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Computational Methods to Predict Protein Interaction Partners

  • Chapter
Protein-protein Interactions and Networks

Part of the book series: Computational Biology ((COBO,volume 9))

Abstract

In the new paradigm for studying biological phenomena represented by Systems Biology, cellular components are not considered in isolation but as forming complex networks of relationships. Protein interaction networks are among the first objects studied from this new point of view. Deciphering the interactome (the whole network of interactions for a given proteome) has been shown to be a very complex task. Computational techniques for detecting protein interactions have become standard tools for dealing with this problem, helping and complementing their experimental counterparts. Most of these techniques use genomic or sequence features intuitively related with protein interactions and are based on “first principles” in the sense that they do not involve training with examples. There are also other computational techniques that use other sources of information (i.e. structural information or even experimental data) or are based on training with examples.

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References

  • Aloy, P. and Russell, R. B. (2002a) Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA, 99, 5896–5901.

    Article  Google Scholar 

  • Aloy, P. and Russell, R. B. (2002b) Potential artefacts in protein-interaction networks. FEBS Lett, 530, 253–254.

    Article  Google Scholar 

  • Aloy, P. and Russell, R. B. (2003) InterPreTS: protein Interaction Prediction through Tertiary Structure. Bioinformatics, 19, 161–162.

    Article  Google Scholar 

  • Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res, 25, 3389–3402.

    Article  Google Scholar 

  • Barker, D., Meade, A. and Pagel, M. (2007) Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics, 23, 14–20.

    Article  Google Scholar 

  • Ben-Hur, A. and Noble, W. S. (2005) Kernel methods for predicting protein-protein interactions. Bioinformatics, 21, i38–46.

    Article  Google Scholar 

  • Bhardwaj, N. and Lu, H. (2005) Correlation between gene expression profiles and protein-protein interactions within and across genomes. Bioinformatics, 21, 2730–2738.

    Article  Google Scholar 

  • Bornberg-Bauer, E., Beaussart, F., Kummerfeld, S. K., Teichmann, S. A. and Weiner, J., 3rd. (2005) The evolution of domain arrangements in proteins and interaction networks. Cell Mol Life Sci, 62, 435–445.

    Article  Google Scholar 

  • Bowers, P. M., Cokus, S. J., Eisenberg, D. and Yeates, T. O. (2004) Use of logic relationships to decipher protein network organization. Science, 306, 2246–2249.

    Article  Google Scholar 

  • Bu, D., Zhao, Y., Cai, L., Xue, H., Zhu, X., Lu, H., Zhang, J., Sun, S., Ling, L., Zhang, N., Li, G. and Chen, R. (2003) Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res, 31, 2443–2450.

    Article  Google Scholar 

  • Chen, X. W. and Liu, M. (2005) Prediction of protein-protein interactions using random decision forest framework. Bioinformatics, 21, 4394–4400.

    Article  Google Scholar 

  • Chen, Y. and Dokholyan, N. V. (2006) The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet, 22, 416–419.

    Article  Google Scholar 

  • Dandekar, T., Snel, B., Huynen, M. and Bork, P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci, 23, 324–328.

    Article  Google Scholar 

  • Date, S. V. and Marcotte, E. M. (2003) Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol, 21, 1055–1062.

    Article  Google Scholar 

  • Enright, A. J., Iliopoulos, I., Kyrpides, N. C. and Ouzounis, C. A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86–90.

    Article  Google Scholar 

  • Fraser, H. B., Hirsh, A. E., Steinmetz, L. M., Scharfe, C. and Feldman, M. W. (2002) Evolutionary rate in the protein interaction network. Science, 296, 750–752.

    Article  Google Scholar 

  • Fraser, H. B., Hirsh, A. E., Wall, D. P. and Eisen, M. B. (2004) Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A, 101, 9033–9038.

    Article  Google Scholar 

  • Fryxell, K. J. (1996) The coevolution of gene family trees. Trends Genet, 12, 364–369.

    Article  Google Scholar 

  • Gaasterland, T. and Ragan, M. A. (1998) Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microb Comp Genomics, 3, 199–217.

