Study of the dynamics of protein folding through minimalistic models

Theoretical Chemistry Accounts

Volumn 109, Issue 1, 2003, Pages 8-21

  Srinivas, Goundla ^a   Bagchi, Biman ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Free energy; HP 36; Landscape; Protein folding

Indexed keywords

VILLIN;

CHICKEN; DYNAMICS; HYDROPHOBICITY; MODEL; PROTEIN ANALYSIS; PROTEIN FOLDING; REVIEW; SIMULATION;

EID: 0037292462     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-002-0390-6     Document Type: Review

References (91)

1. Horwich AL, Weissman JS (1997) Cell 89: 499
2. Walsh DM, Klyubin I, Fadeeva JV, Cullen WK, Anwyl R, Wolfe MS, Rowan MJ, Selkoe DJ (2002) Nature 416: 535
3. Bucciantini M, Giannoni E, Chiti F, Baroni F, Formigli L, Zurdo J, Taddei N, Ramponi G, Dobson CM, Stefani M (2002) Nature 416: 507
4. Levitt M (1991) Curr Opin Struct Biol 1: 224
5. Dill KA (1990) Biochemistry 29: 7133
6. Skolnick J, Kolinski A (1989) Annu Rev Phys Chem 40: 207
7. Onuchic JN, Luthey-Schulten Z, Wolynes PG (1997) Annu Rev Phys Chem 48: 545
8. Brooks CL III, Gruebele M, Onuchic JN, Wolynes PG (1998) Proc Natl Acad Sci USA 95: 1037
9. Shakhnovich EI (1997) Curr Opin Struct Biol 7: 29
10. Anfinsen CB, Haser E, Seli M, White FH (1961) Proc Natl Acad Sci USA 47: 1309
11. Kim PS, Baldwin RL (1990) Annu Rev Biochem 59: 631 and references therein
12. (a) Zhou Y, Hall CK? Karplus M (1996) Phys Rev Lett 77: 2822;
13. (b) Zhou Y, Karplus M, Wichert JM, Hall CK (1997) J Chem Phys 107: 10691
14. Shakhnovich EI, Gutin AM (1990) Nature 346: 773
15. Sali A, Shakhnovich EI, Karplus M (1994) Nature 369: 248
16. Dinner RA, Karplus M (1998) Nature Struct Biol 5: 236
17. Levinthal C: In: Debrunner P, Tsibris JCM, Munck E (eds) Proceedings of a Meeting held at Allerton House, Monticello, I1. Mossbauer spectroscopy in biological systems. University of Illinois Press, Urbana, p 22
18. Dawkins R (1987) The blind watchmaker. Norton, New York, pp 46-50
19. Zwanzig R, Szabo A, Bagchi B (1992) Proc Natl Acad Sci USA 89: 20
20. Leopold PE, Montal M, Onuchic JN (1992) Proc Natl Acad Sci USA 89: 8721
21. Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND (1995) Proc Natl Acad Sci USA 92: 3626
22. Onuchik JN (1998) Proc Natl Acad Sci USA 94: 7129
23. Nymeyer H, Garcia AE, Onuchic JN (1998) Proc Natl Acad Sci USA 95: 5921
24. Schoemaker BA, Portman JJ, Wolynes PG (2000) Proc Natl Acad Sci USA 97: 8868
25. Goldstein RA, Luthey-Schulten Z, Wolynes PG (1992) Proc Natl Acad Sci USA 89: 8029
26. (a) Zwanzig R (1995) Proc Natl Acad Sci USA 92: 9801;
27. (b) Zwanzig R (1997) Proc Natl Acad Sci USA 94: 148
28. (a) Bryngelson JD, Wolynes PG (1987) Proc Natl Acad Sci USA 84: 7524;
29. (b) Bryngelson JD, Wolynes PG (1989) J Phys Chem 93: 6902
30. Dill KA, Alonso DOV, Hutchinson K (1989) Biochemistry 28: 5439
31. de Gennes PG (1990) Scaling concepts in polymer physics. Cornell University Press, Ithaca
32. Sali A, Karplus M, Shaknovich EI (1994) J Mol Biol 235: 1614
33. Wolynes PG (1997) Proc Natl Acad Sci USA 94: 6170
34. Schoemaker BA, Wang J, Wolynes PG (1997) Proc Natl Acad Sci USA 94: 777
35. Shakhnovich EI, Gutin M (1999) Proc Natl Acad Sci USA 90: 7195
36. Grantcharova V, Alm VJ, Baker D, Horwich AL (2001) Curr Opin Struct Biol 11: 70
37. Plaxco KW, Simons KT, Baker D (1998) J Mol Biol 277: 985
38. Laurents DV, Baldwin RL (1998) Biophys J 75: 428
39. Brockwell DJ, Smith DA, Radford SE (2000) Curr Opin Struct Biol 10: 16
