1
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Idrees S, Paudel KR. Proteome-wide assessment of human interactome as a source of capturing domain-motif and domain-domain interactions. J Cell Commun Signal 2024; 18:e12014. [PMID: 38545252 PMCID: PMC10964934 DOI: 10.1002/ccs3.12014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 12/11/2023] [Indexed: 06/29/2024] Open
Abstract
Protein-protein interactions (PPIs) play a crucial role in various biological processes by establishing domain-motif (DMI) and domain-domain interactions (DDIs). While the existence of real DMIs/DDIs is generally assumed, it is rarely tested; therefore, this study extensively compared high-throughput methods and public PPI repositories as sources for DMI and DDI prediction based on the assumption that the human interactome provides sufficient data for the reliable identification of DMIs and DDIs. Different datasets from leading high-throughput methods (Yeast two-hybrid [Y2H], Affinity Purification coupled Mass Spectrometry [AP-MS], and Co-fractionation-coupled Mass Spectrometry) were assessed for their ability to capture DMIs and DDIs using known DMI/DDI information. High-throughput methods were not notably worse than PPI databases and, in some cases, appeared better. In conclusion, all PPI datasets demonstrated significant enrichment in DMIs and DDIs (p-value <0.001), establishing Y2H and AP-MS as reliable methods for predicting these interactions. This study provides valuable insights for biologists in selecting appropriate methods for predicting DMIs, ultimately aiding in SLiM discovery.
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Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Centre for InflammationCentenary Institute and the University of Technology SydneySchool of Life SciencesFaculty of ScienceSydneyNew South WalesAustralia
| | - Keshav Raj Paudel
- Centre for InflammationCentenary Institute and the University of Technology SydneySchool of Life SciencesFaculty of ScienceSydneyNew South WalesAustralia
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2
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Short Linear Motifs in Colorectal Cancer Interactome and Tumorigenesis. Cells 2022; 11:cells11233739. [PMID: 36496998 PMCID: PMC9737320 DOI: 10.3390/cells11233739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Colorectal tumorigenesis is driven by alterations in genes and proteins responsible for cancer initiation, progression, and invasion. This multistage process is based on a dense network of protein-protein interactions (PPIs) that become dysregulated as a result of changes in various cell signaling effectors. PPIs in signaling and regulatory networks are known to be mediated by short linear motifs (SLiMs), which are conserved contiguous regions of 3-10 amino acids within interacting protein domains. SLiMs are the minimum sequences required for modulating cellular PPI networks. Thus, several in silico approaches have been developed to predict and analyze SLiM-mediated PPIs. In this review, we focus on emerging evidence supporting a crucial role for SLiMs in driver pathways that are disrupted in colorectal cancer (CRC) tumorigenesis and related PPI network alterations. As a result, SLiMs, along with short peptides, are attracting the interest of researchers to devise small molecules amenable to be used as novel anti-CRC targeted therapies. Overall, the characterization of SLiMs mediating crucial PPIs in CRC may foster the development of more specific combined pharmacological approaches.
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3
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Chasapis CT. Building Bridges Between Structural and Network-Based Systems Biology. Mol Biotechnol 2019; 61:221-229. [DOI: 10.1007/s12033-018-0146-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Abstract
The implication of several TRP ion channels (e.g., TRPV1) in diverse physiological and pathological processes has signaled them as pivotal drug targets. Consequently, the identification of selective and potent ligands for these channels is of great interest in pharmacology and biomedicine. However, a major challenge in the design of modulators is ensuring the specificity for their intended targets. In recent years, the emergence of high-resolution structures of ion channels facilitates the computer-assisted drug design at molecular levels. Here we describe some computational methods and general protocols to discover channel modulators, including homology modelling, docking and virtual screening, and structure-based peptide design.
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Affiliation(s)
- Magdalena Nikolaeva Koleva
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universitas Miguel Hernández, Elche, Spain
- AntalGenics SL. Ed. Quorum III, University Scientific Park, Universitas Miguel Hernández, Elche, Spain
| | - Gregorio Fernandez-Ballester
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universitas Miguel Hernández, Elche, Spain.
