Evolutionary conservation in multiple faces of protein interaction

Proteins: Structure, Function and Bioinformatics

Volumn 77, Issue 1, 2009, Pages 14-25

  Choi, Yoon Sup ^a   Yang, Jae Seong ^a   Choi, Yonghwan ^a   Ryu, Sung Ho ^a   Kim, Sanguk ^a  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

Author keywords

Docking simulation; Evolutionary conservation; Multiple interfaces; Protein protein interaction

Indexed keywords

ARTICLE; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION;

ANIMALS; EVOLUTION, MOLECULAR; HUMANS; MODELS, MOLECULAR; MODELS, THEORETICAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS;

EID: 70349330141     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22410     Document Type: Article

References (49)

1. Pal C, Papp B, Lercher MJ. An integrated view of protein evolution. Nat Rev Genet 2006;7:337-348.
2. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. Evolutionary rate in the protein interaction network. Science 2002;296:750-752. (Pubitemid 34442006)
3. Fraser HB. Modularity and evolutionary constraint on proteins. Nat Genet 2005;37:351-352.
4. Fraser HB, Wall DP, Hirsh AE. A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol 2003;3:11.
5. Elcock AH, McCammon JA. Identification of protein oligomerization states by analysis of interface conservation. Proc Natl Acad Sci USA 2001;98:2990-2994.
6. Valdar WS, Thornton JM. Conservation helps to identify biologically relevant crystal contacts. J Mol Biol 2001;313:399-416.
7. Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Res 2006;34:3698-3707. (Pubitemid 44400419)
8. Magliery TJ, Regan L. Sequence variation in ligand binding sites in proteins. BMC Bioinformatics 2005;6:240. (Pubitemid 41548715)
9. Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 2004;13:190-202.
10. Guharoy M, Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc Natl Acad Sci USA 2005;102:15447-15452. (Pubitemid 41528077)
11. Bradford JR, Needham CJ, Bulpitt AJ, Westhead DR. Insights into protein-protein interfaces using a Bayesian network prediction method. J Mol Biol 2006;362:365-386. (Pubitemid 44403921)
12. Bordner AJ, Abagyan R. Statistical analysis and prediction of protein-protein interfaces. Proteins 2005;60:353-366. (Pubitemid 41061632)
13. Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005;21:1487-1494.
14. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
15. http://www.rcsb.org/pdb/statistics/clusterStatistics.do.
16. Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 2008;36(Database issue):D419-D425. (Pubitemid 351149760)
17. http://scop.berkeley.edu/.
18. Kim WK, Henschel A, Winter C, Schroeder M. The many faces of protein-protein interactions: a compendium of interface geometry. PLoS Comput Biol 2006;2:e124. (Pubitemid 44495727)
19. Mintseris J, Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 2005;102:10930-10935. (Pubitemid 41105970)
20. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002;415:141-147. (Pubitemid 34059510)
21. Mintz S, Shulman-Peleg A, Wolfson HJ, Nussinov R. Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions. Proteins 2005;61:6-20. (Pubitemid 41262913)
22. http://bioinfo3d.cs.tau.ac.il/Interfaces/Full-Dataset.
23. Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins 2003;53:629-639. (Pubitemid 37352176)
24. http://au.expasy.org/sprot/.
25. Nooren IM, Thornton JM. Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol 2003;325:991-1018.
26. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410. (Pubitemid 20364473)
27. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792-1797. (Pubitemid 38832724)
28. Mayrose I, Graur D, Ben-Tal N, Pupko T. Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol 2004;21:1781-1791. (Pubitemid 39096894)
29. Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 2002;18 (Suppl 1):S71-S77. (Pubitemid 41185639)
30. Bahadur RP, Chakrabarti P, Rodier F, Janin J. Dissecting subunit interfaces in homodimeric proteins. Proteins 2003;53:708-719. (Pubitemid 37352183)
31. Hubbard SJ, Thornton JM.NACCESS. 1993: Computer Program, University College, London.
32. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. Patch-Dock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 2005;33(Web Server issue):W363-W367. (Pubitemid 44529944)
33. Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, Benyamini H, Barzilai A, Dror O, Haspel N, Nussinov R, Wolfson HJ. Taking geometry to its edge: fast unbound rigid (and hingebent) docking. Proteins 2003;52:107-112. (Pubitemid 36648858)
34. Perlmutter RM, Berson B, Griffin JA, Hood L. Diversity in the germline antibody repertoire. Molecular evolution of the T15 VN gene family. J Exp Med 1985;162:1998-2016. (Pubitemid 16149691)
35. DeLano WL. The PyMOL molecular graphics system. Palo Alto, CA: DeLano Scientific; 2002.
36. http://www.pymol.org.
37. Wolfson HJ, Shatsky M, Schneidman-Duhovny D, Dror O, Shulman-Peleg A, Ma B, Nussinov R. From structure to function: methods and applications. Curr Protein Pept Sci 2005;6:171-183.
38. Vajda S. Classification of protein complexes based on docking difficulty. Proteins 2005;60:176-180. (Pubitemid 40934883)
39. Vajda S, Camacho CJ. Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol 2004;22:110-116.
40. Duan Y, Reddy BV, Kaznessis YN. Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. Protein Sci 2005;14:316-328. (Pubitemid 40194583)
41. Huang B, Schroeder M. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol 2006;6:19. (Pubitemid 44570436)
42. Janin J. Specific versus non-specific contacts in protein crystals. Nat Struct Biol 1997;4:973-974.
43. Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998;23:358-361. (Pubitemid 28461869)
44. Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 2000;41:47-57. (Pubitemid 30666912)
45. Teichmann SA. The constraints protein-protein interactions place on sequence divergence. J Mol Biol 2002;324:399-407.
46. Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.
47. Andrusier N, Mashiach E, Nussinov R, Wolfson HJ. Principles of flexible protein-protein docking. Proteins 2008;73:271-289.
48. Chaudhury S, Gray JJ. Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J Mol Biol 2008;381:1068-1087.
49. Akiva E, Itzhaki Z, Margalit H. Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. Proc Natl Acad Sci USA 2008;105:13292-13297.