Molecular dynamics of a 15-residue poly(L-alanine) in water: Helix formation and energetics

Journal of the American Chemical Society

Volumn 121, Issue 4, 1999, Pages 605-612

  Takano, Mitsunori ^a   Yamato, Takahisa ^b   Higo, Junichi ^c   Suyama, Akira ^a   Nagayama, Kuniaki ^d  

^a UNIVERSITY OF TOKYO   (Japan)

^b NAGOYA UNIVERSITY   (Japan)

^c BIOMOL ENG RESEARCH INSTITUTE   (Japan)

^d NATIONAL INSTITUTE FOR PHYSIOLOGICAL SCIENCES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; POLYAMINOACID; WATER;

ALPHA HELIX; ARTICLE; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; EQUILIBRIUM CONSTANT; HIGH TEMPERATURE; HYDROGEN BOND; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PROTEIN DOMAIN; PROTEIN FOLDING; SIMULATION; TEMPERATURE DEPENDENCE;

EID: 0033518605     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja982919c     Document Type: Article

References (67)

1. Ballew, R. M.; Sabelko, J.; Gruebele, M. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 5759-5764.
2. Gilmanshin, R.; Williams, S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 3709-3713.
3. Gilmanshin, R.; Williams, S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Biochemistry 1997, 36, 15006-15012.
4. Gilmanshin, R.; Callender, R. H.; Dyer, R. B. Nat. Struct. Biol. 1998, 5, 363-365.
5. Williams, S.; Causgrove, T. P.; Gilmanshin, R.; Fang, K. S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Biochemistry 1996, 35, 691-697.
6. Thompson, P. A.; Eaton, W. A.; Hofrichter, J. Biochemistry 1997, 36, 9200-9210.
7. Muñoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. A. Nature 1997, 390, 196-199.
8. Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Proteins 1995, 21, 167-195.
9. Fersht, A. R. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 10869-10873.
10. Guo, Z.; Brooks, C. L., III; Boczko, E. M. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 10161-10166.
11. Lazaridis, T.; Karplus, M. Science 1997, 278, 1928-1931.
12. Karplus, M. Folding Des. 1997, 2, S69-S75.
13. Dill, K. A.; Chan, H. S. Nat. Struct. Biol. 1997, 4, 10-19.
14. Duan, Y.; Wang, L.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 9897-9902. Duan, Y.; Kollman, P. A. Science 1998, 282, 740-744.
15. Duan, Y.; Wang, L.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 9897-9902. Duan, Y.; Kollman, P. A. Science 1998, 282, 740-744.
16. Daura, X.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. J. Mol. Biol. 1998, 280, 925-932.
17. Tirado-Rives, J.; Jorgensen, W. L. Biochemistry 1991, 30, 3864-3871.
18. Soman, K. V.; Karime, A.; Case, D. A. Biopolymers 1991, 31, 1351-1361.
19. DiCapua, F. M.; Swaminathan, S.; Beveridge, D. L. J. Am. Chem. Soc. 1991, 113, 6145-6155.
20. Daggett, V.; Levitt, M. J. Mol. Biol. 1992, 223, 1121-1138.
21. De Loof, H.; Nilsson, L.; Rigler, R. J. Am. Chem. Soc. 1992, 114, 4028-4035.
22. van Buuren, A. R.; Berendsen, H. J. C. Biopolymers 1993, 33, 1159-1166.
23. Kovacs, H.; Mark, A. E.; Johansson, J.; van Gunsteren, W. F. J. Mol. Biol. 1995, 247, 808-822.
24. Hirst, J. D.; Brooks, C. L., III Biochemistry 1995, 34, 7614-7621.
25. Okamoto, Y.; Hansmann, U. H. E. J. Phys. Chem. 1995, 99, 11276-11287.
26. Sung, S. S.; Wu, X. W. Proteins 1996, 25, 202-214.
27. Klein, C. T.; Mayer, B.; Kohler, G.; Wolshann, P. J. Mol. Struct. (THEOCHEM) 1996, 370, 33-34.
28. Takano, M.; Takahashi, T.; Nagayama, K. Phys. Rev. Lett. 1998, 80, 5691-5694.
29. Tobias, D. J.; Merts, J. E.; Brooks, C. L., III. Biochemistry 1991, 30, 6054-6058.
