How important are quantum mechanical nuclear motions in enzyme catalysis?

Journal of the American Chemical Society

Volumn 118, Issue 47, 1996, Pages 11745-11751

  Hwang, Jenn Kang ^a   Warshel, Arieh ^b  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CATALYSIS; ENZYME ACTIVITY; QUANTUM CHEMISTRY;

EID: 0029951263     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja962007f     Document Type: Article

References (61)

1. Yuan, C.; Murray, C. J.; Klinman, J. P. Science 1989, 213, 1325.
2. Kraut, J. Science 1988, 248, 533.
3. (a) Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; John Wiley & Sons, Inc.: New York, 1991.
4. (b) Kollman, P. Chem. Rev. 1993, 93, 2395.
5. Warshel, A.; Hwang, J.-K. J. Chem. Phys. 1986, 84, 4938.
6. Warshel, A.: Parson, W. W. Ann. Rev. Phys. Chem. 1991, 42, 279.
7. Bader, J. S.; Kuharski, R. A.; Chandler, D. J. Chem. Phys. 1990, 93, 203.
8. Zheng, C.; McCammon, J. A.; Wolynes, P. G. Chem. Phys. 1991, 158, 261.
9. Nonella, M.; Schulten, K. J. Phys. Chem. 1991, 95, 2059.
10. Wolynes, P. G. J. Chem. Phys. 1987, 87, 6559.
11. Truhlar, D. G.; Liu, Y.-P.; Schemer, G. K.; Garrett, B. C. J. Phys. Chem. 1994, 98, 8396.
12. (a) Borgis, D.; Lee, S.; Hynes, J. T. Chem. Phys. Lett. 1989, 162, 19.
13. (b) Borgis, D.; Hynes, J. T. J. Chem. Phys. 1991, 94, 3619.
14. (a) Li, D.; Voth, G. A. J. Phys. Chem. 1991, 95, 10425.
15. (b) Lobaugh, J.; Voth, G. A. Chem. Phys. Lett. 1992, 198, 311.
16. (c) Lobaugh, J.; Voth. G. A. J. Chem. Phys. 1994, 100, 3039.
17. (d) Lobaugh, J.; Voth, G. A. J. Chem. Phys. 1996, 104, 2056.
18. Hammes-Schiffer, S.; Tully, J. C. J. Phys. Chem. 1995, 99, 5793.
19. (a) Hwang, J.-K.; Chu, Z. T.; Yadav, A.; Warshel, A. J. Phys Chem. 1991, 95, 8445.
20. (b) Warshel, A.; Chu, Z. T. J. Chem Phys. 1990, 93, 4003.
21. Hwang, J.-K.; Warshel, A. J. Phys. Chem. 1993, 97, 10053.
22. Kong, Y. S.; Warshel, A. J. Am. Chem. Soc. 1995, 117, 6234.
23. Gillan, M. J. Phys. Chem. 1987, 20, 3621.
24. (a) Voth, G. A.; Chandler, D.; Miller, W. H. J. Chem Phys. 1989, 91, 7749.
25. (b) Voth, G. A. J. Phys. Chem. 1993, 97, 8365.
26. 20 However the elegant proposal of ref 20 was developed for ground state partition functions and not for calculations of rate constants by centroid approaches. Furthermore, our approach and the work described in ref 14b have introduced the use of FEP/umbrella sampling methods to path integral centroid calculations of rate constants. We consider this to be quite useful and like to point out that many works in this field developed effective simulation approaches for implementation of the original idea of Feynman, rather than invented a new quantum mechanical concept.
27. Doll, J. D.; Myers, L. E. J. Chem. Phys. 1979, 71, 2880.
28. (a) Feynman, R. P.; Hibbs, A. R. Quantum Mechanics and Path Integrals; McGraw-Hill: New York, 1965.
29. (b)Feynman, R. P. Statistical Mechanics; Benjamin: New York, 1972.
30. 40 that the EVB potential surface correctly reproduces the corresponding ab initio surfaces.
31. (a) Silverman, D. N.; Lindskog, S. Acc. Chem. Res. 1988, 21, 30.
32. (b) Venkatasubban, K. S.; Silverman, D. N. Biochemistry 1980, 19, 4984.
33. (c) Silverman, D. N.; Tu, C.; Chen, X.; Tanhauser, S. M.; Kresge, A. J.; Laipis, P. J. Biochemistry 1993, 32, 10757.
34. (d) Taoka, S.; Tu, C.; Kistler, K. A.; Silverman, D. N. J. Biol. Chem. 1994, 269, 17988
