Probing the active site of acetylcholinesterase by molecular dynamics of its phosphonate ester adducts

Journal of the American Chemical Society

Volumn 118, Issue 36, 1996, Pages 8531-8541

  Bencsura, Akos ^a,b   Enyedy, Istvan Y ^a   Kovach, Ildiko M ^a  

^a CATHOLIC UNIVERSITY OF AMERICA   (United States)

^b CTRL RES INSTITUTE FOR CHEMISTRY   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLCHOLINESTERASE; SOMAN;

ARTICLE; COMPUTER SIMULATION; ENZYME ACTIVE SITE; ENZYME ANALYSIS; MOLECULAR DYNAMICS; NONHUMAN; TORPEDO CALIFORNICA;

EID: 0029847276     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja952406v     Document Type: Article

References (64)

1. Sussman, J. L.; Harel, M.; Frolow, F.; Oefner, C.; Goldman, A.; Toker, L.; Silman, I. Science 1991, 253, 872-879.
2. Taylor, P.; Radic, Z. Annu. Rev. Pharmacol. Toxicol. 1994,34, 281-320.
3. Tan, R. C.; Truong, T. N.; McCammon, J. A.; Sussman, J. L. Biochemistry 1993, 32, 401-403.
4. Cygler, M.; Schrag, J. D.; Sussman, J. L.; Harel, M.; Silman, I.; Gentry, M. K.; Doctor, B. P. Protein Sci. 1993, 2, 366-382.
5. Antosiewicz, J.; McCammon, J. A.; Wlodek, S. T.; Gilson, M. K. Biochemistry 1995, 34, 4211-4219.
6. Qian, N.; Kovach, I. M. FEBS Lett. 1993, 336, 263-266.
7. (a) Bencsura, A.; Enyedy, I.; Kovach, I. M. Biochemistry 1995, 34, 8989-8999.
8. (b) Enyedy, I.; Bencsura, A.; Kovach, I. M. Phosphorus, Sulfur and Silicon 1996, 109-110, 249-252.
9. Kovach, I. M.; Qian, N. F.; Bencsura, A. FEBS Lett. 1994, 349, 60-64.
10. Saxena, A.; Qian, N.; Kovach, I. M.; Kozikowski, A. P.; Pang, Y. P.; Vellom, D. C.; Radic, Z.; Quinn, D.; Taylor, P.; Doctor, B. P. Protein Sci. 1994, 3, 1770-1778.
11. Ripoll, D. L.; Faerman, C. H.; Axelsen, P. H.; Silman, I.; Sussman, J. L. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 5128-5131.
12. Gilson, M. K.; Straatsma, T. P.; McCammon, J. A.; Ripoll, D. R.; Faerman, C. H.; Axelsen, P. H.; Silman, I.; Sussman, J. L. Science 1994, 263, 1276-1278.
13. Axelsen, P. H.; Harel, M.; Silman, I.; Sussman, J. L. Protein Sci. 1994, 3, 188-197.
14. Sterri, S. H.; Fonnum, F. Biochem. Pharmacol. 1987, 36, 3937-3942.
15. Kovach, I. M. J. Enzyme Inhib. 1988, 2, 199-208.
16. (a) Kovach, I. M.; Huber-Ashley Harmon, J.; Schowen, R. L. J. Am. Chem. Soc. 1988, 110, 590-593.
17. (b) Kovach, I. M. unpublished data on the inactivation of serine proteases by soman.
18. Bennet, A. J.; Kovach, I. M.; Bibbs, J. A. J. Am. Chem. Soc. 1989, 111, 6424-6427.
19. Kovach, I. M.; Larson, M.; Schowen, R. L. J. Am. Chem. Soc. 1986, 108, 3054-3056.
20. Bennet, A.; Kovach, I. M.; Schowen, R. L. J. Am. Chem. Soc. 1988, 110, 7892-7893.
21. Boter, H. L.; Ooms, A. J. Biochem. Pharmacol. 1967, 16, 1563-1569.
22. De Jong, L. P. A.; Benschop, H. P. In Stereoselectivity of Pesticides; Ariens, E. J., van Rensen, J. J. S., Welling, W., Eds.; Elsevier: Amsterdam, 1988; pp 109-149.
23. Ooms, A. J. J.; van Dijk, C. Biochem. Pharmacol. 1966, 15, 1361 - 1377.
24. Bencsura, A.; Enyedy, I.; Viragh, C.; Akhmetshin, R.; Kovach, I. M. In Proceedings of the Fifth International Meeting on Cholinesterases, Madras, India Quinn, M. D., Doctor, B. P., Eds.; Plenum Publishing. Co.: New York, 1995; pp 155-162.
25. Chambers, J. L.; Stroud, R. M. Acta Crystallogr., Sect. B 1977, 33, 1824.
26. Kossiakoff, A. A.; Spencer, S. A. Biochemistry 1981, 20, 6462-6474.
27. James, M. N. G. Can. J. Biochem. 1980, 58, 251-272.
