Preorganization and reorganization as related factors in enzyme catalysis: The chorismate mutase case

Chemistry - A European Journal

Volumn 9, Issue 4, 2003, Pages 984-991

  Martí, Sergio ^a   Andrés, Juan ^a   Moliner, Vicent ^a   Silla, Estanislao ^b   Tuñón, Iñaki ^b   Bertrán, Juan ^c  

^a UNIVERSITAT JAUME I   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Chorismate mutase; Enzyme catalysis; Molecular dynamics; Pericyclic reaction; QM MM methods

Indexed keywords

CATALYSIS; COMPUTER SIMULATION; QUANTUM THEORY; STATISTICAL MECHANICS; SUBSTRATES;

RATE ENHANCEMENT;

ENZYME KINETICS;

CHORISMATE MUTASE;

AQUEOUS SOLUTION; ARTICLE; BACILLUS SUBTILIS; CATALYSIS; DECOMPOSITION; ELECTRICITY; ELECTROCHEMICAL ANALYSIS; ENERGY METABOLISM; ENZYME ACTIVE SITE; ENZYME KINETICS; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; EVAPORATION; MOLECULAR MECHANICS; NONHUMAN; QUANTUM MECHANICS; STATISTICAL ANALYSIS;

BACILLUS SUBTILIS; CATALYSIS; CHEMISTRY, PHYSICAL; CHORISMATE MUTASE; ELECTROCHEMISTRY; PROTEIN CONFORMATION; SOLUTIONS;

EID: 0037450070     PISSN: 09476539     EISSN: None     Source Type: Journal    
DOI: 10.1002/chem.200390121     Document Type: Article

References (52)

