Coupling between hydration layer dynamics and unfolding kinetics of HP-36

Journal of Chemical Physics

Volumn 125, Issue 8, 2006, Pages

  Bandyopadhyay, Sanjoy ^a   Chakraborty, Sudip ^a   Bagchi, Biman ^b  

^a INDIAN INSTITUTE OF TECHNOLOGY   (India)

^b INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH TEMPERATURE EFFECTS; HYDRATION; MOLECULAR DYNAMICS; MOLTEN MATERIALS; SOLVENT EXTRACTION; WATER;

MOLTEN GLOBULE STATE; PROTEIN HYDRATION LAYERS; PROTEIN SURFACE; SOLVATION DYNAMICS;

PROTEINS;

NEUROFILAMENT PROTEIN; PEPTIDE FRAGMENT; PROTEIN; SOLVENT; VILLIN HEADPIECE SUBDOMAIN PEPTIDE; WATER;

AMINO ACID SEQUENCE; ARTICLE; BIOPHYSICS; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; KINETICS; METHODOLOGY; MOLECULAR GENETICS; PHYSICAL CHEMISTRY; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; TEMPERATURE;

AMINO ACID SEQUENCE; BIOPHYSICS; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; KINETICS; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; NEUROFILAMENT PROTEINS; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEINS; SOLVENTS; TEMPERATURE; WATER;

EID: 33748283319     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2335451     Document Type: Article

References (78)