    Google Scholar 

  • Goh, C.-S., Bogan, A. A., Joachimiak, M., Walther, D. and Cohen, F. E. (2000) Co-evolution of Proteins with their Interaction Partners. J Mol Biol, 299, 283–293.

    Article  Google Scholar 

  • Gomez, M., Alonso-Allende, R., Pazos, F., Graña, O., Juan, D. and Valencia, A. (2005) Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories. In Priami, C. (ed.), Transactions on Computational Systems Biology I: Subseries of Lecture Notes in Computer Science. Springer-Verlag GmbH, Heidelberg, Vol. 3380/2005, pp. 1–13.

    Google Scholar 

  • Hakes, L., Lovell, S., Oliver, S. G. and Robertson, D. L. (2007) Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proc Natl Acad Sci U S A, 104, 7999–8004.

    Article  Google Scholar 

  • Halperin, I., Wolfson, H. and Nussinov, R. (2006) Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. Proteins, 63, 832–845.

    Article  Google Scholar 

  • Han, J. D., Bertin, N., Hao, T., Goldberg, D. S., Berriz, G. F., Zhang, L. V., Dupuy, D., Walhout, A. J., Cusick, M. E., Roth, F. P. and Vidal, M. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 430, 88–93. Epub 2004 Jun 2009.

    Article  Google Scholar 

  • Ideker, T. and Valencia, A. (2006) Bioinformatics in the human interactome project. Bioinformatics, 22, 2973–2974.

    Article  Google Scholar 

  • Izarzugaza, J. M., Juan, D., Pons, C., Ranea, J. A., Valencia, A. and Pazos, F. (2006) TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res, 34, W315–319.

    Article  Google Scholar 

  • Jansen, R., Greenbaum, D. and Gerstein, M. (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res, 12, 37–46.

    Article  Google Scholar 

  • Jansen, R., Yu, H., Greenbaum, D., Kluger, Y., Krogan, N. J., Chung, S., Emili, A., Snyder, M., Greenblatt, J. F. and Gerstein, M. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science, 302, 449–453.

    Article  Google Scholar 

  • Jeong, H., Mason, S. P., Barabási, A. L. and Oltvai, Z. N. (2001) Lethality and centrality in protein networks. Nature, 411, 41–42.

    Article  Google Scholar 

  • Jothi, R., Cherukuri, P. F., Tasneem, A. and Przytycka, T. M. (2006) Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol, 362, 861–875.

    Article  Google Scholar 

  • Jothi, R., Kann, M. G. and Przytycka, T. M. (2005) Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics, 21, i241–i250.

    Article  Google Scholar 

  • Jothi, R., Przytycka, T. M. and Aravind, L. (2007) Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics, 8, 173.

    Article  Google Scholar 

  • Kann, M. G., Jothi, R., Cherukuri, P. F. and Przytycka, T. M. (2007) Predicting protein domain interactions from coevolution of conserved regions. Proteins, 67, 811–820.

    Article  Google Scholar 

  • Kelley, B. P., Sharan, R., Karp, R. M., Sittler, T., Root, D. E., Stockwell, B. R. and Ideker, T. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A, 100, 11394–11399.

    Article  Google Scholar 

  • Kiel, C., Foglierini, M., Kuemmerer, N., Beltrao, P. and Serrano, L. (2007) A Genome-wide Ras-Effector Interaction Network. J Mol Biol, 370, 1020–1032.

    Article  Google Scholar 

  • Lappe, M. and Holm, L. (2004) Unraveling protein interaction networks with near-optimal efficiency. Nat Biotechnol, 22, 98–103.

    Article  Google Scholar 

  • Lee, I., Date, S. V., Adai, A. T. and Marcotte, E. M. (2004) A probabilistic functional network of yeast genes. Science, 306, 1555–1558.

    Article  Google Scholar 

  • Legrain, P., Wojcik, J. and Gauthier, J. M. (2001) Protein-protein interaction maps: a lead towards cellular functions. Trends Genet, 17, 346–352.

