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 523 records · Page 29Linked to original sources
PubMed2006

Sorting nexin 17, a non-self-assembling and a PtdIns(3)P high class affinity protein, interacts with the cerebral cavernous malformation related protein KRIT1.

The mammalian sorting nexin (SNX) proteins are involved in the endocytosis and the sorting machinery of transmembrane proteins. Additionally to the family defining phox homology (PX) domain, SNX17 is the only member with a truncated FERM (4.1, ezrin, radixin, and moesin) domain and a unique C-terminal region (together designated as FC unit). By gel filtration and lipid overlay assays we show that SNX17 is a non-self-assembling and a PtdIns(3)P high class affinity protein. A SNX17 affinity to any other phosphoinositides was not detected. By yeast two-hybrid- and GST-trapping assays we identified KRIT1 (krev1 interaction trapped 1) as a new specific interaction partner of the FC unit of SNX17. KRIT1 binds SNX17 by its N-terminal region like the known interaction partner ICAP1alpha (integrin cytoplasmic domain-associated protein-1). The interaction was also detected in HEK 293 cells transiently expressing GFP-tagged KRIT1 and Xpress-tagged SNX17. KRIT1 mutations cause cerebral cavernous malformation (CCM1). Our finding suggests a SNX17 involvement in the indicated KRIT1 function in cell adhesion processes by integrin signaling.

Carrier Proteins↗
PubMed2005

Not all J domains are created equal: implications for the specificity of Hsp40-Hsp70 interactions.

Heat shock protein 40s (Hsp40s) and heat shock protein 70s (Hsp70s) form chaperone partnerships that are key components of cellular chaperone networks involved in facilitating the correct folding of a broad range of client proteins. While the Hsp40 family of proteins is highly diverse with multiple forms occurring in any particular cell or compartment, all its members are characterized by a J domain that directs their interaction with a partner Hsp70. Specific Hsp40-Hsp70 chaperone partnerships have been identified that are dedicated to the correct folding of distinct subsets of client proteins. The elucidation of the mechanism by which these specific Hsp40-Hsp70 partnerships are formed will greatly enhance our understanding of the way in which chaperone pathways are integrated into finely regulated protein folding networks. From in silico analyses, domain swapping and rational protein engineering experiments, evidence has accumulated that indicates that J domains contain key specificity determinants. This review will critically discuss the current understanding of the structural features of J domains that determine the specificity of interaction between Hsp40 proteins and their partner Hsp70s. We also propose a model in which the J domain is able to integrate specificity and chaperone activity.

Adenosine Triphosphatases↗
PubMed2004

Application of the split-ubiquitin membrane yeast two-hybrid system to investigate membrane protein interactions.

The characterization of protein-protein interactions provides the foundation for further studies concerning protein complex function and regulation. Since the advent of the yeast two-hybrid assay, many additional genetic systems based upon the principle of protein fragment complementation have been designed. One such system, the split-ubiquitin membrane yeast two-hybrid system (MbYTH), is able to analyze the interaction status between two integral membrane proteins. This ability of the MbYTH system augments genetic analysis of protein interactions by covering for the inherent limitation of the yeast two-hybrid system when studying membrane protein interactions. Herein, we provide a description of the MbYTH method and detailed protocols in order to monitor protein interactions and discover novel interacting partners using the MbYTH system.

DNA, Complementary↗
PubMed2006

Structural and functional insights into the B30.2/SPRY domain.

