Discovering protein-protein interaction sites from sequence and structure

Biological Data Mining in Protein Interaction Networks

Volumn , Issue , 2009, Pages 64-79

  La, David ^a   Kihara, Daisuke ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84901534791     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4018/978-1-60566-398-2.ch005     Document Type: Chapter

References (73)

1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res, 25, 3389-3402.
2. Armon, A., Graur, D., & Ben-Tal, N. (2001). ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol, 307, 447-463.
3. Block, P., Paern, J., Hullermeier, E., Sanschagrin, P., Sotriffer, C. A., & Klebe, G. (2006). Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms. Proteins, 65, 607-622.
4. Bogan, A. A., & Thorn, K. S. (1998). Anatomy of hot spots in protein interfaces. J Mol Biol, 280, 1-9.
5. Bradford, J. R., & Westhead, D. R. (2005). Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics, 21, 1487-1494.
6. Burgoyne, N. J., & Jackson, R. M. (2006). Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces. Bioinformatics, 22, 1335-1342.
7. Caffrey, D. R., Somaroo, S., Hughes, J. D., Mintseris, J., & Huang, E. S. (2004). Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci, 13, 190-202.
8. Capra, J. A., & Singh, M. (2007). Predicting functionally important residues from sequence conservation. Bioinformatics, 23, 1875.
9. Chen, R., Mintseris, J., Janin, J., & Weng, Z. (2003). A protein-protein docking benchmark. Proteins, 52, 88-91.
10. Dayhoff, M. O., Barker, W. C., & Hunt, L. T. (1983). Establishing homologies in protein sequences. Methods Enzymol., 91, 524-545.
11. de Vries, S. J., van Dijk, A. D., & Bonvin, A. M. (2006). WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins, 63, 479-489.
12. Dominguez, C., Boelens, R., & Bonvin, A. M. (2003). HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc, 125, 1731-1737.
13. Dosztanyi, Z., Chen, J., Dunker, A. K., Simon, I., & Tompa, P. (2006). Disorder and sequence repeats in hub proteins and their implications for network evolution. J Proteome Res, 5, 2985-2995.
14. Dunker, A. K., Cortese, M. S., Romero, P., Iakoucheva, L. M., & Uversky, V. N. (2005). Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J, 272, 5129-5148.
15. Eisenberg, D., & McLachlan, A. D. (1986). Solvation energy in protein folding and binding. Nature, 319, 199-203.
16. Ekman, D., Light, S., Bjorklund, A. K., & Elofsson, A. 2006. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biology, 2007 8, R192 7:R45.
17. Fernandez-Recio, J., Totrov, M., Skorodumov, C., & Abagyan, R. 2005. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins, 58, 134-143.
18. Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., et al. (2003). A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.
19. Glaser, F., Pupko, T., Paz, I., Bell, R. E., Bechor-Shental, D., Martz, E., & Ben-Tal, N. 2003. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19, 163-164.
20. Glaser, F., Rosenberg, Y., Kessel, A., Pupko, T., and Ben-Tal, N. (2005). The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures. Proteins, 58, 610-617.
21. Goebel, U., Sander, C., Schneider, R., & Valencia, A. (1994). Correlated mutations and residue contacts in proteins. Proteins, 18, 309-317.
22. Halperin, I., Wolfson, H., & Nussinov, R. (2006). Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. Proteins 63, 832-845.
23. Higurashi, M., Ishida, T., & Kinoshita, K. (2008). Identification of transient hub proteins and the possible structural basis for their multiple interactions. Protein Sci, 17, 72-78.
24. Huang, B., & Schroeder, M. (2008). Using protein binding site prediction to improve protein docking. Gene, 422, 14-21.
25. Hwang, H., Pierce, B., Mintseris, J., Janin, J., & Weng, Z. (2008). Protein-protein docking benchmark version 3.0. Proteins.
26. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki,Y. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA, 98, 4569-4574.
27. Janin, J., Rodier, F., Chakrabarti, P., & Bahadur, R. P. (2007). Macromolecular recognition in the Protein Data Bank. Acta Crystallogr D Biol Crystallogr, 63, 1-8.
28. Jones, S., & Thornton, J. M. (1996). Principles of protein-protein interactions. Proc Natl Acad Sci USA, 93, 13-20.
29. Jones, S., & Thornton, J. M. (1997a). Analysis of protein-protein interaction sites using surface patches. J Mol Biol, 272, 121-132.
30. Jones, S. & Thornton, J. M. (1997b). Prediction of protein-protein interaction sites using patch analysis. J Mol Biol, 272, 133-143.
31. Kihara, D., Lu, H., Kolinski, A., & Skolnick, J. (2001). TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc. Natl. Acad. Sci U. S. A, 98, 10125-10130.
32. Kihara, D., & Skolnick, J. (2004). Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins, 55, 464-473.
33. Kihara, D., Zhang, Y., Lu, H., Kolinski, A., & Skolnick, J. (2002). Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci USA, 99, 5993-5998.
34. Kufareva, I., Budagyan, L., Raush, E., Totrov, M., & Abagyan, R. (2007). PIER: Protein interface recognition for structural proteomics. Proteins, 67, 400-417.
35. Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. J Mol Biol, 157, 105-132.
36. Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T., & Ben-Tal, N. (2005). ConSurf 2005: The projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res, 33, W299-W302.
