PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces

Nucleic Acids Research

Volumn 38, Issue 6, 2009, Pages

  Assi, Salam A ^a   Tanaka, Tomoyuki ^a   Rabbitts, Terence H ^a   Fernandez Fuentes, Narcis ^a  

^a ST JAMES S UNIVERSITY HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; BIOINFORMATICS; COMPLEX FORMATION; COMPUTER INTERFACE; COMPUTER NETWORK; COMPUTER PREDICTION; CONTROLLED STUDY; INFORMATION STORAGE; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; QUALITY CONTROL; RESIDUE ANALYSIS; VALIDATION PROCESS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; IMMUNOGLOBULIN VARIABLE REGION; IMMUNOLOGY; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN CONFORMATION; VALIDATION STUDY;

AMINO ACID; PROTEIN; PROTEIN P21;

AMINO ACIDS; BAYES THEOREM; COMPUTATIONAL BIOLOGY; IMMUNOGLOBULIN VARIABLE REGION; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; PROTO-ONCOGENE PROTEINS P21(RAS); SOFTWARE;

EID: 77951273638     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1158     Document Type: Article

References (57)

1. Jones, S. and Thornton, J.M. (1996) Principles of protein-protein interactions. Proc. Natl Acad. Sci. USA, 93, 13.
2. Lo Conte, L., Chothia, C. and Janin, J. (1999) The atomic structure of protein-protein recognition sites. J. Mol. Biol., 285, 2177.
3. Bogan, A.A. and Thorn, K.S. (1998) Anatomy of hot spots in protein interfaces. J. Mol. Biol., 280, 1-9.
4. Blundell, T.L., Sibana, B.L., Montalvao, R.W., Brewerton, S., Chelliah, V., Worth, C.L., Harmer, N.J., Davies, O. and Burke, D. (2006) Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery. Philos. Trans. Roy. Soc. Lond. B Biol. Sci., 361, 413-423.
5. Wells, J.A. and McLendon, C.L. (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature, 450, 1001-1009.
6. Yin, H. and Hamilton, A.D. (2005) Strategies for targetting protein-protein interactions with synthetic agents. Ang. Chem. Int. Edn, 44, 2-35.
7. Clackson, T. and Wells, J.A. (1995) A hot spot of binding energy in a hormone-receptor interface. Science, 267, 383-386.
8. Wells, J.A. (1991) Systematic mutational analyses of protein-protein interfaces. Methods Enzymol., 202, 390-411.
9. Jin, L. and Wells, J.A. (1994) Dissecting the energetics of an antibody-antigen interface by alanine shaving and molecular grafting. Protein Sci., 3, 2351-2357.
10. Guerois, R., Nielsen, J.E. and Serrano, L. (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol., 320, 369-387.
11. Kortemme, T. and Baker, D. (2002) A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl Acad. Sci. USA, 99, 14116-14121.
12. Moreira, I.S., Fernandes, P.A. and Ramos, M.J. (2007) Computational alanine scanning mutagenesis-an improved methodological approach. J. Comput. Chem., 28, 644-654.
13. Lafont, V., Schaefer, M., Stote, R.H., Altschuh, D. and Dejaegere, A. (2007) Protein-protein recognition and interaction hot spots in an antigen-antibody complex: free energy decomposition identifies "efficient amino acids". Proteins, 67, 418-434.
14. Landon, M.R., Lancia, D.R. Jr, Yu, J., Thiel, S.C. and Vajda, S. (2007) Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. J. Med. Chem., 50, 1231-1240.
15. Guney, E., Tuncbag, N., Keskin, O. and Gursoy, A. (2008) HotSprint: database of computational hot spots in protein interfaces. Nucleic Acids Res., 36, D662-D666.
16. Tuncbag, N., Gursoy, A. and Keskin, O. (2009) Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics, 25, 1513-1520.
17. Li, L., Zhao, B., Cui, Z., Gan, J., Sakharkar, M.K. and Kangueane, P. (2006) Identification of hot spot residues at protein-protein interface. Bioinformation, 1, 121-126.
18. Li, X., Keskin, O., Ma, B., Nussinov, R. and Liang, J. (2004) Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J. Mol. Biol., 344, 781-795.
19. Yogurtcu, O.N., Erdemli, S.B., Nussinov, R., Turkay, M. and Keskin, O. (2008) Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations. Biophys. J., 94, 3475-3485.
20. Keskin, O., Ma, B. and Nussinov, R. (2005) Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues. J. Mol. Biol., 345, 1281-1294.
21. Hu, Z., Ma, B., Wolfson, H. and Nussinov, R. (2000) Conservation of polar residues as hot spots at protein interfaces. Proteins, 39, 331-342.
22. Ma, B., Elkayam, T., Wolfson, H. and Nussinov, R. (2003) Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl Acad. Sci. USA, 100, 5772-5777.
23. Ma, B. and Nussinov, R. (2007) Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design. Curr. Top Med. Chem., 7, 999-1005.
24. Ofran, Y. and Rost, B. (2007) Protein-protein interaction hotspots carved into sequences. PLoS Comput. Biol., 3, e119.