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5
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Idrees S, Pérez-Bercoff Å, Edwards RJ. SLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions. PeerJ 2018; 6:e5858. [PMID: 30402352 PMCID: PMC6215436 DOI: 10.7717/peerj.5858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/02/2018] [Indexed: 01/21/2023] Open
Abstract
Many important cellular processes involve protein–protein interactions (PPIs) mediated by a Short Linear Motif (SLiM) in one protein interacting with a globular domain in another. Despite their significance, these domain-motif interactions (DMIs) are typically low affinity, which makes them challenging to identify by classical experimental approaches, such as affinity pulldown mass spectrometry (AP-MS) and yeast two-hybrid (Y2H). DMIs are generally underrepresented in PPI networks as a result. A number of computational methods now exist to predict SLiMs and/or DMIs from experimental interaction data but it is yet to be established how effective different PPI detection methods are for capturing these low affinity SLiM-mediated interactions. Here, we introduce a new computational pipeline (SLiM-Enrich) to assess how well a given source of PPI data captures DMIs and thus, by inference, how useful that data should be for SLiM discovery. SLiM-Enrich interrogates a PPI network for pairs of interacting proteins in which the first protein is known or predicted to interact with the second protein via a DMI. Permutation tests compare the number of known/predicted DMIs to the expected distribution if the two sets of proteins are randomly associated. This provides an estimate of DMI enrichment within the data and the false positive rate for individual DMIs. As a case study, we detect significant DMI enrichment in a high-throughput Y2H human PPI study. SLiM-Enrich analysis supports Y2H data as a source of DMIs and highlights the high false positive rates associated with naïve DMI prediction. SLiM-Enrich is available as an R Shiny app. The code is open source and available via a GNU GPL v3 license at: https://github.com/slimsuite/SLiMEnrich. A web server is available at: http://shiny.slimsuite.unsw.edu.au/SLiMEnrich/.
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Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Åsa Pérez-Bercoff
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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6
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Kelil A, Dubreuil B, Levy ED, Michnick SW. Exhaustive search of linear information encoding protein-peptide recognition. PLoS Comput Biol 2017; 13:e1005499. [PMID: 28426660 PMCID: PMC5417721 DOI: 10.1371/journal.pcbi.1005499] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 05/04/2017] [Accepted: 04/04/2017] [Indexed: 11/24/2022] Open
Abstract
High-throughput in vitro methods have been extensively applied to identify linear information that encodes peptide recognition. However, these methods are limited in number of peptides, sequence variation, and length of peptides that can be explored, and often produce solutions that are not found in the cell. Despite the large number of methods developed to attempt addressing these issues, the exhaustive search of linear information encoding protein-peptide recognition has been so far physically unfeasible. Here, we describe a strategy, called DALEL, for the exhaustive search of linear sequence information encoded in proteins that bind to a common partner. We applied DALEL to explore binding specificity of SH3 domains in the budding yeast Saccharomyces cerevisiae. Using only the polypeptide sequences of SH3 domain binding proteins, we succeeded in identifying the majority of known SH3 binding sites previously discovered either in vitro or in vivo. Moreover, we discovered a number of sites with both non-canonical sequences and distinct properties that may serve ancillary roles in peptide recognition. We compared DALEL to a variety of state-of-the-art algorithms in the blind identification of known binding sites of the human Grb2 SH3 domain. We also benchmarked DALEL on curated biological motifs derived from the ELM database to evaluate the effect of increasing/decreasing the enrichment of the motifs. Our strategy can be applied in conjunction with experimental data of proteins interacting with a common partner to identify binding sites among them. Yet, our strategy can also be applied to any group of proteins of interest to identify enriched linear motifs or to exhaustively explore the space of linear information encoded in a polypeptide sequence. Finally, we have developed a webserver located at http://michnick.bcm.umontreal.ca/dalel, offering user-friendly interface and providing different scenarios utilizing DALEL. Here we describe the first strategy for the exhaustive search of the linear information encoding protein-peptide recognition; an approach that has previously been physically unfeasible because the combinatorial space of polypeptide sequences is too vast. The search covers the entire space of sequences with no restriction on motif length or composition, and includes all possible combinations of amino acids at distinct positions of each sequence, as well as positions with correlated preferences for amino acids.
