An integrated view of molecular coevolution in protein-protein interactions

Molecular Biology and Evolution

Volumn 27, Issue 11, 2010, Pages 2567-2575

  Lovell, Simon C ^a   Robertson, David L ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

coevolution; evolutionary rate; protein expression; protein protein interactions

Indexed keywords

PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; COEVOLUTION; CORRELATION ANALYSIS; GENETIC TRANSCRIPTION; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; EVOLUTION, MOLECULAR; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN BINDING; PROTEINS;

EID: 77958114505     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq144     Document Type: Article

References (92)

1. Agrafioti I, Swire J, Abbott J, Huntley D, Butcher S, Stumpf MP. 2005. Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks. BMC Evol Biol. 5:23.
2. Altschuh D, Lesk AM, Bloomer AC, Klug A. 1987. Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J Mol Biol. 193:693-707.
3. Atchley WR, Wollenberg KR, Fitch WM, Terhalle W, Dress AW. 2000. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol Biol Evol. 17:164-178.
4. Bahadur RP, Chakrabarti P, Rodier F, Janin J. 2003. Dissecting subunit interfaces in homodimeric proteins. Proteins. 53:708-719.
5. Berg J, Lassig M, Wagner A. 2004. Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. BMC Evol Biol. 4:51.
6. Bogan AA, Thorn KS. 1998. Anatomy of hot spots in protein interfaces. J Mol Biol. 280:1-9.
7. Chakrabarti P, Janin J. 2002. Dissecting protein-protein recognition sites. Proteins. 47:334-343.
8. Chao JA, Patskovsky Y, Almo SC, Singer RH. 2008. Structural basis for the coevolution of a viral RNA-protein complex. Nat Struct Mol Biol. 15:103-105.
9. Chelliah V, Chen L, Blundell TL, Lovell SC. 2004. Distinguishing structural and functional restraints in evolution in order to identify interaction sites. J Mol Biol. 342:1487-1504.
10. Clackson T, Wells JA. 1995. A hot spot of binding energy in a hormone-receptor interface. Science. 267:383-386.
11. Clarke ND. 1995. Covariation of residues in the homeodomain sequence family. Protein Sci. 4:2269-2278.
12. Date SV, Marcotte EM. 2003. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol. 21:1055-1062.
13. Davis JC, Brandman O, Petrov DA 2005. Protein evolution in the context of Drosophila development. J Mol Evol. 60:774-785.
14. DeLano WL 2002. Unraveling hot spots in binding interfaces: progress and challenges. Curr Opin Struct Biol. 12:14-20.
15. DePristo MA, Weinreich DM, Hartl DL 2005. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet. 6:678-687.
16. Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. 2005. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA. 102:14338-14343.
17. Drummond DA, Raval A, Wilke CO. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 23:327-337.
18. Duret L, Mouchiroud D. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol. 17:68-74.
19. Dutheil J, Pupko T, Jean-Marie A, Galtier N. 2005. A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol. 22:1919-1928.
20. Ehrlich PR, Raven PH. 1964. Butterflies and plants: a study in coevolution. Evolution. 18:586-608.
21. Evlampiev K, Isambert H. 2008. Conservation and topology of protein interaction networks under duplication-divergence evolution. Proc Natl Acad Sci USA. 105:9863-9868.
22. Fares MA, McNally D. 2006. CAPS: coevolution analysis using protein sequences. Bioinformatics. 22:2821-2822.
23. Fares MA, Travers SA. 2006. A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. Genetics. 173:9-23.
24. Fodor AA, Aldrich RW. 2004. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins. 56:211-221.
25. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. 2002. Evolutionary rate in the protein interaction network. Science. 296:750-752.
26. Gloor GB, Martin LC, Wahl LM, Dunn SD. 2005. Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. Biochemistry. 44:7156-7165.
27. Gobel U, Sander C, Schneider R, Valencia A. 1994. Correlated mutations and residue contacts in proteins. Proteins. 18: 309-317.
28. Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE. 2000. Coevolution of proteins with their interaction partners. J Mol Biol. 299:283-293.
