QM/MM calculations of kinetic isotope effects in the chorismate mutase active site

Organic and Biomolecular Chemistry

Volumn 1, Issue 3, 2003, Pages 483-487

  Martí, Sergio ^a   Moliner, Vicent ^a   Tuñón, Inaki ^b   Williams, Ian H ^c  

^a UNIVERSITAT JAUME I   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c University of Bath   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; COMPUTER SIMULATION; ENZYMES; ISOTOPES; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; POTENTIAL ENERGY; REACTION KINETICS; SOLUTIONS; SUBSTITUTION REACTIONS;

CHORISMATE MUTASE ACTIVE SITE; CLAISEN REARRANGEMENT; KINETIC ISOTOPE;

ORGANIC COMPOUNDS;

CHORISMATE MUTASE; ISOTOPE;

ARTICLE; BACILLUS SUBTILIS; BINDING SITE; CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER PROGRAM; COMPUTER SIMULATION; ENZYMOLOGY; GAS; KINETICS; METABOLISM; PROTEIN CONFORMATION; QUANTUM THEORY; SOLUTION AND SOLUBILITY; THERMODYNAMICS;

BACILLUS SUBTILIS; BINDING SITES; CATALYSIS; CHORISMATE MUTASE; COMPUTER SIMULATION; GASES; ISOTOPES; KINETICS; MODELS, MOLECULAR; PROTEIN CONFORMATION; QUANTUM THEORY; SOFTWARE; SOLUTIONS; THERMODYNAMICS;

EID: 0041317582     PISSN: 14770520     EISSN: None     Source Type: Journal    
DOI: 10.1039/b210508j     Document Type: Article

References (49)

