Using Coevolution to Predict Protein–Protein Interactions

Methods in Molecular Biology

Volumn 781, Issue , 2011, Pages 237-256

  Clark, Gregory W ^a   Dar, Vaqaar un Nisa ^a   Bezginov, Alexandr ^a   Yang, Jinghao M ^a   Charlebois, Robert L ^a   Tillier, Elisabeth R M ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Bioinformatics; Domain domain interactions; Phylogenetic tree; Protein coevolution; Protein interaction network; Protein protein interactions; Proteomics

Indexed keywords

BIOINFORMATICS; COEVOLUTION; COIMMUNOPRECIPITATION; EVOLUTIONARY RATE; GOLD STANDARD; HUMAN; IN VITRO STUDY; MASS SPECTROMETRY; PHYLOGENETIC TREE; PREDICTION; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; EVOLUTION; IMMUNOPRECIPITATION; METABOLISM; METHODOLOGY; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN BINDING;

PROTEIN;

ALGORITHMS; BIOLOGICAL EVOLUTION; COMPUTATIONAL BIOLOGY; IMMUNOPRECIPITATION; PHYLOGENY; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 80054748042     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-276-2_11     Document Type: Chapter

References (63)

1. Fraser HB, Wall DP, and Hirsh AE (2003) A simple dependence between protein evolution rate and the number of protein–protein interactions, BMC Evol Biol 3, 11.
2. Krylov DM, Wolf YI, Rogozin IB, and Koonin EV (2003) Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution, Genome Res 13, 2229–2235.
3. Tillier ERM, and Charlebois RL (2009) The human protein coevolution network, Genome Res 19, 1861–1871.
4. Pazos F, and Valencia A (2001) Similarity of phylogenetic trees as indicator of protein– protein interaction, Protein Eng 14, 609–614.
5. Atchley WR, Wollenberg KR, Fitch WM, Terhalle W, and Dress AW (2000) Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis, Mol Biol Evol 17, 164–178.
6. Bloom JD, Lu Z, Chen D, Raval A, Venturelli OS, and Arnold FH (2007) Evolution favors protein mutational robustness in sufficiently large populations, BMC Biol 5, 29.
7. Worth CL, Gong S, and Blundell TL (2009) Structural and functional constraints in the evolution of protein families, Nat Rev Mol Cell Biol 10, 709–720.
8. Singer MS, Vriend G, and Bywater RP (2002) Prediction of protein residue contacts with a PDB-derived likelihood matrix, Protein Eng 15, 721–725.
9. Saraf MC, Moore GL, and Maranas CD (2003) Using multiple sequence correlation analysis to characterize functionally important protein regions, Protein Eng 16, 397–406.
10. Tillier ERM, Biro L, Li G, and Tillo D (2006) Codep: maximizing coevolutionary interde-pendencies to discover interacting proteins, Proteins 63, 822–831.
11. Choi SS, Li W, and Lahn BT (2005) Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylog-eny-aided structural analysis, Nat Genet 37, 1367–1371.
12. Tress ML, and Valencia A (2010) Predicted residue-residue contacts can help the scoring of 3D models, Proteins 78, 1980–1991.
13. Horner DS, Pirovano W, and Pesole G (2008) Correlated substitution analysis and the prediction of amino acid structural contacts, Brief Bioinform 9, 46–56.
14. Pazos F, and Valencia A (2002) In silico two-hybrid system for the selection of physically interacting protein pairs, Proteins 47, 219–227.
15. Xu Y, and Tillier ERM (2010) Regional cova-riation and its application for predicting protein contact patches, Proteins 78, 548–558.
16. Goh CS, Bogan AA, Joachimiak M, Walther D, and Cohen FE (2000) Coevolution of proteins with their interaction partners, J Mol Biol 299, 283–293.
17. Aytuna AS, Gursoy A, and Keskin O (2005) Prediction of protein–protein interactions by combining structure and sequence conservation in protein interfaces, Bioinformatics 21, 2850–2855.
18. Sato T, Yamanishi Y, Kanehisa M, and Toh H (2005) The inference of protein–protein interactions by coevolutionary analysis is improved by excluding the information about the phylogenetic relationships, Bioinformatics 21, 3482–3489.
19. Hakes L, Lovell SC, Oliver SG, and Robertson DL (2007) Specificity in protein interactions and its relationship with sequence diversity and coevolution, Proc Natl Acad Sci USA 104, 7999–8004.
20. Craig RA, and Liao L (2007) Phylogenetic tree information aids supervised learning for predicting protein–protein interaction based on distance matrices, BMC Bioinformatics 8, 6.
21. Kann MG, Jothi R, Cherukuri PF, and Przytycka TM (2007) Predicting protein domain interactions from coevolution of conserved regions, Proteins 67, 811–820.
22. Juan D, Pazos F, and Valencia A (2008) Coevolution and co-adaptation in protein networks, FEBS Lett 582, 1225–1230.
23. Barabasi AL, and Albert R (1999) Emergence of scaling in random networks, Science 286, 509–512.
24. Rodionov A, Bezginov A, Rose J, and Tillier ERM (2011) A new, fast algorithm for detecting protein coevolution using maximum compatible cliques, Algorithms Mol Biol 6, 17.
25. Pazos F, and Valencia A (2008) Protein coevolution, co-adaptation and interactions, EMBO J 27, 2648–2655.
26. Mintseris J, and Weng Z (2005) Structure, function, and evolution of transient and obligate protein–protein interactions, Proc Natl Acad Sci USA 102, 10930–10935.
27. Drummond DA, Bloom JD, Adami C, Wilke CO, and Arnold FH (2005) Why highly expressed proteins evolve slowly, Proc Natl Acad Sci USA 102, 14338–14343.
28. Rocha EP, and Danchin A (2004) An analysis of determinants of amino acids substitution rates in bacterial proteins, Mol Biol Evol 21, 108–116.