29. Goh CS, Cohen FE. 2002. Co-evolutionary analysis reveals insights into protein-protein interactions. J Mol Biol. 324:177-192.
30. Guan Y, Dunham MJ, Troyanskaya OG. 2007. Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics. 175:933-943.
31. Hakes L, Lovell SC, Oliver SG, Robertson DL 2007. Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proc Natl Acad Sci USA. 104:7999-8004.
32. Halabi N, Rivoire O, Leibler S, Ranganathan R. 2009. Protein sectors: evolutionary units of three-dimensional structure. Cell. 138: 774-786.
33. Hart GT, Lee I, Marcotte ER. 2007. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics. 8:236.
34. Hazkani-Covo E, Wool D, Graur D. 2005. In search of the vertebrate phylotypic stage: a molecular examination of the developmental hourglass model and von Baer's third law. J Exp Zool B Mol Dev Evol. 304:150-158.
35. Hirsh AE, Fraser HB. 2001. Protein dispensability and rate of evolution. Nature 411:1046-1049.
36. Hubbard TJ, Blundell TL 1987. Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng. 1:159-171.
37. Izarzugaza JM, Juan D, Pons C, Pazos F, Valencia A. 2008. Enhancing the prediction of protein pairings between interacting families using orthology information. BMC Bioinformatics. 9:35.
38. Jordan IK, Rogozin IB, Wolf YI, Koonin EV. 2002. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 12:962-968.
39. Jothi R, Cherukuri PF, Tasneem A, Przytycka TM. 2006. Coevolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating proteinprotein interactions. J Mol Biol. 362:861-875.
40. Juan D, Pazos F, Valencia A. 2008a. High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci USA. 105:934-939.
41. Juan D, Pazos F, Valencia A. 2008b. Co-evolution and co-adaptation in protein networks. FEBS Lett. 582:1225-1230.
42. Kann MG, Jothi R, Cherukuri PF, Przytycka TM. 2007. Predicting protein domain interactions from coevolution of conserved regions. Proteins 67:811-820.
43. Kann MG, Shoemaker BA, Panchenko AR, Przytycka TM. 2009. Correlated evolution of interacting proteins: looking behind the mirrortree. J Mol Biol. 385:91-98.
44. Lewis AC, Saeed R, Deane CM. 2010. Predicting protein-protein interactions in the context of protein evolution. Mol Biosyst 6:55-64.
45. Lichtarge O, Sowa MA 2002. Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol. 12:12-27.
46. Madaoui H, Guerois R. 2008. Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking. Proc Natl Acad Sci USA. 105:7708-7713.
47. Maddison WP. 1997. Gene trees in species trees. Syst Biol. 46: 523-536.
48. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285:751-753.
49. Marcotte EM, Xenarios I, van Der Bliek AM, Eisenberg D. 2000. Localizing proteins in the cell from their phylogenetic profiles. Proc Natl Acad Sci USA. 97:12115-12120.
50. Mintseris J, Weng Z. 2005. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA. 102:10930-10935.
51. Mode CJ. 1957. A mathematical model for the co-evolution of obligate parasites and their hosts. Evolution 12:158-165.
52. Moyle WR, Campbell RK, Myers RV, Bernard MP, Han Y, Wang X. 1994. Co-evolution of ligand-receptor pairs. Nature 368:251-255.
53. Najafabadi HS, Salavati R. 2008. Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol. 9:R87.
54. Overington J, Donnelly D, Johnson MS, Sali A, Blundell TL 1992. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci. 1:216-226.
55. Overington J, Johnson MS, Sali A, Blundell TL 1990. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci. 241:132-145.
56. Pal C, Papp B, Hurst LD. 2001. Highly expressed genes in yeast evolve slowly. Genetics. 158:927-931.
57. Pal C, Papp B, Hurst LD. 2003. Genomic function: rate of evolution and gene dispensability. Nature. 421:496-497 discussion 497-498.
58. Pal C, Papp B, Lercher MJ. 2006. An integrated view of protein evolution. Nat Rev Genet. 7:337-348.
59. Pazos F, Helmer-Citterich M, Ausiello G, Valencia A. 1997. Correlated mutations contain information about proteinprotein interaction. J Mol Biol. 271:511-523.
60. Pazos F, Ranea JA, Juan D, Sternberg MJ. 2005. Assessing protein coevolution in the context of the tree of life assists in the prediction of the interactome. J Mol Biol. 352:1002-1015.
