoprocesses and the phenomenology of photoresponses.

Genetic Variation↗
PubMed2005

Novel clustering of sodium channel Na(v)1.1 with ankyrin-G and neurofascin at discrete sites in the inner plexiform layer of the retina.

Voltage-gated sodium channels cluster at sites of action potential generation and propagation by interacting with partner proteins such as neurofascin, an adhesion molecule in the L1 family, and ankyrin-G, a spectrin-binding protein required for sodium channel accumulation at axon initial segments. Here, we describe in the inner plexiform layer of the retina a novel site of high-density sodium channel clustering, marked by ankyrin-G and neurofascin. The sodium channel isoform at this site is Na(v)1.1, instead of the Na(v)1.6 channels more commonly found in association with the clustering machinery. During development, Na(v)1.2 channels first associate with ankyrin-G in the inner plexiform layer but are later replaced by Na(v)1.1, similar to the switch from Na(v)1.2 to Na(v)1.6 at nodes of Ranvier and initial segments. This represents the first instance of high-density clustering of Na(v)1.1 channels, which may contribute to synaptic interactions among retinal neurons in the inner plexiform layer.

Animals↗
PubMed2003

Organization of the G protein-coupled receptors rhodopsin and opsin in native membranes.

G protein-coupled receptors (GPCRs), which constitute the largest and structurally best conserved family of signaling molecules, are involved in virtually all physiological processes. Crystal structures are available only for the detergent-solubilized light receptor rhodopsin. In addition, this receptor is the only GPCR for which the presumed higher order oligomeric state in native membranes has been demonstrated (Fotiadis, D., Liang, Y., Filipek, S., Saperstein, D. A., Engel, A., and Palczewski, K. (2003) Nature 421, 127-128). Here, we have determined by atomic force microscopy the organization of rhodopsin in native membranes obtained from wild-type mouse photoreceptors and opsin isolated from photoreceptors of Rpe65-/- mutant mice, which do not produce the chromophore 11-cis-retinal. The higher order organization of rhodopsin was present irrespective of the support on which the membranes were adsorbed for imaging. Rhodopsin and opsin form structural dimers that are organized in paracrystalline arrays. The intradimeric contact is likely to involve helices IV and V, whereas contacts mainly between helices I and II and the cytoplasmic loop connecting helices V and VI facilitate the formation of rhodopsin dimer rows. Contacts between rows are on the extracellular side and involve helix I. This is the first semi-empirical model of a higher order structure of a GPCR in native membranes, and it has profound implications for the understanding of how this receptor interacts with partner proteins.

Animals↗
PubMed2006

P-glycoprotein and 'lipid rafts': some ambiguous mutual relationships (floating on them, building them or meeting them by chance?).

P-glycoprotein (P-gp) is an active membrane transporter responsible for cell detoxification against numerous amphiphilic compounds, leading to multidrug resistance in tumor cells. It displays entangled connections with its membrane environment since it recognizes its substrates within the cytosolic leaflet and it also translocates some endogenous lipids to the exoplasmic leaflet. Regarding its relationships with membrane microdomains, 'lipid rafts', a literature analysis concludes that (i) P-gp also exists in rafts and non-raft membrane domains, depending on the cell considered, the experimental conditions and the method used to test it; (ii) cholesterol has a positive influence on P-gp function, and this may be a direct effect of the free cholesterol present in membrane or an indirect effect mediated by the cholesterol-enriched microdomains; (iii) when present in rafts, P-gp interacts with protein partners regulating its activity; (iv) P-gp is a lipid translocase that handles the raft-constituting lipids with particular efficiency, and it also influences membrane trafficking in the cell.

ATP Binding Cassette Transporter, Subfamily B, Mem↗