Substrate hydroxylation in methane monooxygenase: quantitative modeling via mixed quantum mechanics/molecular mechanics techniques.
Using broken-symmetry unrestricted density functional theory quantum mechanical (QM) methods in concert with mixed quantum mechanics/molecular mechanics (QM/MM) methods, the hydroxylation of methane and substituted methanes by intermediate Q in methane monooxygenase hydroxylase (MMOH) has been quantitatively modeled. This protocol allows the protein environment to be included throughout the calculations and its effects (electrostatic, van der Waals, strain) upon the reaction to be accurately evaluated. With the current results, recent kinetic data for CH3X (X = H, CH3, OH, CN, NO2) substrate hydroxylation in MMOH (Ambundo, E. A.; Friesner, R. A.; Lippard, S. J. J. Am. Chem. Soc. 2002, 124, 8770-8771) can be rationalized. Results for methane, which provide a quantitative test of the protocol, including a substantial kinetic isotope effect (KIE), are in reasonable agreement with experiment. Specific features of the interaction of each of the substrates with MMO are illuminated by the QM/MM modeling, and the resulting effects upon substrate binding are quantitatively incorporated into the calculations. The results as a whole point to the success of the QM/MM methodology and enhance our understanding of MMOH catalytic chemistry. We also identify systematic errors in the evaluation of the free energy of binding of the Michaelis complexes of the substrates, which most likely arise from inadequate sampling and/or the use of harmonic approximations to evaluate the entropy of the complex. More sophisticated sampling methods will be required to achieve greater accuracy in this aspect of the calculation.
Gherman
Benjamin F
BF
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA.
Lippard
Stephen J
SJ
Friesner
Richard A
RA
D000097:Acetonitriles / Q000737:chemistry / Q000378:metabolism; D002384:Catalysis; D004980:Ethane / Q000737:chemistry / Q000378:metabolism; D057927:Hydrophobic and Hydrophilic Interactions; D006900:Hydroxylation; D007700:Kinetics; D008697:Methane / Q000031:analogs & derivatives / Q000378:metabolism; D000432:Methanol / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D010105:Oxygenases / Q000737:chemistry* / Q000378:metabolism*; D011789:Quantum Theory; D013816:Thermodynamics
D000097:Acetonitriles; D010105:Oxygenases; C021555:methane monooxygenase; D004980:Ethane; D008697:Methane; D000432:Methanol; C032159:acetonitrile