Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates

Journal of the American Chemical Society

Volumn 126, Issue 27, 2004, Pages 8426-8432

  Chavez, Leslie L ^a   Onuchic, José N ^a   Clementi, Cecilia ^b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b RICE UNIVERSITY   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; ENTHALPY; ENTROPY; PROTEINS; REACTION KINETICS; TOPOLOGY;

FREE ENERGY LANDSCAPE; PROTEIN FOLDING;

FREE ENERGY;

ACYLPHOSPHATASE; BACTERIAL PROTEIN; BINDING PROTEIN; CHYMOTRYPSIN INHIBITOR; COLD SHOCK PROTEIN; CONNECTIN; PROTEIN; PROTEIN G; PYRUVATE DEHYDROGENASE; RIBOSOME PROTEIN; VILLIN;

ARTICLE; ENERGY; ENTROPY; GEOMETRY; HUMAN; MEASUREMENT; NONHUMAN; PROTEIN FOLDING; PROTEIN STRUCTURE;

CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; KINETICS; MODELS, CHEMICAL; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 3142782241     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja049510+     Document Type: Article

References (79)

1. Itzhaki, L. S.; Otzen, D. E.; Fersht, A. R. J. Mol. Biol. 1995, 254, 260-288.
2. Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Proteins: Struct., Funct., Genet. 1995, 21, 167-195.
3. Kuhlman, B.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 10383-10388.
4. Bryngelson, J. D.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 7524-7528.
5. Brockwell, D. J.; Smith, D. A.; Radford, S. E. Curr. Opinion Struct. Biol. 2000, 10, 16-25.
6. Grantcharova, V.; Alm, E. J.; Baker, D.; Horwich, A. L. Curr. Opinion Struct. Biol. 2001, 11, 70-82.
7. Gunasekaran, K.; Eyles, S. J.; Hagler, A. T.; Gierasch, L. M. Curr. Opinion Struct. Biol. 2001, 11, 83-93.
8. Alm, E.; Morozov, A. V.; Kortemme, T.; Baker, D. J. Mol. Biol. 2002, 322, 463-476.
9. Dinner, A. R.; Karplus, M. Nat. Struct. Biol. 2001, 8, 21-22.
10. Nymeyer, H.; Socci, N. D.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 634-639.
11. Clementi, C.; Nymeyer, H.; Onuchic, J. N. J. Mol. Biol. 2000, 298, 937-953.
12. Clementi, C.; Jennings, P. A.; Onuchic, J. N. J. Mol. Biol. 2001, 311, 879-890.
13. Clementi, C.; Jennings, P. A.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5871-5876.
14. Clementi, C.; García, A. E.; Onuchic, J. N. J. Mol. Biol. 2003, 326, 933-954.
15. Klimov, D.; Thirumalai, D. J. Mol. Biol. 2002, 317, 721-737.
16. Du, R.; Pande, V. S.; Grosberg, A. Y.; Tanaka, T.; Shakhnovich, E. J. Chem. Phys. 1999, 111, 10375-10380.
17. Plaxco, K. W.; Simmons, K. T.; Baker, D. J. Mol. Biol. 1998, 277, 985-994.
18. Plotkin, S. S.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 6509-6514.
19. Plotkin, S. S.; Onuchic, J. N. J. Chem. Phys. 2002, 116, 5263-5283.
20. Koga, N.; Shoji, T. J. Mol. Biol. 2001, 313, 171-180.
21. Gromiha, M. M.; Selvaraj, S. J. Mol. Biol. 2001, 310, 27-32.
22. Taketomi, H.; Ueda, Y.; Go, N. Int. J. Pept. Protein Res. 1975, 7, 445-459.
23. Wittung-Stafshede, P.; Lee, J. C.; Winkler, J. R.; Gray, H. B. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 6587-6590.
24. Chang, I. J.; Lee, J. C.; Winkler, J. R.; Gray, H. B. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 3838-3840.
25. Chiti, F.; Taddei, N.; van Nuland, N. A. J.; Magherini, F.; Stefani, M.; Ramponi, G. M.; Dobson, C. M. J. Mol. Biol. 1998, 283, 883-891.
26. Roumestand, C.; Boyer, M.; Guignard, L.; Barthe, P.; Royer, C. A. J. Mol. Biol. 2001, 312, 247-259.
27. Martinez, J. C.; Pisabarro, M. T.; Serrano, L. Nat. Struct. Biol, 1998, 5, 721-729.
28. Grantcharova, V. P.; Riddle, D. S.; Santiago, J. V.; Baker, D. Nat. Struct. Biol. 1998, 5, 714-720.
29. Burns, L. L.; Dalessio, P. M.; Ropson, I. J. Proteins: Struct., Funct., Genet. 1998, 33, 107-118.
30. Dalessio, P. M.; Ropson, I. J. Biochemistry 2000, 39, 860-871.
31. Ferguson, N.; Capaldi, A. P.; James, R.; Kleanthous, C.; Radford, S. E. J. Mol. Biol. 1999, 286, 1597-1608.
32. Kim, D.; Fisher, C.; Baker, D. J. Mol. Biol. 2000, 298, 971-984.
33. McCallister, E. L.; Alm, E.; Baker, D. Nat. Struct. Biol. 2000, 7, 669-673.
34. Pappu, R. V.; Srinivasan, R.; Rose, G. D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 12565-12570.
