Theoretical modeling of enzyme catalytic power: Analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

Journal of the American Chemical Society

Volumn 125, Issue 25, 2003, Pages 7726-7737

  Roca, Maite ^a   Martí, Sergio ^a   Andrés, Juan ^a   Moliner, Vicent ^a   Tuñón, Iñaki ^b   Bertrán, Juan ^c   Williams, Ian H ^d  

^a UNIVERSITAT JAUME I   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^d University of Bath Claverton Down   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CHEMICAL ACTIVATION; COMPUTER SIMULATION; DECOMPOSITION; ELECTRIC FIELDS; ELECTROSTATICS; FREE ENERGY; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; NEGATIVE IONS; POSITIVE IONS; POTENTIAL ENERGY; SOLUTIONS; STATISTICAL MECHANICS; SUBSTRATES; WATER;

BIOMOLECULAR REACTIONS;

ENZYMES;

ANION; CATECHOL METHYLTRANSFERASE; CATION; S ADENOSYLMETHIONINE; SOLVENT; SULFONIUM DERIVATIVE; TRIMETHYLSULFONIUM DERIVATIVE; UNCLASSIFIED DRUG; WATER;

AQUEOUS SOLUTION; ARTICLE; CALCULATION; CATALYSIS; CATALYST; CHEMICAL REACTION; CONCENTRATION RESPONSE; CONFORMATIONAL TRANSITION; DECOMPOSITION; ELECTRIC FIELD; ELECTRIC POTENTIAL; ENERGY; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME STABILITY; ENZYME STRUCTURE; FORCE; GAS; MOLECULAR DYNAMICS; POLARIZATION; POLYMERIZATION; REACTION ANALYSIS; SIMULATION; SOLUTE; STRUCTURE ANALYSIS; TECHNIQUE; TEMPERATURE DEPENDENCE; THEORETICAL MODEL; THERMODYNAMICS; TWO HYBRID SYSTEM;

EID: 84961983443     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0299497     Document Type: Article

References (78)

