QM/MM study of the product-enzyme complex in P450cam catalysis

Journal of Physical Chemistry B

Volumn 108, Issue 28, 2004, Pages 10083-10088

  Lin, Hai ^a   Schöneboom, Jan C ^a   Cohen, Shimrit ^b   Shaik, Sason ^b   Thiel, Walter ^a  

^a MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

^b HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; BIOCHEMISTRY; CATALYSIS; CHEMICAL BONDS; COMPLEXATION; CONFORMATIONS; DISSOCIATION; HYDROXYLATION; PROBABILITY DENSITY FUNCTION; SOLVENTS;

CONFORMATIONAL COMPLEXITY; NONPOLAR PROTEINS; PRODUCY-ENZYME COMPLEXES;

PROTEINS;

EID: 3442900466     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0493632     Document Type: Article

References (26)

1. Cytochrome P450: Structure, Mechanisms and Biochemistry, 2nd ed.; Ortiz de Montellano, P. R., Ed.; Plenum Press: New York, 1995; Vol. 2.
2. Li, H.; Narasimhulu, S.; Havran, L. M.; Winkler, J. D.; Poulos, T. L. J. Am. Chem. Soc. 1995, 117, 6297.
3. Lipscomb, J. D. Biochemistry 1980, 19, 3590.
4. Davydov, R.; Makris, T. M.; Kofman, V.; Werst, D. E.; Sligar, S. G.; Hoffman, B. M. J. Am. Chem. Soc. 2001, 123, 1403.
5. Schöneboom, J. C.; Cohen, S.; Lin, H.; Shaik, S.; Thiel, W. J. Am. Chem. Soc. 2004, 126, 4017.
6. Schöneboom, J. C.; Lin, H.; Reuter, N.; Thiel, W.; Cohen, S.; Ogliaro, F.; Shaik, S. J. Am. Chem. Soc. 2002, 124, 8142.
7. Sherwood, P.; de Vries, A. H.; Guest, M. F.; Schreckenbach, G.; Catlow, C. R. A.; French, S. A.; Sokol, A. A.; Bromley, S. T.; Thiel, W.; Turner, A. J. ; Billeter, S.; Terstegen, F.; Thiel, S.; Kendrick, J.; Rogers, S. C.; Casci, J.; Watson, M.; King, F.; Karlsen, E.; Sjovoll, M.; Fahmi, A.; Schäfer, A. ; Lennartz, C. J. Mol. Struct. (THEOCHEM) 2003, 632, 1.
8. (a) Becke, A. D. Phys. Rev. A 1988, 38, 3098.
9. (b) Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 85.
10. (c) Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
11. Reiher, M.; Salomon, O.; Hess, B. A. Theor. Chem. Acc. 2001, 107, 48.
12. Salomon, O.; Reiher, M.; Hess, B. A. J. Chem. Phys. 2002, 117, 4729.
13. Hay, J. P.; Wadt, W. R. J. Chem. Phys. 1985, 82, 299.
14. Ditchfield, R.; Hehre, W. J.; Pople, J. A. J. Chem. Phys. 1971, 54, 724.
15. Bakowies, D.; Thiel, W. J. Phys. Chem. 1996, 100, 10580.
16. Antes, I.; Thiel, W. Hybrid Quantum Mechanical and Molecular Mechanical Methods; Gao, J., Ed.; ACS Symposium Series 712; American Chemical Society; Washington, DC, 1998; pp 50-65.
17. de Vries, A. H.; Sherwood, P.; Collins, S. J.; Rigby, A. M.; Rigutto, M. ; Kramer, G. J. J. Phys. Chem. B 1999, 103, 6133.
18. (a) Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. Chem. Phys. Lett. 1989, 162, 165.
19. (b) Ahlrichs, R.; Bar, M.; Baron, H.-P.; Bauernschmitt, R.; Böcker, S.; Ehrig, M.; Eichkorn, K.; Elliot, S.; Furche, F.; Häser, M.; Horn, H,; Hättig, C.; Huber, C.; Huniar, U.; Kattanneck, M.; Köhn, A.; Kölmel, C.; Kollwitz, M.; May, K.; Ochsenfeld, C.; Öhm, H.; Schäfer, A.; Schneider, U.; Treutler, O.; v. Arnim, M.; Weigend, F.; Weis, P.; Weiss, H. TURBOMOLE 5.5, University of Karlsruhe: Karlsruhe, Germany, 2002.
20. ChemShell is a modular QM/MM program developed in the European QUASI project under the coordination of P. Sherwood. See: http:// www.cse.clrc.ac.uk/qcg/chemshell.
21. CHARMM22 force field: MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586.
22. For details about the generation and geometric features of the snapshot structures, nonstandard force field parameters, and QM/MM geometry optimizations, see ref 6 and Supporting Information thereof.
23. Smith, W.; Forester, T. J. Mol. Graph. 1996, 14, 136.
24. Billeter, S. R.; Turner, A. J.; Thiel, W. Phys. Chem. Chem. Phys. 2000, 2, 2177.
25. Ogliaro, F.; Harris, N.; Cohen, S.; Filatov, M.; de Visser, S. P.; Shaik, S. J. Am. Chem. Soc. 2000, 122, 8977.
26. Schöneboom, J. C.; Thiel, W. J. Phys. Chem. B 2004, 108, 7468.