Coupling between protein and reaction dynamics in enzymatic processes: Application of Grote-Hynes theory to catechol O-methyltransferase

Journal of the American Chemical Society

Volumn 128, Issue 18, 2006, Pages 6186-6193

  Roca, Maite ^a   Moliner, Vicente ^a   Tuñón, Iñaki ^b   Hynes, James T ^c,d  

^a UNIVERSITAT JAUME I   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c ECOLE NORMALE SUPÉRIEURE   (France)

^d UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ENZYMES; METHANOL; MOLECULAR DYNAMICS; RATE CONSTANTS; REACTION KINETICS; SOLUTIONS;

ENZYMATIC COEFFICIENTS; GROTE-HYNES PREDICTIONS; TRANSITION STATE FRICTION KERNELS; TRANSMISSION COEFFICIENTS;

ENZYME KINETICS;

CATECHOL; CATECHOL METHYLTRANSFERASE; METHYL GROUP; S ADENOSYLHOMOCYSTEINE; S ADENOSYLMETHIONINE;

AQUEOUS SOLUTION; ARTICLE; CALCULATION; ENERGY; ENZYME ACTIVE SITE; GROTE HYNES THEORY; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; QUANTUM MECHANICS; THEORY;

EID: 33646524282     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja058826u     Document Type: Article

References (61)

