Computational methods for the study of enzymic reaction mechanisms: 1. Application to the hydride transfer step in the catalysis of dihydrofolate reductase

Journal of Physical Chemistry B

Volumn 106, Issue 38, 2002, Pages 9934-9944

  Cummins, Peter L ^a   Greatbanks, Stephen P ^a   Rendell, Alistair P ^b   Gready, Jill E ^a  

^a Biology and Environment   (Australia)

^b AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; CATALYST ACTIVITY; COMPUTATION THEORY; COMPUTER SIMULATION; ESCHERICHIA COLI; FREE ENERGY; HYDRIDES; IONIZATION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; OPTIMIZATION; PROBABILITY DENSITY FUNCTION;

DENSITY FUNCTIONAL THEORY (DFT);

ENZYME KINETICS;

EID: 0037180004     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp021070q     Document Type: Article

References (60)

1. Gao, J.L. Rev. Comput. Chem. 1996, 7, 119.
2. Amara, P.; Field, M.J. In Encyclopaedia of Computational Chemistry; von Rogue Schleyer, P., Ed.; John Wiley: New York, 1998; p 431.
3. Friesner, R.A.; Beachy, M.D. Curr. Opin. Struct. Biol. 1998, 8, 257.
4. Mordasini, T.Z.; Thiel, W. Chimia 1998, 52, 288.
5. Luque, F.J.; Reuter, N.; Cartier, A.; Ruiz-Lopez, M.F. J. Phys. Chem. A 2000, 104, 10923.
6. Liu, H.; Zhang, Y.; Yang, W.T. J. Am. Chem. Soc. 2000, 122, 6560.
7. Bystroff, C.; Oatley, S.J.; Kraut, J. Biochemistry 1990, 29, 3263.
8. Blakely, R.L. In Advances in Enzymology; Meister, A., Ed.; John Wiley: New York, 1995; Vol. 70, p 23.
9. Cummins, P.L.; Gready, J.E. J. Phys. Chem. B 2000, 104, 4503.
10. Cummins, P.L.; Gready, J.E. J. Mol. Graph. Model. 2000, 18, 42.
11. Cummins, P.L.; Gready, J.E. J. Am. Chem. Soc. 2001, 123, 3418.
12. Donkersloot, M.C.A.; Buck, H.M. J. Am. Chem. Soc. 1981, 103, 6549.
13. Brounts, R.H.A.M.; Buck, H.M. J. Am. Chem. Soc. 1983, 105, 1284.
14. Krechl, J.; Kuthan, J. J. Mol. Struct.: THEOCHEM 1988, 170, 239.
15. Tapia, O.; Candenas, R.; Andres, J.; Colonna-Cesari, F. J. Am. Chem. Soc. 1988, 110, 4046.
16. Cummins, P.L.; Gready, J.E. J. Comput. Chem. 1990, 11, 791.
17. Andres, J.; Safont, V.S.; Martins, J.B.L.; Beltran, A.; Moliner V.J. Mol. Struct.: THEOCHEM 1995, 330, 411.
18. Andres, J.; Moliner, V.; Safont, V.S.; Domingo, L.R.; Picher, M.T.; Krechl, J. Bioorg. Chem. 1996, 24, 10.
19. Castillo, R.; Andres, J.; Moliner, V. J. Am. Chem. Soc. 1999, 121, 12140.
20. Cummins, P.L.; Gready, J.E. J. Comput. Chem. 1998, 19, 977.
21. 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.; 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.; 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.
22. Lee, C.; Yang, W.; Parr, R.G. Phys. Rev. B 1988, 37, 785.
23. Becke, A.D. J. Chem. Phys. 1993, 98, 5648.
24. Koch, W.; Holthausen, M.C. A Chemist's Guide to Density Functional Theory; Wiley-VCH: Weinheim, 2000.
25. Miani, A.; Cane, E.; Palmieri, P.; Trombetti, A.; Handy, N.C. J. Chem. Phys. 2000, 112, 248.
