Experimentally restrained molecular dynamics simulations for characterizing the open states of cytochrome P450cam.
Residual dipolar couplings (RDCs) were used as restraints in fully solvated molecular dynamics simulations of reduced substrate- and carbonmonoxy-bound cytochrome P450(cam) (CYP101A1), a 414-residue soluble monomeric heme-containing camphor monooxygenase from the soil bacterium Pseudomonas putida. The (1)D(NH) residual dipolar couplings used as restraints were measured in two independent alignment media. A soft annealing protocol was used to heat the starting structures while incorporating the RDC restraints. After production dynamics, structures with the lowest total violation energies for RDC restraints were extracted to identify ensembles of conformers accessible to the enzyme in solution. The simulations result in substrate orientations different from that seen in crystallographic structures and a more open and accessible enzyme active site and largely support previously reported differences between the open and closed states of CYP101A1.
Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States.
Eliana K
EK
Asciutto
Marina
M
Dang
Susan Sondej
SS
Pochapsky
Jeffry D
JD
Madura
Thomas C
TC
Pochapsky
D019475:Camphor 5-Monooxygenase / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017434:Protein Structure, Tertiary; D016958:Pseudomonas putida / Q000201:enzymology*; D040681:Structural Homology, Protein; D013379:Substrate Specificity
D019475:Camphor 5-Monooxygenase
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