Gherman Benjamin F, Lippard Stephen J, Friesner Richard A
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA.
J Am Chem Soc. 2005 Jan 26;127(3):1025-37. doi: 10.1021/ja049847b.
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.
结合使用破缺对称性无限制密度泛函理论量子力学（QM）方法与混合量子力学/分子力学（QM/MM）方法，对甲烷单加氧酶羟化酶（MMOH）中中间体Q催化甲烷及取代甲烷的羟基化反应进行了定量建模。该方法能够在整个计算过程中纳入蛋白质环境，并准确评估其对反应的影响（静电作用、范德华力、应变）。基于目前的研究结果，可以合理解释MMOH中CH3X（X = H、CH3、OH、CN、NO2）底物羟基化反应的最新动力学数据（安本多，E. A.；弗里斯纳，R. A.；利帕德，S. J. 《美国化学会志》2002年，124卷，8770 - 8771页）。甲烷的研究结果对该方法进行了定量检验，包括显著的动力学同位素效应（KIE），与实验结果合理吻合。QM/MM建模揭示了每种底物与MMO相互作用的具体特征，并将由此产生的对底物结合的影响定量纳入计算。总体结果表明QM/MM方法取得了成功，加深了我们对MMOH催化化学的理解。我们还发现了在评估底物米氏复合物结合自由能时存在的系统误差，这很可能是由于采样不足和/或使用谐振近似来评估复合物熵所致。在计算的这一方面，需要更复杂的采样方法以获得更高的精度。
