Molecular dynamics simulations of cyclic and linear DPDPE: Influence of the disulfide bond on peptide flexibility

Journal of Physical Chemistry

Volumn 100, Issue 7, 1996, Pages 2555-2563

  Wang, Yan ^a   Kuczera, Krzysztof ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000114578     PISSN: 00223654     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp952669b     Document Type: Article

References (53)

1. Thornton, J. M. J. Mol. Biol. 1981, 151, 261-287.
2. Creighton, T. E. J. Phys. Chem. 1983, 89, 2452-2459.
3. Creighton, T. E., Ed. Protein folding; W. H. Freeman: New York, 1992.
4. Holmgren, A. Annu. Rev. Biochem. 1985, 54, 237-271.
5. Creighton, T. E. Bioessays 1988, 8, 57-63.
6. Nishiuchi, Y.; Sakakibara, S. FEBS Lett. 1982, 148, 260-262.
7. Yanagisawa, M.; Kurihara, H.; Kimura, S.; Tomobe, Y.; Kobayashi, M.; Mitsui, Y.; Yazaki, Y.; Goto, K.; Masaki, T. Nature 1988, 332, 441-415.
8. Hruby, V. J.; Smith, C. W. In The Peptides: Analysis, Synthesis, Bioloqy; Udenfriend, S., Meienhofer, J., Eds.; Academic Press: London, 1987; pp 77-197.
9. Mosberg, H. I.; Hurst, R.; Hruby, V. J.; Gee, K.; Yamamura, H. I.; Galligan, J. J.; Burks, T. F. Proc. Natl. Acad. Sci. U.S.A. 1983, 80, 5871-5874.
10. Hughes, J.; Smith, T. W.; Kosterlitz, H. W.; Forthergill, L. A.; Morgan, B. A.; Morris, H. R. Nature 1975, 258, 577-580.
11. Hruby, V. J. Opioid Peptides: Medicinal Chemistry; Rapaka, R. S., Barnett, G., Hawks, R. L., Eds.; National Institute on Drug Abuse Research Monograph 69; NIDA: Rockville, MD, 1986; pp 128-147.
12. Udenfriend, S., Meienhoferr, J., Eds. The peptides, analysis, synthesis, biology. Opioid peptides: Biology, Chemistry, and Genetics; Academic Press: Orlando, FL, 1984; Vol. 6, pp 147-189.
13. Schiller, P. W. The peptides. analysis, synthesis, biology. Opioid peptides: Biology, Chemistry, and Genetics; Acdemic Press: Orlando, FL, 1984; Vol. 6, pp 219-268.
14. Froimowitz, M.; Hruby, V. J. Int. J. Peptide Protein Res. 1989, 34, 89-96.
15. Nikiforovich, G. V.; Hruby, V. J.; Prakash, O.; Gehrig, C. A. Biopolymers 1991, 31, 941-955.
16. Hruby, V. J.; Kao, L.-F.; Pettitt, B. M.; Karplus, M. J. Am. Chem. Soc. 1988, 110, 3351-3359.
17. Pettitt, B. M.; Matsunaga, T.; Al-Obeidi, F.; Gehrig, C.; Hruby, V. J.; Karplus, M. Biophys. J. 1991, 60, 1540-1544.
18. Smith, P. E.; Dang, L. X.; Pettitt, B. M. J. Am. Chem. Soc. 1991, 113, 67-73.
19. Smith, P. E.; Pettitt, B. M. Biopolymers 1992, 32, 1623-1629.
20. Wilkes, B. C.; Schiller, P. W. J. Comput.-Aided Mol. Des. 1991, 5, 293-302.
21. Chew, C.; Villar, H. O.; Loew, G. H. Mol. Pharm. 1991, 39, 502-510.
22. Flippen-Anderson, J. L.; Hruby, V. J.; Collins, N.; George, C.; Cudney, B. J. Am. Chem. Soc. 1994, 116, 7523-7531.
23. Misicka, A.; Lipkowski, A. W.; Horvath, R.; Davis, P.; Porreca, F.; Yamamura, H. I.; Hruby, V. J. Int. J. Pept. Protein Res. 1994, 44, 80-84.
24. Froimowitz, M. Biopolymers 1990, 30, 1011-1025.
