Association of putative concave protein-binding sites with the fluctuation behavior of residues

Protein Science

Volumn 15, Issue 10, 2006, Pages 2265-2277

  Ertekin, Asli ^a   Nussinov, Ruth ^b,c,d   Haliloglu, Turkan ^a  

^a BOGAZICI UNIVERSITY   (Turkey)

^b SAIC FREDERICK INC   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

^d NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Binding sites; GNM; Protein protein interactions; Protein protein interfaces; Structural dynamics

Indexed keywords

ANTIBODY; ANTIGEN; ENZYME;

ARTICLE; BINDING SITE; DATA BASE; DENSITY; DYNAMICS; INVAGINATION; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RESIDUE ANALYSIS; THEORETICAL MODEL;

AMINO ACIDS; BINDING SITES; MODELS, MOLECULAR; MOTION; PROTEINS; SOFTWARE; VIBRATION;

EID: 33749367332     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.051815006     Document Type: Article

References (48)

1. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., and Watson, J.D. 1994. Molecular biology of the cell.. Garland Publishing, New York.
2. Bahar, I., Atilgan, A., and Erman, B. 1997. Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential. Fold. Des. 2: 173-181.
3. Bahar, I., Atilgan, A.R., Demirel, M.C., and Erman, B. 1998. Vibrational dynamics of proteins: Significance of slow and fast modes in relation to function and stability. Phys. Rev. Lett. 80: 2733-2736.
4. Bartlett, G.J., Porter, T.P., Borkakoti, N., and Thornton, J.M. 2002. Analysis of catalytic residues in enzyme active sites. J. Mol. Biol. 324: 105-121.
5. Brinda, K.V., Kannan, N., and Vishveshwara, S. 2002. Analysis of homodimeric protein interfaces by graph-spectral methods. Protein Eng. 15: 265-277.
6. Casari, G., Sander, C., and Valencia, A. 1995. A method to predict functional residues in proteins. Nat. Struct. Biol. 2: 171-178.
7. Cheng, R., Mintseris, J., Janin, J., and Weng, Z. 2003. A protein-protein docking benchmark. Proteins 52: 88-91.
8. Chothia,, C. 1975. Nature of accessible and buried surfaces in proteins. J. Mol. Biol. 105: 1-14.
9. Clackson, T. and Wells, J.A. 1995. A hot spot of binding energy in a hormone-receptor interface. Science 267: 383-386.
10. Dean, A.M. and Golding, G.B. 2000. Enzyme evolution explained (sort of). pp. 6-17, Pacific Symposium on Biocomputing.
11. DeLano, W.L. 2002. Unraveling hot spots in binding interfaces: Progress and challenges. Curr. Opin. Struct. Biol. 12: 14-20.
12. Demirel, M.C., Atilgan, A.R., Jernigan, R.L., Erman, B., and Bahar, I. 1998. Identification of kinetically hot residues in proteins. Protein Sci. 7: 2522-2532.
13. Dominguez, C., Boelens, R., and Bonvin, A.M. 2003. HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125: 1731-1737.
14. Fariselli, P., Pazos, F., Valencia, A., and Haliloglu, T. 2002. Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur. J. Biochem. 269: 1356-1361.
15. Fernandez-Recio, J., Totrov, M., Skorodumov, C., and Abagyan, R. 2005. Optimal docking area: A new method for predicting protein-protein interaction sites. Proteins 58: 134-143.
16. Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor-Shental, D., Martz, E., and Ben-Tal, N. 2003. ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164.
17. Haliloglu, T., Bahar, I., and Erman, B. 1997. Gaussian dynamics of folded proteins. Phys. Rev. Lett. 79: 3090-3093.
18. Haliloglu, T., Keskin, O., Ma, B., and Nussinov, R. 2005. How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hotspots and conserved residues. Biophys. J. 88: 1552-1559.
19. Huan-Xiang, Z. and Yibing, S. 2001. Prediction of protein interaction sites from sequence profile and residue neighbor. Proteins 44: 336-343.
20. Jambon, M., Imberty, A., Deleage, G., and Geourjon, C. 2003. A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 52: 137-145.
21. Jones, S. and Thornton, J.M. 1997. Prediciton of protein-protein interaction sites using patch analysis. J. Mol. Biol. 272: 133-143.
22. Keskin, O., Tsai, C.J., Wolfson, H., and Nussinov, R. 2004. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci. 13: 1043-1055.
23. 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.
