Low barrier kinetics: Dependence on observables and free energy surface

Journal of Computational Chemistry

Volumn 27, Issue 2, 2006, Pages 125-134

  Ma, Hairong ^a   Gruebele, Martin ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Downhill folding; Free energy surface; Langevin dynamics; Molecular time scale

Indexed keywords

DOWNHILL FOLDING; FREE ENERGY SURFACE; LANGEVIN DYNAMICS; MOLECULAR TIME SCALE;

FREE ENERGY; FUNCTIONS; MATHEMATICAL MODELS;

MOLECULAR DYNAMICS;

ARTICLE; CHEMICAL MODEL; COMPUTER SIMULATION; KINETICS; SURFACE PROPERTY; THERMODYNAMICS;

COMPUTER SIMULATION; KINETICS; MODELS, CHEMICAL; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 33645148429     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20311     Document Type: Article

References (40)

1. Eyring, H. Trans Faraday Soc 1938, 34, 41.
2. Kramers, H. A. Physica 1940, 7, 284.
3. Friedman, L. Ion-Molecule Reactions; Wiley-Interscience: New York, 1970.
4. Bryngelson, J. D.; Onuchic, J, N.; Socci, N. D.; Wolynes, P. G. Proteins Struct Funct Genet 1995, 21, 167.
5. Chandler, D. Modern Statistical Mechanics; Oxford University Press: Oxford, 1989.
6. Berne, B. J. In Activated Barrier Crossing: Applications in Physics, Chemistry and Biology; Hänggi, P.; Fleming, G. R., Eds.; World Scientific: Singapore, 1993, p. 82.
7. Ma, H.; Gruebele, M. Proc Natl Acad Sci USA 2005, 102, 2283.
8. Topaler, M.; Makri, N. J Chem Phys 1994, 101, 7500.
9. Shea, J.; Brooks, C. L. Annu Rev Phys Chem 2001, 52, 499.
10. Ben-Nun, M.; Martinez, T. J. Adv Chem Phys 2002, 121, 439.
11. Car, R.; Parinello, M. Phys Rev Lett 1985, 55, 2471.
12. Muñoz, V.; Henry, E. R.; Hofrichter, J.; Eaton, W. A. Proc Natl Acad Sci USA 1998, 95, 5872.
13. Doshi, U.; Muñoz, V. Chem Phys 2004, 307, 129.
14. Socci, N. D.; Onuchic, J. N.; Wolynes, P. G. J Chem Phys 1996, 104, 5860.
15. Wagner, C.; Kiefhaber, T. Proc Natl Acad Sci USA 1999, 96, 6716.
16. Yang, W.; Gruebele, M. Biophys J 2004, 87, 596.
17. Yang, W. Y.; Gruebele, M. Nature 2003, 423, 193.
18. Yang, W. Y.; Gruebele, M. J Am Chem Soc 2004, 126, 7758.
19. Eigen, M.; Maeyer, L. D. In Technique of Organic Chemistry; Weiss-berger, A., Ed.; Interscience: New York, 1963, p. 895.
20. Metzler, R.; Klafter, J.; Jortner, J. Proc Natl Acad Sci USA 1999, 96, 11085.
21. Shlesinger, M. F.; Zaslavsky, G. M.; Klafter, J. Nature 1993, 363, 31.
22. Pain, R. H., Ed. Mechanisms of Protein Folding; Oxford University Press: Oxford, 2000.
23. Buchner, J.; Kiefhaber, T., Eds. Protein Folding Handbook; Wiley-VCH: Weinheim, 2005.
24. Yang, W. Y.; Gruebele, M. Biochemistry 2004, 43, 13018.
25. Hammond, G. S. J Am Chem Soc 1955, 77, 334.
26. Kubelka, J.; Hofrichter, J.; Eaton, W. A. Curr Opinion Struct Biol 2004, 14, 76.
27. Ozkan, S. B.; Dill, K. A.; Bahar, I. Protein Sci 2002, 11, 1958.
28. Zwanzig, R. J Chem Phys 1995, 103, 9397.
29. Sadqi, M.; Lapidus, L. J.; Muñoz, V. Proc Natl Acad Sci USA 2003, 100, 12117.
30. Muñoz, V. Int J Quantum Chem 2002, 90, 1522.
31. Hagen, S. J. Proteins Struct Funct Genet 2003, 50, 1.
32. Englander, S. W.; Sosnick, T. R.; Mayne, L. C.; Shtilerman, M.; Qi, P. X.; Bai, Y. Acc Chem Res 1998, 31, 767.
33. Bai, Y. W. Biochem Biophys Res Commun 2003, 305, 785.
34. Zwanzig, R. Proc Natl Acad Sci USA 1988, 85, 2029.
35. Silow, M.; Oliveberg, M. Biochemistry 1997, 36, 7633.
36. Bachmann, A.; Kiefhaber, T. J Mol Biol 2001, 306, 375.
37. Oliveberg, M. Acc Chem Res 1998, 31, 765.
38. Pogorelov, T. V.; Luthey-Schulten, Z. Biophys J 2004, 87, 207.
39. Volk, M.; Kholodenko, Y.; Lu, H. S. M.; Gooding, E. A.; DeGrado, W. F.; Hochstrasser, R. M. J Phys Chem 1997, 101, 8607.
40. Sabelko, J.; Ervin, J.; Gruebele, M. Proc Natl Acad Sci USA 1999, 96, 6031.