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Protein Science (2007), 16:420-431. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants

K. Anton Feenstra1, Eugene B. Starikov1, Vlada B. Urlacher2, Jan N.M. Commandeur1, and Nico P.E. Vermeulen1

1 Leiden/Amsterdam Center for Drug Research, Division of Molecular Toxicology, Vrije Universiteit, 1081HV Amsterdam, The Netherlands
2 Institute for Technical Biochemistry, University of Stuttgart, Stuttgart, Germany

(RECEIVED May 8, 2006; FINAL REVISION October 23, 2006; ACCEPTED November 21, 2006)

Hydroxylations of octane and lauric acid by Cytochrome P450-BM3 (CYP102A1) wild-type and three active site mutants—F87A, L188Q/A74G, and F87V/L188Q/A74G—were rationalized using a combination of substrate orientation from docking, substrate binding statistics from molecular dynamics simulations, and barrier energies for hydrogen atom abstraction from quantum mechanical calculations. Wild-type BM3 typically hydroxylates medium- to long-chain fatty acids on subterminal ({omega}–1, {omega}–2, {omega}–3) but not the terminal ({omega}) positions. The known carboxylic anchoring site Y51/R47 for lauric acid, and hydrophobic interactions and steric exclusion, mainly by F87, for octane as well as lauric acid, play a role in the binding modes of the substrates. Electrostatic interactions between the protein and the substrate strongly modulate the substrate's regiodependent activation barriers. A combination of the binding statistics and the activation barriers of hydrogen-atom abstraction in the substrates is proposed to determine the product formation. Trends observed in experimental product formation for octane and lauric acid by wild-type BM3 and the three active site mutants were qualitatively explained. It is concluded that the combination of substrate binding statistics and hydrogen–atom abstraction barrier energies is a valuable tool to rationalize substrate binding and product formation and constitutes an important step toward prediction of product ratios.

Keywords: Cytochrome P450; enzyme catalysis; substrate dynamics; substrate activation barriers; essential dynamics; protein dynamics


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