35. Steiner, H.; Jonsoon, B. H.; Lindskog, S. Eur. J. Biochem. 1975, 59, 253.
36. Krebs, J. F.; Ippolito, J. A.; Christianson, D. W.; Fierke, C. A. J. Biol. Chem. 1993, 268, 27458.
37. Liljas, A.; Kannan, K. K.; Bergstén, P.-C.; Waara, I.; Fidborg, K.; Strandberg, B.; Carlbom, U.; Järup, L.; Lövgren, S.; Petef, M. Nature New Biol. 1972, 235, 131.
38. Kannan, K. K.; Ramanadham, M.; Jones, T. A. Ann. N. Y. Acad. Sci. 1984, 429, 49.
39. (a) Aqvist, A.; Warshel, A. J. Mol. Biol. 1992, 224, 7.
40. (b) Åqvist, A.; Fothergill, M; Warshel, A. J. Am. Chem. Soc. 1993, 115, 631.
41. Liang, J. Y.; Lipscomb, W. N. Biochemistry 1987, 26, 5293.
42. Jacob, O.; Cardenas, R.; Tapia, O. J. Am. Chem Soc. 1990, 112. 8692.
43. Merz, K. M. J. Am. Chem. Soc. 1991, 113, 406.
44. Åqvist, A.; Warshel, A. Chem. Rev. 1993, 93, 2523-2544.
45. Lee, F. S.; Chu, Z. T.; Warshel, A. J. Comput. Chem. 1993, 14, 161.
46. Åqvist, A.; Warshel, A. J. Am. Chem. Soc. 1999, 112, 2860.
47. Lee, F. S.; Warshel, A. J. Chem. Phys, 1992, 97, 3100.
48. The reliability and convergence of FEP calculation in proteins is a rather complex issue. Usual convergence tests, such as forward and backward integration, are not always informative or even appropriate as far as overall accuracy is concerned. An important point to remember in the error analysis is to be consistent with the methodology used to parametrize the model. We and others have invested considerable effort addressing these issues (e.g. refs 33 and 35) and concluded that a useful estimate of the actual error range can be obtained by running a set of simulations with different initial conditions. By this definition we have an error range of about 2 kcal/mol in the absolute value of the activation free energy. The error in the activation free energy difference between D and H transfer reactions is around 0.20 kcal/mol which corresponds to an error range of about ±1.0 in the corresponding isotope effect.
49. Some readers might confuse the many force field parameters of eq 8 with empirical parameters that allow one to adjust the calculated rate constant to any desirable value. However, while our approach refines parameters by reproducing properties of molecules in solution (as is done by all current approaches), it does not allow any of these parameters to change when calculating the difference between the energy of the given reaction in the protein active site and in water.
50. Warshel, A.; Hwang, J.-K.; Åqvist, J. Faraday Discussion 1992, 93, 225.
51. (a) German, E. D.; Kuznetsov, A. M. J. Chem. Soc., Faraday Trans. 1981, 220, 3.
52. (b) Suhnel, J.; Gustav, K. Chem. Phys. 1984, 87, 179.
53. Muller, R. P.; Warshel, A. J. Phys. Chem. 1995, 99, 17516.
54. Warshel, A.; J. Phys. Chem. 1979, 83, 1640.
55. (a) Warshel, A.; Weiss, R. M. J. Am. Chem. Soc. 1980, 102, 6218.
56. (b) Hwang, J.-K.; King, G.; Creighton, S.; Warshel. A. J. Am. Chem. Soc. 1988, 110, 5297.
57. Hawkinson, D. C.; Pollack, R. M.; Ambulos, N. P. J. Biochemistry 1994, 33, 12172.
58. Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 1978, 75, 5250.
59. Kim, H. J.; Hynes, J. T. J. Am. Chem. Soc. 1992, 114, 10508.
60. Bursulaya, B. D.; Zichi, D. A.; Kim, H. J. J. Phys. Chem. 1996, 100, 1392.
61. Bala, P.; Grochowski, P.; Lesyng, B.; McCammon, J. A. J. Phys. Chem. 1996, 100, 2535.