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Affiliation(s)
- Abdellali Kelil
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Benjamin Dubreuil
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emmanuel D. Levy
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, Canada
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Stephen W. Michnick
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, Canada
- * E-mail:
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7
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Evolution of domain-peptide interactions to coadapt specificity and affinity to functional diversity. Proc Natl Acad Sci U S A 2016; 113:E3862-71. [PMID: 27317745 DOI: 10.1073/pnas.1518469113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Evolution of complexity in eukaryotic proteomes has arisen, in part, through emergence of modular independently folded domains mediating protein interactions via binding to short linear peptides in proteins. Over 30 years, structural properties and sequence preferences of these peptides have been extensively characterized. Less successful, however, were efforts to establish relationships between physicochemical properties and functions of domain-peptide interactions. To our knowledge, we have devised the first strategy to exhaustively explore the binding specificity of protein domain-peptide interactions. We applied the strategy to SH3 domains to determine the properties of their binding peptides starting from various experimental data. The strategy identified the majority (∼70%) of experimentally determined SH3 binding sites. We discovered mutual relationships among binding specificity, binding affinity, and structural properties and evolution of linear peptides. Remarkably, we found that these properties are also related to functional diversity, defined by depth of proteins within hierarchies of gene ontologies. Our results revealed that linear peptides evolved to coadapt specificity and affinity to functional diversity of domain-peptide interactions. Thus, domain-peptide interactions follow human-constructed gene ontologies, which suggest that our understanding of biological process hierarchies reflect the way chemical and thermodynamic properties of linear peptides and their interaction networks, in general, have evolved.
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8
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Kelil A, Dubreuil B, Levy ED, Michnick SW. Fast and accurate discovery of degenerate linear motifs in protein sequences. PLoS One 2014; 9:e106081. [PMID: 25207816 PMCID: PMC4160167 DOI: 10.1371/journal.pone.0106081] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 08/01/2014] [Indexed: 11/20/2022] Open
Abstract
Linear motifs mediate a wide variety of cellular functions, which makes their characterization in protein sequences crucial to understanding cellular systems. However, the short length and degenerate nature of linear motifs make their discovery a difficult problem. Here, we introduce MotifHound, an algorithm particularly suited for the discovery of small and degenerate linear motifs. MotifHound performs an exact and exhaustive enumeration of all motifs present in proteins of interest, including all of their degenerate forms, and scores the overrepresentation of each motif based on its occurrence in proteins of interest relative to a background (e.g., proteome) using the hypergeometric distribution. To assess MotifHound, we benchmarked it together with state-of-the-art algorithms. The benchmark consists of 11,880 sets of proteins from S. cerevisiae; in each set, we artificially spiked-in one motif varying in terms of three key parameters, (i) number of occurrences, (ii) length and (iii) the number of degenerate or “wildcard” positions. The benchmark enabled the evaluation of the impact of these three properties on the performance of the different algorithms. The results showed that MotifHound and SLiMFinder were the most accurate in detecting degenerate linear motifs. Interestingly, MotifHound was 15 to 20 times faster at comparable accuracy and performed best in the discovery of highly degenerate motifs. We complemented the benchmark by an analysis of proteins experimentally shown to bind the FUS1 SH3 domain from S. cerevisiae. Using the full-length protein partners as sole information, MotifHound recapitulated most experimentally determined motifs binding to the FUS1 SH3 domain. Moreover, these motifs exhibited properties typical of SH3 binding peptides, e.g., high intrinsic disorder and evolutionary conservation, despite the fact that none of these properties were used as prior information. MotifHound is available (http://michnick.bcm.umontreal.ca or http://tinyurl.com/motifhound) together with the benchmark that can be used as a reference to assess future developments in motif discovery.
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Affiliation(s)
- Abdellali Kelil
- Département de Biochimie and Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Succursale Centre-Ville, Montreal, Quebec, Canada
| | - Benjamin Dubreuil
- Département de Biochimie and Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Succursale Centre-Ville, Montreal, Quebec, Canada
| | - Emmanuel D. Levy
- Département de Biochimie and Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Succursale Centre-Ville, Montreal, Quebec, Canada
- * E-mail: (EDL); (SWM)
| | - Stephen W. Michnick
- Département de Biochimie and Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Succursale Centre-Ville, Montreal, Quebec, Canada
- * E-mail: (EDL); (SWM)
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9
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Mosca R, Céol A, Stein A, Olivella R, Aloy P. 3did: a catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res 2013; 42:D374-9. [PMID: 24081580 PMCID: PMC3965002 DOI: 10.1093/nar/gkt887] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein–protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain–domain interactions in the Protein Data Bank, providing molecular details for such interactions. The current version also includes a pipeline for the discovery and annotation of novel domain–motif interactions. For every interaction, 3did identifies and groups different binding modes by clustering similar interfaces into ‘interaction topologies’. By maintaining a constantly updated collection of domain-based structural interaction templates, 3did is a reference source of information for the structural characterization of protein interaction networks. 3did is updated every 6 months.
