Reaction mechanism of soluble epoxide hydrolase: Insights from molecular dynamics simulations

Journal of the American Chemical Society

Volumn 124, Issue 49, 2002, Pages 14558-14570

  Schiøtt, Birgit ^a   Bruice, Thomas C ^b  

^a AARHUS UNIVERSITY   (Denmark)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; COMPUTER SIMULATION; HYDROGEN BONDS; HYDROLYSIS; MUTAGENESIS; SUBSTRATES;

PROTONATION;

ENZYMES;

ALCOHOL DERIVATIVE; AMINO ACID; AROMATIC COMPOUND; CARBON; EPOXIDE; EPOXIDE HYDROLASE; HISTIDINE; META TYROSINE; METHYLSTYRENE OXIDE; OXIDE; OXYGEN; PHENYL GROUP; TRYPTOPHAN; UNCLASSIFIED DRUG;

ARTICLE; ATOM; CATALYSIS; CONFORMATION; ENZYME ACTIVITY; ENZYME STABILITY; ENZYME STRUCTURE; HYDROGEN BOND; HYDROLYSIS; MOLECULAR DYNAMICS; MUTAGENESIS; PROTON TRANSPORT; REACTION ANALYSIS; SIMULATION; SOLUBILITY; STEREOCHEMISTRY;

ANIMALS; COMPUTER SIMULATION; EPOXIDE HYDROLASES; MICE; MODELS, MOLECULAR; PROTEIN CONFORMATION; SOLUBILITY; STYRENES; THERMODYNAMICS;

EID: 1942517067     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja021021r     Document Type: Article

References (69)