1. E. Haslam, Shikimic Acid: Metabolism and Metabolites, John Wiley & Sons, New York, 1993.
2. U. Weiss, J. M. Edwards, The Biosynthesis of Aromatic Compounds, Wiley, New York, 1980.
3. T. Fitzpatrick, S. Ricken, M. Lanzer, N. Amrhein, P. Macheroux and B. Kappes, Mol. Biol., 2001, 40, 65.
4. E. M. Dirggers, H. S. Cho, C. W. Liu, C. P. Katzka, A. C. Braisted, H. D. Ulrich, D. E. Wemmer and P. G. Schultz, J. Am. Chem. Soc., 1998, 120, 1945.
5. S. G. Sogo, T. S. Widlanski, J. H. Hoare, C. E. Grimshaw, G. A. Berchtold and J. R. Knowles, J. Am. Chem. Soc., 1984, 106, 2701.
6. S. D. Copley and J. R. Knowles, J. Am. Chem. Soc., 1987, 109, 5008.
7. I. H. Williams, Chem. Soc. Rev., 1993, 22, 277.
8. K. D. McMichael and G. L. Korver, J. Am. Chem. Soc., 1979, 101, 2746.
9. J. J. Gajewski and N. D. Conrad, J. Am. Chem. Soc., 1979, 101, 2747.
10. (a) L. Kupczyk-Subotkowska, W. H. Saunders and H. J. Shine, J. Am. Chem. Soc., 1988, 110, 7153
11. L. Kupczyk-Subotkowska, W. Subotkowski, W. H. Saunders and H. J. Shine. J. Am. Chem. Soc., 1992, 114, 3441.
12. L. Kupczyk-Subotkowska, W. H. Saunders, H. J. Shine and W. Subotkowski, J. Am. Chem. Soc., 1993, 115, 5957.
13. M. P. Meyer, A. J. DelMonte and D. A. Singleton, J. Am. Chem. Soc., 1999, 121, 10865.
14. L. Addadi, E. K. Jaffe and J. R. Kowles. Biochemistry, 1983, 22, 4994.
15. W. J. Guilford, S. D. Copley and J. R. Knowles, J. Am. Chem. Soc., 1987, 109, 5013.
16. D. J. Gustin, P. Mattei, P. Kast, O. Wiest, L Lee, W. W. Cleland and D. Hilvert, J. Am. Chem. Soc., 1999, 121, 1756.
17. (a) S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón and J. Bertrán, Theor. Chem., 2001, 105, 207
18. (b) S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón and J. Bertrán, J. Phys. Chem. B., 2000, 104, 11308
19. (c) S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñon, J. Bertrán and M. J. Field, J. Am. Chem. Soc., 2001, 123, 1709
20. (d) S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán, Chem. Eur. J., 2002, in press
21. (e) S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán, Theochem., 2002, in press.
22. A. Warshel and M. Levitt, J. Mol. Biol., 1976, 103, 227.
23. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy and J. J. P. Stewart, J. Am. Chem. Soc., 1985, 107, 3902.
24. (a) A. D. Becke, Phys. Rev. A, 1988, 38, 3098
25. A. D. Becke, J. Chem. Phys., 1993, 98, 5648
26. (b) C. Lee, W. Yang and R. G. Parr, Phys. Rev. B, 1988, 37, 785
27. (c) P. J. Stevens, J. F. Devlin, C. F. Chabalowski and M. J. Frisch, J. Phys. Chem., 1994, 98, 11623.
28. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. 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. P. 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 98, Revision A.6, Gaussian, Inc., Pittsburgh PA, 1998.
29. H. B. Schlegel, J. Comput. Chem., 1982, 3, 214.
30. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, J. Comput. Chem., 1983, 4, 187.
31. (a) V. Moliner, A. J. Turner and I. H. Williams, Chem. Commun., 1997, 1271
32. (b) A. J. Turner, V. Moliner and I. H. Williams, Phys. Chem. Chem. Phys., 1999, 1, 1323.
33. Y. M. Chook, H. Ke and W. N. Lipscomb, Proc. Natl. Acad. Sci. USA, 1993, 90, 8600. Protein Data Bank ID code ICOM.
34. (a) M. W. Schmidt, M. S. Gordon and M. Dupuis, J. Am. Chem. Soc., 1985, 107, 1585
35. (b) J. J. P. Stewart, MOPAC 7 (QCPE 457), QCPE Bull., 1993, 13, 42.
36. B. Roux, Comput. Phys. Commun., 1995, 91, 275.
37. G. M. Torrie and J. P. Valleau, J. Comput. Phys., 1977, 23, 187.
38. M. J. Field, M. Albe, C. Bret, F. Proust de Martin and A. Thomas, J. Comput. Chem., 2000, 21, 1088.
39. F. Proust de Martin, R. Dumas and M. J. Field, J. Am. Chem. Soc., 2000, 122, 7688.
40. (a) I. H. Williams, Chem. Phys. Lett., 1982, 88, 462
41. (b) I. H. Williams, J. Mol. Struct. THEOCHEM, 1983, 11, 275.
42. J. Sühnel, R. L. Schowen, in Enzyme Mechanism from Isotope Effects, ed. P. F. Cook, CRC Press, Boca Raton, 1991.
43. P. D. Lyne, A. J. Mulholland and W. G. Richards, J. Am. Chem. Soc., 1995, 117, 11345.
44. K. N. Houk, J. Gonzalez and Y. Li, Acc. Chem. Res., 1995, 28, 81.
45. (a) B. R. Beno, K. N. Houk and D. A. Singleton, J. Am. Chem. Soc., 1996, 118, 9984
46. (b) D. A. Singleton, S. L. Merrigan, J. Liu and K. N. Houk, J. Am. Chem. Soc., 1997, 119, 3385
47. (c) A. J. Del Monte, J. Haller, K. N. Houk, K. B. Sharpless, D. A. Singleton, T. Strassner and A. A. Thomas, J. Am. Chem. Soc., 1997, 119, 9907.
48. Y. S. Lee, S. E. Worthington, M. Krauss and B. R. Brooks, J. Phys. Chem. B, 2002, 106, 12059.
49. P. Matthei, P. Kast and D. Hilvert, Eur. J. Biochem., 1999, 261-25.