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Affiliation(s)
- Roberto Mosca
- Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158-2330, USA and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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10
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de la Puerta ML, Trinidad AG, Rodríguez MDC, de Pereda JM, Sánchez Crespo M, Bayón Y, Alonso A. The autoimmunity risk variant LYP-W620 cooperates with CSK in the regulation of TCR signaling. PLoS One 2013; 8:e54569. [PMID: 23359562 PMCID: PMC3554717 DOI: 10.1371/journal.pone.0054569] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 12/12/2012] [Indexed: 11/21/2022] Open
Abstract
The protein tyrosine phosphatase LYP, a key regulator of TCR signaling, presents a single nucleotide polymorphism, C1858T, associated with several autoimmune diseases such as type I diabetes, rheumatoid arthritis, and lupus. This polymorphism changes an R by a W in the P1 Pro rich motif of LYP, which binds to CSK SH3 domain, another negative regulator of TCR signaling. Based on the analysis of the mouse homologue, Pep, it was proposed that LYP and CSK bind constitutively to inhibit LCK and subsequently TCR signaling. The detailed study of LYP/CSK interaction, here presented, showed that LYP/CSK interaction was inducible upon TCR stimulation, and involved LYP P1 and P2 motifs, and CSK SH3 and SH2 domains. Abrogating LYP/CSK interaction did not preclude the regulation of TCR signaling by these proteins.
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Affiliation(s)
- María Luisa de la Puerta
- Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Antonio G. Trinidad
- Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, Valladolid, Spain
| | | | - José María de Pereda
- Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Mariano Sánchez Crespo
- Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Yolanda Bayón
- Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Andrés Alonso
- Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, Valladolid, Spain
- * E-mail:
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11
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Hooda Y, Kim PM. Computational structural analysis of protein interactions and networks. Proteomics 2012; 12:1697-705. [PMID: 22593000 DOI: 10.1002/pmic.201100597] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein interactions have been at the focus of computational biology in recent years. In particular, interest has come from two different communities--structural and systems biology. Here, we will discuss key systems and structural biology methods that have been used for analysis and prediction of protein-protein interactions and the insight these approaches have provided on the nature and organization of protein-protein interactions inside cells.
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Affiliation(s)
- Yogesh Hooda
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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12
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A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. Genome Biol 2012; 13:R76. [PMID: 22937800 PMCID: PMC4053744 DOI: 10.1186/gb-2012-13-8-r76] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 08/31/2012] [Indexed: 12/28/2022] Open
Abstract
Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-positive and false-negative rates. Coev2Net is easily applied to thousands of binary protein interactions and has superior predictive performance over existing methods. We experimentally validate selected high-confidence predictions in the human MAPK network and show that predicted interfaces are enriched for cancer -related or damaging SNPs. Coev2Net can be downloaded at http://struct2net.csail.mit.edu.
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13
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Kubrycht J, Sigler K, Souček P. Virtual interactomics of proteins from biochemical standpoint. Mol Biol Int 2012; 2012:976385. [PMID: 22928109 PMCID: PMC3423939 DOI: 10.1155/2012/976385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/18/2012] [Accepted: 05/18/2012] [Indexed: 12/24/2022] Open
Abstract
Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein) docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations.
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Affiliation(s)
- Jaroslav Kubrycht
- Department of Physiology, Second Medical School, Charles University, 150 00 Prague, Czech Republic
| | - Karel Sigler
- Laboratory of Cell Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
| | - Pavel Souček
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
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Weatheritt RJ, Jehl P, Dinkel H, Gibson TJ. iELM--a web server to explore short linear motif-mediated interactions. Nucleic Acids Res 2012; 40:W364-9. [PMID: 22638578 PMCID: PMC3394315 DOI: 10.1093/nar/gks444] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The recent expansion in our knowledge of protein–protein interactions (PPIs) has allowed the annotation and prediction of hundreds of thousands of interactions. However, the function of many of these interactions remains elusive. The interactions of Eukaryotic Linear Motif (iELM) web server provides a resource for predicting the function and positional interface for a subset of interactions mediated by short linear motifs (SLiMs). The iELM prediction algorithm is based on the annotated SLiM classes from the Eukaryotic Linear Motif (ELM) resource and allows users to explore both annotated and user-generated PPI networks for SLiM-mediated interactions. By incorporating the annotated information from the ELM resource, iELM provides functional details of PPIs. This can be used in proteomic analysis, for example, to infer whether an interaction promotes complex formation or degradation. Furthermore, details of the molecular interface of the SLiM-mediated interactions are also predicted. This information is displayed in a fully searchable table, as well as graphically with the modular architecture of the participating proteins extracted from the UniProt and Phospho.ELM resources. A network figure is also presented to aid the interpretation of results. The iELM server supports single protein queries as well as large-scale proteomic submissions and is freely available at http://i.elm.eu.org.