29. Papp B, Pál C, and Hurst LD (2003) Dosage sensitivity and the evolution of gene families in yeast, Nature 424, 194–197.
30. Kann MG, Shoemaker BA, Panchenko AR, and Przytycka TM (2009) Correlated evolution of interacting proteins: looking behind the mirrortree, J Mol Biol 385, 91–98.
31. 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.
32. Huynen M, Snel B, Lathe W, and Bork P (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences, Genome Res 10, 1204–1210.
33. Sharp PM, and Li WH (1987) The codon Adaptation Index–a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Res 15, 1281–1295.
34. Fraser HB, Hirsh AE, Wall DP, and Eisen MB (2004) Coevolution of gene expression among interacting proteins, Proc Natl Acad Sci USA 101, 9033–9038.
35. Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, and Vidal M (2001) Identification of potential interaction networks using sequence-based searches for conserved protein–protein interactions or “interologs,” Genome Res 11, 2120–2126.
36. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, and Bork P (2002) Comparative assessment of large-scale data sets of protein–protein interactions, Nature 417, 399–403.
37. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME. Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabási AL, Tavernier J, Hill DE, and Vidal M (2008) High-quality binary protein interaction map of the yeast interactome network, Science 322, 104–110.
38. Nooren IMA, and Thorton JM (2003) Diversity of protein–protein interactions, The EMBO Journal 22.
39. Wuchty S, Barabási AL, and Ferdig MT (2006) Stable evolutionary signal in a yeast protein interaction network, BMC Evol Biol 6, 8.
40. Yellaboina S, Dudekula DB, and Ko MSh (2008) Prediction of evolutionarily conserved interologs in Mus musculus, BMC Genomics 9, 465.
41. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA (1998) Cell 95, 717–728.
42. Pawson T, and Nash P (2003) Assembly of cell regulatory systems through protein interaction domains, Science 300, 445–452.
43. del Sol A, and Carbonell P (2007) The modular organization of domain structures: insights into protein–protein binding, PLoS Comput Biol 3, e239.
44. Itzhaki Z, Akiva E, Altuvia Y, and Margalit H (2006) Evolutionary conservation of domain– domain interactions, Genome Biol 7, R125.
45. Kim Y, Koyutürk M, Topkara U, Grama A, and Subramaniam S (2006) Inferring functional information from domain coevolution, Bioinformatics 22, 40–49.
46. Jothi R, Cherukuri, PF, Tasneem A, and Przytycka TM (2006) Coevolutionary analysis of domains in interacting proteins reveals insights into domain–domain interactions mediating protein–protein interactions, J Mol Biol 362, 861–875.
47. Wojcik J, and Schächter V (2001) Protein– protein interaction map inference using interacting domain profile pairs, Bioinformatics 17 Suppl 1, S296–S305.
48. Wagner A (2001) The Yeast Protein Interaction Network Evolves Rapidly and Contains Few Redundant Duplicate Genes, Mol Biol Evol 18, 1283–1292.
49. Berg J, Lässig M, and Wagner A (2004) Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications, BMC Evol Biol 4, 51.
50. Katoh K, Kuma K, Miyata T, and Toh H (2005) Improvement in the accuracy of multiple sequence alignment program MAFFT, Genome Inform 16, 22–33.
51. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. University of Washington, Seattle.
52. Veerassamy S, Smith A, and Tillier ERM (2003) A transition probability model for amino acid substitutions from blocks, J Comput Biol 10, 997–1010.
53. Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ (1990) Basic Local Alignment Search Tool, Journal of Molecular Biology 215.
54. Schneider A, Dessimoz C, and Gonnet GH (2007) OMA Browser–exploring orthologous relations across 352 complete genomes, Bioinformatics 23, 2180–2182.
55. Nuin PA, Wang Z, and Tillier ERM (2006) The accuracy of several multiple sequence alignment programs for proteins, BMC Bioinformatics 7, 471.
56. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, and Tyers M (2006) BioGRID: a general repository for interaction datasets, Nucleic Acids Res 34, D535–D539.
57. Gong Y, Kakihara Y, Krogan N, Greenblatt J, Emili A, Zhang Z, and Houry W (2009) An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell, Mol Sys Biol 5, 275.
58. Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI, and Tyers M (2010) A global protein kinase and phosphatase interaction network in yeast, Science 328, 1043–1046.
59. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, and Eisenberg D (2000) DIP: the Database of Interacting Proteins, Nucleic Acids Reseach 28, 289–291.
60. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, and Pandey A (2009) Human Protein Reference Database–2009 update, Nucleic Acids Res 37, D767–D772.
61. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, and Hermjakob H (2007) IntAct– open source resource for molecular interaction data, Nucleic Acids Res 35, D561–D565.
62. Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, and Cesareni G (2010) MINT, the molecular interaction database: 2009 update, Nucleic Acids Res 38, D532–D539.
63. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, and Yaschenko E (2008) Database resources of the National Center for Biotechnology Information, Nucleic Acids Res 36, D13–D21.