A ternary nucleation model for the nucleation pathway of protein folding

Journal of Chemical Physics

Volumn 126, Issue 17, 2007, Pages

  Djikaev, Y S ^a   Ruckenstein, Eli ^a  

^a State University of New York   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHAOS THEORY; ENZYMES; HYDROPHILICITY; HYDROPHOBICITY; NUCLEATION; TERNARY SYSTEMS;

PANCREATIC RIBONUCLEASE; PROTEIN FOLDING TIME; SELF CONSISTENT KINETIC THEORY; TERNARY NUCLEATION FORMALISM;

PROTEIN FOLDING;

ARTICLE; BIOLOGICAL MODEL; HYDROPHOBICITY; PROTEIN FOLDING;

HYDROPHOBICITY; MODELS, BIOLOGICAL; PROTEIN FOLDING;

EID: 34248182883     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2727469     Document Type: Article

References (72)

1. C. B. Anfinsen, Science 181, 223 (1973).
2. C. Ghelis and J. Yan, Protein Folding (Academic, New York, 1982).
3. T. E. Creighton, Proteins: Structure and Molecular Properties (Freeman, San Francisco, 1984).
4. L. Stryer, Biochemistry, 3rd ed. (Freeman, 1988).
5. B. Nölting, Protein Folding Kinetics (Springer-Verlag, Berlin, 2006).
6. J. D. Honeycutt and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 87, 3526 (1990).
7. J. D. Honeycutt and D. Thirumalai, Biopolymers 32, 695 (1992).
8. J. S. Weissman and P. S. Kim, Science 253, 1386 (1991).
9. T. E. Creighton, Nature (London) 356, 194 (1992).
10. C. Levinthal, J. Chim. Phys. Phys.-Chim. Biol. 65, 44 (1968).
11. P. S. Kim and R. I. Baldwin, Annu. Rev. Biochem. 0066-4154 10.1146/annurev.bi.51.070182.002331 51, 459 (1982); P. S. Kim and R. I. Baldwin, Annu. Rev. Biochem. 59, 631 (1990).
12. P. S. Kim and R. I. Baldwin, Annu. Rev. Biochem. 0066-4154 10.1146/annurev.bi.51.070182.002331 51, 459 (1982); P. S. Kim and R. I. Baldwin, Annu. Rev. Biochem. 59, 631 (1990).
13. T. E. Creighton, Biochem. J. 0264-6021 240, 1 (1990); T. E. Creighton, Prog. Biophys. Mol. Biol. 33, 231 (1978).
14. T. E. Creighton, Biochem. J. 0264-6021 240, 1 (1990); T. E. Creighton, Prog. Biophys. Mol. Biol. 33, 231 (1978).
15. Z. Guo, D. Thirumalai, and J. D. Honeycutt, J. Chem. Phys. 97, 525 (1992).
16. Z. Guo and D. Thirumalai, Biopolymers 36, 83 (1995).
17. D. Thirumalai and Z. Guo, Biopolymers 35, 137 (1995).
18. B. Nölting, R. Golbik, J. L. Neira, A. S. Soler-Gonzalez, G. Schreiber, and A. R. Fersht, Proc. Natl. Acad. Sci. U.S.A. 94, 826 (1997).
19. B. Nölting, J. Theor. Biol. 0022-5193 194, 419 (1998); B. Nölting, J. Theor. Biol. 197, 113 (1999).
20. B. Nölting, J. Theor. Biol. 0022-5193 194, 419 (1998); B. Nölting, J. Theor. Biol. 197, 113 (1999).
21. A. R. Fersht, Proc. Natl. Acad. Sci. U.S.A. 92, 10869 (1995).
22. A. R. Fersht, Curr. Opin. Struct. Biol. 7, 3 (1997).
23. E. I. Shakhnovich, Curr. Opin. Struct. Biol. 7, 29 (1997).
24. E. I. Shakhnovich, V. Abkevich, and O. Ptitsyn, Nature (London) 379, 96 (1996).
25. V. I. Abkevich, A. M. Gutin, and E. I. Shakhnovich, J. Chem. Phys. 101, 6052 (1994).
26. A. V. Finkelstein and A. Y. Badretdinov, Folding Des. 2, 115 (1997).
27. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.84.21.7524 84, 7524 (1987); J. D. Bryngelson and P. G. Wolynes, J. Phys. Chem. 93, 6902 (1998).
28. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.84.21.7524 84, 7524 (1987); J. D. Bryngelson and P. G. Wolynes, J. Phys. Chem. 93, 6902 (1998).
29. E. I. Shakhnovich and A. M. Gutin, Nature (London) 0028-0836 10.1038/346773a0 346, 773 (1990); E. I. Shakhnovich and A. M. Gutin, J. Phys. A 22, 1647 (1989).
30. E. I. Shakhnovich and A. M. Gutin, Nature (London) 0028-0836 10.1038/346773a0 346, 773 (1990); E. I. Shakhnovich and A. M. Gutin, J. Phys. A 22, 1647 (1989).
31. J. D. Bryngelson and P. G. Wolynes, Biopolymers 30, 177 (1990).
