Showing papers on "Protein–protein interaction published in 2000"
TL;DR: Examination of large-scale yeast two-hybrid screens reveals interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes.
Abstract: Two large-scale yeast two-hybrid screens were undertaken to identify protein-protein interactions between full-length open reading frames predicted from the Saccharomyces cerevisiae genome sequence. In one approach, we constructed a protein array of about 6,000 yeast transformants, with each transformant expressing one of the open reading frames as a fusion to an activation domain. This array was screened by a simple and automated procedure for 192 yeast proteins, with positive responses identified by their positions in the array. In a second approach, we pooled cells expressing one of about 6,000 activation domain fusions to generate a library. We used a high-throughput screening procedure to screen nearly all of the 6,000 predicted yeast proteins, expressed as Gal4 DNA-binding domain fusion proteins, against the library, and characterized positives by sequence analysis. These approaches resulted in the detection of 957 putative interactions involving 1,004 S. cerevisiae proteins. These data reveal interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes. The results of these screens are shown here.
4,877 citations
TL;DR: This review examines the structural basis for 14-3- 3-ligand interactions, proposed functions of 14-1-3 in various signaling pathways, and emerging views of mechanisms that regulate 14-2-3 actions.
Abstract: The 14-3-3 proteins are a family of conserved regulatory molecules expressed in all eukaryotic cells. A striking feature of the 14-3-3 proteins is their ability to bind a multitude of functionally diverse signaling proteins, including kinases, phosphatases, and transmembrane receptors. This plethora of interacting proteins allows 14-3-3 to play important roles in a wide range of vital regulatory processes, such as mitogenic signal transduction, apoptotic cell death, and cell cycle control. In this review, we examine the structural basis for 14-3-3-ligand interactions, proposed functions of 14-3-3 in various signaling pathways, and emerging views of mechanisms that regulate 14-3-3 actions.
1,549 citations
TL;DR: This approach correctly predicts a functional category for 72% of the 1,393 characterized proteins with at least one partner of known function, and has been applied to predict functions for 364 previously uncharacterized proteins.
Abstract: A global analysis of 2,709 published interactions between proteins of the yeast Saccharomyces cerevisiae has been performed, enabling the establishment of a single large network of 2,358 interactions among 1,548 proteins. Proteins of known function and cellular location tend to cluster together, with 63% of the interactions occurring between proteins with a common functional assignment and 76% occurring between proteins found in the same subcellular compartment. Possible functions can be assigned to a protein based on the known functions of its interacting partners. This approach correctly predicts a functional category for 72% of the 1,393 characterized proteins with at least one partner of known function, and has been applied to predict functions for 364 previously uncharacterized proteins.
1,373 citations
TL;DR: The underlying biochemical mechanisms through which specificity is generated during signal transduction are addressed, and the means by which signaling molecules may act in combination to generate complex biological responses are pursued.
Abstract: Virtually every aspect of cellular function within a metazoan organism, including proliferative status, metabolism, gene expression, cytoskeletal organization, and indeed the cell’s very survival, is dependent on external signaling molecules, either in the form of soluble hormones or proteins anchored to the surface of an adjacent cell or the extracellular matrix (ECM). These factors exert their effects either by binding receptors displayed on the surface of the cell or, in the case of compounds such as steroids, by traversing the plasma membrane and directly engaging intracellular receptors. In addition, these external signals can be linked to intrinsic cues that regulate events such as polarity and asymmetric cell division, and that monitor the molecular composition of the cell, and therefore determine whether suitable conditions prevail for cell growth and division. Over the last two decades, we have achieved considerable understanding of the mechanisms by which signals are conveyed from receptors at the plasma membrane to their targets in the cytoplasm and nucleus. At heart, this is a problem of molecular recognition. Hormones must bind selectively to their receptors and these in turn must interact with specific cytoplasmic targets. To understand signal transduction in a general sense, it is important to know whether different biochemical pathways use related molecular devices to control cellular behavior. To understand specificity in signaling, we need to know how receptors interact with particular targets and how the proteins of one pathway can be insulated from related signaling components. At the same time, it is important to learn how distinct signaling pathways communicate with one another, since the entire cell must ultimately function as a single unit whose different elements respond in an organized fashion to external signals. A cell in the body will be exposed to many different stimuli, which it must integrate into a coherent response. Furthermore, although a rather large fraction of genes within nucleated cells appear to function in the processes of signal transduction and cellular organization (Plowman et al. 1999), it is still remarkable that only a few thousand gene products can control the sophisticated behaviors of many different cell types. This immediately suggests that signaling proteins must act in a combinatorial fashion, since there are insufficient proteins for each to have a single biological role. For example, there are billions of neurons in the human brain, each of which must project its axon to the appropriate target, let alone undertake the complex biochemical events associated with neurotransmission and synaptic plasticity. Clearly, the signaling molecules that function in the process of axon guidance must act in a combinatorial way to generate the extreme complexity of the human nervous system. Here we will address some of the underlying biochemical mechanisms through which specificity is generated during signal transduction, and pursue the means by which signaling molecules may act in combination to generate complex biological responses.