25. Haaseth, R. C.; Sobczyk-Kojiro, K.; Medzihradsky, F.; Smith, C. B.; Mosberg, H. I. Int. J. Pept. Protein Res. 1990, 36, 139-146.
26. Mosberg, H. I.; Sobczyk-Kojiro, K.; Subramanian, P.; Crippen, G. M.; Ramalingam, K.; Woodard, R. W. J. Am. Chem. Soc. 1990, 112, 822-829.
27. Misicka, A.; Nikiforovich, G.; Lipkowski, A. W.; Horvath, R.; Davis, P.; Kramer, T. H.; Yamamura, H. I.; Hruby, V. J. Bioorg. Med. Chem. Lett. 1992, 2, 547-552.
28. Qian, X.; Köver, K. E.; Shenderovich, M. D.; Lou, B.-S.; Misika, A.; Zalewska, T.; Horvath, R.; Davis, P.; Bilsky, E. J.; Porreca, F.; Yamamura, H. I.; Hruby, V. J. J. Med. Chem. 1994, 37, 1746-1575.
29. Smith, P. E.; Marlow, G. E.; Pettitt, B. M. J. Am. Chem. Soc. 1993, 115, 7493-7498.
30. Matsunaga, T. O.; Collins, N.; Ramaswami, V.; Yamamura, S. H.; O'Brien, D. F.; Hruby, V. J. Biochemistry 1993, 32, 13180-13189.
31. Ramaswami, V.; Haaseth, R. C.; Matsunaga, T. O.; Hruby, V. J.; O'Brien, D. F. Biochim. Biophys. Acta 1992, 1109, 195-202.
32. Brownson, E. A.; Abbruscato, T. J.; Gillespie, T. J.; Hruby, V. J.; Davis, T. P. J. Pharmacol. Exp. Ther. 1994, 270 (2), 675-680.
33. Thirumalai, D.; Mountain, R. D. Phys. Rev. A 1990, 42, 4574-4587.
34. Straub, J. E.; Rashkin, A. B.; Thirumalai, D. J. Am. Chem. Soc. 1994, 116, 2049-2063.
35. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
36. Brooks, B. R.; Bruccoleri, R.; Olafson, B.; States, D.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
37. Nikiforrovich, G. V.; Golbraikh, A. A.; Shenderovich, M. D.; Balodis, J. Int. J. Pept. Protein Res. 1990, 36, 209-218.
38. Srinivasan, N.; Sowdhamini, R.; Ramakrishnan, C.; Balaram, P. Int. J. Pept. Protein Res. 1990, 36, 147-155.
39. Tobias, D. J.; Mertz, J. E.; Brooks, C. L., III. Biochemistry 1991, 30, 6054-6058.
40. Bruccoleri, R. E.; Karplus, M. Biopolymers 1990, 29, 1847-1862.
41. Roitberg, A.; Elber, R. J. Chem. Phys. 1992, 95, 9277.
42. Lewis, P. N.; Momany, F. A.; Scheraga, H. A. Biochim. Biophys. Acta 1973, 303, 211-229.
43. Brooks, C. L., III; Karplus, M.; Petitt, B. M. Proteins; John Wiley and Sons: New York, 1988.
44. Bystrov, V. F. Prog. Nucl. Magn. Reson. Spectrosc. 1976, 10, 41-81.
45. de Leeuw, C.; amd Altona, F. A. A. M. Int. J. Pept. Protein Res. 1982, 20, 120-125.
46. McQuarrie, D. A. Statistical Mechanics; Harper & Row: New York, 1976.
47. McConnell, J. Rotational Brownian Motion and Dielectric Theory; Academic Press: London, 1980.
48. Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry: Techniques for the Study of Biological Structure and Function; W. H. Freeman: New York, 1980; Vol. II.
49. Pratt, W. B., Taylor, P., Eds.; Principles of Drug Action; Churchill Livingstone Inc.: New York, 1990.
50. Burgen, A. S. V. J. Pharm. Pharmacol. 1966, 18, 137.
51. Alberty, R. A.; Hammes, G. G. J. Phys. Chem. 1958, 62, 154.
52. Straub, J. E.; Thirumalai, D. Proteins: Structure, Funct., Genet. 1993, 15, 360-373.
53. Kraulis, P. J. J. Appl. Crystallogr. 1991, 24, 946-950.