How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues

Biophysical Journal

Volumn 88, Issue 3, 2005, Pages 1552-1559

  Haliloglu, Turkan ^a   Keskin, Ozlem ^b,c   Ma, Buyong ^c   Nussinov, Ruth ^c,d,e  

^a BOGAZICI UNIVERSITY   (Turkey)

^b KOÇ UNIVERSITY   (Turkey)

^c SAIC FREDERICK INC   (United States)

^d TEL AVIV UNIVERSITY   (Israel)

^e NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTATHIONE TRANSFERASE; PROTEIN; AMINO ACID;

ANTIGEN ANTIBODY COMPLEX; ARTICLE; MATHEMATICAL MODEL; MOLECULAR INTERACTION; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; VIBRATION; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENERGY TRANSFER; MOTION; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION;

AMINO ACIDS; BINDING SITES; COMPUTER SIMULATION; ENERGY TRANSFER; MODELS, CHEMICAL; MODELS, MOLECULAR; MOTION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; VIBRATION;

EID: 21244506296     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.051342     Document Type: Article

References (39)

1. Aloy, P., B. Bottcher, H. Ceulemans, C. Leuwein, C. Mellwig, S. Fischer, A. C. Gavin, P. Bork, G. Superti-Furga, L. Serrano, and R. B. Russel. 2004. Structure-based assembly of protein complexes in yeast. Science. 303:2026-2029.
2. Bahar, I., A. R. Atilgan, M. C. Demirel, and B. Erman. 1998. Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys. Rev. Lett. 80:2733-2736.
3. Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-181.
4. Bahar, I., and R. L. Jernigan. 1997. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266:195-214.
5. Bogan, A. A., and K. S. Thorn. 1998. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280:1-9.
6. Chern, M.-K., T.-C. Wu, C.-H. Hsieh, C.-C. Chou, L.-F. Liu, I.-C. Kuan, Y.-H. Yeh, C.-D. Hsiao, and F. T. Tam. 2000. Tyr115, Gln165 and Trp209 contribute to the 1,2-epoxy-3-(p nitrophenoxy)propane-conjugating activity of glutathione S-transferase cGSTM1-1. J. Mol. Biol. 300:1257-1269.
7. Chothia, C. 1975. Nature of accessible and buried surfaces in proteins. J. Mol. Biol. 105:1-14.
8. Demirel, M. C., A. R. Atilgan, R. L. Jernigan, B. Erman, and I. Bahar. 1998. Identification of kinetically hot residues in proteins. Protein Sci. 7:2522-2532.
9. Fernandez, A., and H. A. Scheraga. 2003. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc. Natl. Acad. Sci. USA. 100:113-118.
10. Fernandez, A., R. Scott, and R. S. Berry. 2004. The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks. Proc. Natl. Acad. Sci. USA. 101:2823-2827.
11. Fersht, A. R. 1976. Nucleation mechanisms in protein folding. Curr. Opin. Struct. Biol. 7:3-9.
12. Gavin, A. C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J. M. Rick, A. M. Michon, C. M. Cruciat, M. Remor, C. Hofert, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:141-147.
13. Halperin, I., H. Wolfson, and R. Nussinov. 2004. Protein-protein interactions: coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure. 12:1027-1038.
14. Hu, Z., B. Ma, H. Wolfson, and R. Nussinov. 2000. Conservation of polar residues as hot spots at protein interfaces. Proteins. 39:331-342.
15. Keskin, O., R. L. Jernigan, and I. Bahar. 2000. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys. J. 78:2093-2106.
16. Keskin, O., B. Ma, and R. Nussinov. 2005. Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues. J. Mol. Biol. 345:1281-1294.
17. Keskin, O., C. J. Tsai, H. Wolfson, and R. Nussinov. 2004. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci. 13:1043-1055.
18. Kortemme, T., and D. Baker. 2002. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. USA. 99:14116-14121.
19. Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
20. Ma, J. P. 2004. New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr. Protein Pept. Sci. 5:119-123.
21. Ma, B., T. Elkayam, H. Wolfson, and R. Nussinov. 2003. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl. Acad. Sci. USA. 100: 5772-5777.
22. Marcotte, E. M., M. Pellegrini, H. L. Ng, D. W. Rice, T. O. Yeates, and D. Eisenberg. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science. 285:751-753.
23. Massova, I., and P. A. Kollman. 1999. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 121:8133-8143.
24. Mirny, L., and E. J. Shakhnovich. 2001. Evolutionary conservation of the folding nucleus. J. Mol. Biol. 308:123-129.
25. Miyazawa, S., and R. L. Jernigan. 1985. Estimation of effective interresidue contact energies from protein crystal-structures: quasi-chemical approximation. Macromolecules. 18:534-552.
26. Papageorgiou, A. C., R. Shapiro, and K. R. Acharya. 1997. Molecular recognition of human angiogenin by placental ribonuclease inhibitor-an X-ray crystallographic study at 2.0 angstrom resolution. EMBO J. 16: 5162-5177.
27. Perrett, S., J. Clarke, A. M. Hounslow, and A. R. Fersht. 1995. Relationship between equilibrium amide proton-exchange behavior and the folding pathway of barnase. Biochemistry. 34:9288-9298.
28. Rader, A. J., and I. Bahar. 2004. Identification of core amino acids stabilizing rhodopsin. Polym. 45:659-668.
29. Rajamani, D., S. Thiel, V. Sandor, and C. J. Camacho. 2004. Anchor residues in protein-protein interactions. Proc. Natl. Acad. Sci. USA. 3:11287-11292.
30. Roder, H., G. A. Elove, and S. W. Englander. 1988. Structural characterization of folding intermediates in cytochrome-c by h-exchange labeling and proton NMR. Nature. 335:700-704.
31. Shakhnovich, E., V. Abkevich, and O. Ptitsyn. 1996. Conserved residues and the mechanism of protein folding. Nature. 379:96-98.
32. Shatsky, M., R. Nussinov, and H. Wolfson. 2004. A method for simultaneous alignment of multiple protein structures. Proteins. 56: 143-156.
33. Shoemaker, B. J., J. Wang, and P. G. Wolynes. 1997. Structural correlations in protein folding funnels. Proc. Natl. Acad. Sci. USA. 94: 777-782.
34. Thorn, K. S., and A. A. Bogan. 2001. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics. 17:284-285.
35. Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
36. Tsai, C. J., D. Xu, and R. Nussinov. 1998. Protein folding via binding and vice versa. Fold. Des. 3:R71-R80.
37. Uetz, P., L. Giot, G. Cagney, T. A. Mansfield, R. S. Judson, J. R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, A. Qureshi-Emili, Y. Li, B. Godwin, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:623-627.
38. Verkhivker, G. M., D. Bouzida, D. K. Gehlhaar, P. A. Rejto, S. T. Freer, and P. W. Rose. 2002. Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface. Proteins. 48:539-557.
39. Wu, Y. H., and J. P. Ma. 2004. Refinement of F-actin model against fiber diffraction data by long-range normal modes. Biophys. J. 86:116-124.