1. a) W. P. Jencks, Adv. Enzymol. 1975, 43, 219-410;
2. b) A. Fersht, Enzyme Structure and Mechanism, W. H. Freeman, New York, 1985.
3. a) L. Pauling, Nature 1948, 161, 707-709;
4. b) L. Pauling, Chem. Eng. News 1946, 24, 1375-1377;
5. c) L. Pauling, Am. Sci. 1948, 36, 51-58.
6. J. E. S. Haldane, Enzymes, Longmans Green, London, 1930.
7. I. H. Williams, Chem. Soc. Rev. 1993, 22, 277.
8. a) A. Warshel, Computer Modeling of Chemical Reactions in Enzymes and Solutions, Wiley, New York, 1991;
9. b) A. Warshel, Acc. Chem. Res. 2002, 35, 385-395.
10. a) M. J. Field, A Practical Introduction to the Simulation of Molecular Systems, Cambridge University Press, Cambridge, 1999;
11. b) M. J. Field, J. Comput. Chem. 2002, 23, 48-58.
12. a) V. Moliner, A. J. Turner, I. H. Willimans, Chem. Commun. 1997, 1271-1272;
13. b) A. J. Turner, V. Moliner, I. H. Williams, Phys. Chem. Chem. Phys. 1999, 1, 1323-1331.
14. a) S. Strajbl, J. Florián, A. Warshel, J. Am. Chem. Soc. 2000, 122, 5354-5366;
15. b) J. Villà, A. Warshel, J. Phys. Chem. B 2001, 105, 7887-7907.
16. a) C. J. Cramer, D. G. Truhlar, Chem. Rev. 1999, 99, 2161-2200;
17. b) C. J. Cramer, D. G. Truhlar, in Solvent Effects and Chemical Reactivity (Eds.: O. Tapia, J. Bertrán), Kluwer, Dordrecht, 1996, pp. 1-80.
18. M. I. Page, W. P. Jencks, Proc. Natl. Acad. Sci. USA, 1971, 68, 1678-1683.
19. a) F. M. Menger, Acc. Chem. Res. 1993, 26, 206-212;
20. b) N. A. Khanjin, J. P. Snyder, F. M. Menger, J. Am. Chem. Soc. 1999, 121, 11831-11846.
21. a) E. Y. Lau, T. C. Bruice, J. Am. Chem. Soc. 1998, 120, 12387-12394;
22. b) R. A. Torres, B. Schiøt, T. C. Bruice, J. Am. Chem. Soc. 1999, 121, 8164-8173;
23. c) F. C. Lightstone, T. C. Bruice, J. Am. Chem. Soc. 1996, 118, 2595-2605;
24. d) T. C. Bruice, F. C. Lightstone, Acc. Chem. Res. 1999, 32, 127-136;
25. e) T. C. Bruice, S. J. Benkovic, Biochemistry 2000, 39, 6267-6274.
26. A. T. Mesecar, B. L. Stoddard, D. E. Koshland Jr., Science 1997, 227, 202-206.
27. a) R. V. Stanton, M. Peräkylä, D. Bakowies, P. A. Kollman, J. Am. Chem. Soc. 1998, 120, 3448-3457;
28. b) P. A. Kollman, B. Khun, O. Donini, M. Peräkylä, R. V. Stanton, D. Bakowies, Acc. Chem. Res. 2001, 34, 72-79;
29. c) P. A. Kollman, B. Kuhn, M. Peräkylä, J. Phys. Chem. B 2002, 106, 1537-1542.
30. J. Hermans, L. Wang, J. Am. Chem. Soc. 1997, 119, 2707-2714.
31. a) E. Haslam, Shikimic Acid: Metabolism and Metabolites, Wiley, New York, 1993;
32. b) B. Golinelli-Pimpaneau, Curr. Opin. Struct. Biol. 2000, 10, 697-708;
33. c) P. Kast, M. Asif-Ullah, D. Hilvert, Tetrahedron Lett. 1996, 37, 2691-2694.
34. S. Martí, J, Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán, J. Phys. Chem. B 2000, 104, 11308-11315.
35. a) S. D. Copley, J. R. Knowles, J. Am. Chem. Soc. 1987, 109, 5008-5013;
36. b) H. A. Carlson, W. L. Jorgensen, J. Am. Chem. Soc. 1996, 118, 8475-8484.
37. A. Warshel, Acc. Chem. Res. 2002, 35, 385-395.
38. a) M. J. S. Dewar, W. Thiel, J. Am. Chem. Soc. 1977, 99, 4899-4907;
39. b) M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, J. J. P. Stewart, J. Am. Chem. Soc. 1985, 107, 3902-3909.
40. B. Roux, Comput. Phys. Commun. 1995, 91, 275-282.
41. G. M. Torrie, J. P. Valleau, J. Comput. Phys. 1977, 23, 187-199.
42. M. J. Field, M. Albe, C. Bret, F. Proust-de Martin, A. Thomas, J. Comput. Chem. 2000, 21, 1088-1100.
43. GAUSSIAN 98, Revision A.6, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. J. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, J. A. Pople, Gaussian Inc., Pittsburgh PA, 1998.
44. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus, J. Comput. Chem. 1983, 4, 187-217.
45. S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán, Theochem 2002, in press.
46. a) W. L. Jorgensen, J. Tirado-Rives, J. Am. Chem. Soc. 1988, 110, 1657-166;
47. b) W. L. Jorgensen, D. S. Maxwell, J. Tirado-Rives, J. Am. Chem. Soc. 1996, 118, 11225-11236.
48. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, J. Chem. Phys. 1983, 79, 926-935.
49. H. Guo, Q. Cui, W. N. Lipscomb, M. Karplus, M. Proc. Natl. Acad. Sci. USA 2001, 98, 9032-9037.
50. S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán, M. J. Field, J. Am. Chem. Soc. 2001, 123, 1709-1712.
51. H. Sun, T. C. Bruice, Proc. Natl. Acad. Sci. USA 2002, 99, 1176-1181.
52. A. Warshel, J. Biol. Chem. 1998, 273, 27035-27038.