61. Pazos F, Valencia A. 2001. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14:609-614.
62. Pazos F, Valencia A. 2008. Protein co-evolution, co-adaptation and interactions. EMBOJ. 27:2648-2655.
63. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA. 96:4285-4288.
64. Pereira-Leal JB, Levy ED, Kamp C, Teichmann SA. 2007. Evolution of protein complexes by duplication of homomeric interactions. Genome Biol. 8:R51.
65. Pinney JW, Amoutzias GD, Rattray M, Robertson DL 2007. Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. Proc Natl Acad Sci USA. 104:20449-20453.
66. Pollock DD, Taylor WR, Goldman N. 1999. Coevolving protein residues: maximum likelihood identification and relationship to structure. J Mol Biol. 287:187-198.
67. Prachumwat A, Li WH. 2006. Protein function, connectivity, and duplicability in yeast. Mol Biol Evol. 23:30-39.
68. Presser A, Elowitz MB, Kellis M, Kishony R. 2008. The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication. Proc Natl Acad Sci USA. 105:950-954.
69. Sato T, Yamanishi Y, Horimoto K, Kanehisa M, Toh H. 2006. Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. Bioinformatics 22:2488-2492.
70. Sato T, Yamanishi Y, Kanehisa M, 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.
71. Sharp PM, 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.
72. Simonis N, Gonze D, Orsi C, van Helden J, Wodak SJ. 2006. Modularity of the transcriptional response of protein complexes in yeast. J Mol Biol. 363:589-610.
73. Simonis N, van Helden J, Cohen GN, Wodak SJ. 2004. Transcriptional regulation of protein complexes in yeast. Genome Biol. 5:R33.
74. Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, Ranganathan R. 2005. Evolutionary information for specifying a protein fold. Nature. 437:512-518.
75. Stumpf MP, Kelly WP, Thorne T, Wiuf C 2007. Evolution at the system level: the natural history of protein interaction networks. Trends Ecol Evol. 22:366-373.
76. Suel GM, Lockless SW, Wall MA, Ranganathan R. 2003. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol. 10:59-69.
77. Tan SH, Zhang Z, Ng SK. 2004. ADVICE: automated detection and validation of interaction by co-evolution. Nucleic Acids Res. 32:W69-W72.
78. Thompson JN. 1994. The coevolutionary process. University of Chicago Press.
79. Travers SA, Fares MA 2007. Functional coevolutionary networks of the Hsp70-Hop-Hsp90 system revealed through computational analyses. Mol Biol Evol. 24:1032-1044.
80. Travers SA, Tully DC, McCormack GP, Fares MA 2007. A study of the coevolutionary patterns operating within the env gene of the HIV-1 group M subtypes. Mol Biol Evol. 24:2787-2801.
81. Valencia A, Pazos F. 2003. Prediction of protein-protein interactions from evolutionary information. Methods Biochem Anal. 44: 411-426.
82. Waddell PJ, Kishino H, Ota R. 2007. Phylogenetic methodology for detecting protein interactions. Mol Biol Evol. 24:650-659.
83. Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MW. 2005. Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci USA. 102:5483-5488.
84. Wang H, Kakaradov B, Collins SR, Karotki L, Fiedler D, Shales M, Shokat KM, Walther T, Krogan NJ, Koller D. 2009. A complexbased reconstruction of the S. cerevisiae interactome. Mol Cell Proteomics. 8:1361-1381.
85. Wang ZO, Pollock DD. 2005. Context dependence and coevolution among amino acid residues in proteins. Methods Enzymol. 395:779-790.
86. Wang ZO, Pollock DD. 2007. Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context. J Mol Evol. 65:485-495.
87. Williams EJ, Hurst LD. 2000. The proteins of linked genes evolve at similar rates. Nature 407:900-903.
88. Williams SG, Lovell SC. 2009. The effect of sequence evolution on protein structural divergence. Mol Biol Evol. 26:1055-1065.
89. Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC 1999. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol. 285:1711-1733.
90. Yeang CH, Haussler D. 2007. Detecting coevolution in and among protein domains. PLoS Comput Biol. 3:e211.
91. Yu H, Braun P, Yildirim MA, et al. (34 co-authors). 2008. Highquality binary protein interaction map of the yeast interactome network. Science 322:104-110.
92. Zotenko E, Mestre J, O'Leary DP, Przytycka TM. 2008. Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol. 4:e1000140.