Conformational free energy surfaces of alaio and aibio peptide helices in solution

Journal of Physical Chemistry B

Volumn 105, Issue 9, 2001, Pages 1863-1876

  Mahadevan, Janaki ^a   Lee, Kyung Hoon ^a   Kuczera, Krzysztof ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; CONFORMATIONS; FREE ENERGY; HYDROGEN BONDS; OPTIMIZATION; SOLUTIONS; SURFACE PROPERTIES; WATER;

PEPTIDES; SOLVATION;

AMINO ACIDS;

EID: 0035281216     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp002474q     Document Type: Article

References (55)

1. Baker, E. N.; Hubbard, R. E. Prag. Biophys. Mol. Biol. 1984, 44, 97-179.
2. Barlow, D. J.; Thornton, J. M. J. Mol. Biol. 1988, 207, 601-619.
3. Yang, D. S. C; Sax, M.; Chakrabartty, A.; Hew, C. L. Nature 1988, 333, 232-237.
4. Scholtz, J. M.; Baldwin, R. L. Annu. Rev. Biophys. Biomol. Struct. 1992, 27, 95-118.
5. DeGrado, W. F.; Walsh, S. T. R.; Roder, H. Proc. Natl. Acad. Sci. 1999, 96, 5486. ;
6. Liu, D.; Williamson, D. A.; Kennedy, M. L.; Williams, T. D.; Morton, M.; Benson, D. R. J. Am. Chem. Soc. 1999, 727, 11798-11812.
7. Pauling, L.; Corey, R. B. Proc. Natl. Acad. Sci. U.S.A. 1950, 37, 235-240.
8. Low, B. W.; Baybutt, R. B. J. Am. Chem. Soc. 1952, 74, 58065807.
9. Donohue, J. Proc. Natl Acad. Sci. U.S.A. 1953, 39, 470- 478.
10. Creighton, T. E. Proteins. Structures and Molecular Properties; W. H. Freeman: New York, 1993.
11. Bavioso, A.; Benedetti, E.; DiBlasio, B.; Pavone, V.; Pedone, C.; Toniolo, C.; Bonora, G. M. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 19881992.
12. Toniolo, C; Crisma, M.; Bonora, G. M.; Benedetti, E.; DiBlasio, B.; Pavone, V.; Pedone, C.; Santini, A. Biopolymers 1991, 37, 129-138.
13. Smythe, M. L.; Huston, S. E.; Marshall, G. E. J. Am. Chem. Soc. 1995, 777, 5445-5452.
14. Weaver, T. Protein Sci. 2000, 9, 201-206.
15. Rajashankar, K. R.; Ramakumar, S. Protein Sci. 1996, 5, 932-946.
16. Sasaki, S.; Yasumoto, Y.; Uematsu, I. Macromolecules 1981, 14, 1797-1801.
17. Musso, G. F.; Patthi, G. S.; Ryskamp, T. C.; Provov, S.; Kaiser, E. T.; Velicelebi, G. Biochemistry 1998, 27, 8174-8181.
18. Kovacs, H.; Mark, A. E.; Johansson, J.; van Gunsteren, W. F. J. . Mol. Biol. 1995, 247, 808-822.
19. Shirley, W. A.; Brooks, C. L., III Proteins 1997, 28, 59-71.
20. Sessions, R. B.; Gibbs, N.; Dempsey, C. E. Biophys. J. 1998, 74, 138-152.
21. Duneau, J.-R; Crouzy, S.; Chapron, Y.; Genest, M. Theor. Chan. Acc. 1999, 101, 87-91.
22. Kuczera, K. J. Comput. Chem. 1996, 17, 1726-1749.
23. Wang, Y.; Kuczera, K. J. Phys. Chem. B 1997, 101, 5205-5213.
24. Wang, Y.; Kuczera, K. Theor. Chem. Acc. 1999, 101, 274-281.
25. Ramachandran, G.; Sasisekharan, H. Adv. Protein Chem. 1968, 23, 284-438.
26. Leach, A. R. Molecular Modeling. Principles and Applications', Longman, Harlow: 1996.
