Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis

Journal of Physical Chemistry B

Volumn 106, Issue 12, 2002, Pages 3283-3293

  Agarwal, Pratul K ^a   Billeter, Salomon R ^a   Hammes Schiffer, Sharon ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME DYNAMICS;

ACTIVATION ENERGY; CATALYSIS; COMPUTER SIMULATION; FREE ENERGY; ISOTOPES; MOLECULAR DYNAMICS; QUANTUM THEORY; X RAY CRYSTALLOGRAPHY;

ENZYMES;

EID: 0037188007     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp020190v     Document Type: Article

References (57)

1. Miller, G.P.; Benkovic, S. J. Chem. Biol. 1998, 5, R105-R113.
2. Fierke, C.A.; Johnson, K.A.; Benkovic, S. J. Biochemistry 1987, 26, 4085.
3. Huang, Z.; Wagner, C.R.; Benkovic, S. J. Biochemistry 1994, 33, 11576.
4. Wagner, C.R.; Huang, Z.; Singleton, S.F.; Benkovic, S. J. Biochemistry 1995, 34, 15671.
5. Cummins, P.L.; Gready, J.E. J. Comput. Chem. 1998, 19, 977.
6. Cummins, P.L.; Gready, J.E. J. Am. Chem. Soc. 2001, 123, 3418.
7. Castillo, R.; Andres, J.; Moliner, V. J. Am. Chem. Soc. 1999, 121, 12140.
8. Sawaya, M.R.; Kraut, J. Biochemistry 1997, 36, 586.
9. Falzone, C.J.; Wright, P.E.; Benkovic, S.J. Biochemistry 1994, 33, 439.
10. Osborne, M.J.; Schnell, J.; Benkovic, S.J.; Dyson, H.J.; Wright, P.E. Biochemistry 2001, 40, 9846.
11. Radkiewicz, J.L.; Brooks, C.L.B., III J. Am. Chem. Soc. 2000, 122, 225.
12. Mildvan, A.S.; Weber, D.J.; Kuliopulos, A. Arch. Biochem. Biophys. 1991, 294, 327.
13. Agarwal, P.K.; Billeter, S.R.; Rajagopalan, P.T.R.; Benkovic, S.J.; Hammes-Schiffer, S. Proc. Nat. Acad. Sci. (in press).
14. Billeter, S.R.; Webb, S.P.; Iordanov, T.; Agarwal, P.K.; Hammes-Schiffer, S. J. Chem. Phys. 2001, 114, 6925.
15. Billeter, S.R.; Webb, S.P.; Agarwal, P.K.; Iordanov, T.; Hammes-Schiffer, S. J. Am. Chem. Soc. 2001, 123, 11262.
16. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; John Wiley: New York, 1991.
17. van Gunsteren, W.F.; Billeter, S.R.; Eising, A.A.; Hünenberger, P.H.; Krüger, P.; Mark, A.E.; Scott, W.R.P.; Tironi, I.G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; Biomos b.v., Zürich and Groningen, VdF Hochschulverlag, ETH Zürich: Zürich, 1996.
18. Scott, A.P.; Radom, L. J. Phys. Chem. 1996, 100, 16502.
19. Frisch, M.J.; Tracks, 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.; 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, revision A.6; Gaussian, Inc.: Pittsburgh, PA, 1998.
20. Eisenberg, D.; Crothers, D. Physical Chemistry with Application to the Life Sciences; Benjamin/Cummings: Menlo Park, CA, 1979.
21. Scott, W.R.P.; Hunenberger, P.H.; Tironi, I.G.; Mark, A.; Billeter, S.R.; Fennen, J.; Torda, A.E.; Huber, T.; Kruger, P.; van Gunsteren, W.F. J. Phys. Chem. A 1999, 103, 3596.