25. Hsu, C.M., Chen, C.Y., Liu, B.J., Huang, C.C., Laio, M.H., Lin, C.C. and Wu, T.L. (2007) Identification of hot regions in protein-protein interactions by sequential pattern mining. BMC Bioinformatics, 8(Suppl. 5), S8.
26. DeLano, W.L. (2002) Unraveling hot spots in binding interfaces: progress and challenges. Curr. Opin. Struct. Biol., 12, 14-20.
27. Pearl, J. (1988) Probabilistic Reasoning in Intelligent Systems: Networks of plausible inference. Morgan Kaufmann Publisher Inc, San Francisco.
28. Jordan, M.I. (1988) Learning in graphical models. Kluwer Academic Publishers, Boston, USA.
29. 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.
30. Troyanskaya, O.G., Dolinski, K., Owen, A.B., Altman, R.B. and Botstein, D. (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc. Natl Acad. Sci. USA, 100, 8348-8353.
31. Pudimat, R., Schukat-Talamazzini, E.G. and Backofen, R. (2005) A multiple-feature framework for modelling and predicting transcription factor binding sites. Bioinformatics, 21, 3082-3088
32. Cai, D., Delcher, A., Kao, B. and Kasif, S. (2000) Modeling splice sites with Bayes networks. Bioinformatics, 16, 152-158.
33. Husmeier, D. (2003) Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics, 19, 2271-2282.
34. Friedman, N. (2004) Inferring cellular networks using probabilistic graphical models. Science, 303, 799-805.
35. Bradford, J.R., Needham, C.J., Bulpitt, A.J. and Westhead, D.R. (2006) Insights into protein-protein interfaces using a Bayesian network prediction method. J. Mol. Biol., 362, 365-386.
36. Needham, C.J., Bradford, J.R., Bulpitt, A.J. and Westhead, D.R. (2006) Inference in Bayesian networks. Nat. Biotechnol., 24, 51-53.
37. Tanaka, T., Williams, R.L. and Rabbitts, T.H. (2007) Tumour prevention by a single antibody domain targeting the interaction of signal transduction proteins with RAS. EMBO J., 26, 3250-3259.
38. Darnell, S.J., Page, D. and Mitchell, J.C. (2007) An automated decision-tree approach to predicting protein interaction hot spots. Proteins, 68, 813-823.
39. Thorn, K.S. and Bogan, A.A. (2001) ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics, 17, 284-285.
40. Fischer, T.B., Arunachalam, K.V., Bailey, D., Mangual, V., Bakhru, S., Russo, R., Huang, D., Paczkowski, M., Lalchandani, V., Ramachandra, C. et al. (2003) The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces. Bioinformatics, 19, 1453-1454.
41. Sobolev, V., Sorokine, A., Prilusky, J., Abola, E.E. and Edelman, M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332.
42. Levy, E. (2007) PiQSi: protein quaternary structure investigation. Structure, 15, 1364-1367.
43. Fernandez-Fuentes, N., Rai, B.K., Madrid-Aliste, C.J., Fajardo, J.E. and Fiser, A. (2007) Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments. Bioinformatics, 23, 2558-2565.
44. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
45. 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. Nucleic Acids Res., 25, 3389.
46. Rai, B.K., Madrid-Aliste, C.J., Fajardo, J.E. and Fiser, A. (2006) MMM: a sequence-to-structure alignment protocol. Bioinformatics, 22, 2691-2692.
47. Pei, J. and Grishin, N. (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics, 17, 700-712.
48. Landgraf, R., Xenarios, I. and Eisenberg, D. (2001) Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol., 307, 1487
49. Murphy, B. (2001) The Bayes Net Toolbox for Matlab. Comput. Sci. Stat., 33, 331-350.
50. Bottcher, S. and Dethlefsen, C. (2003) Deal: a package for learning Bayesian networks. J. Stat. Software, 8, 1-40.
51. Sham, P. (1998) Statistics in Human Genetics. Edward Arnorld, London.
52. Edwards, A. (1997) What did Fisher mean by "inverse probability" in 1912-1922? Stat. Sci., 12, 177-184.
53. Mclachlan, G. and Krishnan, T. (1997) The EM Algorithm and Extensions. John Wiley & Sons, New york, USA.
54. Tucker, K.L., Beard, C., Dausmann, J., Jackson-Grusby, L., Laird, P.W., Lei, H., Li, E. and Jaenisch, R. (1996) Germ-line passage is required for establishment of methylation and expression patterns of imprinted but not of nonimprinted genes. Genes Dev., 10, 1008-1020.
55. Pazos, F. and Valencia, A. (2008) Protein co-evolution, co-adaptation and interactions. EMBO J., 27, 2648-2655.
56. Hage, T., Sebald, W. and Reinemer, P. (1999) Crystal structure of the interleukin-4/receptor alpha chain complex reveals a mosaic binding interface. Cell, 97, 271-281.
57. Scheidig, A.J., Hynes, T.R., Pelletier, L.A., Wells, J.A. and Kossiakoff, A.A. (1997) Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities. Protein Sci., 6, 1806-1824.