745 citations
TL;DR: A web-based database is developed that can predict a putative CRS location within a given protein sequence, identify the subclass to which it may belong, and structural and biophysical parameters such as hydrophobicity, hydrophobic moment, and propensity for a -helix formation.
Abstract: The intracellular calcium sensor protein calmodulin (CaM) interacts with a large number of proteins to regulate their biological functions in response to calcium stimulus. This molecular recognition process is diverse in its mechanism, but can be grouped into several classes based on structural and sequence information. We have developed a web-based database (http://calcium.uhnres.utoronto.ca/ctdb) for this family of proteins containing CaM binding sites or, as we propose to call it herein, CaM recruitment signaling (CRS) motifs. At present the CRS motif found in approximately 180 protein sequences in the databases can be divided into four subclasses, each subclass representing a distinct structural mode of molecular recognition involving CaM. The database can predict a putative CRS location within a given protein sequence, identify the subclass to which it may belong, and structural and biophysical parameters such as hydrophobicity, hydrophobic moment, and propensity for a -helix formation.
533 citations
TL;DR: 14-3-3 proteins play a key regulatory role in signal transduction, checkpoint control, apoptotic, and nutrient-sensing pathways, and they can also promote the nuclear localization of other partners, such as the catalytic subunit of telomerase (TERT).
407 citations
TL;DR: In the majority of cases, one of the interacting proteins was known to be involved in DNA replication, transcription, virion structure, or host evasion, thereby providing a clue to the role of the other uncharacterized protein in a specific process.
Abstract: To detect interactions between proteins of vaccinia virus, we carried out a comprehensive two-hybrid analysis to assay every pairwise combination. We constructed an array of yeast transformants that contained each of the 266 predicted viral ORFs as Gal4 activation domain hybrid proteins. The array was individually mated to transformants containing each ORF as a Gal4–DNA-binding domain hybrid, and diploids expressing the two-hybrid reporter gene were identified. Of the ≈70,000 combinations, we found 37 protein–protein interactions, including 28 that were previously unknown. In some cases, e.g., late transcription factors, both proteins were known to have related roles although there was no prior evidence of physical associations. For some other interactions, neither protein had a known role. In the majority of cases, however, one of the interacting proteins was known to be involved in DNA replication, transcription, virion structure, or host evasion, thereby providing a clue to the role of the other uncharacterized protein in a specific process.
287 citations
TL;DR: Tyrosine sulfation is a post-translational modification of many secreted and membrane-bound proteins that is implicated in protein-protein interactions involved in leukocyte adhesion, hemostasis and chemokine signaling.
251 citations
TL;DR: It is maintained that an increase in the first-encounter rate is too small to be responsible for truly enhanced signal transduction, and an important structural constraint imposed by this mechanism on signalTransduction proteins that might also account for the presence of adaptor proteins are discussed.
240 citations
TL;DR: Combinatorial control is a characteristic property of Ets family members, involving interaction between Ets and other key transcriptional factors such as AP-1, NFκB and Pax family members.
Abstract: Ets proteins are a family of transcription factors that share an 85 amino acid conserved DNA binding domain, the ETS domain. Over 25 mammalian Ets family members control important biological processes, including cellular proliferation, differentiation, lymphocyte development and activation, transformation and apoptosis by recognizing the GGA core motif in the promoter or enhancer of their target genes. Protein–protein interactions regulates DNA binding, subcellular localization, target gene selection and transcriptional activity of Ets proteins. Combinatorial control is a characteristic property of Ets family members, involving interaction between Ets and other key transcriptional factors such as AP-1, NFκB and Pax family members. Specific domains of Ets proteins interact with many protein motifs such as bHLH, bZipper and Paired domain. Such interactions coordinate cellular processes in response to diverse signals including cytokines, growth factors, antigen and cellular stresses.