1. Greene, J. F.; Newman, J. W.; Williamson, K. C.; Hammock, B. D. Chem. Res. Tox. 2000. 13, 217-226.
2. Fretland, A. J.; Omiecinski, C. J. Chem. Biol. Interac. 2000, 129, 41-59.
3. Oesch, F. Xenobiotica 1973, 3, 305-340.
4. Ota, K.; Hammock, B. D. Science 1980, 207, 1479-1481.
5. Wixtram, R. N.; Hammock, B. D. Biochemical Pharmacology and Toxicology; Zakim, D., Vessey, D. A., Eds.; Wiley: New York, 1985; Vol. 1, 1-93.
6. (a) Zeldin, D.; Wei, S.; Falck, J. R.; Hammock, B. D.; Snapper, J. R.; Capdevila, J. H. Arch. Biochem. Biophys. 1995, 316, 443-451.
7. (b) Morriseau, C.; Beetham, J. K.; Pinot, F.: Debernard, S.; Newman, J. W.; Hammock, B. D. Arch. Biochem. Biophys. 2000, 378, 321-332.
8. (c) Armstrong, R. N. Drug Metab. Rev. 1999, 31, 71-86.
9. Archer, I. V. J. Tetrahedron 1997, 53, 15 617-15 662.
10. Pedragosa-Moreau, S.; Archelas, A.; Furstoss, R. J. Org. Chem. 1993, 58, 5533-5536.
11. Mischitz, M.; Kroutil, W.; Wandel, U.; Faber, K. Tetrahedron: Asymmetry 1995, 6, 1261-1272.
12. Orru, R. V. A.; Faber, K. Curr. Opion. Chem. Biol. 1999, 3, 16-21.
13. Chiappe, C.; Rubertis, A. D.; Marioni, F.; Pelagotti, F. J. Mol. Catal. B 2001, 14, 125-129.
14. Archelas, A.; Furstoss, R. Curr. Opion. Chem. Biol. 2001, 5, 112-119; Archelas, A.; Furstoss, R. Trends Biotech. 1998, 16, 108-116.
15. Archelas, A.; Furstoss, R. Curr. Opion. Chem. Biol. 2001, 5, 112-119; Archelas, A.; Furstoss, R. Trends Biotech. 1998, 16, 108-116.
16. Beetham, J. K.; Grant, D.; Arand, M.; Garbarino, J.; Kiyosue, T.; Pinot, F.; Oesch, F.; Belknap, W. R.; Shinozaki, K.; Hammock, B. D. DNA Cell Biol. 1995, 14, 61-71.
17. Nardini, M.; Dijkstra, W. Curr. Opion. Struct. Biol. 1999, 9, 732-737.
18. (a) Arand, M.; Wagner, H.; Oesch, F. J. Chem. Biol. 1996, 271, 4223-4229;
19. (b) Rink, R.; Fenneman, M.; Smids, M.; Dehmel, U.; Janssen, D. B. J. Biol. Chem. 1997, 272, 14 650-14 657.
20. (a) Lacourciere, G. M.; Armstrong, R. N. J. Am. Chem. Soc. 1993, 115 10466-10 467.
21. (b) Borhan, B.; Jones, A. D.; Pinot, F.; Grants, D. F.; Kurth M. J.; Hammock, B. D. J. Biol. Chem. 1995, 270, 26 923-26 930.
22. (a) Rink, R.; Spelberg, J. H. L.; Pieters, R. J.; Kingma, J.; Nardini, M. Kellogg, R. M.; Dijksatra, B. W.; Janssen, D. B. J. Am. Chem. Soc. 1999 121, 7417-7418;
23. (b) Rink, R.; Kingma, J.; Spelberg, J. H. L.; Janssen, D. B. Biochemistry 2000, 39, 5600-5613;
24. (c) Yamada, T.; Morisseau, C.; Maxwell, J. E. M. A. Argiriadi, Christianson, Hammock, B. D. J. Biol. Chem. 2000, 275, 23 082-23 088.
25. Argiriadi, M. A.; Morrisseau, C.; Hammock, B. D.; Christianson, D. W. Proc. Natl. Acad. Sci. 1999, 96, 10 637-10 642.
26. Nardini, M.; Ridder, I. S.; Rozeboom, H. J.; Kalk, K. H.; Rink, R.; Janssen, D. B.; Dijkstra, B. W. J. Biol. Chem. 1999, 274, 14 579-14 586.
27. Zou, J.; Hallberg, B. M.; Bergfors, T.; Oesch, F.; Arand, M.; Mowbray, S. L.; Jones, T. A. Structure 2000, 8, 111-122.
28. Argiriadi, M. A.; Morrisseau, C.; Goodrow, M. H.; Dowdy, D. L.; Hammock, B. D.; Christianson, D. W. J. Biol. Chem. 2000, 275, 15 265-15 270.
29. Armstrong, R. N.; Cassidy, C. S. Drug Metab. Rev. 2000, 32, 327-338.
30. Laughlin, L. T.; Tzeng, H.-F.; Lin, S.; Armstrong, R. N. Biochemistry 1998, 37, 2897-3904.
31. Brooks, B. R; Brucolleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
