Computational structural analysis of protein interactions and networks

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.

[1]  P. Bork,et al.  Structure-Based Assembly of Protein Complexes in Yeast , 2004, Science.

[2]  Gary D Bader,et al.  The multiple-specificity landscape of modular peptide recognition domains. , 2011 .

[3]  Benjamin A. Shoemaker,et al.  Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners , 2007, PLoS Comput. Biol..

[4]  Martin Vingron,et al.  IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..

[5]  Michael Y. Galperin,et al.  Who's your neighbor? New computational approaches for functional genomics , 2000, Nature Biotechnology.

[6]  M. Yaffe,et al.  A motif-based profile scanning approach for genome-wide prediction of signaling pathways , 2001, Nature Biotechnology.

[7]  C. Prieto,et al.  Structural domain–domain interactions: Assessment and comparison with protein–protein interaction data to improve the interactome , 2010, Proteins.

[8]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[9]  Ozlem Keskin,et al.  Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example† †This article is part of a Molecular BioSystems themed issue on Computational and Systems Biology. , 2009, Molecular bioSystems.

[10]  Mike Tyers,et al.  Evolutionary and Physiological Importance of Hub Proteins , 2006, PLoS Comput. Biol..

[11]  Nir London,et al.  The structural basis of peptide-protein binding strategies. , 2010, Structure.

[12]  Wei Zhang,et al.  Characterization of Domain-Peptide Interaction Interface , 2009, Molecular & Cellular Proteomics.

[13]  Sean R. Collins,et al.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.

[14]  Ozlem Keskin,et al.  Interaction prediction and classification of PDZ domains , 2010, BMC Bioinformatics.

[15]  Lincoln Stein,et al.  Reactome knowledgebase of human biological pathways and processes , 2008, Nucleic Acids Res..

[16]  T. Pawson,et al.  Assembly of Cell Regulatory Systems Through Protein Interaction Domains , 2003, Science.

[17]  S. Wodak,et al.  Docking and scoring protein complexes: CAPRI 3rd Edition , 2007, Proteins.

[18]  P. Bork,et al.  Linear Motif Atlas for Phosphorylation-Dependent Signaling , 2008, Science Signaling.

[19]  Juan Fernández-Recio,et al.  Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments , 2009, PLoS Comput. Biol..

[20]  Frederick P. Roth,et al.  Predicting co-complexed protein pairs using genomic and proteomic data integration , 2004, BMC Bioinformatics.

[21]  Mike Tyers,et al.  BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..

[22]  P. Bradley,et al.  Inferring PDZ Domain Multi-Mutant Binding Preferences from Single-Mutant Data , 2010, PloS one.

[23]  P. Aloy,et al.  Three-dimensional modeling of protein interactions and complexes is going 'omics. , 2011, Current opinion in structural biology.

[24]  Alfonso Valencia,et al.  Protein co-evolution, co-adaptation and interactions , 2008, The EMBO journal.

[25]  M. Gerstein,et al.  A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data , 2003, Science.

[26]  D. Fry,et al.  NMR characterization of interleukin‐2 in complexes with the IL‐2Rα receptor component, and with low molecular weight compounds that inhibit the IL‐2/IL‐Rα interaction , 2003, Protein science : a publication of the Protein Society.

[27]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

[28]  Bonnie Berger,et al.  Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction , 2005, Pacific Symposium on Biocomputing.

[29]  Lan V. Zhang,et al.  Evidence for dynamically organized modularity in the yeast protein–protein interaction network , 2004, Nature.

[30]  William Stafford Noble,et al.  Large-scale prediction of protein-protein interactions from structures , 2010, BMC Bioinformatics.

[31]  D. Eisenberg,et al.  Use of Logic Relationships to Decipher Protein Network Organization , 2004, Science.

[32]  Richard J. Edwards,et al.  SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent , 2006, Nucleic acids research.

[33]  Nikolaj Blom,et al.  Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins , 2004, BMC Bioinformatics.

[34]  Hui Lu,et al.  Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. , 2003, Genome research.

[35]  Alfonso Valencia,et al.  Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions. , 2009, Journal of molecular biology.

[36]  Alexandre M J J Bonvin,et al.  Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. , 2010, Journal of proteome research.

[37]  H Videler,et al.  Protein-protein interactions in colicin E9 DNase-immunity protein complexes. 2. Cognate and noncognate interactions that span the millimolar to femtomolar affinity range. , 1995, Biochemistry.

[38]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[39]  S. Jones,et al.  Prediction of protein-protein interaction sites using patch analysis. , 1997, Journal of molecular biology.

[40]  Petras J. Kundrotas,et al.  GWIDD: Genome-wide protein docking database , 2009, Nucleic Acids Res..

[41]  Bermseok Oh,et al.  Prediction of phosphorylation sites using SVMs , 2004, Bioinform..

[42]  Alex Bateman,et al.  Reuse of structural domain–domain interactions in protein networks , 2007, BMC Bioinformatics.

