QM-FE and molecular dynamics calculations on catechol O- methyltransferase: Free energy of activation in the enzyme and in aqueous solution and regioselectivity of the enzyme-catalyzed reaction

Journal of the American Chemical Society

Volumn 122, Issue 11, 2000, Pages 2586-2596

  Kuhn, Bernd ^a   Kollman, Peter A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATECHOL METHYLTRANSFERASE; TRYPSIN;

ARTICLE; CATALYSIS; CHEMICAL ANALYSIS; ENERGY TRANSFER; ENZYME ACTIVATION; ENZYME MECHANISM; MOLECULAR DYNAMICS; QUANTUM MECHANICS; STEREOCHEMISTRY;

EID: 0034701258     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja992218v     Document Type: Article

References (66)

1. Hegazi, M. F.; Borchardt, R. T.; Schowen, R. L. J. Am. Chem. Soc. 1979, 101, 4359-4365.
2. Woodard, R. W.; Tsai, M. D.; Floss, H. G.; Crooks, P. A.; Coward, J. K. J. Biol. Chem. 1980, 255, 9124-9127.
3. Knipe, J. O.; Vasquez, P. J.; Coward, J. K. J. Am. Chem. Soc. 1982, 104, 3202-3209.
4. Rodgers, J.; Femec, D. A.; Schowen, R. L. J. Am. Chem. Soc. 1982, 104, 3263-3268.
5. Zheng, Y. J.; Bruice, T. C. J. Am. Chem. Soc. 1997, 119, 8137-8145.
6. Lau, E. Y.; Bruice, T. C. J. Am. Chem. Soc. 1998, 120, 12387-12394.
7. Lightstone, F. C.; Bruice, T. C. J. Am. Chem. Soc. 1996, 118, 2595-2605.
8. Mihel, I.; Knipe, J. O.; Coward, J. K.; Schowen, R. L. J. Am. Chem. Soc. 1979, 101, 4349-4351.
9. Stanton, R. V.; Perakyla, M.; Bakowies, D.; Kollman, P. A. J. Am. Chem. Soc. 1998, 120, 3448-3457.
10. Vidgren, J.; Svensson, L. A.; Liljas, A. Nature 1994, 368, 354-358.
11. Creveling, C. R.; Dalgard, N.; Shimizu, H.; Daly, J. W. Mol. Pharmacol. 1970, 6, 691-696.
12. Creveling, C. R.; Morris, N.; Shimizu, H.; Ong, H. H.; Daly, J. Mol. Pharmacol. 1972, 8, 398-409.
13. Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 154-162.
14. Chandrasekhar, J.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 2974-2975.
15. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280.
16. Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117.
17. Ovaska, M.; Yliniemela, A. J. Comput.- Aided Mol. Des. 1998, 12, 301-307.
18. Barratt, M. D. Toxicol. Lett. 1995, 80, 69-74.
19. Paetzel, M.; Dalbey, R. E. Trends Biochem. Sci. 1997, 22, 28-31.
20. a Prediction for Organic Acids and Bases; Chapman and Hall: London and New York, 1981.
21. Stryer, L. Biochemistry, 3rd ed.; W. H. Freeman and Company: New York, 1988.
22. Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. J. Am. Chem. Soc. 1998, 120, 9401-9409.
23. Kuhn, B.; Kollman, P. A. J. Am. Chem. Soc., in press.
24. Massova, I.; Kollman, P. A. J. Am. Chem. Soc. 1999, 121, 8133-8143.
25. 28 Solute entropy corrections -TS were neglected because they are expected to be similar for the monoanionic and dianionic complex formations and would thus cancel in the thermodynamic cycle (2) and in eq 3.
26. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
27. Fox, T.; Kollman, P. A. J. Phys. Chem. B 1998, 102, 8070-8079.
28. Aqvist, J. J. Phys. Chem. 1990, 94, 8021-8024.
29. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
30. Berendsen, H. J. C.; Potsma, J. P. M.; van Gunsteren, W. F.; DiNola, A. D.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
