On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

Journal of the American Chemical Society

Volumn 127, Issue 30, 2005, Pages 10648-10655

  Roca, Maite ^a   Andrés, Juan ^a   Moliner, Vicent ^a   Tuñón, Iñaki ^b   Bertrán, Juan ^c  

^a UNIVERSITAT JAUME I   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL ENGINEERING; CATALYSIS; ENZYMES; FREE ENERGY; HYDROXYLATION;

CATECHOLS; FREE ENERGY BARRIERS; NUCLEOPHILIC; TRANSITION STATE;

MOLECULAR DYNAMICS;

CATECHOL METHYLTRANSFERASE; MAGNESIUM; METHYL GROUP; OXYGEN; S ADENOSYLMETHIONINE; TRANSITION ELEMENT;

ARTICLE; CATALYSIS; CHEMICAL REACTION; ELECTROCHEMICAL ANALYSIS; ENERGY; ENZYME CHEMISTRY; ENZYME MECHANISM; MOLECULAR DYNAMICS;

CATECHOL O-METHYLTRANSFERASE; CATECHOLS; MODELS, MOLECULAR; QUANTUM THEORY; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 23044469487     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja051503d     Document Type: Article

References (43)

1. Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 444-448.
2. Benkovic, S. J.; Hammes-Schiffer, S. Science 2003, 301, 1196-1202.
3. Radkiewicz, J. L.; Brooks, C. L., III. J. Am. Chem. Soc. 2000, 122, 225-231.
4. Antonious, D.; Schwartz, S. D. J. Phys. Chem. B 2001, 105, 5553-5558.
5. Cameron, C. E.; Benkovic, S. J. Biochemistry 1997, 36, 15792-15800.
6. Martí, S.; Roca, M.; Andrés, J.; Moliner, V.; Tuñón, I.; Bertrán J. Chem. Soc. Rev. 2004, 33, 98-107.
7. (a) Villa, J.; Warshel, A. J. Phys. Chem. B 2001, 105, 7887-7907.
8. (b) Warshel, A. J. Biol. Chem. 1998, 273, 27035-27038.
9. García-Viloca, M.; Gao, J.; Karplus, M.; Truhlar D. G. Science 2004, 303, 186-195.
10. For a more detailed discussion about the relationship between activation free energies and PMFs, see: Schemer, G. K.; Garrett, B. C.; Truhlar, D. G. J. Chem. Phys. 2003, 119, 5828-5833.
11. (a) Pauling, L. Chem. Eng. News 1946, 24, 1375-1377.
12. (b) Pauling, L. Am. Sci. 1948, 36, 51-58.
13. (c) Pauling, L. Nature 1948, 161, 707-709.
14. Gao, J. Curr. Opin. Struct. Biol. 2003, 13, 184-192.
15. Nam, K.; Prat-Resina, X.; Garcia-Viloca, M.; Devi-Kesavan, L. S.; Gao, J. J. Am. Chem. Soc. 2004, 126, 1369-1376.
16. Neria, E.; Karplus, M. Chem. Phys. Lett. 1977, 267, 23-30.
17. Takusagawa, F.; Fujioka, M.; Spies, A.; Schowen, R. L. In Comprehensive Biological Catalysts; Sinnot, M., Ed.; Academic Press: San Diego, CA, 1998; Vol. 1, pp 1-30.
18. Gulberg, H. C.; Marsden, C. A. Pharmacol. Rev. 1975, 27, 135-206.
19. (a) Hegazi, M. F.; Borchardt, R. T.; Schowen, R. L. J. Am. Chem. Soc. 1979, 101, 4359-4365.
20. (b) Rodgers, J.; Femec, D. A.; Schowen, R. L. J. Am. Chem. Soc. 1982, 104, 3263-3268.
21. (a) Woodard, R. W.; Tsai, M. D.; Floss, H. G.; Crooks, P. A.; Coward, J. K. J. Biol. Chem. 1980, 255, 9124-9127.
22. (b) Knipe, J. O.; Vasquez, P. J.; Coward, J. K. J. Am. Chem. Soc. 1982, 104, 3202-3209.
23. (a) Zheng, Y. J.; Bruice, T. C. J. Am. Chem. Soc. 1997, 119, 8137-8145.
24. (b) Kahn, K.; Bruice, T. C. J. Am. Chem. Soc. 2000, 122, 46-51.
25. (a) Lau, E. Y.; Bruice, T. C. J. Am. Chem. Soc. 1998, 120, 12387-12394.
26. (b) Lau, E. Y.; Bruice, T. C. J. Am. Chem. Soc. 2000, 122, 7165-7171.
27. Kuhn, B.; Kollman, P. A. J. Am. Chem. Soc. 2000, 122, 2586-2596.
28. Roca, M.; Martí, S.; Andrés, J.; Moliner, V.; Tuñón, I.; Bertrán, J.; Williams, I. H. J. Am. Chem. Soc. 2003, 125, 7726-7737.
29. Vidgren, J.; Svensson, L. A.; Liljas, A. Nature 1994, 368, 354-358.
30. Field, M. J.; Albe, M.; Bret, C.; Proust-de Martin, F.; Thomas, A. J. Comput. Chem. 2000, 21, 1088-1100.
31. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-199.
32. (a) Ferrenberg, A. M.; Swedsen, R. H. Phys. Rev. Lett. 1989, 63, 1195-1198.
33. (b) Kumar, J.; Bouzida, D.; Swedsen, R. H.; Kollman, P.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
34. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902-3909.
35. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
36. (a) Moliner, V.; Turner, A. J.; Williams, I. H. J. Chem. Soc., Chem. Commun. 1997, 14, 1271-1272.
37. (b) Turner, A. J.; Moliner, V.; Williams, I. H. Phys. Chem. Chem. Phys. 1999, 1, 1323-1331.
38. Strnad, M.; Martins-Costa, M. T. C.; Millot, C.; Tuñón, I.; Ruiz-López, M. F.; Rivail, J. L. J. Chem. Phys. 1997, 106, 3643-3657.
39. Bergsma, J. P.; Gertner, K. R.; Wilson, K. R.; Hynes, J. T. J. Chem. Phys. 1987, 86, 1356-1376.
40. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon: Oxford, 1989.
41. For details of the error estimation procedure, see: Bradley, J.; Gertner, K. R.; Wilson, K. R.; Hynes, J. T. J. Chem. Phys. 1989, 90, 3537-3558.
42. Olsson, M. H. M.; Warshel, A. J. Am. Chem. Soc. 2004, 126, 15167-15179.
43. Soriano, A.; Silla, E.; Tuñón, I.; Ruiz-López, M. F. J. Am. Chem. Soc. 2005, 127, 1946-1957.