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Affiliation(s)
- Robert J Weatheritt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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15
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Trabuco LG, Lise S, Petsalaki E, Russell RB. PepSite: prediction of peptide-binding sites from protein surfaces. Nucleic Acids Res 2012; 40:W423-7. [PMID: 22600738 PMCID: PMC3394340 DOI: 10.1093/nar/gks398] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Complex biological functions emerge through intricate protein–protein interaction networks. An important class of protein–protein interaction corresponds to peptide-mediated interactions, in which a short peptide stretch from one partner interacts with a large protein surface from the other partner. Protein–peptide interactions are typically of low affinity and involved in regulatory mechanisms, dynamically reshaping protein interaction networks. Due to the relatively small interaction surface, modulation of protein–peptide interactions is feasible and highly attractive for therapeutic purposes. Unfortunately, the number of available 3D structures of protein–peptide interfaces is very limited. For typical cases where a protein–peptide structure of interest is not available, the PepSite web server can be used to predict peptide-binding spots from protein surfaces alone. The PepSite method relies on preferred peptide-binding environments calculated from a set of known protein–peptide 3D structures, combined with distance constraints derived from known peptides. We present an updated version of the web server that is orders of magnitude faster than the original implementation, returning results in seconds instead of minutes or hours. The PepSite web server is available at http://pepsite2.russelllab.org.
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16
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Weatheritt RJ, Luck K, Petsalaki E, Davey NE, Gibson TJ. The identification of short linear motif-mediated interfaces within the human interactome. ACTA ACUST UNITED AC 2012; 28:976-82. [PMID: 22328783 PMCID: PMC3315716 DOI: 10.1093/bioinformatics/bts072] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein-protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by short linear motifs (SLiMs), particularly the canonical and ubiquitous SH2, SH3 and PDZ domain-binding motifs. However, these motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of motif instances. RESULTS In this article, interaction data are analysed to identify and characterize an important subset of PPIs, those involving SLiMs binding to globular domains. To do this, we introduce iELM, a method to identify interactions mediated by SLiMs and add molecular details of the interaction interfaces to both interacting proteins. The method identifies SLiM-mediated interfaces from PPI data by searching for known SLiM-domain pairs. This approach was applied to the human interactome to identify a set of high-confidence putative SLiM-mediated PPIs. AVAILABILITY iELM is freely available at http://elmint.embl.de CONTACT toby.gibson@embl.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- R J Weatheritt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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17
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Luck K, Fournane S, Kieffer B, Masson M, Nominé Y, Travé G. Putting into practice domain-linear motif interaction predictions for exploration of protein networks. PLoS One 2011; 6:e25376. [PMID: 22069443 PMCID: PMC3206016 DOI: 10.1371/journal.pone.0025376] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 09/02/2011] [Indexed: 12/22/2022] Open
Abstract
PDZ domains recognise short sequence motifs at the extreme C-termini of proteins. A model based on microarray data has been recently published for predicting the binding preferences of PDZ domains to five residue long C-terminal sequences. Here we investigated the potential of this predictor for discovering novel protein interactions that involve PDZ domains. When tested on real negative data assembled from published literature, the predictor displayed a high false positive rate (FPR). We predicted and experimentally validated interactions between four PDZ domains derived from the human proteins MAGI1 and SCRIB and 19 peptides derived from human and viral C-termini of proteins. Measured binding intensities did not correlate with prediction scores, and the high FPR of the predictor was confirmed. Results indicate that limitations of the predictor may arise from an incomplete model definition and improper training of the model. Taking into account these limitations, we identified several novel putative interactions between PDZ domains of MAGI1 and SCRIB and the C-termini of the proteins FZD4, ARHGAP6, NET1, TANC1, GLUT7, MARCH3, MAS, ABC1, DLL1, TMEM215 and CYSLTR2. These proteins are localised to the membrane or suggested to act close to it and are often involved in G protein signalling. Furthermore, we showed that, while extension of minimal interacting domains or peptides toward tandem constructs or longer peptides never suppressed their ability to interact, the measured affinities and inferred specificity patterns often changed significantly. This suggests that if protein fragments interact, the full length proteins are also likely to interact, albeit possibly with altered affinities and specificities. Therefore, predictors dealing with protein fragments are promising tools for discovering protein interaction networks but their application to predict binding preferences within networks may be limited.
