Self-organization and mismatch tolerance in protein folding: General theory and an application

Journal of Chemical Physics

Volumn 112, Issue 11, 2000, Pages 5212-5222

  Fernández, Ariel ^a,b   Berry, R Stephen ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSIDAD NACIONAL DEL SUR   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 2242421816     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.481076     Document Type: Article

References (51)

1. R. Jaenicke, in Protein Structure and Protein Engineering, edited by E. L. Winnacker and R. Huber (Springer-Verlag, Berlin, 1988), p. 16.
2. O. B. Ptitsyn and B. V. Semisotnov, in Conformations and Forces in Protein Folding, edited by B. Nall, B. Dill, and K. Dill (American Association for the Advancement of Science, Washington, 1991), p. 155.
3. R. Zwanzig, A. Szabo, and B. Bagchi, Proc. Natl. Acad. Sci. USA 89, 20 (1992).
4. R. L. Baldwin, Proc. Natl. Acad. Sci. USA 93, 2627 (1996).
5. K. A. Dill and H. S. Chan, Nat. Struct. Biol. 4, 10 (1997).
6. J. Bohr, H. Bohr, and S. Brunak, Europhys. News 27, 50 (1996).
7. T. E. Creighton, N. J. Darby, and J. Kemmink, FASEB J. 10, 110 (1996).
8. M. Jamin and R. L. Baldwin, Nat. Struct. Biol. 3, 613 (1996).
9. A. Fernández and G. Appingnanesi, Phys. Rev. Lett. 78, 2668 (1997).
10. K. Dill, K. M. Fiebig, and H. S. Chan, Proc. Natl. Acad. Sci. USA 90, 1942 (1993).
11. N. Go and H. A. Scheraga, J. Chem. Phys. 51, 4751 (1969).
12. N. Go and H. A. Scheraga, Macromolecules 9, 535 (1976).
13. H. Cendra, A. Fernández, and W. Reartes, J. Math. Chem. 19, 331 (1996).
14. S. He and H. A. Scheraga, J. Chem. Phys. 108, 287 (1998).
15. S. He and H. A. Scheraga, J. Chem. Phys. 108, 271 (1998).
16. A. Fernández, J. Stat, Phys. 92, 237 (1998).
17. Z. Guo and D. Thirumalai, Biopolymers 36, 83 (1995).
18. M. Guenza and K. F. Freed, J. Chem. Phys. 105, 3823 (1996).
19. A. Fernández and A. Colubri, Physica A 248, 336 (1998).
20. R. E. Kunz and R. S. Berry, J. Chem. Phys. 103, 1904 (1995).
21. K. D. Ball and R. S. Berry, J. Chem. Phys. 109, 8541 (1998).
22. K. D. Ball and R. S. Berry, J. Chem. Phys. 109, 8557 (1998).
23. K. D. Ball and R. S. Berry, J. Chem. Phys. 111, 2060 (1999).
24. C. Cantor and P. Schimmel, Biophysical Chemistry (W. H. Freeman, New York, 1980).
25. R. F. Gesteland and J. F. Atkins, The RNA World (Cold Spring Harbor Press, New York, 1993).
26. T. E. Creighton, Proteins (Freeman and Co., New York, 1993).
27. N. Go, Annu. Rev. Biophys. Bioeng. 12, 183 (1983).
28. J. D. Bryngelson and P. G. Wolynes, J. Phys. Chem. 93, 6902 (1989).
29. R. Zwanzig, Proc. Natl. Acad, Sci. USA 92, 9801 (1995).
30. H. Frauenfelder, S. G. Sugar, and P. G. Wolynes, Science 254, 1598 (1991).
31. D. E. Rumelhart, J. C. McClelland and t. P. R. Group, Parallel Distributed Processing (MIT Press, Cambridge, 1988).
32. C. L. Brooks, M. Petitt, and M. Karplus, Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics (Wiley, New York, 1988).
33. J. S. Richardson and D. C. Richardson, in Protein Folding, edited by L. M. Gierasch and J. King (American Association for the Advancement of Science, Washington, 1990), p. 5.
34. T. G. Oas and P. S. Kim, in Protein Folding, edited by L. M. Gierasch and J. King (American Association for the Advancement of Science, Washington, 1990), p. 123.
35. D. Bashford, M. Karplus, and D. Weaver, in Protein Folding, edited by L. M. Gierasch and J. King (American Association for the Advancement of Science, Washington, 1990), p. 283.
36. T. E. Creighton, in Protein Folding, edited by L. M. Gierasch and J. King (American Association for the Advancement of Science, Washington, 1990), p. 157.
37. K. D. Ball, R. S. Berry, A. Proykova, R. E. Kunz, and D. J. Wales, Science 271, 963 (1996); see also R. S. Berry, N. Elmaci, J. P. Rose, and B. Vekhter, Proc. Natl. Acad. Sci. USA 94, 9520 (1997), for application of this method to a protein model.
38. K. D. Ball, R. S. Berry, A. Proykova, R. E. Kunz, and D. J. Wales, Science 271, 963 (1996); see also R. S. Berry, N. Elmaci, J. P. Rose, and B. Vekhter, Proc. Natl. Acad. Sci. USA 94, 9520 (1997), for application of this method to a protein model.
39. T. E. Creighton, J. Mol. Biol. 113, 275 (1977).
40. T. E. Creighton, Prog. Biophys. Mol. Biol. 33, 231 (1978).
41. C. J. Camacho and D. Thirumalai, Proc. Natl. Acad. Sci. USA 92, 1277 (1995).
42. A. Ansari, J. Berendzen, S. F. Browne, H. Frauenfelder, I. E. T. Iben, T. B. Sauke, E. Shyamsunder, and R. D. Young, Proc. Natl. Acad. Sci. USA 82, 5000 (1985).
43. B. Vekhter and R. S. Berry, J. Chem. Phys. 110, 2195 (1999).
44. J. D. Honeycutt and D. Thirumalai, Proc. Natl. Acad. Sci. USA 87, 3526 (1990).
45. J. D. Honeycutt and D. Thirumalai, Biopolymers 32, 695 (1992).
46. P. A. Laskowski, M. W. MacArthur, D. S. Moss, and J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1993).
47. M. Dadlez, Biochem. J. 36, 2788 (1997).
48. T. R. Sosnick, L. Mayne, and S. W. Englander, Proteins: Struct, Funct., Genet. 24, 413 (1996).
49. R. L. Baldwin and G. Rose, Trends Biol. Sci. 24, 26 (1999).
50. A. Fernandez, K. Kostov, and R. S. Berry, Proc. Natl. Acad. Sci. USA 96, 12991 (1999).
51. A. Fernández, K. Kostov, and R. S. Berry, J. Chem. Phys. 112, 5223 (2000) (following paper).