30. Bashford, D.; Case, D. A.; Choi, C.; Gippert, G. P. J. Am. Chem. Soc. 1997, 119, 4964-4971.
31. O'Neil, K. T.; DeGrado, W. F. Science 1990, 250, 646-651.
32. Lyu, P. C.; Liff, M. I.; Marky, L. A.; Kallenbach, N. R. Science 1990, 250, 669-673.
33. Chakrabartty, A.; Kortemme, T.; Baldwin, R. L. Protein Sci. 1994, 3, 843-852.
34. Padmanabhan, S.; York, E. J.; Gera, J.; Stewart, J. M.; Baldwin, R. L. Biochemistry 1994, 33, 8604-8609.
35. Okamoto, Y. Proteins 1994, 19, 14-23.
36. Marqusee, S.; Robbins, V. H.; Baldwin, R. L. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 5286-5290.
37. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. J. Comput. Chem. 1986, 7, 230-252.
38. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; Reidel: Dordrecht, 1981; pp 331-342.
39. Haar, L.; Gallagher, J. S.; Kell, G. S. NBS/NRC Steam Tables: Hemisphere Publication Corp.; Washington DC, 1984.
40. Ripoll, D. R.; Scheraga, H. A. Biopolymers 1988, 27, 1283-1303.
41. Sung, S. S. Biophys. J. 1995, 68, 826-834.
42. Hockney, R. W. Methods Comput. Phys. 1970, 9, 135-211.
43. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
44. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Di Nicola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
45. Morikami, K.; Nakai, T.; Kidera, A.; Saito, M.; Nakamura, H. Comput. Chem. 1992, 16, 243-248.
46. Higo, J.; Endo, S.; Nagayama, K.; Ito, T.; Fukushige, T.; Ebisuzaki, T.; Sugimoto, D.; Miyagawa, H.; Kitamura, K.; Makino, J. J. Comput. Chem. 1994, 15, 1372-1376.
47. Komeiji, Y.; Uebayasi, M.; Takata, R.; Shimizu, A.; Itsukashi, K.; Taiji, M. J. Comput. Chem. 1997, 18, 1546-1563.
48. Press: W. H.; Teukolsky, S. A.; Veterling, W. T.; Flannery, B. P. Numerical Recipes in Fortran: The Art of Scientific Computing, 2nd ed.; Cambridge University Press: New York, 1996; pp 655-660.
49. Young, W. S.; Brooks, C. L., III. J. Mol. Biol. 1996, 259, 560-572.
50. Millhauser, G. L.; Stenland, C. J.; Hanson, P.; Bolin, K. A.; van de Ven, F. J. M. J. Mol. Biol. 1997, 267, 963-974.
51. Sheinerman, F. B.; Brooks, C. L., III. J. Am. Chem. Soc. 1995, 117, 10098-10103.
52. Rose, G. D.; Gierasch, L. M.; Smith, J. A. Adv. Protein Chem. 1985, 37, 1-109.
53. Pear, M. R.; Northrup, S. H.; McCammon, J. A.; Karplus, M.; Levy, R. M. Biopolymers 1981, 20, 629-632.
54. Helfand, E. Science 1984, 226, 647-650.
55. Shirley, W. A.; Brooks, C. L., III. Proteins 1997, 28, 59-71.
56. Kramers, H. A. Physica 1940, 7, 284-304.
57. Steinfeld, J. I.; Francisco, J. S.; Hase, W. L. Chemical Kinetics and Dynamics; Prentice Hall Inc.; New Jersey, 1989; pp 410-414.
58. Brooks, C. L., III. J. Phys. Chem. 1996, 100, 2546-2549.
59. Krynicki, K.; Green, C. D.; Sawyer, W. Faraday Discuss. Chem. Soc. 1978, 66, 199-208.
60. Alberty, R. A. Physical Chemistry, 7th ed.; John Wiley: New York, 1987.
61. Scholtz, J. M.; Marqusee, S.; Baldwin, R. L.; York, E. J.; Stewart, J. M.; Santoro, M.; Bolen, D. W. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 2854-2858.
62. Ooi, T.; Oobatake, M. J. Biochem. (Tokyo) 1988, 103, 114-120.
63. Ooi, T.; Oobatake, M. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 2859-2863.
64. Avbelj, F.; Fele, L. J. Mol. Biol. 1998, 279, 665-684.
65. Yang, A. S.; Honig, B. J. Mol. Biol. 1995, 252, 351-365.
66. Wang, L.; O'Connell, T.; Tropsha, A.; Hermans, J. Biopolymers 1996, 39, 479-489.
67. Braxenthaler, M.; Avbelj, F.; Moult, J. J. Mol. Biol. 1995, 250, 239-257.