35. Clementi, C.; Plotkin, S. S. Protein Sci., in press.
36. Plaxco, K. W.; Simons, K. T.; Ruczinski, I.; Baker, D. Biochemistry 2000, 39, 11177-11183.
37. Lindberg, M. O.; Tangrot, J.; Otzen, D. E.; Dolgikh, D. A.; Finkelstein, A.; Oliveberg, M. J. Mol. Biol. 2001, 314, 891-900.
38. Ivankov, D. N.; Finkelstein, A. V. Biochemistry 2001, 40, 9957-9961.
39. Finkelstein, A. V.; Badretdinov, A. Folding Des. 1997, 2, 115-121.
40. Micheletti, C. Proteins: Struct., Funct., Genet. 2003, 51, 74-84.
41. Ivankov, D. N.; Garbuzynskiy, S. O.; Alm, E.; Plaxco, K. W.; Baker, D.; Finkelstein, A. V. Protein Sci. 2003, 12, 2057-2062.
42. Galzitskaya, O. V.; Garbuzynskiy, S. O.; Ivankov, D. N.; Finkelstein, A. V. Proteins: Struct., Funct., Genet. 2003, 51, 162-166.
43. Baker, D. Nature 2000, 405, 39-42.
44. Jones, K.; Wittung-Stafshede, P. J. Am. Chem. Soc. 2003, 125, 9606-9607.
45. Tang, K. S.; Fersht, A. R.; Itzhaki, L. S. Structure 2003, 11, 67-73.
46. Plotkin, S. S.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A 2000, 97, 6509-6514.
47. Plotkin, S. S.; Onuchic, J. N. Q. Rev. Biophys. 2002, 35, 111-167.
48. Plotkin, S. S.; Onuchic, J. N. Q. Rev. Biophys. 2002, 35, 205-286.
49. Aronsson, G.; Brorsson, A. C.; Sahlman, L.; Jonsson, B. H. FEBS Lett. 1997, 411, 359-364.
50. Kuszewski, J.; Clore, G. M.; Gronenborn, A. M. Protein Sci. 1994, 3, 1945-1952.
51. Park, S. H.; Oneil, K. T.; Roder, H. Biochemistry 1997, 36, 14277-14283.
52. Lindberg, M. O.; Tangrot, J.; Oliveberg, M. Nat. Struct. Biol. 2002, 9, 818-822.
53. Vendruscolo, M.; Paci, E.; Dobson, C. M.; Karplus, M. Nature 2001, 409, 641-645.
54. Micheletti, C.; Banavar, J.; Maritan, A.; Seno, F. Phys. Rev. Lett. 1999, 82, 3372-3375.
55. Alm, E.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11305-11310.
56. Munoz, V.; Eaton, W. A. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11311-11316.
57. Klimov, D. K.; Thirumalai, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 7254-7259.
58. Garcia, A. E.; Onuchic, N. J. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13898-13903.
59. Scalley, M. L.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 94, 10636-10640.
60. Kuhlman, B.; Luisi, D. L.; Evans, P. A.; Raleigh, D. P. J. Mol. Biol. 1998, 284, 1661-1670.
61. Cobos, E. S.; Filimonov, V. V.; Vega, M. C.; Mateo, P. L.; Serrano, L.; Martinez, J. C. J. Mol. Biol. 1998, 328, 221-233.
62. Clarke, J.; Cota, E.; Fowler, S. B.; Hamill, S. Structure with Folding and Design 1999, 7, 1145-1153.
63. Wang, M.; Tang, Y.; Sato, S.; Vugmeyster, L.; McKnight, C. J.; Raleigh, D. P. J. Am. Chem. Soc. 2003, 125, 6032-6033.
64. Yang, W. Y.; Gruebele, M. Nature 2003, 423, 193-197.
65. Spector, S.; Raleigh, D. P. J. Mol. Biol. 1999, 293, 763-768.
66. Perl, D.; Jacob, M.; Stupak, M.; Antalik, M.; Schmid, F. X. Biophys. Chem. 2002, 96, 173-190.
67. Schindler, T.; Schmid, F. Biochemistry 1996, 35, 16833-16842.
68. Jacob, M.; Geeves, M.; Holtermann, G.; Schmid, F. X. Nat. Struct. Biol. 1999, 6, 923-926.
69. Alexander, P.; Orban, J.; Bryan, P. Biochemistry 1992, 31, 7243-7248.
70. Jackson, S. E.; Fersht, A. R. Biochemistry 1991, 30, 10436-10443.
71. Oliveberg, M.; Tan, Y.-J.; Fersht, A. R. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 8926-8929.
72. Tan, Y.; Oliveberg, M.; Fersht, A. J. Mol. Biol. 1996, 264, 377-389.
73. Friel, C. T.; Capaldi, A. P.; Radford, S. E. J. Mol. Biol. 2003, 326, 293-305.
74. Riddle, D. S.; Grantcharova, V. P.; Santiago, J. V.; Alm, E.; Ruczinski, I.; Baker, D. Nat. Struct. Biol. 1999, 6, 1016-1024.
75. Martinez, J. C.; Serrano, L. Nat. Struct. Biol. 1999, 6, 1010-1016.
76. Fowler, S. B.; Clarke, J. Structure with Folding and Design 2001, 9, 355-366.
77. Van Nuland, N. A. J.; Meijberg, W.; Forge, V.; Scheek, R. M.; Robillard, G. T. M.; Dobson, C. M. Biochemistry 1998, 37, 622-637.
78. Chiti, F.; Taddei, N.; White, P. M.; Bucciantini, M.; Magherini, F.; Stefani, M. M.; Dobson, C. M. Nat. Struct. Biol. 1999, 6, 1005-1009.
79. Kitahara, R.; Royer, C.; Yamada, H.; Boyer, M.; Soldana, J.-L.; Akasaka, K.; Roumestand, C. J. Mol. Biol. 2002, 320, 609-628.