Modeling the interplay between geometrical and energetic effects in protein folding

Journal of Physical Chemistry B

Volumn 109, Issue 34, 2005, Pages 16503-16510

  Suzuki, Yoko ^a   Onuchic, José N ^b  

^a MEISEI UNIVERSITY   (Japan)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHYMOTRYPSIN INHIBITORS; CONFIGURATIONAL ENTROPY; MANY-BODY CORRECTIONS; PROTEIN FOLDING;

COMPUTER SIMULATION; ENTROPY; ENZYME INHIBITION; FREE ENERGY; POLYMERS;

PROTEINS;

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; ENTROPY; METABOLISM; PROBABILITY; PROTEIN CONFORMATION; PROTEIN FOLDING; SRC HOMOLOGY DOMAIN; THERMODYNAMICS;

ENTROPY; MODELS, MOLECULAR; PROBABILITY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SRC HOMOLOGY DOMAINS; THERMODYNAMICS;

EID: 24944568200     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0512863     Document Type: Article

References (46)

1. Onuchic, J. N.; Luthey-Schulten, Z.; Wolynes, P. G. Annu. Rev. Phys. Chem. 1997, 48, 545.
2. Onuchic, J. N.; Nymeyer, H.; Garcia, A. E.; Chahine, J.; Socci, N. D. Adv. Protein. Chem. 2000, 53, 87.
3. Bryngelson, J. D.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 7524.
4. Leopold, P. E.; Montai, M.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 8721.
5. Shea, J. E.; Brooks, C. L., III Annu. Rev. Phys. Chem. 2001, 52, 499.
6. Eaton, W. A.; Muñoz, V.; Thompson, P.; Chan, C. K.; Hofrichter, J. Curr. Opin. Struct. Biol. 1997, 7, 10.
7. Fersht, A. R. Curr. Opin. Struct. Biol. 1997, 7, 3.
8. Miranker, A. D.; Dobson, C. M. Curr. Opin. Struct. Biol. 1996, 6, 31.
9. Gruebele, M. Annu. Rev. Phys. Chem. 1999, 50, 485.
10. Taketomi, H.; Ueda, Y.; Go, N. Int. J. Pept. Res. 1975, 7, 445.
11. Socci, N. D.; Onuchic, J. N. J. Chem. Phys. 1995, 103, 4732.
12. Gutin, A.; Sali, A.; Abkevich, V.; Karplus, M.; Shakhnovich, E. I. J. Chem. Phys. 1998, 108, 6466.
13. Hardin, C.; Eastwood, M. P.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 14235.
14. Hardin, C.; Eastwood, M. P.; Prentiss, M. C.; Luthey-Schulten, Z. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1679.
15. Jin, W. Z.; Kambara, O.; Sasakawa, H.; Tamura, A.; Takada, S. Structure 2003, 11, 581.
16. Onuchic, J. N.; Wolynes, P. G.; Luthey-Schulten, Z.; Socci, N. D. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 3626.
17. Ozkan, S. B.; Bahar, I.; Dill, K. A. Nat. Struct. Biol. 2001, 8, 765.
18. Levitt, M.; Warshel, A. Nature 1975, 253, 694.
19. Friedrichs, M. S.; Goldstein, R. A.; Wolynes, P. G. J. Mol. Biol. 1991, 222, 1013.
20. Irbäck, A.; Peterson, C.; Potthast, F.; Sommelius, O. J. Chem. Phys. 1997, 107, 273.
21. Guo, Z.; Thirumalai, D.; Honeycutt, J. D. J. Chem. Phys. 1992, 92, 525.
22. Boczko, E. M.; Brooks, C. L., III Science 1995, 269, 393.
23. Ghosh, A.; Eiber, R.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 10394.
24. Duan, Y.; Kollman, P. A. Science 1998, 252, 740.
25. Snow, C. D.; Nguyen, N.; Pande, V. S.; Gruebele, M. Nature 2002, 420, 102.
26. García, A. E.; Sanbonmatsu, K. Y. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2782.
27. Daggett, V.; Fersht, A. Nat. Rev. Mol. Cell. Biol. 2003, 4, 497.
28. Fersht, A.; Daggett, V. Cell 2002, 108, 573.
29. Paci, E.; Vendruscolo, M.; Dobson, C. M.; Karplus, M. J. Mol. Biol. 2002, 324, 151.
30. Clementi, C.; Nymeyer, H.; Onuchic, J. N. J. Mol. Biol. 2000, 295, 937.
31. Clementi, C.; Jennings, P. A.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5871.
32. Koga, N.; Takada, S. J. Mol. Biol. 2001, 313, 171.
33. Papoian, G. A.; Wolynes, P. G. Biopolymers 2003, 68, 333.
34. Levy, Y.; Wolynes, P. G.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2003, 101, 511.
35. Shoemaker, B. A.; Portman, J. J.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 8868.
36. Plotkin, S. S.; Onuchic, J. N. Q. Rev. Biophys. 2002, 35, 111.
37. Plotkin, S. S.; Onuchic, J. N. Q. Rev. Biophys. 2002, 35, 205.
38. Plotkin, S. S.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 6509.
39. Plotkin, S. S.; Onuchic, J. N. J. Chem. Phys. 2002, 116, 5263.
40. Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 6170.
41. Portman, J. J.; Takada, S.; Wolynes, P. G. Phys. Rev. Lett. 1998, 81, 5237.
42. Eastwood, M. P.; Wolynes, P. G. J. Chem. Phys. 2001, 114, 4702.
43. Fersht, A. R. Curr. Opin. Struct. Biol. 1995, 5, 79.
44. Chan, H. S.; Shimizu, S.; Kaya, H. Methods Enzymol. 2004, 380, 350.
45. A contact is counted between residue i and residue j when all atoms (excluding hydrogen atoms) of residue i are within ∼4 Å of any atom of residue j for |i -j| > 3.
46. This temperature may be slightly different from the specific heat peak since the system is finite.