[43]  Gabriele Ausiello,et al.  MINT: the Molecular INTeraction database , 2006, Nucleic Acids Res..

[44]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[45]  Leszek Rychlewski,et al.  ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins , 2003, Nucleic Acids Res..

[46]  Tanja Kortemme,et al.  Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. , 2010, Journal of molecular biology.

[47]  A. Valencia,et al.  Similarity of phylogenetic trees as indicator of protein-protein interaction. , 2001, Protein engineering.

[48]  William Stafford Noble,et al.  Kernel methods for predicting protein-protein interactions , 2005, ISMB.

[49]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[50]  Gary D. Bader,et al.  Proteome scanning to predict PDZ domain interactions using support vector machines , 2010, BMC Bioinformatics.

[51]  J. Ferrell,et al.  Mechanisms of specificity in protein phosphorylation , 2007, Nature Reviews Molecular Cell Biology.

[52]  P. Bork,et al.  Systematic Discovery of In Vivo Phosphorylation Networks , 2007, Cell.

[53]  M. Tyers,et al.  From large networks to small molecules. , 2004, Current opinion in chemical biology.

[54]  L. Iakoucheva,et al.  The importance of intrinsic disorder for protein phosphorylation. , 2004, Nucleic acids research.

[55]  Sarah A. Teichmann,et al.  Principles of protein-protein interactions , 2002, ECCB.

[56]  D. Frishman,et al.  A domain interaction map based on phylogenetic profiling. , 2004, Journal of molecular biology.

[57]  S. J. Deminoff,et al.  An evolutionary proteomics approach identifies substrates of the cAMP-dependent protein kinase. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[58]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[59]  Bruce Stillman,et al.  Deciphering Protein Kinase Specificity through Large-scale Analysis of Materials Supplemental Deciphering Protein Kinase Specificity through Large-scale Analysis of Yeast Phosphorylation Site Motifs , 2010 .

[60]  Ziv Bar-Joseph,et al.  Evaluation of different biological data and computational classification methods for use in protein interaction prediction , 2006, Proteins.

[61]  Mark Gerstein,et al.  Open Access Methodology Article Motips: Automated Motif Analysis for Predicting Targets of Modular Protein Domains , 2022 .

[62]  J. H. Shinn,et al.  Minimotif Miner: a tool for investigating protein function , 2006, Nature Methods.

[63]  Alfonso Valencia,et al.  Towards the prediction of protein interaction partners using physical docking , 2011, Molecular systems biology.

[64]  Xingming Zhao,et al.  Computational Systems Biology , 2013, TheScientificWorldJournal.

[65]  Gavin MacBeath,et al.  Predicting PDZ domain–peptide interactions from primary sequences , 2008, Nature Biotechnology.

[66]  T. Clackson,et al.  Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity. , 1998, Journal of molecular biology.

[67]  A. Hopkins Network pharmacology: the next paradigm in drug discovery. , 2008, Nature chemical biology.

[68]  Christian von Mering,et al.  STRING: a database of predicted functional associations between proteins , 2003, Nucleic Acids Res..

[69]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[70]  T. Clackson,et al.  A hot spot of binding energy in a hormone-receptor interface , 1995, Science.

[71]  Patrick Aloy,et al.  Interrogating protein interaction networks through structural biology , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[72]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[73]  Albert-László Barabási,et al.  Error and attack tolerance of complex networks , 2000, Nature.

[74]  Yu Xue,et al.  GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy *S , 2008, Molecular & Cellular Proteomics.

[75]  Philip M. Kim,et al.  The role of disorder in interaction networks: a structural analysis , 2008, Molecular systems biology.

[76]  Andrew Chatr-aryamontri,et al.  DOMINO: a database of domain–peptide interactions , 2006, Nucleic Acids Res..

[77]  H. Kitano Systems Biology: A Brief Overview , 2002, Science.

[78]  Pedro Beltrão,et al.  Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions , 2005, PLoS Comput. Biol..

[79]  J. Thornton,et al.  Diversity of protein–protein interactions , 2003, The EMBO journal.

[80]  Jakub Pas,et al.  ELM: the status of the 2010 eukaryotic linear motif resource , 2009, Nucleic Acids Res..

[81]  D. Ingber,et al.  High-Betweenness Proteins in the Yeast Protein Interaction Network , 2005, Journal of biomedicine & biotechnology.

[82]  Philip M. Kim,et al.  Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights , 2006, Science.

[83]  José A. Encinar,et al.  ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs , 2009, Bioinform..

[84]  Pedro Beltrão,et al.  Specificity and Evolvability in Eukaryotic Protein Interaction Networks , 2007, PLoS Comput. Biol..

[85]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[86]  Ozlem Keskin,et al.  PRISM: protein-protein interaction prediction by structural matching. , 2008, Methods in molecular biology.

[87]  Alan M. Moses,et al.  Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions , 2012, Science Signaling.