Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?

Proceedings of the National Academy of Sciences of the United States of America

Volumn 99, Issue 20, 2002, Pages 12777-12782

  Zhou, Ruhong ^a   Berne, Bruce J ^b  

^a IBM T J WATSON RESEARCH CENTER   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN G; SOLVENT; WATER;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CONFORMATION; INTERMETHOD COMPARISON; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SIMULATION; TEMPERATURE DEPENDENCE;

ANIMALS; BIOPHYSICS; COMPUTER SIMULATION; MODELS, MOLECULAR; MODELS, STATISTICAL; MODELS, THEORETICAL; NERVE TISSUE PROTEINS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS; WATER;

EID: 0036789950     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.142430099     Document Type: Article

References (36)

1. McCammon, J. A. & Wolynes, P. G. (2002) Current Opinion in Structural Biology (Current Biology Press, London).
2. Wales, D. J. & Scheraga, H. A. (1999) Science 285, 1368-1372.
3. Blanco, F. J., Rivas, G. & Serrano, L. (1994) Nat. Struct. Biol. 1, 584-590.
4. Blanco, F. J. & Serrano, L. (1995) Eur. J. Biochem. 230, 634-649.
5. Munoz, V., Thompson, P. A., Hofrichter, J. & Eaton, W. A. (1997) Nature (London) 390, 196-199.
6. Munoz, V., Henry, E. R., Hofrichter, J. & Eaton, W. A. (1998) Proc. Natl. Acad. Sci. USA 95, 5872-5879.
7. Honig, B. & Nicholls, A. (1995) Science 268, 1144-1149.
8. Still, W. C., Tempczyk, A., Hawley, R. C. & Hendrickson, T. (1990) J. Am. Chem. Soc. 112, 6127-6129.
9. Ghosh, A., Rapp, C. S. & Friesner, R. A. (1998) J. Phys. Chem. 102, 10983-10990.
10. Lazaridis, T. & Karplus, M. (1999) Proteins 35, 133-152.
11. Pande, V. S. & Rokhsar, D. S. (1999) Proc. Natl. Acad. Sci. USA 96, 9062-9067.
12. Zagrovic, B., Sorin, E. J. & Pande, V. S, (2001) J. Mol. Biol. 313, 151-169.
13. Dinner, A. R., Lazaridis, T. & Karplus, M. (1999) Proc. Natl. Acad. Sci. USA 96, 9068-9073.
14. Garcia, A. E. & Sanbonmatsu, K. Y. (2001) Proteins 42, 345-354.
15. Roccatano, D., Amadei, A., Nola, A. D. & Berendsen, H. J. (1999) Protein Sci. 10, 2130-2143.
16. Kolinski, A., Ilkowski, B. & Skolnick, J. (1999) Biophys. J. 77, 2942-2952.
17. Klimov, D. K. & Thirumalai, D. (2000) Proc. Natl. Acad. Sci. USA 97, 2544-2549.
18. Zhou, R., Berne, B. J. & Germain, R. (2001) Proc. Natl. Acad. Sci. USA 98, 14931-14936.
19. Zhou, R., Harder, E., Xu, H. & Berne, B. J. (2001) J. Chem. Phys. 115, 2348-2358.
20. Hukushima, K. & Nemoto, K. (1996) J. Phys. Soc. Jpn. 65, 1604-1608.
21. Hunenberger, P. H. & McCammon, J. A. (1999) J. Chem. Phys. 110, 1856-1872.
22. Weber, W., Hunenberger, P. H. & McCammon, J. A. (2000) J. Phys. Chem. B104, 3668-3675.
23. Zhou, R. & Berne, B. J. (1997) J. Chem. Phys. 107, 9185-9196.
24. Duane, S., Kennedy, A. D. Pendleton, B. J. & Roweth, D. (1987) Phys. Lett. B 195, 216-222.
25. Sugita, Y. & Okamoto, Y. (1999) Chem. Phys. Lett. 314, 141-151.
26. Gallicchio, E., Zhang, L. Y. & Levy, R. M. (2002) J. Comput. Chem. 23, 517-529.
27. Schutz, C. N. & Warshel, A. (2001) Proteins 44, 400-417.
28. Garcia-Moreno, E. Dwyer, J., Gittis, A., Lattman, E., Spenser, D. & Stites, W. (1997) Biophys. Chem. 64, 211-224.
29. Garcia, A. E. (1992) Phys. Rev. Lett. 68, 2696-2699.
30. Bashford, D. & Case, D. (2000) Annu. Rev. Phys. Chem. 51, 129-152.
31. Chen, S. W. & Honig, B. (1997) J. Phys. Chem. B 101, 9113-9118.
32. Burykin, A., Schutz, C. N., Villa. J. & Warshel, A. (2002) Proteins 47, 265-280.
33. Frishman, D. & Argos, P. (1995) Proteins 23, 566-579.
34. Wallqvist, A., Gallicchio, E., Felts, A. K. & Levy, R. (2002) Adv. Chem. Phys. 120, 459-486.
35. Sendrovic-Rapp, C. & Friesner, R. A. (1999) Proteins 103, 1913-1928.
36. Zhou, R. & Silverman, B. D. (2002) Proceedings of the Pacific Symposium on Biocomputing, eds. Altman, R. B., Dunker, A. K., Hunter, L., Lauderdale, K. & Klein, T. E. (World Scientific, Singapore), pp. 673-684.