Transition-path sampling of β-hairpin folding

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

Volumn 100, Issue 21, 2003, Pages 12129-12134

  Bolhuis, Peter G ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEIN G B1; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; ATOMIC PARTICLE; CALCULATION; CARBOXY TERMINAL SEQUENCE; DYNAMICS; ENERGY; HYDROGEN BOND; KINETICS; PRIORITY JOURNAL; PROTEIN FOLDING; ROOM TEMPERATURE;

ALGORITHMS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BIOPHYSICS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; THERMODYNAMICS;

EID: 0142027789     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.1534924100     Document Type: Article

References (34)

1. Chandler, D. (1978) J. Chem. Phys. 68, 2959-2970.
2. Bennett, C. H. (1977) in Algorithms for Chemical Computations, ed. Christoffersen, R. (Am. Chem. Soc., Washington, DC), pp. 63-97.
3. Dellago, C., Bolhuis, P. G., Csajka, F. S. & Chandler, D. (1998) J. Chem. Phys. 108, 1964-1977.
4. Dellago, C., Bolhuis, P. G. & Chandler, D. (1998) J. Chem. Phys. 108, 9236-9245.
5. Bolhuis, P. G., Dellago, C. & Chandler, D. (1998) Faraday Discuss. 110, 421-436.
6. Dellago, C., Bolhuis, P. G. & Chandler, D. (1999) J. Chem. Phys. 110, 6617-6625.
7. Bolhuis, P. G., Chandler, D., Dellago, C. & Geissler, P. L. (2002) Annu. Rev. Phys. Chem. 54, 291-318.
8. Dellago, C., Bolhuis, P. G. & Geissler, P. L. (2002) Adv. Chem. Phys. 123, 1-78.
9. Dellago, C., Bolhuis, P. G. & Chandler, D. (2000) Proc. Natl. Acad. Sci. USA 97, 5877-5882.
10. Bolhuis, P. G. & Chandler, D. (2000) J. Chem. Phys. 113, 8154-8160.
11. Blanco, F. J., Rivas, G. & Serrano, L. (1994) Nat. Struct. Biol. 1, 584-590.
12. Blanco, F. J. & Serrano, L. (1995) Eur. J. Biochem. 230, 634-649.
13. Muñoz, V., Thomson, P. A., Hofrichter, J. & Eaton, W. A. (1997) Nature 390, 196-199.
14. Muñoz, V., Henry, E. R., Hofrichter, J. & Eaton, W. A. (1998) Proc. Natl. Acad. Sci. USA 95, 5872-5879.
15. Honda, S., Kobayashi, N. & Munekata, E. (2000) J. Mol. Biol. 295, 269-278.
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. Dinner, A. R., Lazaridis, T. & Karplus, M. (1999) Proc. Natl. Acad. Sci. USA 96, 9068-9073.
19. Zagrovic, B., Sorin, E. J. & Pande, V. (2001) J. Mol. Biol. 313, 151-169.
20. Pande, V. S. & Rokhsar, D. S. (1999) Proc. Natl. Acad. Sci. USA 96, 9062-9067.
21. Roccatano, D., Amadel, A., Di Nola, A. & Berendsen, H. J. C. (1999) Protein Sci. 8, 2130-2143.
22. Ma, B. & Nussinov, R. (2000) J. Mol. Biol. 296, 1091-1104.
23. Eastman, P., Gronbech-Jensen, N. & Doniach, S. (2001) J. Chem. Phys. 114, 3823-3841.
24. Garcia, A. E. & Sanbonmatsu, K. Y. (2001) Proteins Struct. Funct. Genet. 42, 345-354.
25. Zhou, R., Berne, B. J. & Germain, R. (2001) Proc. Natl. Acad. Sci. USA 98, 14931-14936.
26. Tsai, J. & Levitt, M. (2002) Biophys. Chem. 101, 187-201.
27. Zhou, R. & Berne, B. J. (2002) Proc. Natl. Acad. Sci. USA 99, 12777-12782.
28. Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K. & Schulten, K. (1999) J. Comput. Phys. 151, 283-312.
29. MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) J. Phys. Chem. B 102, 3586-3616.
30. Andersen, H. C. (1983) J. Comput. Phys. 52, 24-34.
31. Bolhuis, P. G. (2003) J. Phys. Condens. Matter 15, S113-S120.
32. van Erp, T., Moroni, D. & Bolhuis, P. G. (2003) J. Chem. Phys. 118, 7762-7774.
33. Humphrey, W., Dalke, A. & Schulten, K. (1996) J. Mol. Graphics 14, 33-38.
34. Andersen, H. C. (1980) J. Chem. Phys. 72, 2384-2393.