The B30.2/SPRY domain is present in approximately 700 eukaryotic (approximately 150 human) proteins, including medically important proteins such as TRIM5alpha and Pyrin. Nonetheless, the functional role of this modular domain remained unclear. Here, we report the crystal structure of an SPRY-SOCS box family protein GUSTAVUS in complex with Elongins B and C, revealing a highly distorted two-layered beta-sandwich core structure of its B30.2/SPRY domain. Ensuing studies identified one end of the beta-sandwich as the surface interacting with an RNA helicase VASA with a 40 nM dissociation constant. The sequence variation in TRIM5alpha responsible for HIV-1 restriction and most of the mutations in Pyrin causing familial Mediterranean fever map on this surface, implicating the corresponding region in many B30.2/SPRY domains as the ligand-binding site. The amino acids lining the binding surface are highly variable among the B30.2/SPRY domains, suggesting that these domains are protein-interacting modules, which recognize a specific individual partner protein rather than a consensus sequence motif.

Amino Acid Motifs↗
PubMed1999

MAF1, a novel plant protein interacting with matrix attachment region binding protein MFP1, is located at the nuclear envelope.

The interaction of chromatin with the nuclear matrix via matrix attachment region (MAR) DNA is considered to be of fundamental importance for chromatin organization in all eukaryotic cells. MAR binding filament-like protein 1 (MFP1) from tomato is a novel plant protein that specifically binds to MAR DNA. Its filament protein-like structure makes it a likely candidate for a structural component of the nuclear matrix. MFP1 is located at nuclear matrix-associated, specklelike structures at the nuclear envelope. Here, we report the identification of a novel protein that specifically interacts with MFP1 in yeast two-hybrid and in vitro binding assays. MFP1 associated factor 1 (MAF1) is a small, soluble, serine/threonine-rich protein that is ubiquitously expressed and has no similarity to known proteins. MAF1, like MFP1, is located at the nuclear periphery and is a component of the nuclear matrix. These data suggest that MFP1 and MAF1 are in vivo interaction partners and that both proteins are components of a nuclear substructure, previously undescribed in plants, that connects the nuclear envelope and the internal nuclear matrix.

Amino Acid Sequence↗
PubMed2005

Using Drosophila to decipher how mutations associated with human branchio-oto-renal syndrome and optical defects compromise the protein tyrosine phosphatase and transcriptional functions of eyes absent.

Eyes absent (EYA) proteins are defined by a conserved C-terminal EYA domain (ED) that both contributes to its function as a transcriptional coactivator by mediating protein-protein interactions and possesses intrinsic protein tyrosine phosphatase activity. Mutations in human EYA1 result in an autosomal dominant disorder called branchio-oto-renal (BOR) syndrome as well as congenital cataracts and ocular defects (OD). Both BOR- and OD-associated missense mutations alter residues in the conserved ED as do three missense mutations identified from Drosophila eya alleles. To investigate the molecular mechanisms whereby these mutations disrupt EYA function, we tested their activity in a series of assays that measured in vivo function, phosphatase activity, transcriptional capability, and protein-protein interactions. We find that the OD-associated mutations retain significant in vivo activity whereas those derived from BOR patients show a striking decrease or loss of in vivo functionality. Protein-protein interactions, either with its partner transcription factor Sine oculis or with EYA itself, were not significantly compromised. Finally, the results of the biochemical assays suggest that both loss of protein tyrosine phosphatase activity and reduced transcriptional capability contribute to the impaired EYA function associated with BOR/OD syndrome, thus shedding new light into the molecular mechanisms underlying this disease.

Alleles↗
PubMed1994

Subunit interaction in the CCAAT-binding heteromeric complex is mediated by a very short alpha-helix in HAP2.

We dissected the domain of HAP2 that mediates subunit association in the heteromeric CCAAT-binding complex, first by genetic mutational analysis and then by structural studies. The mutational data suggest that a very short region in HAP2 mediates protein-protein association and that the structure of this domain is likely to be an alpha-helix. The CD analyses of a 15-residue synthetic oligopeptide covering this region confirm this surmise. The oligopeptide indeed formed an unusually thermal stable alpha-helix in aqueous solution. Eight amino acids that lie along one face of this helix, including three arginines, are found to be critical for protein-protein association. The partner that interacts with this helical motif is likely to be another subunit in the HAP complex, since the CCAAT-binding factor is shown to contain one molecule of HAP2. Our results suggest that very short regions in proteins can encode precise structures and mediate stable and specific protein-protein recognition and interactions.