238 citations
TL;DR: It is hypothesized that the novel protein domain designated PWWP domain, present in proteins of nuclear origin and plays a role in cell growth and differentiation, is involved in protein–protein interactions.
TL;DR: In this article, the authors used surface plasmon resonance (SPR) to examine the association and dissociation of AKAPs with all four R-subunit isoforms immobilized on a modified cAMP surface.
TL;DR: Evidence is provided that the homeodomain of PDX-1 acts as a protein-protein interaction domain to recruit multiple proteins, including E47/Pan1, BETA2/NeuroD1, and high-mobility group protein I(Y), to an activation complex on the E2A3/4 minienhancer.
Abstract: Activation of insulin gene transcription specifically in the pancreatic beta cells depends on multiple nuclear proteins that interact with each other and with sequences on the insulin gene promoter to build a transcriptional activation complex. The homeodomain protein PDX-1 exemplifies such interactions by binding to the A3/4 region of the rat insulin I promoter and activating insulin gene transcription by cooperating with the basic-helix-loop-helix (bHLH) protein E47/Pan1, which binds to the adjacent E2 site. The present study provides evidence that the homeodomain of PDX-1 acts as a protein-protein interaction domain to recruit multiple proteins, including E47/Pan1, BETA2/NeuroD1, and high-mobility group protein I(Y), to an activation complex on the E2A3/4 minienhancer. The transcriptional activity of this complex results from the clustering of multiple activation domains capable of interacting with coactivators and the basal transcriptional machinery. These interactions are not common to all homeodomain proteins: the LIM homeodomain protein Lmx1.1 can also activate the E2A3/4 minienhancer in cooperation with E47/Pan1 but does so through different interactions. Cooperation between Lmx1.1 and E47/Pan1 results not only in the aggregation of multiple activation domains but also in the unmasking of a potent activation domain on E47/Pan1 that is normally silent in non-beta cells. While more than one activation complex may be capable of activating insulin gene transcription through the E2A3/4 minienhancer, each is dependent on multiple specific interactions among a unique set of nuclear proteins.
TL;DR: The yeast Rad51 interacts with human Rad51 and XRCC3, suggesting Rad51 conservation since the human yeast divergence and suggests that these proteins may participate in one complex or multiple smaller ones.
TL;DR: Six tryptophan-rich peptides that preferentially bind pathologic-length polyglutamine domain proteins are identified and selective inhibition of pathologic interactions of expanded polyGLutamine domains with themselves or other proteins may be a useful strategy for preventing disease onset or for slowing progression of the polyglUTamine repeat diseases.
TL;DR: The results suggest that dimerization is a latent property of the FKBP fold: the crystal structure reveals a remarkably complementary interaction between the monomer binding sites, with only subtle changes in side-chain disposition accounting for the dramatic change in quaternary structure.
Abstract: Chemically induced dimerization provides a general way to gain control over intracellular processes. Typically, FK506-binding protein (FKBP) domains are fused to a signaling domain of interest, allowing crosslinking to be initiated by addition of a bivalent FKBP ligand. In the course of protein engineering studies on human FKBP, we discovered that a single point mutation in the ligand-binding site (Phe-36 → Met) converts the normally monomeric protein into a ligand-reversible dimer. Two-hybrid, gel filtration, analytical ultracentrifugation, and x-ray crystallographic studies show that the mutant (FM) forms discrete homodimers with micromolar affinity that can be completely dissociated within minutes by addition of monomeric synthetic ligands. These unexpected properties form the basis for a “reverse dimerization” regulatory system involving FM fusion proteins, in which association is the ground state and addition of ligand abolishes interactions. We have used this strategy to rapidly and reversibly aggregate fusion proteins in different cellular compartments, and to provide an off switch for transcription. Reiterated FM domains should be generally useful as conditional aggregation domains (CADs) to control intracellular events where rapid, reversible dissolution of interactions is required. Our results also suggest that dimerization is a latent property of the FKBP fold: the crystal structure reveals a remarkably complementary interaction between the monomer binding sites, with only subtle changes in side-chain disposition accounting for the dramatic change in quaternary structure.
