CRK: An evolutionary approach for distinguishing biologically relevant interfaces from crystal contacts

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 12, 2010, Pages 2707-2713

  Schärer, Martin A ^a,b   Grütter, Markus G ^b   Capitani, Guido ^a,b  

^a PAUL SCHERRER INSTITUTE   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

K a K s; Protein protein interactions; Selection pressure; Structural bioinformatics

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE;

COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; EVOLUTION; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 77955781875     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22787     Document Type: Article

References (29)

1. Nishiyama M, Horst R, Eidam O, Herrmann T, Ignatov O, Vetsch M, Bettendorff P, Jelesarov I, Grutter MG, Wuthrich K, Glockshuber R, Capitani G. Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD. EMBO J 2005;24:2075-2086.
2. Janin J. Specific versus non-specific contacts in protein crystals. Nat Struct Mol Biol 1997;4:973-974.
3. Bahadur RP, Chakrabarti P, Rodier F, Janin J. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 2004;336:943-955.
4. Elcock AH, McCammon JA. Identification of protein oligomerization states by analysis of interface conservation. Proc Natl Acad Sci USA 2001;98:2990-2994.
5. Guharoy M, Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc Natl Acad Sci USA 2005;102:15447-15452.
6. Krissinel E, Henrick K. Detection of protein assemblies in crystals. In: Berthold MR, Glen R, Diederichs K, Kohlbacher O, Fischer I, editors. Computational life sciences, proceedings, Vol. 3695. Lecture notes in computer science. Berlin: Springer-Verlag; 2005. pp 163-174.
7. Krissinel E, Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 2007;372:774-797.
8. Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 2000;41:47-57.
9. Zhu H, Domingues F, Sommer I, Lengauer T. NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics 2006;7:27.
10. Bernauer J, Bahadur RP, Rodier F, Janin J, Poupon A. DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions. Bioinformatics 2008;24:652-658.
11. Kobe B, Guncar G, Buchholz R, Huber T, Maco B, Cowieson N, Martin JL, Marfori M, Forwood JK. Crystallography and proteinprotein interactions: biological interfaces and crystal contacts. Biochem Soc Trans 2008;36(Part 6):1438-1441.
12. Stern A, Doron-Faigenboim A, Erez E, Martz E, Bacharach E, Pupko T. Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res 2007;35(Web Server Issue):W506-W511.
13. Doron-Faigenboim A, Stern A, Mayrose I, Bacharach E, Pupko T. Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics 2005;21:2101-2103.
14. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
15. Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000;302:205-217.
16. 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.
17. Uniprot-Consortium. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 2009;37(Database Issue):D169-D174.
18. Yang Z, Nielsen R, Goldman N, Pedersen A-M. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 2000;155:431-449.
19. Percudani R, Peracchi A. A genomic overview of pyridoxal-phosphate- dependent enzymes. EMBO Rep 2003;4:850-854.
20. Dey S, Pal A, Chakrabarti P, Janin J. The subunit interfaces of weakly associated homodimeric proteins. J Mol Biol 2010;398:146-160.
21. Eliot AC, Kirsch JF. Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. Annu Rev Biochem 2004;73:383-415.
22. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, III, Snoeyink J, Richardson JS, Richardson DC. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 2007;35(Web Server Issue):W375-W383.
23. DeLano WL. The PyMOL molecular graphics system. 2002. DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org.
24. Coulibaly F, Chiu E, Ikeda K, Gutmann S, Haebel PW, Schulze-Briese C, Mori H, Metcalf P. The molecular organization of cypovirus polyhedra. Nature 2007;446:97-101.
25. Reyes CL, Chang G. Structure of the ABC transporter MsbA in complex with ADP.vanadate and lipopolysaccharide. Science 2005;308:1028-1031.
26. Ward A, Reyes CL, Yu J, Roth CB, Chang G. Flexibility in the ABC transporter MsbA: alternating access with a twist. Proc Natl Acad Sci USA 2007;104:19005-19010.
27. Lubkowski J, Wlodawer A. Decamers observed in the crystals of bovine pancreatic trypsin inhibitor. Acta Crystallogr D Biol Crystallogr 1999;55(Part 1):335-337.
28. Gottschalk M, Venu K, Halle B. Protein self-association in solution: the bovine pancreatic trypsin inhibitor decamer. Biophys J 2003;84:3941-3958.
29. Hamiaux C, Perez J, Prange T, Veesler S, Ries-Kautt M, Vachette P. The BPTI decamer observed in acidic pH crystal forms pre-exists as a stable species in solution. J Mol Biol 2000;297:697-712.