Amino Acid Sequence↗
PubMed2002

Co-evolutionary analysis reveals insights into protein-protein interactions.

Protein-protein interactions play crucial roles in biological processes. Experimental methods have been developed to survey the proteome for interacting partners and some computational approaches have been developed to extend the impact of these experimental methods. Computational methods are routinely applied to newly discovered genes to infer protein function and plausible protein-protein interactions. Here, we develop and extend a quantitative method that identifies interacting proteins based upon the correlated behavior of the evolutionary histories of protein ligands and their receptors. We have studied six families of ligand-receptor pairs including: the syntaxin/Unc-18 family, the GPCR/G-alpha's, the TGF-beta/TGF-beta receptor system, the immunity/colicin domain collection from bacteria, the chemokine/chemokine receptors, and the VEGF/VEGF receptor family. For correlation scores above a defined threshold, we were able to find an average of 79% of all known binding partners. We then applied this method to find plausible binding partners for proteins with uncharacterized binding specificities in the syntaxin/Unc-18 protein and TGF-beta/TGF-beta receptor families. Analysis of the results shows that co-evolutionary analysis of interacting protein families can reduce the search space for identifying binding partners by not only finding binding partners for uncharacterized proteins but also recognizing potentially new binding partners for previously characterized proteins. We believe that correlated evolutionary histories provide a route to exploit the wealth of whole genome sequences and recent systematic proteomic results to extend the impact of these studies and focus experimental efforts to categorize physiologically or pathologically relevant protein-protein interactions.

Algorithms↗
PubMed2002

Immunolocalization of PICK1 in the ascending auditory pathways of the adult rat.

Protein that interacts with C-kinase alpha (PICK1) is a PDZ domain protein that interacts with many binding partners in the central nervous system (CNS), including activated protein kinase Calpha and subunits of the AMPA subtype of glutamate receptor. Almost nothing is known about the anatomic distribution of PICK1 in the intact adult CNS. By using PICK1 antisera and peroxidase immunocytochemistry, we report on the distribution of PICK1 in the ascending pathways of the central auditory system of the adult rat. PICK1-immunoreactivity (ir) was observed in many component nuclei of the central auditory system, including the dorsal cochlear nucleus, anteroventral cochlear nucleus, posteroventral cochlear nucleus, some divisions of the superior olivary complex, inferior colliculus, medial geniculate body, and primary auditory cortex. The general staining pattern for PICK1-immunoreactivity was somatodendritic with scattered puncta in neuropil and somatodendritic regions. The distribution of PICK1 partially overlaps with PKCalpha and glutamate receptor subunits such as GluR2. These data suggest that PICK1 may function in the regulation of PKCalpha and GluR2 localization in components of the rat auditory system, which may be a fundamental mechanism of synaptic transmission and/or plasticity. J. Comp. Neurol.

Animals↗
PubMed2004

The cholesterol membrane anchor of the Hedgehog protein confers stable membrane association to lipid-modified proteins.

The Hedgehog proteins are potent organizers of animal development. They carry a cholesterol ester at the C terminus of their signaling domain. The membrane anchoring mediated by this lipophilic modification was studied by means of an approach integrating cell biology, biochemistry, biophysics, and organic chemistry techniques. Sterol-modified and fluorescent-labeled Hedgehog-derived peptides and proteins were synthesized and investigated in biophysical and cell-biological assays. These experiments revealed that cholesterol alone anchors proteins to membranes with significant strength and half-times for spontaneous desorption of several hours. Its membrane anchoring ability is comparable to dual lipidation motifs such as double geranylgeranylation or S-palmitoylation plus S-farnesylation found in other lipidated proteins. The experiments also demonstrate that membrane binding changes dramatically if short lipidated peptides are equipped with a large protein. These data suggest that for Hedgehog release and subsequent signaling an interaction partner such as the Dispatched protein is necessary. In addition to these findings the described approach allows one to correlate biophysical data obtained with model peptides with data determined with fully functional proteins and to combine results from in vitro and in vivo experiments. It should be generally applicable to other membrane anchors and proteins.