27. Sharp, K. A.; Honig, B. Amu. Rev. Biophys. Biophys. Chem. 1990, 19, 30l.
28. Marrone, T. J.; Gilson, M. K.; McCammon, J. A. J. Phys. Chem. 1996, 100, 1439-1441.
29. Scarsi, M.; Apostolakis, J.; Caflisch, A. J. Phys. Chem. B 1998, 702, 3637-3641.
30. Vorobjev, Y. N.; Hermans, J. Biophys. Chem. 1999, 78, 195-205.
31. Brooks, C. L., Ill; Case, David A. Chem. Rev. 1993, 93, 2487-2502.
32. Hermans, J. Curr. Opin. Struct. Biol. 1993, 3, 270-276.
33. Tirado-Rives, J.; Maxwell, D. S.; Jorgensen, W. L. J. Am. Chem. Soc. 1993, 775, 11590-11593.
34. Huston, S. E.; Marshall, G. E. Biopolymers 1994, 34, 75-90.
35. Zhang, L.; Hermans, J. J. Am. Chem. Soc. 1994, 116, 11915-11921.
36. Basu, G.; Hirata, F.; Go, N. J. Am. Chem. Soc. 1994, 776, 6307-6315.
37. Brooks, B. R.; Bruccoleri, R.; Olafson, B.; States, D.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
38. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattös, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stole, R.; Sträub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Karplus, M. J. Phys. Chem. B 1998, 702, 3386-3616.
39. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
40. Allen, M. P.; Tildesley, D. J. Computer Simulations of Liquids; Oxford Science Publications: London, 1987.
41. Feller, S. E.; Zhang, Y.; Pastor, R. W. J. Chem. Phys. 1995, 701, 4613-4621.
42. Tobias, D. J.; Brooks, C. L., III J. Chem. Phys. 1988, 59, 51 IS-5127.
43. Tobias, D. J.; Brooks, C. L., III J. Chem. Phys. 1990, 92, 2582-2592.
44. Carter, E. A.; Ciccotti, G.; Hynes, J. T.; Kapral, R. Chem. Phys. Lett. 1989, 756, 472-477.
45. H. W.; Flannery, B. P.; Teukolsky, S. A.; Vetterling, W. T. Numerical Recipes: The Art of Scientific Computing; Cambridge University Press: Cambridge, 1986.
46. Schlick, T. Optimization Methods in Computational Chemistry. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1992; Vol. 3, pp 1-71.
47. Bevington, P. R. Data Reduction and Error Analysis for the Physical Sciences, 2nd ed.; McGraw-Hill: New York, 1992.
48. Brooks, C. L., Ill; Karplus, M.; Petitt, B. M. Proteins: A Tlieoretical Perspective of Dynamics, Structure, and Thermodynamics; John Wiley and Sons: New York, 1988.
49. Marshall, G. R.; Beusen, D. D. Structural Basis of Peptide Channel Formation. In Biomembrane Electrochemistry; Blank, M., Vodyanoy, I., Eds.; American Chemical Society: Washington, DC, 1994; pp 259-314.
50. Karle, I. L.; Flippen-Andersen, J.; Uma, K.; Balaram, P. Curr. Sci. 1990, 59, 875-885.
51. Chotia, C. Annu. Rev. Biochem. 1984, 53, 537-572.
52. Honig, B.; Nicholls, A. Science 1995, 265, 1144-49.
53. Simonson, T.; Brunger, A. J. Phys. Chem. 1994, 98, 4683-4694.
54. Otoda, K.; Yasuyuki, K.; Kimura, S.; Imanishi, Y. Biopolymers 1993, 33, 1337-1345.
55. Kraulis, P. J. J. Appl. Cryst. 1991, 24, 946-950.