Understanding folding and design: Replica-exchange simulations of "Trp-cage" miniproteins

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

Volumn 100, Issue 13, 2003, Pages 7587-7592

  Pitera, Jed W ^a   Swope, William ^a  

^a IBM ALMADEN RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MUTANT PROTEIN; SOLVENT;

ARTICLE; MELTING POINT; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; SIMULATION; THERMODYNAMICS;

BIOPHYSICS; COMPUTER SIMULATION; HEAT; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; TEMPERATURE; THERMODYNAMICS; TRYPTOPHAN;

EID: 0037934616     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.1330954100     Document Type: Article

References (37)

1. Neidigh, J. W., Fesinmeyer, R. M. & Andersen, N. H. (2002) Nat. Struct. Biol. 9, 425-430.
2. Neidigh, J. W., Fesinmeyer, R. M., Pricket, K. S. & Andersen, N. H. (2001) Biochemistry 40, 13188-13200.
3. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, T., Shindyalov, I. N. & Bourne, P. E. (2000) Nucleic Acids Res. 28, 235-242.
4. Simmerling, C., Strockbine, B. & Roitberg, A. E. (2002) J. Am. Chem. Soc. 38, 11258-11259.
5. Wang, J. M., Cieplak, P. & Kollman, P. A. (2000) J. Comput. Chem. 21, 1049-1074.
6. Qiu, L. L., Pabit, S. A., Roitberg, A. E. & Hagen, S. J. (2002) J. Am. Chem. Soc. 124, 12952-12953.
7. Snow, C. D., Zagrovic, B. & Pande, V. S. (2002) J. Am. Chem. Soc. 124, 14548-14549.
8. Hansmann, U. H. E. (1997) Chem. Phys. Lett. 281, 140-150.
9. Mitsutake, A., Sugita, Y. & Okamoto, Y. (2001) Biopolymers 60, 96-123.
10. Kihara, D., Lu, H., Kolinski, A. & Skolnick, J. (2001) Proc. Natl. Acad. Sci. USA 98, 10125-10130.
11. Garcia, A. E. & Sanbonmatsu, K. Y. (2002) Proteins 42, 345-354.
12. Zhou, R. H., Germain, R. & Berne, B. J. (2001) Proc. Natl. Acad. Sci. USA 98, 14931-14936.
13. Munoz, V., Thompson, P. A., Hofrichter, J. & Eaton, W. A. (1997) Nature 390, 196-199.
14. Zhou, R. H. & Berne, B. J. (2002) Proc. Natl. Acad. Sci. USA 99, 12777-12782.
15. Zagrovic, B., Sorin, E. J. & Pande, V. (2001) J. Mol. Biol. 313, 151-169.
16. Wu, H. W., Wang, S. M. & Brooks, B. R. (2002) J. Am. Chem. Soc. 124, 5282-5283.
17. Okur, A., Strockbine, B., Hornak, V. & Simmerling, C. (2003) J. Comput. Chem. 24, 21-31.
18. Jang, S., Shin, S. & Pak, Y. (2002) J. Am. Chem. Soc. 124, 4976-4977.
19. Snow, C. D., Nguyen, N., Pande, V. S. & Gruebele, M. (2002) Nature 420, 102-106.
20. Ferrara, P. & Caflisch, A. (2000) Proc. Natl. Acad. Sci. USA 97, 10780-10785.
21. Daura, X., Jaun, B., Seebach, D., van Gunsteren, W. F. & Mark, A. E. (1998) J. Mol. Biol. 280, 925-932.
22. Daura, X., Gademann, K., Schafer, H., Jaun, B., Seebach, D. & van Gunsteren, W. F. (2001) J. Am. Chem. Soc. 123, 2393-2404.
23. Cornell, W. D. Cieplak, P., Bayly, C.I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. & Kollman, P. A. (1995) J. Am. Chem. Soc. 117, 5179-5197.
24. Sitkoff, D., Sharp, K. A. & Honig, B. (1994) J. Phys. Chem. 98, 1978-1988.
25. Tsui, V. & Case, D. A. (2001) Biopolymers 56, 275-291.
26. Ryckaert, J.-P., Ciccotti, G. & Berendsen, H. J. C. (1977) Comput. Phys. 23, 327-341.
27. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. & Haak, J. R. (1984) J. Chem. Phys. 81, 3684-3690.
28. Onuchic, J. (1997) Proc. Natl. Acad. Sci. USA 94, 7129-7131.
29. Zagrovic, B., Snow, C. D., Khaliq, S., Shirts, M. R. & Pande, V. S. (2002). J. Mol. Biol. 323, 153-164.
30. Privalov, P. L. (1979) Adv. Protein Chem. 33, 167-241.
31. Privalov, P. L. & Gill, S. J. (1989) Pure Appl. Chem. 61, 1097-1104.
32. Bursulaya, B. D. & Brooks, C. L. (2000) J. Phys. Chem. B 104, 12378-12383.
33. Cornell, W. D., Caldwell, J. W. & Kollman, P. A. (1997) J. Chim. Phys.-Chim. Biol. 94, 1417-1435.
34. Kaminski, G. A., Friesner, R. A., Tirado-Rives, J. & Jorgensen, W. L. (2001) J. Phys. Chem. B 105, 6474-6487.
35. MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Gluo, H., Ha, S., et al. (1998) J. Phys. Chem. B 102, 3586-3616.
36. Allen, F., Almasi, G., Andreoni, W., Beece, D., Berne, B. J., Bright, A., Brunheroto, J., Cascaval, C., Castanos, J., Coteus, P., et al. (2001) IBM Syst. J. 40, 310-327.
37. Kofke, D. A. (2002) J. Chem. Phys. 117, 6911-6914.