Animals↗
PubMed2001

Hepatitis B virus large envelope protein interacts with gamma2-adaptin, a clathrin adaptor-related protein.

For the outcome of a hepatitis B virus (HBV) infection, the viral L envelope protein with its pre-S domain performs pivotal functions by mediating attachment of HBV to liver cells, envelopment of viral capsids, release of (sub)viral particles, regulation of supercoiled DNA amplification, and transcriptional transactivation. To assess its multiple functions and host-protein assistance involved, we initiated a two-hybrid screen using the L-specific pre-S1 domain as bait. With this approach, we have identified gamma2-adaptin, a putative member of the clathrin adaptor proteins responsible for protein sorting and trafficking, as a specific binding partner of L protein. Evidence for a physical interaction between L protein and gamma2-adaptin was also demonstrated by affinity chromatography and coimmunoprecipitation, and the binding sites were mapped to the L-specific pre-S1 domain and the gamma2-adaptin-specific ear domain. The specificity of the interaction was further sustained by the failure of gamma1-adaptin, a closely related gamma2-adaptin homologue, to associate with L protein. Analysis of an L mutant protein indicates that the L-gamma2-adaptin interaction strictly depends on the pre-S1 domain of transmembrane L protein oriented to the cytosol and thus appears to occur in the cytosolic environment. Interestingly, coexpression of the two interacting partners in transfected cells resulted in recruitment of gamma2-adaptin by L protein onto cis-Golgi-like structures, strongly indicating that the association is physiologically relevant. Together, the results suggest a role for gamma2-adaptin in L-mediated processes of viral biogenesis and/or pathogenesis, such as facilitating and guiding HBV assembly.

Adaptor Protein Complex gamma Subunits↗
PubMed2005

A mechanism for death receptor discrimination by death adaptors.

The death domain and death effector domain are two common motifs that mediate protein-protein interactions between components of cell death signaling complexes. The mechanism by which these domains engage their binding partners has been explored by extensive mutagenesis of two death adaptors, FADD and TRADD, suggesting that a death adaptor can discriminate its intended binding partners from other proteins harboring similar motifs. Death adaptors are found to utilize one of two topologically conserved surfaces for protein-protein interaction, whether that partner is another adaptor or its cognate receptor. These surfaces are topologically related to the interaction between death domains observed in the x-ray crystal structure of the Drosophila adaptor Tube bound to Pelle kinase. Comparing the topology of protein-protein interactions for FADD complexes to TRADD complexes reveals that FADD uses a Tube-like surface in each of its death motifs to engage either CD95 or TRADD. TRADD reverses these roles, employing a Pelle-like surface to interact with either receptor TNFR1 or adaptor FADD. Since death adaptors display a Tube-like or Pelle-like preference for engaging their binding partners, Tube/Pelle-like pairing provides a mechanism for death adaptor discrimination of death receptors.

Adaptor Proteins, Signal Transducing↗
PubMed2004

What do we learn from high-throughput protein interaction data?

The biological significance of protein interactions, their method of generation and reliability is briefly reviewed. Protein interaction networks adopt a scale-free topology that explains their error tolerance or vulnerability, depending on whether hubs or peripheral proteins are attacked. Networks also allow the prediction of protein function from their interaction partners and therefore, the formulation of analytical hypotheses. Comparative network analysis predicts interactions for distantly related species based on conserved interactions, even if sequences are only weakly conserved. Finally, the medical relevance of protein interaction analysis is discussed and the necessity for data integration is emphasized.