1. (a) Fersht, A. Enzyme Structure and Mechanism; W. H. Freeman and Company: New York, 1985.
2. (b) Jencks, W. P. Adv. Enzymol. 1975, 43, 219-410.
3. (a) Pauling, L. Chem. Eng. News 1946, 24, 1375-1377.
4. (b) Pauling, L. Nature 1948, 161, 707-709.
5. (a) Warshel, A. P. Natl. Acad. Sci. U.S.A. 1978. 75, 5250-5254.
6. (b) Warshel, A. J. Biol. Chem. 1998, 273, 27035-27038.
7. (a) Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161-2200.
8. (b) Cramer, C. J.; Truhlar, D. G. In Solvent Effects and Chemical Reactivity; Tapia, O., Bertrán, J., Eds. Kluwer: Dordrecht, The Netherlands, 1996; pp 1-80.
9. (a) Menger, F. M. Acc. Chem. Res. 1993, 26, 206-212.
10. (b) Khanjin, N. A.; Snyder, J. P.; Menger, F. M. J. Am. Chem. Soc. 1999, 121, 11831-11846.
11. (a) Lau, E. Y.; Bruice, T. C. J. Am. Chem. Soc. 1998, 120, 12387-12394.
12. (b) Torres R. A.; Schiøt B.; Bruice T. C. J. Am. Chem. Soc. 1999, 121, 8164-8173.
13. (c) Lightstone, F. C.; Bruice, T. C. J. Am. Chem. Soc. 1996, 118, 2595-2605.
14. (d) Bruice, T. C.; Lightstone, F. C. Acc. Chem. Res. 1999, 32, 127-136.
15. (e) Bruice, T. C.; Benkovic, S. J. Biochemistry 2000, 39, 6267-6274. Bruice, T. C. Acc. Chem. Res. 2002, 35, 139-148.
16. (e) Bruice, T. C.; Benkovic, S. J. Biochemistry 2000, 39, 6267-6274. Bruice, T. C. Acc. Chem. Res. 2002, 35, 139-148.
17. Mesecar, A. T.; Stoddard, B. L.; Koshland, D. E. Science 1997, 227, 202-206.
18. Westheimer, F. H. Adv. Enzymol. 1962, 24, 441-482.
19. Page, M. I.; Jencks, W. P. Proc. Natl. Acad. Sci. U.S.A. 1971, 68, 1678.
20. Hermans, J.; Wang, L. J. Am. Chem. Soc. 1997, 119, 2707-2714.
21. (a) Stanton, R. V.; Peräkylä, M.; Bakowies, D.; Kollman, P. A. J. Am. Chem. Soc. 1998, 120, 3448-3457.
22. (b) Kollman, P. A.; Kuhn, B.; Donini, O.; Peräkylä, M.; Stanton, R. V.; Bakowies, D. Acc. Chem. Res. 2001, 34, 72-79.
23. Villà, J.; Strajbl, M.; Glennon, T. M.; Sham, Y. Y.; Chu, Z. T.; Warshel, A. P. Natl. Acad. Sci. U.S.A. 2000, 97, 11899-11904.
24. (a) Martí, S.; Andrés, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J. Theor. Chem. 2001, 105, 207-212.
25. (b) Martí, S.; Andrés, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J. J. Phys. Chem. B. 2000, 104, 11308-11315.
26. (c) Martí, S.; Andrés, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J.; Field, M. J. J. Am. Chem. Soc. 2001, 123, 1709-1712.
27. (d) Martí, S.; Andrés, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J. P. Chem.-Eur. J. 2003, 9, 984-991.
28. (e) Martí, S.; Andrés, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J. P. THEOCHEM, in press.
29. Roux, B. Comput. Phys. Commun. 1995, 91, 275-282.
30. Takusagawa, F.; Fujioka, M.; Spies, A.; Schowen. R. L. In Comprehensive Biological Catalyzis; Sinnott, M., Ed.; Academic Press: San Diego, CA, 1998; Vol. 1, pp 1-30.
31. Gulberg, H. C.; Marsden, C. A. Pharmacol. Rev. 1975, 27, 135-206.
32. (a) Hegazi, M. F.; Borchardt, R. T.; Schowen, R. L. J. Am. Chem. Soc. 1979, 101, 4359-4365.
33. (b) Rodgers, J.; Femec, D. A.; Schowen, R. L. J. Am. Chem. Soc. 1982, 104, 3263-3268.
34. (a) Woodard, R. W.; Tsai, M. D.; Floss, H. G.; Crooks, P: A. Coward, J. K. J. Biol. Chem. 1980, 255, 9124-9127.
35. (b) Knipe, J. O.; Vasquez, P. J.; Coward, J. K. J. Am. Chem. Soc. 1982, 104, 3202-3209.
36. (a) Zheng, Y. J.; Bruice, T. C. J. Am. Chem. Soc. 1997, 119, 8137-8145.
37. (b) Kahn, K.; Bruice, T. C. J. Am. Chem. Soc. 2000, 122, 46-51.