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Affiliation(s)
- Katja Luck
- Group Onco-Proteins, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, BP 10413, Illkirch, France
| | - Sadek Fournane
- Group Onco-Proteins, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, BP 10413, Illkirch, France
| | - Bruno Kieffer
- Biomolecular NMR group, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, BP 10413, Illkirch, France
| | - Murielle Masson
- Group Onco-Proteins, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, BP 10413, Illkirch, France
| | - Yves Nominé
- Group Onco-Proteins, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, BP 10413, Illkirch, France
| | - Gilles Travé
- Group Onco-Proteins, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, BP 10413, Illkirch, France
- * E-mail:
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18
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Impact of the 237th residue on the folding of human carbonic anhydrase II. Int J Mol Sci 2011; 12:2797-807. [PMID: 21686151 PMCID: PMC3116157 DOI: 10.3390/ijms12052797] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/07/2011] [Accepted: 04/12/2011] [Indexed: 02/08/2023] Open
Abstract
The deficiency of human carbonic anhydrase II (HCAII) has been recognized to be associated with a disease called CAII deficiency syndrome (CADS). Among the many mutations, the P237H mutation has been characterized to lead to a significant decrease in the activity of the enzyme and in the Gibbs free energy of folding. However, sequence alignment indicated that the 237th residue of CAII is not fully conserved across all species. The FoldX theoretical calculations suggested that this residue did not significantly contribute to the overall folding of HCAII, since all mutants had small ΔΔG values (around 1 kcal/mol). The experimental determination indicated that at least three mutations affect HCAII folding significantly and the P237H mutation was the most deleterious one, suggesting that Pro237 was important to HCAII folding. The discrepancy between theoretical and experimental results suggested that caution should be taken when using the prediction methods to evaluate the details of disease-related mutations.
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19
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Acuner Ozbabacan SE, Engin HB, Gursoy A, Keskin O. Transient protein-protein interactions. Protein Eng Des Sel 2011; 24:635-48. [DOI: 10.1093/protein/gzr025] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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20
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Stein A, Mosca R, Aloy P. Three-dimensional modeling of protein interactions and complexes is going 'omics. Curr Opin Struct Biol 2011; 21:200-8. [PMID: 21320770 DOI: 10.1016/j.sbi.2011.01.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 01/11/2011] [Accepted: 01/13/2011] [Indexed: 10/18/2022]
Abstract
High-throughput interaction discovery initiatives have revealed the existence of hundreds of multiprotein complexes whose functions are regulated through thousands of protein-protein interactions (PPIs). However, the structural details of these interactions, often necessary to understand their function, are only available for a tiny fraction, and the experimental difficulties surrounding complex structure determination make computational modeling techniques paramount. In this manuscript, we critically review some of the most recent developments in the field of structural bioinformatics applied to the modeling of protein interactions and complexes, from large macromolecular machines to domain-domain and peptide-mediated interactions. In particular, we place a special emphasis on those methods that can be applied in a proteome-wide manner, and discuss how they will help in the ultimate objective of building 3D interactome networks.
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Affiliation(s)
- Amelie Stein
- Institute for Research in Biomedicine (IRB Barcelona), Joint IRB-BSC Program in Computational Biology, c/Baldiri i Reixac 10-12, 08028 Barcelona, Spain
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21
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Hosur R, Xu J, Bienkowska J, Berger B. iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. J Mol Biol 2011; 405:1295-310. [PMID: 21130772 PMCID: PMC3028939 DOI: 10.1016/j.jmb.2010.11.025] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 11/10/2010] [Accepted: 11/12/2010] [Indexed: 11/23/2022]
Abstract
Current homology modeling methods for predicting protein-protein interactions (PPIs) have difficulty in the "twilight zone" (<40%) of sequence identities. Threading methods extend coverage further into the twilight zone by aligning primary sequences for a pair of proteins to a best-fit template complex to predict an entire three-dimensional structure. We introduce a threading approach, iWRAP, which focuses only on the protein interface. Our approach combines a novel linear programming formulation for interface alignment with a boosting classifier for interaction prediction. We demonstrate its efficacy on SCOPPI, a classification of PPIs in the Protein Databank, and on the entire yeast genome. iWRAP provides significantly improved prediction of PPIs and their interfaces in stringent cross-validation on SCOPPI. Furthermore, by combining our predictions with a full-complex threader, we achieve a coverage of 13% for the yeast PPIs, which is close to a 50% increase over previous methods at a higher sensitivity. As an application, we effectively combine iWRAP with genomic data to identify novel cancer-related genes involved in chromatin remodeling, nucleosome organization, and ribonuclear complex assembly. iWRAP is available at http://iwrap.csail.mit.edu.
