Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam

Journal of Inorganic Biochemistry

Volumn 81, Issue 3, 2000, Pages 121-131

  Das, Bedamati ^b   Helms, Volkhard ^c   Lounnas, Valère ^d   Wade, Rebecca C ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b FLORIDA STATE UNIVERSITY   (United States)

^c MAX PLANCK INSTITUTE OF BIOPHYSICS   (Germany)

^d NV 5340 BH Oss   (Netherlands)

Author keywords

Alternative ligand binding modes; Camphor; Cytochrome P450; High temperature molecular dynamics; Locally enhanced sampling (LES)

Indexed keywords

CAMPHOR; CAMPHOR 5 MONOOXYGENASE; IMIDAZOLE DERIVATIVE; IRON; OXYGEN; PHENYLIMIDAZOLE; THIOCAMPHOR; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER SIMULATION; CONFORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENANTIOMER; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; HYDROXYLATION; LIGAND BINDING; MOLECULAR DYNAMICS; SPECTROSCOPY; TECHNIQUE; TEMPERATURE;

BINDING SITES; CAMPHOR; CAMPHOR 5-MONOOXYGENASE; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; SOFTWARE; TEMPERATURE; WATER;

EID: 0034739054     PISSN: 01620134     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0162-0134(00)00095-7     Document Type: Article

References (35)

1. Porter T.D., Coon M.J. J. Biol. Chem. 266:1991;13469-13472.
2. Guengerich F.P. J. Biol. Chem. 266:1991;10019-10022.
3. Poulos T.L., Raag R. FASEB J. 6:1992;674-679.
4. Poulos T.L., Finzel B.C., Howard A.J. J. Mol. Biol. 195:1987;687-700.
5. Griffin B.W., Peterson J.A. Biochemistry. 11:1972;4740-4746.
6. Raag R., Poulos T.L. Biochemistry. 30:1991;2674-2684.
7. Paulsen M.D., Ornstein R.L. Protein Eng. 6:1993;359-365.
8. Poulos T.L., Howard A.J. Biochemistry. 26:1987;8165-8174.
9. Kadkhodayan S., Coulter E.D., Maryniak D.M., Bryson T.A., Dawson J.H. J. Biol. Chem. 270:1995;28042-28048.
10. Maryniak D.M., Kadkhodayan S., Crull G.B., Bryson T.A., Dawson J.H. Tetrahedron. 49:1993;9373.
11. Schulze H., HuiBonHoa G., Helms V., Wade R.C., Jung C. Biochemistry. 35:1996;14127-14138.
12. Schlichting I., Jung C., Schulze H. FEBS Lett. 415:1997;253-257.
13. Elber R., Karplus M. J. Am. Chem. Soc. 112:1990;9161-9175.
14. Zheng Q., Rosenfeld R., Kyle D.J. J. Chem. Phys. 99:1993;8892-8896.
15. Roitberg A., Elber R. J. Chem. Phys. 95:1991;9277-9287.
16. Simmerling C.L., Elber R. Proc. Natl. Acad. Sci. USA. 92:1995;3190-3193.
17. Ulitsky A., Elber R. J. Phys. Chem. 98:1994;1034-1043.
18. Raag R.H., Li H., Jones B.C., Poulos T.L. Biochemistry. 32:1993;4571-4578.
19. Straub L.E., Karplus M. J. Chem. Phys. 94:1991;6737-6739.
20. Mohanty D., Elber R., Thirumalai D., Beglov D., Roux B. J. Mol. Biol. 272:1997;423-442.
21. Helms V., Deprez E., Gill E., Barret C., HuiBonHoa G., Wade R.C. Biochemistry. 35:1996;1485-1499.
22. Straatsma T.P., McCammon J.A. J. Comp. Chem. 11:1990;943-951.
23. W.F. van Gunsteren, H.J.C. Berendsen, Groningen Molecular Simulation Library, Groningen, 1987.
24. Helms V., Wade R.C. J. Comp. Chem. 18:1997;449-462.
25. Berendsen H.J.C., Grigera J.R., Straatsma T.P. J. Phys. Chem. 91:1987;6269-6271.
26. Ryckaert J.P., Ciccotti G., Berendsen H.J.C. J. Comp. Phys. 23:1977;327-341.
27. Sobolev V., Wade R.C., Vriend G., Edelman M. Proteins. 25:1996;120-129.
28. Sobolev V., Moallem T.M., Wade R.C., Vriend G., Edelman M. Proteins Suppl. 1:1997;210-214.
29. Poulos T.L., Finzel B.C., Howard A.J. Biochemistry. 25:1986;5314-5322.
30. Wade R.C. J. Comp. Aid. Mol. Des. 4:1990;199-204.
31. Helms V., Wade R.C. Biophys. J. 69:1995;810-824.
32. Harris D., Loew G. J. Am. Chem. Soc. 117:1995;2738-2746.
33. Lee H., Ortiz de Montellano P.R., McDermott A.E. Biochemistry. 38:1999;10808-10813.
34. Helms V., Wade R.C. Proteins. 32:1998;381-396.
35. Helms V., Wade R.C. J. Am. Chem. Soc. 120:1998;2710-2713.