Animals↗
PubMed2006

Mammalian gene expression program resiliency: the roles of multiple coactivator mechanisms in hypoxia-responsive transcription.

CBP and its paralog p300 (CBP/p300 collectively) are transcriptional coactivators that are among the most interconnected proteins in the mammalian protein-protein "interactome" with over 315 described interaction partners. CBP/p300 are protein/histone acetyltransferases, but most of the protein-binding domains of CBP/p300 are unique to these two coactivators, indicating that CBP/p300 should be highly limiting. The CH1 domain of CBP/p300 was considered essential for most, if not all, hypoxia-inducible transcription by binding to hypoxia-inducible-factor-1alpha (HIF-1alpha). Mutating CH1 had little effect, however, on the hypoxia-induced transcription of the HIF-target genes Higd1a, Egln1 (prolyl-hydroxylase), Bnip3 (Bcl2-interacting-protein-3), and Pfkl (phosphofructokinase). In contrast, HIF-targets Pgf (placental growth factor) and Egln3 were strongly affected by the CH1 mutation, while Stc1 (stanniocalcin-1) and Slc2a1 (glucose-transporter-1) were moderately affected. HIF targets were also dependent on coactivation mechanisms that are sensitive to trichostatin A (TSA(S)). Paradoxically, TSA inhibits histone deacetylases (HDACs) that are usually associated with transcriptional repression, implying that HDACs can also function as coactivators. Thus, activator-specific transcription in mammals requires seemingly unrelated coactivator mechanisms, and individual target genes vary in their requirements for each mechanism. Gene expression program resiliency is therefore coupled with gene specific regulation by avoiding uniform reliance on a "keystone" coactivator interaction.

Animals↗
PubMed2002

Adenovirus protein involved in virus internalization recruits ubiquitin-protein ligases.

Adenovirus penton base protein is involved in virus internalization. Searching for the cellular partners of this protein, we used dodecahedra, adenovirus subviral particles composed of 12 bases, for screening a human lung expression library. This screen yielded three ubiquitin-protein ligases, WWP1, WWP2, and AIP4, all of which belong to the HECT family and contain multiple WW domains. The xPPxY motif, known to interact with WW domains in partner proteins occurs twice in the N-terminal part of the base polypeptide chain. The recruitment of three ubiquitin-protein ligases was shown for two distinct virus serotypes, Ad2 and Ad3. The first N-terminal xPPxY motif in the base protein sequence is indispensable for the interaction. The association in vitro was shown by the protein overlay technique and in vivo by cotransfection followed by immunoprecipitation. The binding parameters studied by surface plasmon resonance confirmed the interaction of base protein with three ubiquitin-protein ligases. In case of WWP1 when the saturation of binding was achieved, the apparent dissociation constant of 65nM was calculated. This is the first demonstration of the interaction of nonenveloped viruses with ubiquitin-protein ligases of host cells.

Adenoviruses, Human↗
PubMed1988

Electron-transfer studies involving flavodoxin and a natural redox partner, the iron protein of nitrogenase. Conformational constraints on protein-protein interactions and the kinetics of electron transfer within the protein complex.