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Affiliation(s)
- R. Hosur
- Computer Science and Artificial Intelligence Laboratory, MIT
- Department of Materials Science and Engineering, MIT
| | - J. Xu
- Computer Science and Artificial Intelligence Laboratory, MIT
- Toyota Technological Institute at Chicago
| | - J. Bienkowska
- Computer Science and Artificial Intelligence Laboratory, MIT
- Computational Biology Group, BiogenIdec
| | - B. Berger
- Computer Science and Artificial Intelligence Laboratory, MIT
- Department of Mathematics, MIT
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22
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The structural and dynamic response of MAGI-1 PDZ1 with noncanonical domain boundaries to the binding of human papillomavirus E6. J Mol Biol 2011; 406:745-63. [PMID: 21238461 DOI: 10.1016/j.jmb.2011.01.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 01/06/2011] [Accepted: 01/07/2011] [Indexed: 11/23/2022]
Abstract
PDZ domains are protein interaction domains that are found in cytoplasmic proteins involved in signaling pathways and subcellular transport. Their roles in the control of cell growth, cell polarity, and cell adhesion in response to cell contact render this family of proteins targets during the development of cancer. Targeting of these network hubs by the oncoprotein E6 of "high-risk" human papillomaviruses (HPVs) serves to effect the efficient disruption of cellular processes. Using NMR, we have solved the three-dimensional solution structure of an extended construct of the second PDZ domain of MAGI-1 (MAGI-1 PDZ1) alone and bound to a peptide derived from the C-terminus of HPV16 E6, and we have characterized the changes in backbone dynamics and hydrogen bonding that occur upon binding. The binding event induces quenching of high-frequency motions in the C-terminal tail of the PDZ domain, which contacts the peptide upstream of the canonical X-[T/S]-X-[L/V] binding motif. Mutations designed in the C-terminal flanking region of the PDZ domain resulted in a significant decrease in binding affinity for E6 peptides. This detailed analysis supports the notion of a global response of the PDZ domain to the binding event, with effects propagated to distal sites, and reveals unexpected roles for the sequences flanking the canonical PDZ domain boundaries.
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23
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Stein A, Céol A, Aloy P. 3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res 2010; 39:D718-23. [PMID: 20965963 PMCID: PMC3013799 DOI: 10.1093/nar/gkq962] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. 3did exploits the availability of structural data to provide molecular details on interactions between two globular domains as well as novel domain–peptide interactions, derived using a recently published method from our lab. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The 3did web server at http://3did.irbbarcelona.org visualizes these interfaces along with atomic details of individual interactions using Jmol. The complete contents are also available for download.
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Affiliation(s)
- Amelie Stein
- Institute for Research in Biomedicine, Join IRB-BSC Program in Computational Biology, 08028 Barcelona, Spain
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24
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Aucher W, Becker E, Ma E, Miron S, Martel A, Ochsenbein F, Marsolier-Kergoat MC, Guerois R. A strategy for interaction site prediction between phospho-binding modules and their partners identified from proteomic data. Mol Cell Proteomics 2010; 9:2745-59. [PMID: 20733106 DOI: 10.1074/mcp.m110.003319] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Small and large scale proteomic technologies are providing a wealth of potential interactions between proteins bearing phospho-recognition modules and their substrates. Resulting interaction maps reveal such a dense network of interactions that the functional dissection and understanding of these networks often require to break specific interactions while keeping the rest intact. Here, we developed a computational strategy, called STRIP, to predict the precise interaction site involved in an interaction with a phospho-recognition module. The method was validated by a two-hybrid screen carried out using the ForkHead Associated (FHA)1 domain of Rad53, a key protein of Saccharomyces cerevisiae DNA checkpoint, as a bait. In this screen we detected 11 partners, including Cdc7 and Cdc45, essential components of the DNA replication machinery. FHA domains are phospho-threonine binding modules and the threonines involved in both interactions could be predicted using the STRIP strategy. The threonines T484 and T189 in Cdc7 and Cdc45, respectively, were mutated and loss of binding could be monitored experimentally with the full-length proteins. The method was further tested for the analysis of 63 known Rad53 binding partners and provided several key insights regarding the threonines likely involved in these interactions. The STRIP method relies on a combination of conservation, phosphorylation likelihood, and binding specificity criteria and can be accessed via a web interface at http://biodev.extra.cea.fr/strip/.