40. Portman JJ, Takada S, Wolynes PG (1998) Phys Rev Lett 81: 5237
41. (a) Portman JJ, Takada S, Wolynes PG (2001) J Chem Phys 114: 5069;
42. (b) Portman JJ, Takada S, Wolynes PG (2001) 114: 5082
43. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Proteins 21: 167
44. Hansmann UHE, Onuchic JN (2001) J Chem Phys 1601: 115
45. Socci ND, Onuchic JN, Wolynes PG (1996) J Chem Phys 104: 5860
46. Miller MA, Wales DJ (1999) J Chem Phys 111: 6610
47. Kauzmann W (1959) Adv Protein Chem 14: 1
48. Tanford C (1980) The hydrophobic effect, 2nd edn. Wiley, New York
49. (a) Lim WA, Sauer RT (1992) Biochemistry 219: 319;
50. (b) Mathews BW (1993) Biochemistry 62: 139
51. Dill KA (1999) Protein Sci 8: 1166
52. Predki PF, Agarwal V, Brunger AT, Regan L (1996) Nature Struct Biol 3: 54
53. Kurodu Y, Hamada D, Tanaka T, Goto Y (1996) Folding Design 4: 255
54. Roy S, Ratnaswamy G, Boice JA, Fariman D, McLendon G, Hecht MH (1997) J Am Chem Soc 116: 5302
55. (a) Yue K, Dill KA (1993) Phys Rev E 48: 2267;
56. (b) Chan HS, Dill KA (1990) Proc Natl Acad Sci USA 87: 6368
57. Skolnick J, Kolinski A (1990) Science 250: 1121
58. Kolinski A, Galazaka W, Skolnick J (1996) Proteins 26: 271
59. Pande VS, Rokhsar DS (1999) Proc Natl Acad Sci USA 96: 1273
60. Taketomi H, Ueda Y, Go N (1975) Int J Pept Protein Res 7: 445
61. (a) Honeycutt JD, Thirumalai D (1990) Proc Natl Acad Sci USA 87: 3526;
62. (b) Honeycutt JD, Thirumalai D (1992) Biopolymers 32: 695
63. (a) Guo Z, Thirumalai D, Honeycutt JD (1992) J Chem Phys 97: 525;
64. (b) Klimov D, Thirumlai D (1996) Proteins 26: 411
65. Makarov DE, Hansma PK, Metiu H (2001) J Chem Phys 114: 9663
66. Duan Y, Kollman PA (1998) Science 282: 740
67. Boczko EM, Brooks CL III (1997) Science 269: 393
68. Hansmann UHE, Masuya M, Okamato Y (1997) Proc Natl Acad Sci USA 94: 10652
69. Hansmann UHE, Okamato Y (1997) J Comput Chem 18: 920
70. Pande VS, Rokhsar DS (1999) Proc Natl Acad Sci USA 96: 9062
71. Srinivas G, Yethiraj A, Bagchi B (2001) J Phys Chem B 105: 2475
72. Deniz AA, Laurence TA, Beligere GS, Dahan M, Martin AB, Chemla DS, Dawson PE, Schultz PG, Weiss S (2000) Proc Natl Acad Sci USA 97: 5179
73. Weiss S (1999) Science 283: 676
74. Srinivas G, Bagchi B (2002) Phys Chem Commun 5: 59
75. Zhou Y, Hall CK, Karplus M (1996) Phys Rev Lett 77: 2822
76. Alm E, Baker D (1999) Proc Natl Acad Sci USA 96: 11305
77. Riddle DS, Gratcharova VP, Alm E, Ruczinski I, Baker D (1999) Nature Struct Biol 6: 1016
78. Plaxco KW, Guijarro JI, Morton CJ, Pitkeathly M, Campbell ID, Dobson CM (1998) Biochemistry 37: 2259
79. Srinivas G, Bagchi B (2002) J Chem Phys 116: 0000
80. Srinivas G, Bagchi B (2002) Curr Sci 82: 179
81. McKnight JC, Doering DS, Matsudaria PT, Kim PS (1996) J Mol Biol 260: 126
82. Stryer L (1995) Biochemistry, 4th edn. Freeman, New York
83. Nelson DL, Cox MM (1993) Lehninger principles of biochemistry, 3rd edn. Worth, New York
84. (a) Cheng Y-K, Rossky PJ (1998) Nature 392: 696;
85. (b) Cheng Y-K, Sheu WS, Rossky PJ (1999) Biophys J 76: 1734
86. Srinivas G, Bagchi B (2002) J Phys Chem B (submitted)
87. Ansari A, Kuznetsov SV, Shen Y (2001) Proc Natl Acad Sci USA 98: 7771
88. Scheffler IE, Elson EL, Baldwin RL (1968) J Mol Biol 36: 291
89. Gralla J, Crothers DM (1973) J Mol Biol 73: 497
90. Bonnet G, Krichevsky O, Libchaber A (1998) Proc Natl Acad Sci USA 95: 8602
91. Wallace MI, Ying L, Balasubramanian S, Klenerman D (2000) J Phys Chem B 104: 11551