38. (c) Lau, E. Y.; Bruice, T. C. J. Am. Chem. Soc. 2000, 122, 7165-7171.
39. Kuhn, B.; Kollman, P. A. J. Am. Chem. Soc. 2000, 122, 2586-2596.
40. Schultz, E.; Nissinen, E. Biochem. Pharmacol. 1989, 38, 3953-2956.
41. Strajbl, M.; Florian, J.; Warshel, A. J. Phys. Chem. B. 2001, 105, 4471-4484.
42. (a) Moliner, V.; Turner, A. J.; Williams, I. H. J. Chem. Soc., Chem. Commun. 1997, 1271.
43. (b) Turner, A. J.; Moliner, V.; Williams, I. H. J. Phys. Chem. Chem. Phys. 1999, 1, 1323-1331.
44. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
45. (a) Schmidt, M. W.; Gordon, M. S.; Dupuis, M. J. Am. Chem. Soc. 1985, 107, 2585-2589.
46. (b) Stewart, J. J. P. MOPAC 7, (QCPE 457). Quantum Chem. Program Exch. Bull. 1993, 13, 42.
47. Vidgren, J.; Svensson, L. A.; Liljas, A. Nature 1994, 368, 354-358.
48. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935. Note that CHARMM contains a modified TIP3P potential that includes intramolecular terms.
49. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; J. Tomasi; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, revision A.6; Gaussian. Inc.; Pittsburgh, PA, 1998.
50. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902-3909.
51. (a) Head-Gordon, M.; Pople, J. A.; Frisch, M. J. Chem. Phys. Lett. 1988, 153, 503-506.
52. (b) Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 275-280.
53. (c) Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 281-289.
54. Brooks, C. L.; Karplus, M. J. Mol. Biol. 1989, 208, 159-181.
55. Field, M. J.; Albe, M.; Bret, C.; Proust-de Martin, F.; Thomas, A. J. Comput. Chem. 2000, 21, 1088-1100.
56. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-199.
57. Miertu, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117-129.
58. (b) Cammi, R.; Tomasi, J. J. Chem. Phys. 1994, 100, 7495-7502.
59. (a) Gurney, R. W. Ionic Processes in Solution; McGraw-Hill: New York, 1953; pp 88-91.
60. (b) Yu, Y. B.; Privalov, P. L.; Hodges, R. S. Biophys. J. 2001, 81, 1632-1642.
61. Swain, C. G.; Taylor L. J. J. Am. Chem. Soc. 1962, 84, 2456-2457.
62. Coward, J. K.; Sweet, W. D. J. Org. Chem. 1971, 36, 2337-2346.
63. Paetzel, M.; Dalbey, R. E. Trends Biochem. Sci. 1997, 22, 28-31.
64. Kenyon, G. L.; Gerlt, J. A.; Petsko, G. A.; Kozarich, J. W. Acc. Chem. Res. 1995, 28, 178-186.
65. Cramer, C. J. Essentials of Computational Chemistry: Theories and Models; Wiley: Chichester, U.K., 2002; p 378.
66. Williams, I. H. Chem. Phys. Lett. 1982, 88, 462-466.
67. Williams, I. H. J. Mol. Struct. THEOCHEM 1983, 11, 275-284.
68. Williams, I. H.; Spangler, D.; Femec, D. A.; Maggiora, G. M.; Schowen, R. L. J. Am. Chem. Soc. 1983, 105, 31-40.
69. Wertz, D. H. J. Am. Chem. Soc. 1980, 102, 5316-5322.
70. Abraham, M. H. J. Am. Chem. Soc. 1982, 104, 2085-2094.
71. Ben-Naim, A.; Marcus, Y. J. Chem. Phys. 1984, 81, 2016-2027.
72. Strajbl, M.; Sham, Y. Y.; Villà, J.; Chu, Z.-T.; Warshel, A. J. Phys. Chem. B 2000, 104, 4578-4584.
73. Sham, Y. Y.; Chu, Z.-T.; Tao, H.; Warshel, A. Proteins: Struct., Funct., Genet. 2000, 39, 393-407.
74. Warshel, A.; Parson, W. W. Q. Rev. Biophys. 2001, 34, 563-679.
75. Solà, M.; Lledós, A.; Durán, M.; Bertrán, J.; Abboud, J. L. M. J. Am. Chem. Soc. 1991, 113, 2873-2879.
76. Gao, J.; Xia, X. J. Am. Chem. Soc. 1993, 115, 9667-9675.
77. Dillet, V.; Rinaldi, D.; Bertrán, J.; Rivail, J. L. J. Chem. Phys. 1996, 104, 9437-9444.
78. Florian, J.; Goodman, M. F.; Warshel, A. J. Phys. Chem. B. 2002, 106, 5739-5753.