    Article  Google Scholar 

  • Marcotte, E. M., Pellegrini, M., Ho-Leung, N., Rice, D. W., Yeates, T. O. and Eisenberg, D. (1999a) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751–753.

    Google Scholar 

  • Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O. and Eisenberg, D. (1999b) A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83–86.

    Google Scholar 

  • Mateu, M. G. and Fersht, A. R. (1999) Mutually compensatory mutations during evolution of the tetramerization domain of tumor suppressor p53 lead to impaired hetero-oligomerization. Proc Natl Acad Sci U S A, 96, 3595–3599.

    Article  Google Scholar 

  • Mintseris, J. and Weng, Z. (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A, 102, 10930–10935.

    Article  Google Scholar 

  • Morett, E., Korbel, J. O., Rajan, E., Saab-Rincon, G., Olvera, L., Olvera, M., Schmidt, S., Snel, B. and Bork, P. (2003) Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol, 21, 790–795.

    Article  Google Scholar 

  • Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D. and Maltsev, N. (1999) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol, 1, 93–108.

    Google Scholar 

  • Pages, S., Belaich, A., Belaich, J. P., Morag, E., Lamed, R., Shoham, Y. and Bayer, E. A. (1997) Species-specificity of the cohesin-dockerin interaction between Clostridium thermocellum and Clostridium cellulolyticum: prediction of specificity determinants of the dockerin domain. Proteins, 29, 517–527.

    Article  Google Scholar 

  • Pazos, F., Helmer-Citterich, M., Ausiello, G. and Valencia, A. (1997) Correlated mutations contain information about protein-protein interaction. J Mol Biol, 271, 511–523.

    Article  Google Scholar 

  • Pazos, F., Ranea, J. A. G., Juan, D. and Sternberg, M. J. E. (2005) Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J Mol Biol, 352, 1002–1015.

    Article  Google Scholar 

  • Pazos, F. and Valencia, A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng, 14, 609–614.

    Article  Google Scholar 

  • Pazos, F. and Valencia, A. (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins, 47, 219–227.

    Article  Google Scholar 

  • Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. and Yeates, T. O. (1999) Assigning protein functions by comparative genome analysis: Protein pylogenetic profiles. Proc Natl Acad Sci USA, 96, 4285–4288.

    Article  Google Scholar 

  • Qi, Y., Ye, P. and Bader, J. S. (2005) Genetic Interaction Motif Finding by expectation maximization–a novel statistical model for inferring gene modules from synthetic lethality. BMC Bioinformatics, 6, 288.

    Article  Google Scholar 

  • Qin, H., Lu, H. H., Wu, W. B. and Li, W. H. (2003) Evolution of the yeast protein interaction network. Proc Natl Acad Sci U S A, 100, 12820–12824.

    Article  Google Scholar 

  • Ramani, A. K. and Marcotte, E. M. (2003) Exploiting the co-evolution of interacting proteins to discover interaction specificity. J Mol Biol, 327, 273–284.

    Article  Google Scholar 

  • Sato, T., Yamanishi, Y., Kanehisa, M. and Toh, H. (2005) The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics, 21, 3482–3489.

    Article  Google Scholar 

  • Shen, J., Zhang, J., Luo, X., Zhu, W., Yu, K., Chen, K., Li, Y. and Jiang, H. (2007) Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci U S A, 104, 4337–4341.

    Article  Google Scholar 

  • Sprinzak, E., Altuvia, Y. and Margalit, H. (2006) Characterization and prediction of protein-protein interactions within and between complexes. Proc Natl Acad Sci U S A, 103, 14718–14723.

    Article  Google Scholar 

  • Sprinzak, E. and Margalit, H. (2001) Correlated sequence-signatures as markers of protein-protein interactions. J Mol Biol, 311, 681–692.

    Article  Google Scholar 

  • Sun, J., Xu, J., Liu, Z., Liu, Q., Zhao, A., Shi, T. and Li, Y. (2005) Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics, 21, 3409–3415.