1. Wolfenden, R.; Snider, M. J. Acc. Chem. Res. 2001, 34, 938-945.
2. Benkovic, S. J.; Hammes-Schiffer, S. Science 2003, 301, 1196-1202.
3. Agarwal, P. K. J. Am. Chem. Soc. 2005, 127, 15248-15256.
4. Kohen, A. Prog. React. Kinet. Mech. 2003, 28, 119-156.
5. Fenimore, P. W.; Frauenfelder, H.; McMahon, B. H.; Young, R. D. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14408-14413.
6. Min, W.; English, B. P.; Luo, G.; Cherayil, B. J.; Kou, S. C.; Xie, X. S. Acc. Chem. Res. 2005, 38, 923-931.
7. Glasstone, S.; Laidler, K. J.; Eyring, H. The Theory of Rate Processes; McGraw-Hill: New York, 1941.
8. Keck, J. C. Adv. Chem. Phys. 1967, 13, 85-121.
9. Truhlar, D. G.; Garret, B. C.; Klippenstein, S. J. J. Phys. Chem. 1996, 100, 12771-12800.
10. García-Viloca, M.; Gao, J.; Karplus, M.; Truhlar, D. G. Science 2004, 303, 186-195.
11. Nam, K.; Prat-Resina, X.; García-Viloca, M.; Devi-Kesavan, L. S.; Gao. J. J. Am. Chem. Soc. 2004, 126, 1369-1376.
12. Truhlar, D. G.; Gao, J.; García-Viloca, M.; Alhambra, C.; Corchado, J.; Sanchez, M. L.; Poulsen, T. D. Int. J. Quantum Chem. 2004, 100, 1136-1152.
13. Villà, J.; Warshel, A. J. Phys. Chem. B 2001, 105, 7887-7907.
14. Warshel, A. J. Biol. Chem. 1998, 273, 27035-27038.
15. Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 1978, 75, 5250-5254.
16. Page, M. I.; Jencks, W. J. Proc. Natl. Acad. Sci. U.S.A. 1971, 68, 1678-1683.
17. Kollman, P. A.; Kuhn, B.; Donini, O.; Peräkylä, M.; Stanton, R. V.; Bakowies, D. Acc. Chem. Res. 2001, 34, 72-79.
18. Mesecar, A. D.; Stoddard, B. L.; Koshland, D. E. Science 1997, 277, 202-206.
19. Bruice, T. C. Acc. Chem. Res. 2002, 55, 139-148.
20. Menger, F. M. Acc. Chem. Res. 1993, 26, 206-212.
21. Martí, S.; Roca, M.; Andres, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J. Chem. Soc. Rev. 2004, 55, 98-107.
22. Neria, E.; Karplus, M. Chem. Phys. Lett. 1997, 267, 23-30.
23. In this reference the proton motion was treated classically. An alternative approach, s. a. t. u. i. Staib, A.; Hynes, J. T.; Borgis, D. J. Chem. Phys. 1995, 102, 2487-2505 is more appropiate.
24. Soriano, A.; Silla, E.; Tuñón, I.; Ruiz-Lopez, M. F. J. Am. Chem. Soc. 2005, 127, 1946-1957.
25. Roca, M.; Andrés, J.; Moliner, V.; Tuñón, I.; Bertrán, J. J. Am. Chem. Soc. 2005, 127, 10648-10655.
26. Alhambra, C.; Corchado, J. C.; Sanchez, M. L.; García-Viloca, M.; Gao, J.; Truhlar, D. G. J. Phys. Chem. B 2001, 105, 11326-11340.
27. Agarwal, P. K.; Billeter, S. R.; Hammes-Schiffer, S. J. Phys. Chem. B 2002, 106, 3283-3293.
28. García-Viloca, M.; Truhlar, D. G.; Gao, J. Biochemistry 2003, 42, 13558-13575.
29. García-Viloca, M.; Alhambra, C.; Truhlar, D. G.; Gao, J. J. Comput. Chem. 2003, 24, 177-190.
30. Alhambra, C.; Sanchez, M. L.; Corchado, J. C.; Gao, J.; Truhlar, D. G. Chem. Phys. Lett. 2002, 355, 388-394.
31. Hammes-Schiffer, S. Biochemistry 2002, 41, 13335-13343.
32. Grote, R. F.; Hynes, J. T. J. Chem. Phys. 1980, 73, 2715-2732.
33. The Theory of Chemical Reaction Dynamics; Hynes, J. T.; Baer, M., Eds.; CRC: Boca Raton, FL, 1985; Vol. IV, p 171.
34. Gertner, B. J.; Wilson, K. R.; Hynes, J. T. J. Chem. Phys. 1989, 90, 3537-3558.
35. Note that this is a statement for solution reactions and does not address the issue of the influence of the external solvent on protein dynamics considered in: Tournier, A. L.; Xu, J.; Smith, J. C. Biophysical Journal 2003, 85, 1871-1875, refs 3 and 5.
36. Ciccotti, C.; Ferrario, M.; Hynes, J. T.; Kapral, R. Chem. Phys. 1989, 129, 241-251.
37. Bergsma, J. P.; Reimers, J. R.; Wilson, K. R.; Hynes, J. T. J. Chem. Phys. 1986, 85, 5625-5643.
38. Gertner, B. J.; Bergsma, J. P.; Wilson, K. R.; Lee, S.; Hynes, J. T. J. Chem. Phys. 1987, 86, 1377-1386.
39. Comprehensive Biological Catalysis; Takusagawa, F., Fujioka, M., Spies, A., Schowen, R. L., Sinnott, M., Eds. Academic Press: San Diego, CA, 1998; Vol. 1, pp 1-30.
40. Gulberg, H. C.; Marsden, C. A. Pharmacol. Rev. 1975, 27, 135-206.
41. Gertner, B. J.; Whitnell, R. M.; Wilson, J. C.; Hynes, J. T. J. Am. Chem. Soc. 1991, 113, 74-87.
42. Roca, M.; Martí, S.; Andrés, J.; Moliner, V.; Tuñón, I.; Bertrán, J.; Williams, I. H. J. Am. Chem. Soc. 2003, 125, 7726-7737.
43. Vidgren, J.; Svensson, L. A.; Liljas, A. Nature 1994, 368, 354-358.
44. Zheng, Y. J.; Bruice, T. C. J. Am. Chem. Soc. 1997, 119, 8137-8145.
45. Field, M. J.; Albe, M.; Bret, C.; Proust-De Martin, F.; Thomas, A. J. Comput. Chem. 2000, 21, 1088-1100.
46. Bergsma, J. P.; Gertner, B. J.; Wilson, K. R.; Hynes, J. T. J. Chem. Phys. 1987, 86, 1356-1376.
47. van der Zwan, G.; Hynes, J. T. J. Chem. Phys. 1982, 76, 2993-3001.
48. van der Zwan, G.; Hynes, J. T. J. Chem. Phys. 1983, 78, 4174-4185.
49. van der Zwan, G.; Hynes, J. T. Chem. Phys. 1984, 90, 21-35.
50. Kramers, H. A. Physica 1940, 7, 284-304.
51. Andersen, H. C. J. Comput. Phys. 1983, 52, 24-34.
52. Verlet, L. Phys. Rev. 1967, 159, 98-103.
53. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637-649.
54. See also the references cited in ref 35.
55. Brown, K. G.; Erfurth, S. C.; Small, E. W.; Peticolas, W. L. Proc. Natl. Acad. Sci. U.S.A. 1972, 69, 1467-1469.
56. Go, N.; Noguti, T.; Nishikawa, T. Proc. Natl. Acad. Sci. U.S.A. 1983, 80, 3696-3700.
57. Chou, K. C. Biochem. J. 1983, 215, 465-469.
58. Lau, E. Y.; Bruice, T. C. J. Am. Chem. Soc. 2000, 122, 7165-7171.
59. Berens, P. H.; Mackay, D. H. J.; White, G. M.; Wilson, K. R. J. Chem. Phys. 1983, 79, 2375-2389.
60. Olsson, M. H. M.; Warshel, A. J. Am. Chem. Soc. 2004, 126, 15167-15179.
61. Since the transmission coefficient in the enzyme case is so well described by the nonadiabatic limit, this could be also alternatively analyzed from the various perspectives presented in ref 38.