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Affiliation(s)
- Willy Aucher
- Laboratoire du Métabolisme de l'ADN et Réponses aux Génotoxiques, Gif-sur-Yvette F-91191, France
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25
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Smith CA, Kortemme T. Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. J Mol Biol 2010; 402:460-74. [PMID: 20654621 DOI: 10.1016/j.jmb.2010.07.032] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 07/07/2010] [Indexed: 11/27/2022]
Abstract
Protein-protein recognition, frequently mediated by members of large families of interaction domains, is one of the cornerstones of biological function. Here, we present a computational, structure-based method to predict the sequence space of peptides recognized by PDZ domains, one of the largest families of recognition proteins. As a test set, we use a considerable amount of recent phage display data that describe the peptide recognition preferences for 169 naturally occurring and engineered PDZ domains. For both wild-type PDZ domains and single point mutants, we find that 70-80% of the most frequently observed amino acids by phage display are predicted within the top five ranked amino acids. Phage display frequently identified recognition preferences for amino acids different from those present in the original crystal structure. Notably, in about half of these cases, our algorithm correctly captures these preferences, indicating that it can predict mutations that increase binding affinity relative to the starting structure. We also find that we can computationally recapitulate specificity changes upon mutation, a key test for successful forward design of protein-protein interface specificity. Across all evaluated data sets, we find that incorporation backbone sampling improves accuracy substantially, irrespective of using a crystal or NMR structure as the starting conformation. Finally, we report successful prediction of several amino acid specificity changes from blind tests in the DREAM4 peptide recognition domain specificity prediction challenge. Because the foundational methods developed here are structure based, these results suggest that the approach can be more generally applied to specificity prediction and redesign of other protein-protein interfaces that have structural information but lack phage display data.
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Affiliation(s)
- Colin A Smith
- Graduate Program in Biological and Medical Informatics, University of California San Francisco, 600 16th Street, MC 2240, San Francisco, CA 94158, USA
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26
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Singh R, Park D, Xu J, Hosur R, Berger B. Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Res 2010; 38:W508-15. [PMID: 20513650 PMCID: PMC2896152 DOI: 10.1093/nar/gkq481] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 05/02/2010] [Accepted: 05/13/2010] [Indexed: 01/22/2023] Open
Abstract
Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein-protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of the PPI interactome remains inadequate. We believe that Struct2Net is the first community-wide resource to provide structure-based PPI predictions that go beyond homology modeling. Also, most web-resources for predicting PPIs currently rely on functional genomic data (e.g. GO annotation, gene expression, cellular localization, etc.). Our structure-based approach is independent of such methods and only requires the sequence information of the proteins being queried. The web service allows multiple querying options, aimed at maximizing flexibility. For the most commonly studied organisms (fly, human and yeast), predictions have been pre-computed and can be retrieved almost instantaneously. For proteins from other species, users have the option of getting a quick-but-approximate result (using orthology over pre-computed results) or having a full-blown computation performed. The web service is freely available at http://struct2net.csail.mit.edu.
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Affiliation(s)
- Rohit Singh
- Computer Science and Artificial Intelligence Laboratory, Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, Toyota Technological Institute at Chicago, Chicago, IL and Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel Park
- Computer Science and Artificial Intelligence Laboratory, Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, Toyota Technological Institute at Chicago, Chicago, IL and Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jinbo Xu
- Computer Science and Artificial Intelligence Laboratory, Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, Toyota Technological Institute at Chicago, Chicago, IL and Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Raghavendra Hosur
- Computer Science and Artificial Intelligence Laboratory, Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, Toyota Technological Institute at Chicago, Chicago, IL and Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, Toyota Technological Institute at Chicago, Chicago, IL and Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
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