Elastic properties of proteins: Insight on the folding process and evolutionary selection of native structures

Journal of Molecular Biology

Volumn 321, Issue 5, 2002, Pages 909-921

  Micheletti, Cristian ^a   Lattanzi, Gianluca ^b   Maritan, Amos ^a,c  

^a SISSA   (Italy)

^b HAHN MEITNER INSTITUT   (Germany)

^c ABDUS SALAM INTERNATIONAL CENTRE FOR THEORETICAL PHYSICS   (Italy)

Author keywords

B factors; Folding rates; Key folding sites; Protein flexibility; Vibrational dynamics

Indexed keywords

PROTEIN; PROTEINASE;

ACCURACY; ARTICLE; CONTROLLED STUDY; ELASTICITY; EQUILIBRIUM CONSTANT; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR EVOLUTION; NONHUMAN; PHASE TRANSITION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STRUCTURE; QUALITATIVE ANALYSIS; STATISTICAL ANALYSIS; THEORETICAL STUDY; THERMODYNAMICS; VALIDATION PROCESS;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0036385839     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00710-6     Document Type: Article

References (67)

1. Baker, D. A. (2000). Surprising simplicity to protein folding. Nature, 405, 39-42.
2. Maritan, A., Micheletti, C., Trovato, A. & Banavar, J. R. (2000). Optimal shapes of compact strings. Nature, 406, 287.
3. Micheletti, C., Banavar, J. R., Maritan, A. & Seno, F. (1999). Protein structures and optimal folding from a geometrical variational principle. Phys. Rev. Letters, 82, 26.3372-26.3375.
4. Banavar, J., Maritan, A., Micheletti, C. & Trovato, A. (2002). Geometry and physics of proteins. Proteins: Struct. Funct. Genet. 47, 315-322.
5. ben Avraham, D. (1993). Vibrational normal-mode spectrum of globular proteins. Phys. Rev. ser. B, 47, 14559-14560.
6. Plaxco, K. W., Simons, K. T. & Baker, D. (1998). Contact order and transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277, 985-994.
7. Chan, H. S. (1998). Matching speed and locality. Nature, 392, 761-762.
8. Cecconi, F., Micheletti, C., Carloni, P. & Maritan, A. (2001). Molecular dynamics studies of HIV-1 protease: drug resistance and folding pathways. Proteins: Struct. Funct. Genet. 43, 365-372.
9. Jacobs, D. J., Rader, A. J., Kuhn, L. A. & Thorpe, M. F. (2001). Protein flexibility predictions using graph theory. Proteins: Struct. Funct. Genet. 44, 150-165.
10. Rader, A. J., Heispenheide, B. M., Kuhn, L. A. & Thorpe, M. F. (2002). Protein unfolding: rigidity lost. Proc. Natl Acad. Sci. USA, 99, 3540-3545.
11. Tirion, M. M. (1996). Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Letters, 77, 1905-1908.
12. Go, N. & Scheraga, H. A. (1976). On the use of classical statistical mechanics in the treatment of polymer chain conformations. Macromolecules, 9, 535-542.
13. Galzitskaya, O. V. & Finkelstein, A. V. (1999). A theoretical search for folding/unfolding nuclei in 3D protein structure. Proc. Natl Acad. Sci. USA, 96, 11299-11304.
14. Munoz, V., Henry, E. R., Hofrichter, J. & Eaton, W. A. (1999). A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl Acad. Sci. USA, 95, 5872.
15. Alm, E. & Baker, D. (1999). Prediction of protein folding mechanisms from free energy landscapes derived from native structures. Proc. Natl Acad. Sci. USA, 96, 11305-11310.
16. Klimov, D. K. & Thirumalai, D. (2000). Native topology determines force-induced unfolding pathways in globular proteins. Proc. Natl Acad. Sci. USA, 97, 7254-7259.
17. Clementi, C., Nymeyer, H. & Onuchic, J. N. (2000). Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J. Mol. Biol. 298, 937-953.
18. Micheletti, C., Banavar, J. & Maritan, A. (2001). Conformations of proteins in equilibrium. Phys. Rev. Letters, 87 DOI:088102-1-088102-4.
19. Baldwin, R. L. & Rose, G. D. (1999). Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem. Sci. 24, 26-33.
20. Denton, M. & Marshall, C. (2001). Laws of form revisited. Nature, 410, 417.
21. Chothia, C. (1984). Principles that determine the structure of proteins. Annu. Rev. Biochem. 53, 537-572.
22. Chan, H. S. & Dill, K. A. (1990). The effects of internal constraints on the configurations of chain molecules. J. Chem. Phys. 92, 3118-3135.
23. Socci, N. D., Bialek, W. S. & Onuchic, J. N. (1994). Properties and origins of protein secondary structures. Phys. Rev. ser. E, 49, 3440-3443.
24. Levitt, M., Sander, C. & Stern, P. S. (1985). Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181, 423-447.
25. Horiuchi, T. & Go, N. (1991). Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme. Proteins: Struct. Funct. Genet. 10, 106-116.
26. Amadei, A., Linssen, A. B. M. & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins: Struct. Funct. Genet. 17, 412-425.
27. Bahar, I., Atilgan, A. R. & Erman, B. (1997). Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential. Fold. Des. 2, 173-181.
28. Haliloglu, T., Bahar, I. & Erman, B. (1997). Gaussian dynamics of folded proteins. Phys. Rev. Letters, 79, 3090-3093.
29. Bahar, I., Atilgan, A. R., Demirel, M. C. & Erman, B. (1998). Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys. Rev. Letters, 80, 2733-2736.
30. Jackson, S. E. (1998). How do small single-domain proteins fold? Fold. Des. 3, R81-R91.
31. Bollobas, B. (1985). Random Graphs, Academic, London.
32. Merris, R. (1994). Laplacian matrices of graphs: a survey. Lin. Alg. Appl. 197, 143-176.