32. K. A. Dill, Biochemistry 0006-2960 10.1021/bi00327a032 24, 1501 (1985); K. A. Dill, Biochemistry 29, 7133 (1990).
33. K. A. Dill, Biochemistry 0006-2960 10.1021/bi00327a032 24, 1501 (1985); K. A. Dill, Biochemistry 29, 7133 (1990).
34. J. Lothe and G. M. J. Pound, in Nucleation, edited by, A. C. Zettlemoyer, (Marcel-Dekker, New York, 1969).
35. Y. S. Djikaev and E. Ruckenstein, J. Phys. Chem. B 111, 886 (2007).
36. G. Narsimhan and E. Ruckenstein, J. Colloid Interface Sci. 128, 549 (1989).
37. E. Ruckenstein and B. Nowakowski, J. Colloid Interface Sci. 137, 583 (1990).
38. B. Nowakowski and E. Ruckenstein, J. Colloid Interface Sci. 139, 500 (1990).
39. Y. S. Djikaev and E. Ruckenstein, J. Chem. Phys. 123, 214503 (2005).
40. Y. S. Djikaev and E. Ruckenstein, J. Chem. Phys. 124, 124521 (2006).
41. Y. S. Djikaev and E. Ruckenstein, J. Chem. Phys. 124, 194709 (2006).
42. M. Levitt and R. Sharon, Proc. Natl. Acad. Sci. U.S.A. 85, 8557 (1988).
43. J. Skolnik, A. Kolinski, and R. Yaris, Biopolymers 28, 937 (1989).
44. A. Kolinski, J. Skolnik, and R. Yaris, Biopolymers 28, 937 (1989).
45. A. Sikorski and J. Skolnik, Biopolymers 0006-3525 10.1002/bip.360280605 28, 1097 (1989); A. Sikorski and J. Skolnik, J. Mol. Biol. 213, 183 (1990).
46. A. Sikorski and J. Skolnik, Biopolymers 0006-3525 10.1002/bip.360280605 28, 1097 (1989); A. Sikorski and J. Skolnik, J. Mol. Biol. 213, 183 (1990).
47. J. Skolnik and A. Kolinski, Science 250, 1121 (1990).
48. C. Levinthal, in Mössbauer Spectroscopy in Biological Systems, edited by, P. Debrunner, J. C. M. Tsibris, and, E. Mönck, (University of Illinois Press, Urbana, 1968).
49. D. Wetlaufer, Proc. Natl. Acad. Sci. U.S.A. 70, 697 (1973).
50. T. Y. Tsong, R. Baldwin, and P. McPhie, J. Mol. Biol. 63, 453 (1972).
51. J. Moult and R. Unger, Biochemistry 30, 3816 (1991).
52. K. Dill, K. Fiebig, and H. S. Chan, Proc. Natl. Acad. Sci. U.S.A. 90, 1942 (1993).
53. C. Flageollet, M. Dihn Cao, and P. Mirabel, J. Chem. Phys. 72, 544 (1980).
54. G. Wilemski, J. Phys. Chem. 0022-3654 10.1021/j100294a011 91, 2492 (1987); G. Wilemski, J. Chem. Phys. 80, 1370 (1984).
55. G. Wilemski, J. Phys. Chem. 0022-3654 10.1021/j100294a011 91, 2492 (1987); G. Wilemski, J. Chem. Phys. 80, 1370 (1984).
56. A. Laaksonen, J. Chem. Phys. 97, 1983 (1992).
57. Y. S. Djikaev, I. Napari, and A. Laaksonen, J. Chem. Phys. 120, 9752 (2004).
58. F. F. Abraham, Homogeneous Nucleation Theory (Academic, New York, 1974).
59. S. Chandrasekhar, Rev. Mod. Phys. 15, 1 (1949).
60. C. W. Gardiner, Handbook of Stochastic Methods (Springer, New York, 1983).
61. N. Agmon, J. Chem. Phys. 81, 3644 (1984).
62. Nucleation Theory and Applications, edited by, J. Schmelzer, G. Röpke, and, V. B. Priezzhev, (JINR, Dubna, 1999).
63. D. Kashchiev, Nucleation: Basic Theory with Applications (Butterworth-Heinemann, Oxford, 2000).
64. H. Trinkaus, Phys. Rev. B 27, 7372 (1983).
65. F. M. Kuni, A. A. Melikhov, T. Yu. Novozhilova, and I. A. Terent'ev, Theor. Math. Phys. 83, 530 (1990).
66. W. H. Elliott and D. C. Elliott, Biochemistry and Molecular Biology (Oxford University Press, New York, 2003).
67. W. L. Jorgensen and J. Tirado-Rives, J. Am. Chem. Soc. 110, 1657 (1988).
68. Y. Harpaz, M. Gerstein, and C. Chothia, Structure (London) 2, 641 (1994).
69. D. M. Huang and D. Chandler, Proc. Natl. Acad. Sci. U.S.A. 15, 8324 (2000).
70. J. O. Hirshfelder, C. F. Curtiss, and R. B. Bird, Molecular Theory of Gases and Liquids (Wiley, New York, 1964); W. A. Wakeham, J. Phys. B 6, 372 (1973).
71. J. O. Hirshfelder, C. F. Curtiss, and R. B. Bird, Molecular Theory of Gases and Liquids (Wiley, New York, 1964); W. A. Wakeham, J. Phys. B 6, 372 (1973).
72. H. Sano and M. Tachia, J. Chem. Phys. 71, 1276 (1979).