32. MacKerell Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher III, W. E.; Roux, B.; Schlenkrih, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3585-3616.
33. MidasPlus Version 2.1, Computer Graphics Lab., University of California, San Francisco, 1997.
34. Lau, E. Y.; Newby, Z. E.; Bruice, T. C. J. Am. Chem. Soc. 2001, 123, 3350-3357.
35. Breneman, C. M.; Wiberg, K. B. J. Comput. Chem. 1990, 11, 361-373.
36. QUANTA: Molecular Simulations Inc.: San Diego, CA, 1998, as of July 2001, Accelrys.
37. Brooks III, C. L.; Karplus, M. J. Mol. Biol. 1989, 208, 159-181.
38. Jorgensen, W. L.; Chandrasekhar. J.; Madura, J. D.; Impley, R. W.; Klein, M-. L. J. Chem. Phys. 1983, 79, 925-935.
39. Brünger, A. T.; Brooks, C. L.; Karplus, M. Proc. Natl. Acad. Sci. 1985, 82, 8458-8462.
40. McCammon, J. A.; Harvey, S. C. Dynamics of Proteins and Nucleic Acids: Cambridge University Press: Cambridge, 1987.
41. Verlet, L. Phys. Rev. 1967, 159, 98-113.
42. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667-683.
43. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Chem. 1977, 23, 327-341.
44. Ichiye, T.; Karplus, M. Proteins 1991, 11, 205-217.
45. Sinnokrot, M. O.; Valeev, E. F.; Sherrill, C. D. J. Am. Chem. Soc. 2002, 124, 10887-10893.
46. Clarage, J. B.; Romo, T.; Andrews, B. K.; Pettitt, B. M.; Phillips, G. N. Proc. Natl. Acad. Sci. 1995, 92, 3288-3292.
47. Iversen, B. B.; Larsen, F. K.; Figgis, B. N.; Reynolds, P. A.; Schultz, A. J. Acta Cryst, 1996, B52, 932-931.
48. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: A Theoretical Prespective of Dynamics, Structure and Thermodynamics; John Wiley and Sons: New York, 1987.
49. Mazumder, D.; Bruice, T. C. J. Am. Chem. Soc. In Press.
50. (a) Lightstone, F. C.; Bruice, T. C. J. Am. Chem. Soc. 1996, 118, 2595.
51. (b) Lightstone, F. C.; Bruice, T. C. Acc. Chem. Res. 1999, 32, 127-136.
52. Bruice, T. C. Acc. Chem. Res 2002, 35, 139-148.
53. Kollman, P. A.; Kuhn, B.; Peräkylä, M J. Phys. Chem. B 2002, 106, 1537-1542.
54. Field, M. J. J. Comput. Chem. 2002, 23, 48-58.
55. Daggett, V. Curr. Opion. Struct. Biol. 2000, 10, 160-164.
56. Lau, E. Y.; Bruice, T. C. J. Am. Chem. Soc. 1998, 120, 12 387-12 395.
57. Radkiewicz, J. L.; Brooks III, C. L. J. Am. Chem. Soc. 2000, 122, 225-231.
58. Bruice, T. C.; Benkovic, S. J. Biochemistry 2000, 39, 6267-6274.
59. Hammes, G. G. Biochemistry, 2002, 41, 8221-8228.
60. Swaminathan, S.; Harte, Jr., W. E.; Beveridge, D. L. J. Am. Chem. Soc. 1991, 113, 2717-2721.
61. Eisenmesser, E. Z.; Bosco, D. A. Akke, M.; Kern, D. Science 2002, 295, 1520-1523.
62. (a) Billeter, S. R.; Webb, S. P.; Argawal, P. K., Iordanov, T.; Hammes-Schiffer, S. J. Am. Chem. Soc. 2001, 123, 11 262-11 272.
63. (b) Agarwal, P. K.; Billeter, A. R.; Ravi Rajagopalan, P. T.; Benkovic, S. J.; Hammes-Schiffer, S. Proc. Natl. Acad. Sci. 2002, 99, 2794-2799.
64. Meijer, J.; Depierre, J. W. Eur. J. Biochem. 1985, 150, 7-16.
65. Guenther, T. M.; Oesch, F. J. Biol. Chem. 1983, 258, 15054-15061.
66. Tzeng, H.-F., Laughlin, L, T.; Armstrong, R. N. Biochemistry 1998, 37, 2905-2911.
67. Tzeng, H.-F.; Laughlin, L. T.; Lin, S,; Armstrong, R. N. J. Am. Chem. Soc. 1996, 118, 9436-9437.
68. Willamson, K. C.; Morrisseau, C.; Maxwell, J. E. Hammock, B. D. Tetrahedron Asymmetry 2000, 11, 4451-4462.
69. Lin, B.; Whalen, D. L. J. Org. Chem. 1995, 59, 1638-1641.