A hybrid-potential free-energy study of the isomerization step of the acetohydroxy acid isomeroreductase reaction

Journal of the American Chemical Society

Volumn 122, Issue 32, 2000, Pages 7688-7697

  Proust De Martin, Flavien ^a   Dumas, Renaud ^b   Field, Martin J ^a  

^a INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^b SANOFI   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ISOMERASE; OXIDOREDUCTASE;

ARTICLE; CATALYSIS; ENERGY TRANSFER; ENZYME CONFORMATION; ENZYME SUBSTRATE COMPLEX; ISOMERISM; MOLECULAR DYNAMICS; PROTON TRANSPORT; REACTION ANALYSIS;

EID: 0000556829     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja000414s     Document Type: Article

References (38)

1. Schulz, A.; Spönemann, P.; Köcher, H.; Wengenmayer, F. FEBS Lett. 1988, 238, 375-378.
2. Aulabaugh, A.; Schloss, J. V. Biochemistry 1990, 29, 2824-2830.
3. Dumas, R.; Cornillon-Bertrand, C.; Guigue-Talet, P.; Genix, P.; Douce, R.; Job, D. Biochem. J. 1994, 301, 813-820.
4. Dumas, R.; Butikofer, M. C.; Job, D.; Douce, R. Biochemistry 1995, 34, 6026-6036.
5. Biou, V.; Dumas, R.; Cohen-Addad, C.; Douce, R.; Job, D.; Pebay-Peyroula, E. EMBO J. 1997, 16, 3405-3415.
6. Field, M. J. The Simulation of Chemical Reactions, in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; van Gunsteren, W. F., Weiner, P. K., Wilkinson, A. J., Eds.; ESCOM: Leiden, 1993; Vol. 2, pp 82-123.
7. Gao, J. Methods and Applications of Combined Quantum and Molecular Mechanical Potentials. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1995; Vol. 7, pp 119-185.
8. Stewart, J. J. P. Mopac 7.0, QCPE 688; Quantum Chemistry Program Exchange: Bloomington, IN, 1993.
9. Jaguar 3.5; Schrödinger Inc.: Portland, OR, 1998.
10. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902-3909.
11. Stewart, J. J. P. J. Comput. Chem. 1989, 10, 209-220.
12. Stewart, J. J. P. J. Comput. Chem. 1989, 10, 221-264.
13. Becke, A. D. J. Chem. Phys. 1993, 98, 1372-77; 1993, 98, 5648- 5652.
14. Becke, A. D. J. Chem. Phys. 1993, 98, 1372-77; 1993, 98, 5648-5652.
15. Hehre, W. J.; Radom, L.; Schleyer, P. v. R.; Pople, J. A. Ab Initio Molecular Orbital Theory; J. Wiley & Sons: New York, 1986.
16. AMPAC-5.0 Manual; Semichem, 12715, W. 66th Terrace, Shawnee, KS 66216; 1994.
17. Field, M. J. A Practical Introduction to the Simulation of Molecular Systems; Cambridge University Press: Cambridge, UK, 1999.
18. Field, M. J.; Albe, M.; Bret, C.; Proust-de Martin, F.; Thomas, A. J. Comput. Chem. 2000, 21, 1088-1100.
19. Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11, 700-733.
20. Hutter, M. C.; Reimers, J. R.; Hush, N. S. J. Phys. Chem. B 1998, 102, 8080-8090.
21. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
22. Jorgensen, W. L.; Chandrasekar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
23. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F., Jr.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. J. Mol. Biol. 1977, 112, 535-542.
24. Wessel, P.; Biou, V.; Douce, R.; Dumas, R. Biochemistry 1998, 37, 12753-12760.
25. Insight II; Molecular Simulations Inc.: San Diego, CA, 1993.
26. Kirkwood, J. G. J. Chem. Phys. 1935, 3, 300-313.
27. Valleau, J. P.; Torrie, G. M. A Guide for Monte Carlo for Statistical Mechanics. In Statistical Mechanics; Berne, B. J., Ed.; Plenum Press: New York, 1977; Part A, pp 169-194.
28. Torrie, G. M.; Valleau, J. P. Chem. Phys. Lett. 1974, 28, 578-581.
29. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
30. Roux, B. Comput. Phys. Commun. 1995, 91, 275-282.
31. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Oxford, UK, 1987.
32. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667-683.
33. 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. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, Revision A.7; Gaussian, Inc.: Pittsburgh, PA, 1998.
34. Chunduru, S. K.; Mrachko, G. T.; Calvo, K. C. Biochemistry 1989, 28, 486-493.
35. Hu, H.; Liu, H.; Shi, Y. Proteins: Struct., Funct. Genet. 1997, 27, 545-555.
36. Dewar, M. J. S.; Dieter, K. M. J. Am. Chem. Soc. 1986, 108, 8075-8086.
37. Thomas, A.; Jourand, D.; Bret, C.; Amara, P.; Field, M. J. J. Am. Chem. Soc. 1999, 121, 9693-9702.
38. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes in Fortran: The Art of Scientific Computing, 2nd ed.; Cambridge University Press: Cambridge, UK, 1992.