TL;DR: Surface plasmon resonance-based methods and analytical ultracentrifugation data indicate that SLAM-SLAM interactions are in fact considerably weaker than most other well characterized protein-protein interactions at the cell surface, which raises important questions regarding the physiological role and/or properties of such interactions.
TL;DR: The 1.7 A crystal structure of the 24.5 kDa complex formed between the endonuclease domain of colicin E9 and its cognate immunity protein Im9 is reported, which provides a molecular rationale for this mechanism and highlights how specificity is achieved by very different interactions in the two complexes.
TL;DR: The possible phosphorelay networks in an Arabidopsis two‐component system are discussed and a specific interaction between ATHK1 and ATHP1 is detected, and it is indicated that ATHp2 could interact with ATRR4, and that AthP3 could interactWith ATRR1 or ATRR 4, however, ATH P1 could not interact with any ATRRs.
TL;DR: The generality of the PCA strategy is demonstrated with examples of assays that are designed on the basis of other enzymes including glycinamide ribonucleotide transformylase, aminoglycoside kinase, and hygromycin B kinase.
Abstract: Publisher Summary This chapter presents the basic concept of protein fragment complementation assays (PCAs) and how they are designed, with particular attention to the system developed based on murine dihydrofolate reductase (mDHFR). It then discusses several applications of the assay, including a simple, large-scale library-versus-library screening strategy in Escherichia coli . The implementation of mammalian assays is discussed, including applications to the quantitative detection of induced protein interactions and allosteric transitions in intact cells. Finally, the generality of the PCA strategy is demonstrated with examples of assays that are designed on the basis of other enzymes including glycinamide ribonucleotide transformylase, aminoglycoside kinase, and hygromycin B kinase.
TL;DR: FRET data demonstrate the utility of FRET in mapping dynamic protein interactions in a genetic system and indicate that an importin and exportin have overlapping pathways through the NPC.
TL;DR: The results suggest that the interaction of ULK1 and GABARAP is important to vesicle transport and axonal elongation in mammalian neurons.
TL;DR: This review describes some of the many systems used to select or screen for protein-protein interactions based on the regulation of reporter constructs by hybrid proteins expressed in bacteria, including recent implementations of generalizable two-hybrid systems for Escherichia coli.
TL;DR: This chapter describes methods for constructing and screening a protein array that contains most of the proteins present in S. cerevisiae, and develops an array format to increase the throughput of proteins that can be screened by the two-hybrid method.
Abstract: Publisher Summary The accumulation of large amounts of genomic sequence data has prompted studies in protein biology on an unprecedented scale. Determining the functions of uncharacterized open reading frames (ORFs) from yeast and other organisms is a major challenge, and traditional biochemical and genetic approaches are struggling to keep up with sequence data. One strategy to help determine the functions is to identify protein–protein interactions using the two-hybrid system, a genetic assay that takes place within living yeast cells. An array format is developed in the chapter to increase the throughput of proteins that can be screened by the two-hybrid method. An array is a spatially ordered set of separated elements in which each element is a unique protein potentially available for interaction. This chapter describes methods for constructing and screening a protein array that contains most of the proteins present in S. cerevisiae . However, the array may represent any group of proteins: all the expressed proteins present in an organism a family of related proteins, or even a set of proteins or peptides, not found in nature.
TL;DR: The application of a semi quantitative method based on a comparative analysis of molecular interaction fields to gain insights into the recognition properties of blue copper proteins shows that comparison of the molecular electrostatic potentials provides useful information complementary to that highlighted by sequence analysis.