28. Frey, P. A.; Whitt, S. A.; Tobin, J. B. Science 1994, 264, 1927-1930.
29. Quinn, D. M.; Sutton, L. D. In Enzyme Mechanism from Isotope Effects; Cook, P. F., Ed.; CRC Press: Boston, MA, 1991; pp 73-126.
30. Venkatasuban, K. S.; Schowen, R. L. CRC Crit. Rev. Biochem. 1985, 17, 1-44.
31. Quinn, D. M. Chem. Rev. 1987, 87, 955-975.
32. Quinn, D. M.; Pryor, A. N.; Selwood, T.; Lee, B. H.; Acheson, S. A.; Barlow, P. N. In Cholinesterases: Structure, Function, Mechanism, Genetics. and Cell Biology; Massoulie, J., Bacou, F., Barnard, E., Chatonnet, A., Doctor, B. P., Quinn, D. M., Eds.; American Chemical Society: Washington DC, 1991; pp 252-257.
33. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. J.; Kosecki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993, 14, 1347-1363.
34. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
35. Zhao, Q.; Kovach, I. M.; Bencsura, A.; Papathanassiu, A. Biochemistry 1994, 33, 8128-8138.
36. Walter, J.; Steigemann, W.; Singh, T. P.; Bartunik, H.; Bode, W.; Huber, R. Acta Crystallogr., Sect. B 1982, 38, 1462-1472.
37. Dixon, M. M.; Mathews, B. W. Biochemistry 1989, 28, 7033-7038.
38. (a) Vedani, A.; Huhta, D. V.; Jacober, S. P. J. Am. Chem. Soc. 1989, 111, 4075-4080.
39. (b) Vedani, A. J. J. Comput. Chem. 1988, 9, 269-280.
40. Hosea, N. A.; Berman, H. A.; Taylor, P. Biochemistry 1995, 34, 11528-11536.
41. Stroud, R. M.; Kay, L.; Dickerson, R. E. J. Mol. Biol. 1974, 83, 185-208.
42. (a) Polgar, L. Mechanisms of Protease Action, CRC Press, Inc.: Boca Raton, FL, 1990.
43. (b) Polgar, L. In Hydrolytic Enzymes; Neuberger, A., Brocklehurst, K., Eds.; Elsevier Sci. Pub. Co.: Amsterdam, 1987; pp 159-200.
44. Ordentlich, A.; Kronman, C.; Barak, D.; Stein, D.; Ariel, N.; Marcus, D.; Velan, B.; Shafferman, A. FEBS Lett. 1993, 334, 215-220.
45. Saxena, A.; Doctor, B. P.; Maxwell, D. M.; Lenz, D. E.; Radic, Z.; Taylor, P. Biochem. Biophys. Res. Commun. 1993, 197, 343-349.
46. Westheimer, F. H. Acc. Chem. Res. 1968, 1, 70-78.
47. McCammon, J. A.; Harvey, S. C. Dynamics of Proteins and Nucleic Acids; Cambridge University Press: Cambridge. 1989; pp 1-234.
48. Karplus, M.; McCammon, J. A. CRC Crit. Rev. Biochem. 1981, 293-349.
49. (a) Kovach, I. M.; Huhta, D.; Baptist, S. Theochem. 1991, 72, 99-110.
50. (b) Kovach, I. M. Theochem. 1988, 47, 159-169.
51. Kovach, I. M.; Huhta, D. Theochem. 1991, 79, 335-342.
52. (a) Kovach, I. M.; Larson, M.; Schowen, R. L. J. Am. Chem. Soc. 1986, 108, 5490-5495.
53. (b) Kovach, I. M.; Bennet, A. J. Phosphorus, Sulfur and Silicon 1990, 51/52, 51 -56.
54. Aslanian, D.; Grof, P.; Renault, F.; Masson, P. Biochim. Biophys. Acta 1995, 1249, 37-44.
55. Dewar, S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902-3909.
56. Porubcan, M. A.; Westler, W. M.; Ibanez, I. B.; Markley, J. L. Biochemistry 1979, 18, 4108-4116.
57. (a) Brooks III, C. L.; Brunger, A.; Karplus, M. Biopolymers 1985, 24, 843-865.
58. (b) Brunger, A. T.; Brooks, C. L. III; Karplus, M. Chem. Phys. Lett. 1984, 105,495-500.
59. (c) Berkowitz, M.; McCammon J. A. Chem. Phys. Lett. 1982, 90, 215-217.
60. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
61. Steinbach, P. J.; Brooks, B. R. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 9135-9139.
62. Nakagawa, S.; Yu, H.; Karplus, M.; Umeyama, H. Proteins: Struct. Func. Gen. 1993, 16, 172-194.
63. MacKerell Jr., A. D.; Karplus, M. unpublished.
64. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667-683.