Protein sequence design by energy landscaping

Journal of Physical Chemistry B

Volumn 106, Issue 3, 2002, Pages 599-609

  Betancourt, Marcos R ^a   Thirumalai, D ^b  

^a DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

^b Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENERGY LANDSCAPING; PROTEIN SEQUENCES;

ALGORITHMS; MOLECULAR STRUCTURE; MONTE CARLO METHODS; REACTION KINETICS;

PROTEINS;

EID: 0037165470     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp012014c     Document Type: Article

References (41)

1. Drexler, K.E. Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 5275.
2. Regan, L.; De Grado, W.F. Science 1988, 241, 976.
3. Metropolis, N.; Rosenbluth, A.W.; Rosenbluth, M.N.; Teller, A.H. J. Chem. Phys. 1953, 21, 1087.
4. Kirkpatrick, S.; Gelatt, C.D.; Vecchi, M.P. Science 1983, 220, 671.
5. Shakhnovich, E.I.; Gutin, A.M. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 7195.
6. Hellinga, H.W.; Richards, F.M. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 5803.
7. Jones, D.T. Protein Sci. 1994, 3, 567.
8. Friedrichs, M.S.; Goldstein, R.A.; Wolynes, P.G. J. Mol. Biol. 1991, 222, 1013.
9. Goldstein, R.A.; Luthey-Schulten, Z.A.; Wolynes, P.G. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 4918.
10. Yue, K.; Dill, K.A. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 4163.
11. Dahiyat, B.I.; Mayo, S.L. Science 1997, 278, 82.
12. Shakhnovich, E.I. Phys. Rev. Lett. 1994, 72, 3907.
13. Sasai, M. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 8438.
14. Godzik, A. Protein Eng. 1995, 8, 409.
15. Bowie, J.E.; Lüthy, R.; Eisenberg, D. Science 1991, 253, 164.
16. Kurosky, T.; Deutsch, J.M. J. Phys. 1995, A27, L387.
17. Deutsch, J.M.; Kurosky, T. Phys. Rev. Lett. 1996, 76, 323.
18. Seno, F.; Vendruscolo, M.; Martian, A.; Banavar, J. Phys. Rev. Lett. 1996, 77, 1901.
19. Morrissey, M.P.; Shakhnovich, E. Folding Design 1996, 1, 391.
20. Iba, Y.; Tokita, K.; Kikuchi, M. Preprint, 1998.
21. Betancourt, M.R.; Onuchic, J.N. J. Chem. Phys. 1995, 103, 773.
22. Bryngelson, J.D.; Wolynes, P.G. J. Phys. Chem. 1989, 93, 6902.
23. Dill, K.A.; Chan, H.S. Nat. Struct. Biol. 1997, 4, 10.
24. Camacho, C.; Thirumalai, D. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 6369.
25. Klimov, D.K.; Thirumalai, D. Proteins Struct. Funct. Genet. 1996, 26, 411.
26. Betancourt, M.R. J. Chem. Phys. 1998, 109, 1545.
27. Ueda, Y.; Taketomi, H.; Gō, N. Int. J. Pept. Protein Res. 1975, 7, 445.
28. Chan, H.S.; Dill, K.A. J. Chem. Phys. 1989, 90, 492.
29. Betancourt, M.R.; Thirumalai, D. Protein Sci. 1999, 8, 1.
30. αβ are the parameters from Table 3 in: Miyazawa, S.; Yernigan, R.L. J. Mol. Biol. 1996, 256, 623. t is the index for the threonine residue.
31. Rosenbluth, M.N.; Rosenbluth, A.W. J. Chem. Phys. 1955, 23, 356.
32. Jacobson, H.; Stockmayer, W.H. J. Chem. Phys. 1950, 18, 1600.
33. Thirumalai, D. J. Phys. Chem. B 1999, 103, 608.
34. Abkevich, V.; Mirny, L.; Shakhnovich, E. Monte Carlo approach to Biopolymers and Protein Folding; Grassberger, P., Bankana, G.T., Nadler, W., Eds.; World Scientific: Singapore, 1998; pp 1-18.
35. Ferrenberg, A.M.; Swendsen, R.H. Phys. Rev. Lett. 1989, 63, 1195.
36. Shakhnovich, E.I. Folding Design 1998, 3, R45.
37. Klimov, D.K.; Thirumalai, D. J. Chem. Phys. 1998, 109, 4119.
38. Thirumalai, D.; Klimov, D.K. Folding Design 1998, 3, R112.
39. Govindarajan, S.; Goldstein, R. Biopolymers 1995, 36, 43.
40. Muñoz, V.; Serrano, L. Folding Design 1996, 1, R71.
41. Lacroix, E.; Viguera, A.; Serrano, L. Folding Design 1998, 3, 79.