26. Cohen, A.J.; Handy, N.C. Chem. Phys. Lett. 2000, 316, 160.
27. McAllister, M.A. Can. J. Chem. 1997, 75, 1195.
28. McAllister, M.A. J. Mol. Struct.: THEOCHEM 1998, 427, 39.
29. Pan, Y.P.; McAllister, M.A. J. Mol. Struct.: THEOCHEM 1998, 427, 221.
30. Lozynski, M.; Rusinskaroszak, D.; Mack, H.G. J. Phys. Chem. 1998, 102, 2899.
31. Greatbanks, S.P.; Gready, J.E.; Limaye, A.C.; Rendell, A.P. Proteins: Struct., Funct., Genet. 1999, 37, 157.
32. Domene, C.; Fowler, P.W.; Jemmer, P.; Madden, P. Chem. Phys. Lett. 1999, 299, 51.
33. Greatbanks, S.P.; Gready, J.E.; Limaye, A.C.; Rendell, A.P. J. Comput. Chem. 2000, 21, 788.
34. Champagne, B.; Perpete, E.A.; Jacquemin, D.; van Gisbergen, S. J.A.; Baerends, E.J.; Soubra-Ghaoui, C.; Robins, K.A.; Kirtman, B. J. Phys. Chem. A. 2000, 104, 4755.
35. Rothman, M.J.; Lohr, L.L. Chem. Phys. Lett. 1980, 70, 405.
36. Burket, U.; Allinger, N.L. J. Comput. Chem. 1982, 3, 40.
37. Schlegel, H.B. Adv. Chem. Phys. 1987, 67, 249.
38. Sawaya, M.R.; Kraut, J. Biochemistry 1997, 36, 586.
39. Cummins, P.L.; Gready, J.E. J. Comput. Chem. 1996, 17, 1598.
40. Cornell, W.D.; Cieplak, P.; Bayly, C.I.; Gould, I.R.; Merz, K.M., Jr.; Ferguson, D.M.; Spellmeyer, D.C.; Fox, T.; Caldwell, J.W.; Kollman, P.A. J. Am. Chem. Soc. 1995, 117, 5179.
41. Jorgensen, W.L.; Chandrasekhar, J.; Madura, J.D.; Impey, R.W.; Klein, M.L. J. Chem. Phys. 1983, 79, 926.
42. Cummins, P.L.; Gready, J.E. J. Comput. Chem. 1997, 18, 1496.
43. Cummins, P.L.; Gready, J.E. J. Comput. Chem. 1999, 20, 1028.
44. Cummins, P.L. Molecular Orbital Programs for Simulations (MOPS) 1996.
45. Gao, J.; Xia, X. J. Am. Chem. Soc. 1993, 115, 9667.
46. Ho, L.L.; MacKerell, A.D.; Bash, P.A. J. Phys. Chem. 1996, 100, 4466.
47. van Gunsteren, W.F.; Berendsen, H.J.C. Mol. Phys. 1977, 34, 1311.
48. Lee, F.S.; Chu, Z.T.; Bolger, M.B.; Warshel, A. Protein Eng. 1992, 5, 215.
49. Åqvist, J.; Medina, C.; Samuelsson, J.-E. Protein Eng. 1994, 7, 385.
50. Ivery, M.T.G.; Gready, J.E. Biochemistry 1995, 34, 3724.
51. Jeong, S.-S.; Gready, J.E. Biochemistry 1995, 34, 3734.
52. Fiercke, C.A.; Johnson, K.A.; Benkovic, S.J. Biochemistry 1987, 26, 4085.
53. Thillet, J.; Adams, J.A.; Benkovic, S.J. Biochemistry 1990, 29, 5195.
54. Andrews, J.; Fiercke, C.A.; Birdsall, B.; Ostler, G.; Feeney, J.; Roberts, G.C.K.; Benkovic, S.J. Biochemistry 1989, 28, 5743.
55. Kong, Y.S.; Warshel, A. J. Am. Chem. Soc. 1995, 117, 6234.
56. Hwang, J.K.; Chu, Z.T.; Yadav, A.; Warshel, A. J. Phys. Chem. 1991, 95, 8445.
57. Osborne, M.J.; Schnell, J.; Benkovic, S.J.; Dyson, H.J.; Wright, P.E. Biochemistry 2001, 40, 9846.
58. Radkiewicz, J.L.; Brooks, C.L., III J. Am. Chem. Soc. 2000, 122, 225.
59. Rossi, I.; Truhlar, D.G. Chem. Phys. Lett. 1995, 233, 231.
60. Bash, P.A.; Ho, L.L.; MacKerell, A.D.; Levine, D.; Hallstrom, P. Proc. Nat. Acad. Sci. U.S.A. 1996, 93, 3698.