Substrate hydroxylation in methane monooxygenase: Quantitative modeling via mixed quantum mechanics/molecular mechanics techniques
Substrate hydroxylation in methane monooxygenase: Quantitative modeling via mixed quantum mechanics/molecular mechanics techniques
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DOI：
10.1021/ja049847b
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发表时间：
2005-01-26
影响因子：
15
通讯作者：
Friesner, RA
中科院分区：
文献类型：
--
作者：
Gherman, BF;Lippard, SJ;Friesner, RA
采用非限制性密度泛函量子力学（QM）方法和混合量子力学/分子力学（QM/MM）方法，对甲烷单加氧酶（MMOH）中中间体Q对甲烷和取代甲烷的羟基化反应进行了定量模拟.该方案允许在整个计算过程中包括蛋白质环境，并准确评估其对反应的影响（静电、货车范德华力、应变）。根据目前的结果，MMOH中CH 3X（X = H，CH 3，OH，CN，NO2）底物羟基化的最新动力学数据（Ambundo，E.一、弗里斯纳河，巴西-地一、Lippard，S. J·J·Am. 2002，124，8770-8771）可以合理化。甲烷的结果，提供了一个定量测试的协议，包括大量的动力学同位素效应（KIE），是在合理的协议与实验。每个基板与MMO的相互作用的具体功能被照亮的QM/MM建模，并定量地纳入到计算中所产生的影响后，基板结合。结果作为一个整体指向QM/MM方法的成功，并提高我们的理解MMOH催化化学。我们还确定了系统性的错误，在评价的自由能结合的米氏络合物的基板，这最有可能产生的采样不足和/或使用谐波近似来评估复杂的熵。在这方面的计算中，要达到更高的准确性，就需要采用更复杂的抽样方法。
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.