Φ-value analysis by molecular dynamics simulations of reversible folding

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

Volumn 102, Issue 3, 2005, Pages 628-633

  Settanni, Giovanni ^a   Rao, Francesco ^a   Caflisch, Amedeo ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Peptide folding; Transition state

Indexed keywords

ARTICLE; BETA SHEET; BINDING KINETICS; CALCULATION; GENE MUTATION; MOLECULAR DYNAMICS; MONTE CARLO METHOD; NONHUMAN; PARALLEL DESIGN; PHI VALUE ANALYSIS; POINT MUTATION; PRIORITY JOURNAL; PROTEIN FOLDING; SIMULATION; SINGLE POINT MUTATION; THERMODYNAMICS; THERMOSTABILITY;

COMPUTER SIMULATION; KINETICS; MODELS, MOLECULAR; POINT MUTATION; PROTEIN FOLDING; THERMODYNAMICS;

EID: 14144255497     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0406754102     Document Type: Article

References (41)

1. Fersht, A. R., Matouschek, A. & Serrano, L. (1992) J. Mol. Biol. 224, 771-782.
2. Fersht, A. R. (1999) Structure and Mechanism in Protein Science: Guide to Enzyme Catalysis and Protein Folding (Freeman, New York).
3. Daggett, V. & Fersht, A. (2003) Nat. Rev. Mol. Cell Biol. 4, 497-502.
4. Li, A. J. & Daggett, V. (1996) J. Mol. Biol. 257, 412-429.
5. Vendruscolo, M., Paci, E., Dobson, C. M. & Karplus, M. (2001) Nature 409, 641-645.
6. Li, L. & Shakhnovich, E. I. (2001) Proc. Natl. Acad. Sci. USA 98, 13014-13018.
7. Paci, E., Vendruscolo, M., Dobson, C. M. & Karplus, M. (2002) J. Mol. Biol. 324, 151-163.
8. Gsponer, J. & Caflisch, A. (2002) Proc. Natl. Acad. Sci. USA 99, 6719-6724.
9. Lindorff-Larsen, K., Vendruscolo, M., Paci, E. & Dobson, C. M. (2004) Nat. Struct. Mol. Biol. 11, 443-449.
10. Settanni, G., Gsponer, J. & Caflisch, A. (2004) Biophys. J. 86, 1691-1701.
11. Cho, J. H., Sato, S. & Raleigh, D. P. (2004) J. Mol. Biol. 338, 827-837.
12. Nauli, S., Kuhlman, B. & Baker, D. (2001) Nat. Struct. Biol. 8, 602-605.
13. Wright, C. F., Lindorff-Larsen, K., Randles, L. G. & Clarke, J. (2003) Nat. Struct. Biol. 10, 658-662.
14. Shimada, J. & Shakhnovich, E. I. (2002) Proc. Natl. Acad. Sci. USA 99, 11175-11180.
15. Hubner, I. A., Shimada, J. & Shakhnovich, E. I. (2004) J. Mol. Biol. 336, 745-761.
16. Du, R., Pande V. S., Grosberg, A. Y., Tanaka, T. & Shakhnovich, E. I. (1998) J. Chem. Phys. 108, 334-350.
17. Chandler, D. (1978) J. Chem. Phys. 68, 2959-2970.
18. Northrup, S. H., Pear, M. R., Lee, C. Y., McCammon, J. A. & Karplus, M. (1982) Proc. Natl. Acad. Sci. USA 79, 4035-4039.
19. Lenz, P., Zagrovic, B., Shapiro, J. & Pande, V. S. (2004) J. Chem. Phys. 120, 6769-6778.
20. Rao, F. & Caflisch, A. (2004) J. Mol. Biol. 342, 299-306.
21. De Alba, E., Santoro, J., Rico, M. & Jiménez, M. A. (1999) Protein Sci. 8, 854-865.
22. Ferrara, P. & Caflisch, A. (2000) Proc. Natl. Acad. Sci. USA 97,10780-10785.
23. Sanchez, I. E. & Kiefhaber, T. (2003) J. Mol. Biol. 334, 1077-1085.
24. Fersht, A. R. & Sato, S. (2004) Proc. Natl. Acad. Sci. USA 101, 7976-7981.
25. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983) J. Comput. Chem. 4, 187-217.
26. Ferrara, P., Apostolakis, J. & Caflisch, A. (2002) Proteins 46, 24-33.
27. Cavalli, A., Ferrara, P. & Caflisch, A. (2002) Proteins 47, 305-314.
28. Ferrara, P., Apostolakis, J. & Caflisch, A. (2000) J. Phys. Chem. B 104, 5000-5010.
29. Eaton, W. A., Munoz, V., Hagen, S. J., Jas, G. S., Lapidus, L. J., Henry, E. R. & Hofrichter, J. (2000) Annu. Rev. Biophys. Biomol. Struct. 29, 327-359.
30. Ferrara, P. & Caflisch, A. (2001) J. Mol. Biol. 306, 837-850.
31. Hartigan, J. A. (1975) Clustering Algorithms (Wiley, New York).
32. Tou, J. T. & Gonzalez, R. C. (1974) Pattern Recognition Principles (Addison-Wesley, Reading, MA).
33. Fersht, A. R. (2004) Proc. Natl. Acad. Sci. USA 101, 14338-14342.
34. Baldwin, R. L. & Rose, G. D. (1999) Trends Biochem. Sci. 24, 77-83.
35. Karplus, M. & Weaver, D. L. (1976) Nature 260, 404-406.
36. Itzhaki, L. S., Otzen, D. E. & Fersht, A. R. (1995) J. Mol. Biol. 254, 260-288.
37. Daggett, V., Li, A. J., Itzhaki, L. S., Otzen, D. E. & Fersht, A. R. (1996) J. Mol. Biol. 257, 430-440.
38. Davis, R., Dobson, C. M. & Vendruscolo, M. (2002) J. Chem. Phys. 117, 9510-9517.
39. Warshel, A., Schweins, T. & Fothergill, M. (1994) J. Am. Chem. Soc. 116, 8437-8442.
40. Garcia-Mira, M. M., Boehringer, D. & Schmid, F. X. (2004) J. Mol. Biol. 339, 555-569.
41. Friel, C. T., Capaldi, A. P. & Radford, S. E. (2003) J. Mol. Biol. 326, 293-305.