The kinetics of electron-transfer reactions involving flavodoxins from Klebsiella pneumoniae (KpFld), Azotobacter chroococcum (AcFld), Anacystis nidulans (AnFld) and Megasphaera elsdenii (MeFld), the free, MgADP-bound and MgATP-bound forms of the Fe protein component of nitrogenase from K. pneumoniae [Kp2, Kp2(MgADP)2 and Kp2(MgATP)2] and Na2S2O4 were studied by stopped-flow spectrophotometry. Kinetic evidence was obtained for the formation of binary protein complexes involving KpFldSQ (semiquinone) with either Kp2(MgADP)2 (KD = 49 microM) or Kp2(MgATP)2 (KD = 13 microM) but not with Kp2 (KD greater than 730 microM). The binding of 2MgATP or 2MgADP to Kp2 therefore not only shifts the midpoint potential (Em) of the [4Fe-4S] centre from -200 mV to -320 mV or -350 mV respectively but also changes the affinity of Kp2 for KpFldSQ. Thermodynamically unfavourable electron from Kp2(MgADP)2 and Kp2(MgATP)2 to KpFldSQ occurs within the protein complexes with k = 1.2 s-1 (delta E = -72 mV) and 0.5 s-1 (delta E = -120 mV) respectively. Although AcFldSQ is reduced by Kp2, Kp2(MgADP)2 and Kp2(MgATP)2 (k = 8 x 10(3), 2.4 x 10(3) and 9 x 10(2) M-1.s-1 respectively), protein-complex formation is weak in each case (KD greater than 700 microM). Electron transfer in the physiologically important and thermodynamically favourable direction from Kp2FldHQ (hydroquinone) and AcFldHQ to Kp2ox.(MgADP)2 (the state of Kp2 that accepts electrons from FldHQ in the catalytic cycle of nitrogenase) is rapid (k greater than 10(6) M-1.s-1). The second-order rate constants for the reduction of KpFldSQ, AcFldSQ, AnFldSQ and MeFldSQ by SO2.- (active reductant formed by the predissociation of S2O4(2-) ion) exhibited the linear free-energy relationship predicted by the Marcus theory of electron transfer.

Adenosine Diphosphate↗
PubMed2007

Erosion of interaction networks in reduced and degraded genomes.

Unlike eukaryotes, which often recruit duplicated genes into existing protein-protein interaction (PPI) networks, the low levels of gene duplication coupled with the high probability of lateral transfer of novel genes alters the manner in which PPI networks can evolve in bacteria. By inferring the PPIs present in the ancestor to contemporary Gammaproteobacteria, we were able to trace the changes in gene repertoires, and their consequences on PPI network evolution, in several bacterial lineages that have independently undergone reductions in genome size and genome contents. As genomes degrade, virtually all multi-partner proteins have lost interactors; however, the overall average number of connections increases due to the preferential elimination of proteins that interact with only one other protein partner. We also studied the effect of lateral gene transfer on PPI network evolution by analyzing the connectivity of genes that have been gained along the Escherichia coli lineage, as well as those acquired genes subsequently silenced in Shigella flexneri, since diverging from the gammaproteobacterial ancestor. The situation in PPI networks, in which newly acquired genes preferentially attach to the hubs of the network, contrasts that observed in metabolic networks, which evolve by the peripheral gain and loss of genes, and in regulatory networks, in which high connectivity increases the propensity of loss.

Gammaproteobacteria↗
PubMed2006

FTIR studies of the redox partner interaction in cytochrome P450: the Pdx-P450cam couple.

Recently we have developed a new approach to study protein-protein interactions using Fourier transform infrared spectroscopy in combination with titration experiments and principal component analysis (FTIR-TPCA). In the present paper we review the FTIR-TPCA results obtained for the interaction between cytochrome P450 and the redox partner protein in two P450 systems, the Pseudomonas putida P450cam (CYP101) with putidaredoxin (P450cam-Pdx), and the Bacillus megaterium P450BM-3 (CYP102) heme domain with the FMN domain (P450BMP-FMND). Both P450 systems reveal similarities in the structural changes that occur upon redox partner complex formation. These involve an increase in beta-sheets and alpha-helix content, a decrease in the population of random coil/3(10)-helix structure, a redistribution of turn structures within the interacting proteins and changes in the protonation states or hydrogen-bonding of amino acid carboxylic side chains. We discuss in detail the P450cam-Pdx interaction in comparison with literature data and conclusions drawn from experiments obtained by other spectroscopic techniques. The results are also interpreted in the context of a 3D structural model of the Pdx-P450cam complex.

Bacillus megaterium↗