Abstract: Blue copper proteins are type-I copper-containing redox proteins whose role is to shuttle electrons from an electron donor to an electron acceptor in bacteria and plants. A large amount of experimental data is available on blue copper proteins; however, their functional characterization is hindered by the complexity of redox processes in biological systems. We describe here the application of a semiquantitative method based on a comparative analysis of molecular interaction fields to gain insights into the recognition properties of blue copper proteins. Molecular electrostatic and hydrophobic potentials were computed and compared for a set of 33 experimentally-determined structures of proteins from seven blue copper subfamilies, and the results were quantified by means of similarity indices. The analysis provides a classification of the blue copper proteins and shows that (I) comparison of the molecular electrostatic potentials provides useful information complementary to that highlighted by sequence analysis; (2) similarities in recognition properties can be detected for proteins belonging to different subfamilies, such as amicyanins and pseudoazurins, that may be isofunctional proteins; (3) dissimilarities in interaction properties, consistent with experimentally different binding specificities, may be observed between proteins belonging to the same subfamily, such as cyanobacterial and eukaryotic plastocyanins; (4) proteins with low sequence identity, such as azurins and pseudoazurins, can have sufficient similarity to bind to similar electron donors and acceptors while having different binding specificity profiles.
TL;DR: The ability to self-associate provides a mechanism for EBP50 to expand its capacity to form multiprotein complexes and regulate membrane transport events.
TL;DR: Using an in vitro binding assay, concomitant association of several components of the complex on immobilized p38 could be demonstrated, and the involvement of synergistic effects for association of weakly interacting proteins was revealed.
TL;DR: The yeast two-hybrid method (or interaction trap) is a powerful technique for detecting protein interactions as discussed by the authors, which is performed using transcriptional activation of a dual reporter system in yeast to identify interactions between a protein of interest (the bait protein) and the candidate proteins for interaction.
Abstract: The yeast two-hybrid method (or interaction trap) is a powerful technique for detecting protein interactions. The procedure is performed using transcriptional activation of a dual reporter system in yeast to identify interactions between a protein of interest (the bait protein) and the candidate proteins for interaction. The method can be used to screen a protein library for interactions with a bait protein or to test for association between proteins that are expected to interact based on prior evidence. Interaction mating facilitates the screening of a library with multiple bait proteins.
TL;DR: Genetic analysis revealed that Nhp6B, a member of the HMG1 family of DNA-binding proteins, can influence transcriptional activation as well as repression at a specific locus in the chromosome of the yeast S. cerevisiae.
Abstract: The split-ubiquitin assay detects protein interactions in vivo. To identify proteins interacting with Gal4p and Tup1p, two transcriptional regulators, we converted the split-ubiquitin assay into a generally applicable screen for binding partners of specific proteins in vivo. A library of genomic Saccharomyces cerevisiae DNA fragments fused to the N-terminal half of ubiquitin was constructed and transformed into yeast strains carrying either Gal4p or Tup1p as a bait. Both proteins were C-terminally extended by the C-terminal half of ubiquitin followed by a modified Ura3p with an arginine in position 1, a destabilizing residue in the N-end rule pathway. The bait fusion protein alone is stable and enzymatically active. However, upon interaction with its prey, a native-like ubiquitin is reconstituted. RUra3p is then cleaved off by the ubiquitin-specific proteases and rapidly degraded by the N-end rule pathway. In both screens, Nhp6B was identified as a protein in close proximity to Gal4p as well as to Tup1p. Direct interaction between either protein and Nhp6B was confirmed by coprecipitation assays. Genetic analysis revealed that Nhp6B, a member of the HMG1 family of DNA-binding proteins, can influence transcriptional activation as well as repression at a specific locus in the chromosome of the yeast S. cerevisiae.
TL;DR: Conformational stability of the molecule increased linearly with the van der Waals volume of the side chains, and activity loss appears to correlate with the decrease in the rate of the conformational switch during complex formation with a target protease.
Abstract: In common globular proteins, the native form is in its most stable state. In contrast, each native form exists in a metastable state in inhibitory serpins (serine protease inhibitors) and some viral membrane fusion proteins. Metastability in these proteins is critical to their biological functions. Mutational analyses and structural examination have previously revealed unusual interactions, such as side-chain overpacking, buried polar groups, and cavities as the structural basis of the native metastability. However, the mechanism by which these structural defects regulate protein functions has not been elucidated. We report here characterization of cavity-filling mutations of α1-antitrypsin, a prototype serpin. Conformational stability of the molecule increased linearly with the van der Waals volume of the side chains. Increasing conformational stability is correlated with decreasing inhibitory activity. Moreover, the activity loss appears to correlate with the decrease in the rate of the conformational switch during complex formation with a target protease. These results strongly suggest that the native metastability of proteins is indeed a structural design that regulates protein functions.