31. Ryckaert, J. P.; Cicotti, C.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
32. Mulholland, A. J.; Richards, W. G. Int. J. Quantum Chem. 1994, 51, 161-172.
33. 4′) = -83.7°.
34. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
35. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
36. Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623-11627.
37. Hehre, W. J.; Radom, L.; Schleyer, P. v. R.; Pople, J. A. Ab Initio Molecular Orbital Theory; John Wiley: New York, 1986.
38. Kendall, R. A.; Dunning, T. H.; Harrison, R. J. J. Chem. Phys. 1992, 96, 6796-6806.
39. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; 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. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98; Gaussian, Inc.: Pittsburgh, PA, 1998.
40. ∈) to their QM-optimized values for each point of the reaction path to reproduce the inversion of the transferring methyl group.
41. Beveridge, D. L.; DiCapua, F. M. Annu. Rev. Biophys. Biophys. Chem. 1989, 18, 431-492.
42. Cossi, M.; Tomasi, J.; Cammi, R. Int. J. Quantum Chem. 1995, 695-702.
43. Floris, F. M.; Tomasi, J.; Ahuir, J. L. P. J. Comput. Chem. 1991, 12, 784-791.
44. Cossi, M.; Mennucci, B.; Cammi, R. J. Comput. Chem. 1996, 17, 57-73.
45. Barone, V.; Cossi, M.; Tomasi, J. J. Chem. Phys. 1997, 107, 3210-3221.
46. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092.
47. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
48. Glukhovtsev, M. N.; Bach, R. D.; Pross, A.; Radom, L. Chem. Phys. Lett. 1996, 260, 558-564.
49. Schultz, E.; Nissinen, E. Biochem. Pharmacol. 1989, 38, 3953-3956.
50. Cramer, C. J.; Truhlar, D. G. J. Comput.-Aided Mol. Des. 1992, 6, 629-666.
51. Lotta, T.; Vidgren, J.; Tilgmann, C.; Ulmanen, I.; Melen, K.; Julkunen, I.; Taskinen, J. Biochemistry 1995, 34, 4202-4210.
52. Borges, N.; VieiraCoelho, M. A.; Parada, A.; SoaresdaSilva, P. J. Enzyme Inhib. 1998, 13, 473-483.
53. Cheng, X. D. Annu. Rev. Biophys. Biomol. Struct. 1995, 24, 293-318.
54. Fu, Z. J.; Hu, Y. B.; Konishi, K.; Takata, Y.; Ogawa, H.; Gomi, T.; Fujioka, M.; Takusagawa, F. Biochemistry 1996, 35, 11985-11993.
55. Swain, C. G.; Taylor, L. J. J. Am. Chem. Soc. 1962, 84, 2456-2457.
56. Rived, F.; Roses, M.; Bosch, E. Anal. Chim. Acta 1998, 374, 309-324.
57. Dougherty, D. A.; Staufter, D. A. Science 1990, 250, 1558-1560.
58. Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 4177-4178.
59. Mitchell, J. B. O.; Nandi, C. L.; McDonald, I. K.; Thornton, J. M.; Price, S. L. J. Mol. Biol. 1994, 239, 315-331.
60. Sussman, J. L.; Harel, M.; Frolow, F.; Oefner, C.; Goldman, A.; Toker, L.; Silman, I. Science 1991, 253, 872-879.
61. Basran, J.; Mewies, M.; Mathews, F. S.; Scrutton, N. S. Biochemistry 1997, 36, 1989-1998.
62. Miyamoto, S.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402-8406.
63. Misra, V. K.; Hecht, J. L.; Yang, A. S.; Honig, B. Biophys. J. 1998, 75, 2262-2273.
64. Singh, S. B.; Kollman, P. A. J. Am. Chem. Soc. 1999, 121, 3267-3271.
65. Lee, L.-P.; Tidor, B. J. Chem. Phys. 1997, 106, 8681-8690.
66. Kangas, E.; Tidur, B. J. Chem. Phys. 1998, 109, 7522-7545.