Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

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

Volumn 100, Issue SUPPL. 2, 2003, Pages 13898-13903

  García, Angel E ^a   Onuchic, José N ^b  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN A;

ARTICLE; CHEMICAL REACTION KINETICS; COMPUTER SIMULATION; ENTHALPY; ENTROPY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; TEMPERATURE DEPENDENCE;

BIOPHYSICS; COMPUTER SIMULATION; MODELS, MOLECULAR; PROTEIN FOLDING; STAPHYLOCOCCAL PROTEIN A; THERMODYNAMICS;

EID: 0345133287     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.2335541100     Document Type: Article

References (45)

1. Bryngelson, J. & Wolynes, P. (1987) Proc. Natl. Acad. Sci. USA 84, 7524-7528.
2. Leopold, P. E., Montal, M. & Onuchic, J. N. (1992) Proc. Natl. Acad. Sci. USA 89, 8721-8725.
3. Baldwin, R. L. (1995) J. Biomol. NMR 5, 103-109.
4. Onuchic, J. N., Luthey-Schulten, Z. & Wolynes, P. G. (1997) Annu. Rev. Phys. Chem. 48, 545-600.
5. Sugita, Y. & Okamoto, Y. (1999) Chem. Phys. Lett. 314, 141-151.
6. Gouda, H., Torigoe, H., Saito, A., Sato, M., Arata, Y. & Shimada, I. (1992) Biochemistry 31, 9665-9672.
7. Boczko, E. M. & Brooks, C. L., III (1995) Science 269, 393-396.
8. Shea, J. E., Onuchic, J. N. & Brooks, C. L., III (1999) Proc. Natl. Acad. Sci. USA 96, 12512-12517.
9. Guo, Z., Brooks, C. L., III & Boczko, E. M. (1997) Proc. Natl. Acad. Sci. USA 94, 10161-10166.
10. Takada, S., Luthey-Schulten, Z. & Wolynes, P. (1999) J. Chem. Phys. 110, 11616-11629.
11. Favrin, G., Irback, A. & Wallin, S. (2002) Proteins 47, 99-105.
12. Ghosh, A., Elber, R. & Scheraga, H. A. (2002) Proc. Natl. Acad. Sci. USA 99, 10394-10398.
13. Kolinski, A. & Skolnick, J. (1994) Proteins 18, 353-366.
14. Zhou, Y. & Karplus, M. (1999) J. Mol. Biol. 293, 917-951.
15. Alonso, D. O. & Daggett, V. (2000) Proc. Natl. Acad. Sci. USA 97, 133-138.
16. Onuchic, J. N., Wolynes, P. G., Luthey-Schulten, Z. & Socci, N. D. (1995) Proc. Natl. Acad. Sci. USA 92, 3626-3630.
17. Berriz, G. & Shakhnovich, E. (2001) J. Mol. Biol. 310, 673-685.
18. Witte, K., Skolnick, J. & Wong, C. (1998) J. Am. Chem. Soc. 120, 13042.
19. Bai, Y., Karimi, A., Dyson, H. J. & Wright, P. E. (1997) Protein Sci. 6, 1449-1457.
20. Snow, C. D., Nguyen, H., Pande, V. S. & Gruebele, M. (2002) Nature 420, 102-106.
21. Klimov, D. K., Newfield, D. & Thirumalai, D. (2002) Proc. Natl. Acad. Sci. USA 99, 8019-8024.
22. Lapidus, L. J., Eaton, W. A. & Hofrichter, J. (2000) Proc. Natl. Acad. Sci. USA 97, 7220-7225.
23. Williams, S., Causgrove, T. P., Gilmanshin, R., Fang, K. S., Callender, R. H., Woodruff, W. H. & Dyer, R. B. (1996) Biochemistry 35, 691-697.
24. Munoz, V., Thompson, P. A., Hofrichter, J. & Eaton, W. A. (1997) Nature 390, 196-199.
25. Mayor, U., Johnson, C. M., Daggett, V. & Fersht, A. R. (2000) Proc. Natl. Acad. Sci. USA 97, 13518-13522.
26. Duan, Y. & Kollman, P. A. (1998) Science 282, 740-744.
27. Cornell, W. D., Cieplak, P., Bayley, C. I., Gould, R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. & Kollman, P. A. (1995) J. Am. Chem. Soc. 117, 5179-5197.
28. García, A. E. & Sanbonmatsu, K. Y. (2002) Proc. Natl. Acad. Sci. USA 99, 2782-2787.
29. Hummer, G., Soumpasis, D. & Neumann, M. (1994) J. Phys. Condens. Matter 6, A141-A144.
30. Berendsen, H. J. C., Postma, J. P., van Gunsteren, W. F., DiNola, A. & Haak, J. R. (1984) J. Chem. Phys. 81, 3684-3690.
31. Matouschek, A., Kellis, J. T., Jr., Serrano, L. & Fersht, A. R. (1989) Nature 340, 122-126.
32. Mayor, U., Guydosh, N. R., Johnson, C. M., Grossmann, J. G., Sato, S., Jas, G. S., Freund, S. M. V., Alonso, D. O. V., Daggett, V. & Fersht, A. R. (2003) Nature 421, 863-867.
33. Blanco, F. J., Serrano, L. & Forman-Kay, J. D. (1998) J. Mol. Biol. 284, 1153-1164.
34. Kim, D. E., Fisher, C. & Baker, D. (2000) J. Mol. Biol. 298, 971-984.
35. Oliveberg, M. (2001) Curr. Opin. Struct. Biol. 11, 94-100.
36. Sheinerman, F. B. & Brooks, C. L., III (1998) Proc. Natl. Acad. Sci. USA 95, 1562-1567.
37. Hillson, N., Onuchic, J. N. & García, A. E. (1999) Proc. Natl. Acad. Sci. USA 96, 14848-14853.
38. Cheung, M., García, A. & Onuchic, J. (2002) Proc. Natl. Acad. Sci. USA 99, 685-690.
39. ten Wolde, P. R. & Chandler, D. (2002) Proc. Natl. Acad. Sci. USA 99, 6539-6543.
40. Shea, J., Onuchic, J. & Brooks, C. (2002) Proc. Natl. Acad. Sci. USA 99, 16064-16068.
41. Shea, J. E. & Brooks, C. L., III (2001) Annu. Rev. Phys. Chem. 52, 499-535.
42. Hummer, G., Garde, S., García, A. E., Pohorille, A. & Pratt, L. R. (1996) Proc. Natl. Acad. Sci. USA 93, 8951-8955.
43. Garde, S., Hummer, G., García, A. E., Paulaitis, M. E. & Pratt, L. R. (1996) Phys. Rev. Lett. 77, 4966-4968.
44. Hummer, G., Garde, S., García, A. E. & Pratt, L. R. (2000) Chem. Phys. 258, 349-370.
45. Flyvbjerg, H. & Petersen, H. (1989) J. Chem. Phys. 91, 461-466.