    Article  Google Scholar 

  • Tillier, E. R., Biro, L., Li, G. and Tillo, D. (2006) Codep: maximizing co-evolutionary interdependencies to discover interacting proteins. Proteins, 63, 822–831.

    Article  Google Scholar 

  • Tong, A. H., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Page, N., Robinson, M., Raghibizadeh, S., Hogue, C. W., Bussey, H., Andrews, B., Tyers, M. and Boone, C. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science, 294, 2364–2368.

    Article  Google Scholar 

  • Tong, A. H., Lesage, G., Bader, G. D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G. F., Brost, R. L., Chang, M., Chen, Y., Cheng, X., Chua, G., Friesen, H., Goldberg, D. S., Haynes, J., Humphries, C., He, G., Hussein, S., Ke, L., Krogan, N., Li, Z., Levinson, J. N., Lu, H., Menard, P., Munyana, C., Parsons, A. B., Ryan, O., Tonikian, R., Roberts, T., Sdicu, A. M., Shapiro, J., Sheikh, B., Suter, B., Wong, S. L., Zhang, L. V., Zhu, H., Burd, C. G., Munro, S., Sander, C., Rine, J., Greenblatt, J., Peter, M., Bretscher, A., Bell, G., Roth, F. P., Brown, G. W., Andrews, B., Bussey, H. and Boone, C. (2004) Global mapping of the yeast genetic interaction network. Science, 303, 808–813.

    Article  Google Scholar 

  • Tsoka, S. and Ouzounis, C. A. (2000) Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nature Genet, 26, 141–142.

    Article  Google Scholar 

  • Uetz, P. and Finley, R. L., Jr. (2005) From protein networks to biological systems. FEBS Lett, 579, 1821–1827.

    Article  Google Scholar 

  • von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P. and Snel, B. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res, 31, 258–261.

    Article  Google Scholar 

  • von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S. and Bork, P. (2002) Comparative assessment of large scale data sets of protein-protein interactions. Nature, 417, 399–403.

    Article  Google Scholar 

  • Wuchty, S., Oltvai, Z. N. and Barabasi, A. L. (2003) Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet, 35, 176–179.

    Article  Google Scholar 

  • Yamanishi, Y., Vert, J. P. and Kanehisa, M. (2004) Protein network inference from multiple genomic data: a supervised approach. Bioinformatics, 20, I363–I370.

    Article  Google Scholar 

  • Ye, P., Peyser, B. D., Pan, X., Boeke, J. D., Spencer, F. A. and Bader, J. S. (2005) Gene function prediction from congruent synthetic lethal interactions in yeast. Mol Syst Biol, 1, 2005.0026.

    Article  Google Scholar 

  • Yeger-Lotem, E. and Margalit, H. (2003) Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation. Nucleic Acids Res, 31, 6053–6061.

    Article  Google Scholar 

  • Zheng, Y., Roberts, R. J. and Kasif, S. (2002) Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biology, 3, research0060.0061-0060.0069.

    Article  Google Scholar 

  • Zhou, Y., Wang, R., Li, L., Xia, X. and Sun, Z. (2006) Inferring functional linkages between proteins from evolutionary scenarios. J Mol Biol, 359, 1150–1159.

    Article  Google Scholar 

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Authors and Affiliations

  1. Spanish National Cancer Research Centre (CNIO), Structural Computational Biology Programme, Madrid, Spain

    Alfonso Valencia

  2. Computational Systems Biology Group, National Center for Biotechnology (CNB-CSIC), Madrid, Spain

    Florencio Pazos

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  1. Alfonso Valencia
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  2. Florencio Pazos
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Correspondence to Alfonso Valencia .

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  1. National Institutes of Health, Bethesda, Maryland, USA

    Anna Panchenko  & Teresa Przytycka  & 

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Valencia, A., Pazos, F. (2008). Computational Methods to Predict Protein Interaction Partners. In: Panchenko, A., Przytycka, T. (eds) Protein-protein Interactions and Networks. Computational Biology, vol 9. Springer, London. https://doi.org/10.1007/978-1-84800-125-1_4

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  • DOI: https://doi.org/10.1007/978-1-84800-125-1_4

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