22. Hammes-Schiffer, S.; Tully, J.C. J. Chem. Phys. 1994, 101, 4657.
23. Hammes-Schiffer, S. J. Phys. Chem. A 1998, 102, 10443.
24. Warshel, A.; Chu, Z.T. J. Chem. Phys. 1990, 93, 4003.
25. Laria, D.; Ciccotti, G.; Ferrario, M.; Kapral, R. J. Chem. Phys. 1992, 97, 378.
26. Cao, J.; Voth, G.A. J. Chem. Phys. 1993, 99, 10070.
27. Cao, J.; Voth, G.A. J. Chem. Phys. 1994, 100, 5093.
28. Cao, J.; Voth, G.A. J. Chem. Phys. 1994, 100, 5106.
29. Cao, J.; Voth, G.A. J. Chem. Phys. 1994, 101, 6157.
30. Staib, A.; Borgis, D.; Hynes, J.T. J. Chem. Phys. 1995, 102, 2487.
31. Billeter, S.R.; van Gunsteren, W.F. Comput. Phys. Comm. 1997, 107, 61.
32. Tuckerman, M.E.; Marx, D.; Klein, M.L.; Parrinello, M. Science 1997, 275, 817.
33. Bala, P.; Grochowski, P.; Nowinski, K.; Lesyng, B.; McCammon, J.A. Biophys. J. 2000, 79, 1253.
34. Alhambra, C.; Corchado, J.C.; Sanchez, M.L.; Gao, J.; Truhlar, D.G. J. Am. Chem. Soc. 2000, 122, 8197.
35. Villa, J.; Warshel, A. J. Phys. Chem. B 2001, 105, 7887.
36. Antoniou, D.; Schwartz, S.D. J. Phys. Chem. B 2001, 105, 5553.
37. Webb, S.P.; Hammes-Schiffer, S. J. Chem. Phys. 2000, 113, 5214.
38. Iordanov, T.; Billeter, S.R.; Webb, S.P.; Hammes-Schiffer, S. Chem. Phys. Lett 2001, 338, 389.
39. Wigner, E. Phys. Rev. 1932, 40, 749.
40. Marcus, R.A. Annu. Rev. Phys. Chem. 1964, 15, 155.
41. Zusman, L.D. Chem. Phys. 1980, 49, 295.
42. Warshel, A. J. Phys. Chem. 1982, 86, 2218.
43. King, G.; Warshel, A. J. Chem. Phys. 1990, 93, 8682.
44. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H.J.C. J. Comput. Phys. 1977, 23, 327.
45. Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; DiNola, A.; Haak, J.R. J. Chem. Phys. 1994, 81, 3684.
46. Neria, E.; Karplus, M. J. Chem. Phys. 1996, 105, 10812.
47. Tully, J.C. J. Chem. Phys. 1990, 93, 1061.
48. Bennett, C.H. Algorithms for Chemical Computation; American Chemical Society: Washington, DC, 1997.
49. Keck, J.C. J. Chem. Phys. 1960, 32, 1035.
50. Anderson, J.B. J. Chem. Phys. 1973, 58, 4684.
51. Hammes-Schiffer, S.; Tully, J.C. J. Chem. Phys. 1995, 103, 8528.
52. Allen, M.P.; Tildesley, D.J. Computer Simulation of Liquids; Clarendon Press: Oxford, U.K., 1989.
53. Andersen, H.C. J. Comput. Phys. 1983, 52, 24.
54. Pretsch, E.; Seibl, J.; Clerc, T.; Simon, W. Tables of Spectral Data for Structure Determination of Organic Compounds, 2nd ed.; Springer-Verlag: Berlin, 1983.
55. Lu, H.P.; Xun, L.; Xie, S. Science 1988, 282, 1877.
56. Cameron, C.E.; Benkovic, S.J. Biochemistry 1997, 36, 15792.
57. Chen, J.-T.; Taira, K.; Tu, C.; Benkovic, S.J. Biochemistry 1994, 33, 7021.