A minimum-reaction-flux solution to master-equation models of protein folding

Journal of Chemical Physics

Volumn 128, Issue 19, 2008, Pages

  Zhou, Huan Xiang ^a  

^a Florida State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; EQUILIBRIUM CONSTANTS; MATHEMATICAL MODELS; NUMERICAL METHODS; RATE CONSTANTS;

EQUILIBRIUM DISTRIBUTION; MASTER-EQUATION MODELS; TRANSITION STATE THEORY; UNFOLDED STATE;

PROTEIN FOLDING;

PROTEIN;

ALGORITHM; ARTICLE; BIOPHYSICS; CHEMICAL MODEL; CHEMISTRY; CONFORMATION; METHODOLOGY; PHYSICAL CHEMISTRY; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; STATISTICAL MODEL; SURFACE PROPERTY; THEORETICAL MODEL; THERMODYNAMICS;

ALGORITHMS; BIOPHYSICS; CHEMISTRY, PHYSICAL; MODELS, CHEMICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEINS; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 44349162212     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2929824     Document Type: Article

References (22)

1. R. Zwanzig, A. Szabo, and B. Bagchi, Proc. Natl. Acad. Sci. U.S.A. 89, 20 (1992).
2. R. Zwanzig, Proc. Natl. Acad. Sci. U.S.A. 92, 9801 (1995).
3. R. Doyle, K. Simons, H. Qian, and D. Baker, Proteins 29, 282 (1997).
4. M. Cieplak, M. Henkel, J. Karbowski, and J. R. J. R. Banavar, Phys. Rev. Lett. 80, 3650 (1998).
5. V. Muoz, E. R. Henry, J. Hofrichter, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. 95, 5872 (1998).
6. P. A. Thompson, V. Muoz, G. S. Jas, E. R. Henry, W. A. Eaton, and J. Hofrichter, J. Phys. Chem. B 104, 378 (2000).
7. E. Alm, A. V. Morozov, T. Kortemme, and D. Baker, J. Mol. Biol. 322, 463 (2002).
8. D. Makarov, C. A. Keller, K. W. Plaxco, and H. Metiu, Proc. Natl. Acad. Sci. U.S.A. 99, 3535 (2002).
9. S. B. Ozkan, K. A. Dill, and I. Bahar, Protein Sci. 11, 1958 (2002).
10. S. B. Ozkan, K. A. Dill, and I. Bahar, Biopolymers 68, 35 (2003).
11. J. Schonbrun and K. A. Dill, Proc. Natl. Acad. Sci. U.S.A. 100, 12678 (2003).
12. D. A. Evans and D. J. Wales, J. Chem. Phys. 121, 1080 (2004).
13. T. R. Weikl, M. Palassini, and K. A. Dill, Protein Sci. 13, 822 (2004).
14. C. Merlo, K. A. Dill, and T. R. Weikl, Proc. Natl. Acad. Sci. U.S.A. 102, 10171 (2005).
15. H.-X. Zhou, Phys. Biol. 2, R1 (2005).
16. J. C. Keck, J. Chem. Phys. 32, 1035 (1960).
17. V. Muoz, P. A. Thompson, J. Hofrichter, and W. A. Eaton, Nature (London) 390, 196 (1997).
18. A. Berezhkovskii and A. Szabo, J. Chem. Phys. 121, 9186 (2004).
19. H. Eyring, J. Chem. Phys. 3, 107 (1935).
20. J. Chahine, R. J. Oliveira, V. B. Leite, and J. Wang, Proc. Natl. Acad. Sci. U.S.A. 104, 14646 (2007).
21. M. K. Gilson, Proteins 15, 266 (1993).
22. http://computation.llnl.gov/casc/odepack/download/lsode_agree.html.