37. Li, B., Turuvekere, S., Agrawal, M., La, D., Ramani, K., & Kihara, D. (2008). Characterization of local geometry of protein surfaces with the visibility criterion. Proteins, 71, 670-683.
38. Liang, S., Zhang, C., Liu, S., & Zhou, Y. (2006). Protein binding site prediction using an empirical scoring function. Nucleic Acids Res, 34, 3698-3707.
39. Liang, S., Zhang, J., Zhang, S., & Guo, H. (2004). Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores. Proteins 57, 548-557.
40. Lichtarge, O., Bourne, H. R., & Cohen, F. E. (1996a). An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol, 257, 342-358.
41. Lichtarge, O., Bourne, H. R., & Cohen, F. E. (1996b). Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex. Proc Natl Acad Sci USA, 93, 7507-7511.
42. Lo Conte, L., Chothia, C., & Janin, J. (1999). The atomic structure of protein-protein recognition sites. J Mol Biol, 285, 2177-2198.
43. Mihalek, I., Res, I., & Lichtarge, O. (2007). On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues. J Mol Biol, 369, 584-595.
44. Mihalek, I., Res, I., Yao, H., & Lichtarge, O. (2003). Combining inference from evolution and geometric probability in protein structure evaluation. J Mol Biol, 331, 263-279.
45. Miller, S., Janin, J., Lesk, A. M., & Chothia, C. (1987). Interior and surface of monomeric proteins. J Mol Biol, 196, 641-656.
46. Mintseris, J., & Weng, Z. (2005). Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA, 102, 10930-10935.
47. Mintseris, J., Wiehe, K., Pierce, B., Anderson, R., Chen, R., Janin, J., & Weng, Z. (2005). Protein-Protein Docking Benchmark 2.0: an update. Proteins, 60, 214-216.
48. Mirny, L. A., & Shakhnovich, E. I. (1999). Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol, 291, 177-196.
49. Murakami, Y., & Jones, S. (2006). SHARP2: protein-protein interaction predictions using patch analysis. Bioinformatics, 22, 1794-1795.
50. Murga, L. F., Ondrechen, M. J., & Ringe, D. (2008). Prediction of interaction sites from apo 3D structures when the holo conformation is different. Proteins.
51. Negi, S. S., & Braun, W. (2007). Statistical analysis of physical-chemical properties and prediction of proteinprotein interfaces. Journal of molecular modeling, 13, 1157-1167.
52. Negi, S. S., Schein, C. H., Oezguen, N., Power, T. D., & Braun, W. (2007). InterProSurf: a Web server for predicting interacting sites on protein surfaces. Bioinformatics, 23, 3397-3399.
53. Neuvirth, H., Heinemann, U., Birnbaum, D., Tishby, N., & Schreiber, G. (2007). ProMateus--an open research approach to protein-binding sites analysis. Nucleic Acids Res, 35, W543-W548.
54. Neuvirth, H., Raz, R., & Schreiber, G. (2004). ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol, 338, 181-199.
55. Nooren, I. M., & Thornton, J. M. (2003a). Diversity of protein-protein interactions. EMBO J, 22, 3486-3492.
56. Nooren, I. M., & Thornton, J. M. (2003b). Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol, 325, 991-1018.
57. Oldfield, C. J., Meng, J., Yang, J. Y., Yang, M. Q., Uversky, V. N., & Dunker, A. K. (2008). Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC genomics, 9(Suppl 1), S1.
58. Pazos, F., Helmer-Citterich, M., Ausiello, G., & Valencia, A. (1997). Correlated mutations contain information about protein-protein interaction. J Mol Biol, 271, 511-523.
59. Pazos, F., & Valencia, A. (2002). In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins, 47, 219-227.
60. Pettit, F. K., Bare, E., Tsai, A., & Bowie, J. U. (2007). HotPatch: a statistical approach to finding biologically relevant features on protein surfaces. J Mol Biol, 369, 863-879.
61. Pletneva, E. V., Laederach, A. T., Fulton, D. B., & Kostic, N. M. (2001). The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains. J Am Chem Soc, 123, 6232-6245.
62. Porollo, A., & Meller, J. (2007). Prediction-based fingerprints of protein-protein interactions. Proteins, 66, 630-645.
63. Pupko, T., Bell, R. E., Mayrose, I., Glaser, F., and Ben-Tal, N. (2002). Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics, (18 Suppl 1), S71-S77.
64. Qin, S., & Zhou, H. X. (2007). meta-PPISP: A Meta Web Server for Protein-Protein Interaction Site Prediction. Bioinformatics.
65. Res, I., Mihalek, I., & Lichtarge, O. (2005). An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics, 21, 2496-2501.
66. Shannon, C. E. (2001). A mathematical theory of communication. ACM SIGMOBILE Mobile Computing and Communications Review.
67. Shulman-Peleg, A., Shatsky, M., Nussinov, R., & Wolfson, H. J. (2007). Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol, 5, 43.
68. Singh, G. P., Ganapathi, M., & Dash, D. (2007). Role of intrinsic disorder in transient interactions of hub proteins. Proteins, 66, 761-765.
69. Tjong, H., Qin, S., & Zhou, H. X. (2007). PI2PE: protein interface/interior prediction engine. Nucleic Acids Res, 35, W357-W362.
70. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., & Rothberg, J. M. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
71. Valdar, W. S. (2002). Scoring residue conservation. Proteins, 48, 227-241.
72. Zhou, H. X., & Qin, S. (2007). Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics, 23, 2203-2209.
73. Zhou, H. X., & Shan, Y. (2001). Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins, 44, 336-343.