33. McKay, B. D. (1981). The expected eigenvalue distribution of a large regular graph. Lin. Alg. Appl. 40, 203-216.
34. Monasson, R. (1999). Diffusion, localization and dispersion relations on "small-world" lattices. Eur. Phys. J. sect. B, 12, 555-567.
35. Biroli, G. & Monasson, R. (1999). A single defect approximation for localized states on random lattices. J. Phys. ser. A, 32, L255-L261.
36. Anderson, P. W. (1958). Absence of diffusion in certain random lattices. Phys. Rev. 109, 1492-1505.
37. Anderson, P. W. (1978). Local moments and localized states. Rev. Mod. Phys. 50, 191-201.
38. Tirion, M. M. & ben Avraham, D. (1993). Normal mode analysis of g-actin. J. Mol. Biol. 230, 186-195.
39. Bahar, I., Atilgan, A. R., Jernigan, R. L. & Erman, B. (1997). Understanding the recognition of protein structural classes by amino acid composition. Proteins: Struct. Funct. Genet. 29, 172-185.
40. Lustig, B., Bahar, I. & Jernigan, R. L. (1998). Rna bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access. Nucl. Acids Res. 26, 5212-5217.
41. Bahar, I., Wallqvist, A., Covell, D. G. & Jernigan, R. L. (1998). Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry, 39, 1067-1075.
42. Bahar, I. & Jernigan, R. L. (1998). Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. J. Mol. Biol. 281, 871-884.
43. Jernigan, R. L., Demirel, M. C. & Bahar, I. (1999). Relating structure to function through the dominant modes of motion of DNA topoisomerase II. Int. J. Quant. Chem. 75, 301-312.
44. Bahar, I., Erman, B., Jernigan, R. L., Atilgan, A. R. & Covell, D. G. (1999). Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. J. Mol. Biol. 285, 1023-1037.
45. Haliloglu, T. & Bahar, I. (1999). Structure based analysis of protein dynamics. Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Proteins: Struct. Funct. Genet. 37, 654-667.
46. Bahar, I. & Jernigan, R. L. (1999). Cooperative fluctuations and subunit communication in tryptophan synthase. Biochemistry, 38, 3478-3490.
47. Keskin, O., Bahar, I. & Jernigan, R. L. (2000). Proteins with similar architectures exhibit similar large-scale dynamic behavior. Biophys. J. 78, 2093-2106.
48. Atilgan, A. R., Durell, S. R., Jernigan, R. L., Demirel, M. C., Keskin, O. & Bahar, I. (2001). Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80, 505-515.
49. Cieplak, M. & Hoang, T. X. (2001). Kinetic non-optimality and vibrational stability of proteins. Proteins: Struct. Funct. Genet. 44, 20-25.
50. Hoang, T. X. & Cieplak, M. (2000). Molecular dynamics of folding of secondary structures in Go-type models of proteins. J. Chem. Phys. 112, 6851-6862.
51. Hoang, T. X. & Cieplak, M. (2000). Sequencing of folding events in Go-type proteins. J. Chem. Phys. 113, 8319-8328.
52. Diamond, R. (1990). On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor. Acta Crystallog. sect. A, 46, 425-435.
53. Doruker, P., Jernigan, R. L. & Bahar, I. (2002). Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23, 119-127.
54. Halle, B. (2002). Flexibility and packing in proteins. Proc. Natl Acad. Sci. USA, 99, 1274-1279.
55. Micheletti, C., Seno, F. & Maritan, A. (2000). Recurrent oligomers in proteins - an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies. Proteins: Struct. Funct. Genet. 40, 662-674.
56. Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. E., Brice, M. D., Rodgers, J. R. et al. (1977). The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
57. Condra, J. H. et al. (1995). In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors. Nature, 374, 569-571.
58. Ala, P. J., Huston, E. E., Klabe, R. M., Jadhav, P. K., Lam, P. Y. S. & Chang, C. H. (1998). Counteracting HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with XV638 and SD146, cyclic urea amides with broad specificities. Biochemistry, 37, 15042-15049.
59. Gulnik, S., Erickson, J. W. & Xie, D. (2000). Vitamins and hormones-advances in research and applications. Vitam. Horm. 58, 213-256.
60. Wlodawer, A. & Erickson, J. W. (1993). Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62, 543-585. and references therein..
61. Reddy, P. & Ross, J. (1999). Amprenavir - a protease inhibitor for the treatment of patients with HIV-1 infection. Formulary, 34, 567-675.
62. Tisdale, M. et al. (1995). Cross-resistance analysis of human-immunodeficiency-virus type-1 variants individually selected for resistance to 5 different protease inhibitors. Antimicrob. Agents Chemother. 39, 1704-1710.
63. Piana, S., Carloni, P. & Parrinello, M. (2002). Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. J. Mol. Biol. 319, 567-583.
64. Settanni, G., Hoang, T., Micheletti, C. & Maritan, A. (2002). Folding pathways of prion and doppel. Biophys. J. In the press.
65. Debe, D. A. & Goddard, W. A., III (1999). First principles prediction of protein folding rates. J. Mol. Biol. 294, 619-625.
66. Dinner, A. R. & Karplus, M. (2001). The roles of stability and contact order in determining protein folding rates. Nature Struct. Biol. 8, 21-22.
67. Ivankov, D. N. & Finkelstein, A. (2001). Theoretical study of a landscape of protein folding-unfolding pathways. folding rates and midtransition. Biochemistry, 40, 9957-9961.