24. Kini, R.M. and Evans, H.J. 1995. A hypothetical structural role for proline residues in the flanking segments of protein-protein interaction sites. Biochem. Biophys. Res. Commun. 212: 1115-1124.
25. Kinoshita, K. and Nakamura, H. 2005. Identification of the ligand binding sites on the molecular surface of proteins. Protein Sci. 14: 711-718.
26. Kortemme, T. and Baker, D. 2002. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. 99: 14116-14121.
27. Landgraf, R., Xenarios, I., and Eisenberg, D. 2001. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol. 307: 1487-1502.
28. Lee, B. and Richards, F.M. 1971. The interpretation of protein structures estimation of static accessibility. J. Mol. Biol. 55: 379-400.
29. Li, X., Keskin, O., Ma, B., Nussinov, R., and Liang, J. 2004. Protein-protein interactions: Hotspots and structurally conserved residues often locate in the complemented pockets that pre-organized in the unbound states: Implications for docking. J. Mol. Biol. 344: 781-795.
30. Lichtarge, O., Bourne, H.R., and Cohen, F.E. 1996. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257: 342-358.
31. Lim, D., Park, H.U., DeCastro, L., Kang, S., Lee, H.S., Jensen, S., Lee, K.J., and Strynadka, N.C. 2001. Crystal structure and kinetic analysis of β-lactamase inhibitor protein-II in complex with TEM-1 β-lactamase. Nat. Struct. Biol. 8: 848-852.
32. Livingston, C.D. and Barton, G.J. 1993. Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation. Comp. Appl. Biosci. 6: 645-656.
33. Luque, I. and Freire, E. 2000. Structural stability of binding sites: Consequences for binding affinity and allosteric effects. Proteins 4: 63-71.
34. 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. 100: 5772-5777.
35. Madabushi, S., Yao, H., Marsh, M., Kristensen, D.M., Philippi, A., Sowa, M.E., and Lichtarge, O. 2002. Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J. Mol. Biol. 316: 139-154.
36. Marti-Renom, M.A., Stuart, A.C., Fiser, A., Sanchez, R., Melo, F., and Sali, A. 2000. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29: 291-325.
37. Neuvirth, H., Raz, R., and Scheiber, G. 2004. ProMate: A structure based prediction program to identify the location of protein-protein binding sites. J. Mol. Biol. 338: 181-199.
38. Nimrod, G., Glaser, F., Steinberg, D., Ben-Tal, N., and Pupko, T. 2005. In silico identification of functional regions in proteins. Bioinformatics 21 (Suppl 1): i328-i337.
39. Pazos, F., Helmer-Citterich, M., Ausiello, G., and Valencia, A. 1997. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271: 511-523.
40. Rader, A.J. and Bahar, I. 2004. Folding core predictions from network models of proteins. Polymer 45: 659-668.
41. Rader, A.J., Anderson, G., Isin, B., Khorana, H.G., Bahar, I., and Klein-Seetharaman, J. 2004. Identification of core amino acids stabilizing rhodopsin. Proc. Natl. Acad. Sci. 101: 7246-7251.
42. Sandak, B., Wolfson, H., and Nussinov, R. 1998. Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers. Proteins 32: 159-174.
43. Smith, G.R. and Sternberg, M.J.E. 2005. The relationship between the flexibility of proteins and conformational states on forming protein-protein complexes with an application to protein-protein docking. J. Mol. Biol. 347: 1077-1101.
44. Szilagyi, A., Grimm, V., Arakaki, A.K., and Skolnick, J. 2005. Prediction of physical protein-protein interactions. Phys. Biol. 2: 1-16.
45. Todd, A.E., Orengo, C.A., and Thornton, J.M. 2001. Evolution of funciton in protein superfamilies, from a structural perspective. J. Mol. Biol. 307: 1113-1143.
46. Wagnikar, P.P., Tendulka, A.V., Ramya, S., Mail, D.N., and Sarawagi, S. 2003. Functional sites in protein families uncovered via an objective and automated graph theoretic approach. J. Mol. Biol. 326: 955-978.
47. Yang, L.W. and Bahar, I. 2005. Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes. Structure 13: 893-904.
48. Yao, H., Kristensen, D.M., Mihalek, I., Sowa, M.E., Shaw, C., Kimmel, M., Kavraki, L., and Lichtarge, O. 2003. An accurate, sensitive and scalable method to identify functional sites in protein structures. J. Mol. Biol. 326: 255-261.