1. C. B. Anfinsen, Science 181, 223 (1973).
2. H. J. Dyson and P. E. Wright, Chem. Rev. (Washington, D.C.) 104, 3607 (2004).
3. M. Wang, Y. Tang, S. Sato, L. Vugmeyster, C. J. McKnight, and D. P. Raleigh, J. Am. Chem. Soc. 125, 6032 (2003);
4. Y. Tang, D. J. Rigotti, R. Fairman, and D. P. Raleigh, Biochemistry 43, 3264 (2004).
5. D. M. Vu, E. S. Peterson, and R. B. Dyer, J. Am. Chem. Soc. 126, 6546 (2004).
6. P. Sen, S. Mukherjee, P. Dutta, A. Halder, D. Mandai, R. Banerjee, S. Roy, and K. Bhattacharyya, J. Phys. Chem. B 107, 14563 (2003);
7. S. Guha, K. Sahu, D. Roy, S. K. Mondai, S. Roy, and K. Bhattacharyya, Biochemistry 44, 8940 (2005).
8. E. V. Pletneva, H. B. Gray, and J. R. Winkler, J. Mol. Biol. 345, 855 (2005);
9. J. Am. Chem. Soc. 127, 15370 (2005).
10. T. Kiefhaber, Proc. Natl. Acad. Sci. U.S.A. 92, 9029 (1995).
11. R. Kitahara and K. Akasaka, Proc. Natl. Acad. Sci. U.S.A. 100, 3167 (2003).
12. A. Sali, E. Shakhnovich, and M. Karplus, Nature (London) 369, 248 (1994).
13. Y. Duan and P. A. Kollman, Science 282, 740 (1998);
14. Y. Duan, L. Wang, and P. A. Kollman, Proc. Natl. Acad. Sci. U.S.A. 95, 9897 (1998).
15. F. B. Sheinerman and C. L. Brooks III, Proc. Natl. Acad. Sci. U.S.A. 95, 1562 (1998).
16. X. Daura, W. F. van Gunsteren, and A. E. Mark, Proteins: Struct., Funct., Genet. 34, 269 (1999).
17. E. Paci, L. J. Smith, C. M. Dobson, and M. Karplus, J. Mol. Biol. 306, 329 (2001).
18. A. E. Garcia and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 100, 13898 (2003).
19. M. Tarek, D. A. Neumann, and D. J. Tobias, Chem. Phys. 292, 435 (2003).
20. S. Jang, E. Kim, S. Shin, and Y. Pak, J. Am. Chem. Soc. 125, 14841 (2003).
21. J. M. Borreguero, F. Ding, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, Biophys. J. 87, 521 (2004).
22. G. A. Arteca and O. Tapia, Chem. Phys. Lett. 383, 462 (2004).
23. C. C. Wei, M. H. Ho, W. H. Wang, and Y. C. Sun, J. Phys. Chem. B 109, 19980 (2005).
24. B. Zagrovic, C. D. Snow, S. Khaliq, M. R. Shirts, and V. S. Pande, J. Mol. Biol. 323, 153 (2002);
25. B. Zagrovic, C. D. Snow, M. R. Shirts, and V. S. Pande, J. Mol. Biol. ibid. 323, 927 (2002);
26. C. D. Snow, B. Zagrovic, and V. S. Pande, J. Am. Chem. Soc. 124, 14548 (2002).
27. V. Daggett, Acc. Chem. Res. 35, 422 (2002);
28. B. Rizzuti, V. Daggett, R. Guzzi, and L. Sportelli, Biochemistry 43, 15604 (2004);
29. R. Day and V. Daggett, Proc. Natl. Acad. Sci. U.S.A. 102, 13445 (2005).
30. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 84, 7524 (1987);
31. J. Phys. Chem. 93, 6902 (1989);
32. J. V. Saven and P. G. Wolynes, J. Mol. Biol. 257, 199 (1996).
33. K. A. Dill, Biochemistry 29, 7133 (1990);
34. K. A. Dill, K. M. Fiebig, and H. S. Chan, Proc. Natl. Acad. Sci. U.S.A. 90, 1942 (1993).
35. J. N. Onuchic and P. G. Wolynes, Curr. Opin. Struct. Biol. 14, 70 (2004);
36. J. N. Onuchic, Z. Luthey-Schulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. 48, 545 (1997);
37. J. N. Onuchic, H. Nymeyer, A. E. Garcia, J. Chahine, and N. D. Socci, Adv. Protein Chem. 53, 87 (2000).
38. J. D. Honeycutt and D. Thirumalai, Proc. Nad. Acad. Sci. U.S.A. 87, 3526 (1990);
39. D. K. Klimov and D. Thirumalai, Proteins: Struct., Funct., Genet. 26, 411 (1996);
40. M. S. Li, D. K. Klimov, and D. Thirumalai, Phys. Rev. Lett. 93, 268107 (2004).
41. A. Mukherjee and B. Bagchi, J. Chem. Phys. 118, 4733 (2003);
42. G. Srinivas and B. Bagchi, J. Phys. Chem. B 107, 11768 (2003);
43. A. Mukherjee, P. Bhimalapuram, and B. Bagchi, J. Chem. Phys. 123, 014901 (2005).
44. N. D. Socci and J. N. Onuchic, J. Chem. Phys. 103, 4732 (1995).
45. J. Wang, J. G. Saven, and P. G. Wolynes, J. Chem. Phys. 105, 11276 (1996).
46. E. I. Shakhnovich, A. Abkevich, and O. B. Ptitsyn, Nature (London) 379, 96 (1996).
47. O. B. Ptitsyn, CUIT. Opin. Struct. Biol. 5, 74 (1995).
48. C. Levinthal, J. Chim. Phys. Phys.-Chim. Biol. 65. 44 (1968).
49. A. Van der vaart, B. D. Bursulaya, C. L. Brooks III, and K. M. Merz, J. Phys. Chem. B 104, 9554 (2000).
50. T. Head-Gordon and S. Brown, Curr. Opin. Struct. Biol. 13, 160 (2003).
51. G. A. Papoian, J. Ulander, M. P. Eastwood, Z. Luthey-Schulten, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 101, 3352 (2004).
52. Y. Harano and M. Kinoshita, Chem. Phys. Lett. 399, 342 (2004).
53. R. Chang and A. Yethiraj, J. Chem. Phys. 114, 7688 (2001).
54. C. J. McKnight, P. T. Matsudaira, and P. S. Kim, Nat. Struct. Biol. 4, 180 (1997);
55. C. J. McKnight, D. S. Doering, P. T. Matsudaira, and P. S. Kim, J. Mol. Biol. 260, 126 (1996).
56. D. S. Doering and P. Matsudaira, Biochemistry 35, 12677 (1996);
57. B. Pope, M. Way, P. T. Matsudaira, and A. Weeds, FEBS Lett. 338, 58 (1994).
58. S. Bandyopadhyay, S. Chakraborty, S. Balasubramanian, S. Pal, and B. Bagchi, J. Phys. Chem. B 108, 12608 (2004).
59. S. Bandyopadhyay, S. Chakraborty, S. Balasubramanian, and B. Bagchi, J. Am. Chem. Soc. 127, 4071 (2005);
60. S. Bandyopadhyay, S. Chakraborty, and B. Bagchi, J. Am. Chem. Soc. ibid. 127, 16660 (2005).
61. M. E. Tuckerman, D. A. Yarne, S. O. Samuelson, A. L. Hughs, and G. J. Martyna, Comput. Phys. Commun. 128, 333 (2000).
62. A. D. MacKerell, Jr., D. Bashford, M. Bellott et al., J. Phys. Chem. B 102, 3586 (1998).
63. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
64. G. J. Martyna, M. E. Tuckerman, D. J. Tobias, and M. L. Klein, Mol. Phys. 87, 1117 (1996).
65. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).
66. P. Procacci, T. Darden, and M. Marchi, J. Phys. Chem. 100, 10464 (1996);
67. P. Procacci, M. Marchi, and G. J. Martyna, J. Chem. Phys. 108, 8799 (1998).
68. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
69. S. M. Le Grand and K. M. Merz, J. Comput. Chem. 14, 349 (1993).
70. D. Eliezer and P. E. Wright, J. Mol. Biol. 263, 531 (1996).
71. N. Smolin and R. Winter, J. Phys. Chem. B 108, 15928 (2004).
72. MOL-VOLUME is a free program available in the MDTools utilities (a NIH Resource for Macromolecular Modeling and Bioinformatics) developed by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign (http://www.ks.uiuc.edu/Development/MDTools).
73. D. I. Svergun, S. Richard, M. H. J. Koch, Z. Sayers, S. Kuprin, and G. Zaccai, Proc. Natl. Acad. Sci. U.S.A. 95, 2267 (1998).
74. M. Levitt and R. Sharan, Proc. Natl. Acad. Sci. U.S.A. 85, 7557 (1988).
75. F. Merzel and J. C. Smith, Proc. Natl. Acad. Sci. U.S.A. 99, 5378 (2002).
76. S. J. Perkins, Eur. J. Biochem. 157, 169 (1986).
77. N. Nandi and B. Bagchi, J. Phys. Chem. 100, 13914 (1996);
78. J. Phys. Chem. B 101, 10954 (1997).