Computing the transition state populations in simple protein models

Biopolymers

Volumn 68, Issue 1, 2003, Pages 35-46

  Ozkan, S Banu ^a,b   Dill, Ken A ^c   Bahar, Ivet ^a,b  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^b BOGAZICI UNIVERSITY   (Turkey)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Go model; Kinetics of protein folding; Master equation method; Transition state; Two state fast folding

Indexed keywords

DECAY (ORGANIC); ENZYME KINETICS;

TRANSITION STATE POPULATION;

PROTEINS;

ARTICLE; CALCULATION; KINETICS; MOLECULAR MODEL; PROTEIN CONFORMATION; PROTEIN FOLDING;

KINETICS; MATHEMATICAL COMPUTING; MODELS, CHEMICAL; PROBABILITY; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 0346003771     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/bip.10280     Document Type: Article

References (25)

1. Widom, B. Science 1965, 148, 1555-15560.
2. Widom, B. J Chem Phys 1971, 55, 44-52.
3. Oppenheim, I.; Shuler, K. E.; Weiss, G. H. Adv Mol Relax Processes 1967, 1, 13-68.
4. Bahar, I. J Chem Phys 1989, 91, 6525-6531.
5. Gardiner, G. W. Handbook of Stochastic Methods for Physics, Chemistry, and Natural Sciences; Springer-Verlag: London 1990.
6. Van Kampen, N. G. Stochastic Processes in Physics and Chemistry; Elsevier: North Holland, 1992.
7. Leopold, P. E.; Montal;, M.; Onuchic, J. N. Proc Natl Acad Sci USA 1992, 89, 8721-8725.
8. Chan, H. S.; Dill, K. A. J Chem Phys 1993, 99, 2116-2127.
9. Zwanzig, R. Proc Natl Acad Sci USA 1997, 94, 148-150.
10. Zwanzig, R. Proc Natl Acad Sci USA 1995, 92, 9801-9804.
11. Ye, Y. J.; Ripoll, D. R.; Scheraga, H. A. Comp Theor Polymer Sci 1999, 9, 359-370.
12. Cieplak, M.; Henkel, M.; Karbowski, J.; Banavar, J. R. Phys Rev Lett 1998, 80, 3654-3657.
13. Munoz, V.; Henry, E. R.; Hofrichter, J.; Eaton, W. A. Proc Natl Acad Sci USA 1998, 95, 5872-5879.
14. Zhang, W. B.; Chen, S. J. Proc Natl Acad Sci USA 2002, 99, 1931-1936.
15. Ozkan, S. B.; Bahar, I.; Dill, K. A. Nat Struct Biol 2001, 8, 765-769.
16. Stollenwerk, N.; Briggs, K. M. Phys Lett A 2000, 274, 84-91.
17. Goel, N. S.; Richter, Dyn N. Dynamic Stochastic Models in Biology; Academia: New York, 1974.
18. Paci, E.; Vendruscolo, M.; Karplus, M. Proteins 2002, 47, 379-392.
19. Hoang, T. X.; Cieplak, M. J Chem Phys 2000, 113, 8319-8328.
20. Pande, V. S.; Rokhsar, D. S. Proc Natl Acad Sci USA 1999, 96, 1273-1278.
21. Klimov, D. K.; Thirumalai, D. J Mol Biol 1998, 282, 471-492.
22. Jacob, M.; Schmid, F. X. Biochemistry 1999, 38, 13773-13779.
23. Englander, S. W. Ann Rev Biophys Biomol Struct 2000, 29, 213-238.
24. Ozkan, S. B.; Dill, K. A.; Bahar, I. Protein Sci 2002, 11, 1958-1970.
25. Ueda, Y.; Taketomi, T.; Go, N. Int J Peptide Res 1975, 7, 445-449.