Energetic decomposition of the α-helix-coil equilibrium of a dynamic model system

Biopolymers

Volumn 39, Issue 4, 1996, Pages 479-489

  Wang, Lu ^a   O'Connell, Thomas ^b   Tropsha, Alexander ^b   Hermans, Jan ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DECOMPOSITION; ELECTROSTATICS; FREE ENERGY; HYDROGEN BONDS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; MOLECULES; PERMITTIVITY; VAN DER WAALS FORCES;

ALANINE OLIGOMERS; DYNAMIC MODEL SYSTEM; ENERGETIC DECOMPOSITION; MOLECULAR TRANSFORMATION; VAN DER WAALS INTERACTIONS;

OLIGOMERS;

ALANINE; OLIGOMER;

ALPHA HELIX; ARTICLE; DECOMPOSITION; DIELECTRIC CONSTANT; ELECTRICITY; ENTROPY; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; PROTEIN STABILITY;

EID: 0030271002     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0282(199610)39:4<479::aid-bip1>3.0.co;2-u     Document Type: Article

References (44)

1. Scholtz, J. M. & Baldwin, R. L. (1992) Ann. Rev. Biophys. Biomol. Struct. 21, 95-118.
2. Sundaralingam, M., Sekharudu, Y. C., Yathindra, N. & Ravichandran, V. (1987) Proteins Struct. Fund. Genet. 2, 64-71.
3. Richardson, J. S. & Richardson, D. C. (1988) Science 240, 1648-1652.
4. Presta, L. G. & Rose, G. D. (1988) Science 240, 1632-1641.
5. Doty, P. & Yang, J. T. (1956) J. Am. Chem. Soc. 78, 498-500.
6. Brown, J. E. & Klee, W. A. (1971) Biochemistry 10, 470-476.
7. Schellman, J. A. (1955) Compt. rend. trav. lab. Carlsberg, Sér. chim. 29, 230-259.
8. Bixon, M., Scheraga, H. A. & Lifson, S. (1963) Biopolymers 1, 419-429.
9. Blader, M., Zhang, X. J. & Matthews, B. M. (1993) Science 260, 1637-1640.
10. Shoemaker, K. R., Kim, P. S., York, E. J., Stewart, J. M. & Baldwin, R. L. (1987) Nature 326, 563-567.
11. Marqusee, S. & Baldwin, R. L. (1987) Proc. Natl. Acad. Sci. USA 84, 8898-8902.
12. Armstrong, K. M., Fairman, R. & Baldwin, R. L. (1993) J. Mol. Biol. 230, 284-291.
13. Zhou, H. X., Lyu, P. C., Wemmer, D. E. & Kallenbach, N. R. (1994) Proteins Struct. Funct. Genet. 18, 1-7.
14. Zimm, B. H. & Bragg, J. K. (1959) J. Chem. Phys. 31, 526-535.
15. Wojcik, J., Altman, K.-H. & Scheraga, H. A. (1990) Biopolymers 30, 121-134.
16. Chakrabartty, A., Kortemme, T. & Baldwin, R. L. (1994) Protein Sci. 3, 843-852.
17. O'Neil, K. T. & DeGrado, W. F. (1990) Science 250, 646-656.
18. Go, M., Go, N. & Scheraga, H. A. (1971) J. Chem. Phys. 54, 4489-4503.
19. Hermans, J. & Anderson, A. G. (1990) in Theoretical Biochemistry and Molecular Biophysics, A Comprehensive Survey, Beveridge, D. L. & Lavery, R., Ed., Adenine Press, Schenectady, NY, pp. 45-62.
20. Daggett, V., Kollman, P. A. & Kuntz, I. R. (1991) Biopolymers 31, 1115-1134.
21. Daggett, V. & Levitt, M (1992) J. Mol. Biol. 223, 1121-1138.
22. Tirado-Rives, J. & Jorgensen, W. L. (1991) Biochemistry 30, 3864-3871.
23. Tirado-Rives, J., Maxwell, D. S. & Jorgensen, W. L. (1993) J. Am. Chem. Soc. 115, 11590-11593.
24. Tobias, D. J. & Brooks, C. L. (1991) Biochemistry 30, 6059-6070.
25. Yang, A.-S. & Honig, B. (1995) J. Mol. Biol. 252, 351-365.
26. Chakrabartty, A., Schellman, J. A. & Baldwin, R. L. (1991) Nature 351, 586-588.
27. Wang, L., O'Connell, T., Tropsha, A. & Hermans, J. (1995) Proc. Natl. Acad. Sci. USA 92, 10924-10928.
28. Tropsha, A., Yan, Y., Schneider, S. E., Li, L. & Erickson, B. W. (1994) in Peptides: Chemistry, Structure and Biology, Hodges, R. S. & Smith, J. A., Ed., Escom, Leiden, pp. 883-885.
29. Ferro, D. R., McQueen, J. E., McCown, J. T. & Hermans, J. (1980) J. Mol. Biol. 136, 1-18.
30. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F. & Hermans, J. (1981) in Intermolecular Forces, Pullman, B., Ed., Reidel, Dordrecht, Holland, pp. 331-342.
31. Lifson, S. & Sander, C. (1979) Nature 282, 109-111.
32. Yun, R. H. & Hermans, J. (1991) Protein Eng. 4, 761-766.
33. Hermans, J., Yun, R. H. & Anderson, A. G. (1992) J. Comp. Chem. 13, 429-442.
34. Hermans, J. (1966) J. Am. Chem. Soc. 88, 2418-2422.
35. Cantor, C. R. & Schimmel, P. R. (1980) Biophysical Chemistry, Vol. 3, Freeman, San Francisco, pp. 1041-1073.
36. Hine, J. & Mookerjee, P. K. (1975) J. Org. Chem. 40, 292-298.
37. Wolfenden, R. (1983) Science 222, 1087-1093.
38. McAuliffe, C. (1966) J. Phys. Chem. 70, 1267-1275.
39. Gill, S. J. & Wadsö, I. (1976) Proc. Natl Acad. Sci. USA 73, 2955-2958.
40. Serrano, L., Neira, J., Sancho, J. & Fersht, A. (1992) Nature 356, 453-455.
41. Sitkoff, D., Sharp, K. A. & Honig, B. (1994) J. Phys. Chem. 98, 1978-1988.
42. Shi, Y. Y., Mark, A. E., Wang, C., Huang, F., Berendsen, H. J. C. & van Gunsteren, W. F. (1993) Protein Eng. 6, 289-295.
43. Smith, P. E. & van Gunsteren, W. F. (1994) J. Phys. Chem. 98, 13735-13740.
44. Boresch, S., Archontis, G. & Karplus, M. (1994) Proteins Struct. Funct. Genet. 20, 25-33.