How Do Perfluorinated Alkanoic Acids Elicit Cytochrome P450 to Catalyze Methane Hydroxylation? An MD and QM/MM Study.
How Do Perfluorinated Alkanoic Acids Elicit Cytochrome P450 to Catalyze Methane Hydroxylation? An MD and QM/MM Study.
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DOI：
10.1039/c2ra22294a
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发表时间：
2013-03-07
期刊：
影响因子：
3.9
通讯作者：
Shaik S
中科院分区：
文献类型：
--
作者：
Li C;Shaik S
最近的实验研究表明，使用全氟癸酸（PFDA）作为虚拟底物，可以引发P450 BM 3进行小烷烃（如甲烷）的羟基化（参考文献）。和丙烷（参考文献和参考文献）。为了理解PFDA增强P450 BM 3催化小烷烃羟基化的机制，我们使用了分子动力学（MD）和混合量子力学/分子力学（QM/MM）计算。MD结果表明，在没有PFDA的情况下，甲烷逃离活性位点，而PFDA的存在可能会诱导一个生产性的Cpd I-甲烷并置快速氧化。然而，当PFDA附近只有一个甲烷分子时，它仍然在不到一纳秒的时间内逃离口袋。然而，当三个甲烷分子存在于口袋中时，它们准周期性地交替，使得在所有时间（10 ns内），甲烷分子总是以反应性构象存在于Cpd I附近。我们的研究结果进一步表明，PFDA不施加任何静电催化，无论PFDA是在质子化或去质子化的形式。综上所述，我们得出结论，甲烷羟基化需要，除了PFDA，甲烷的高分压，这将导致高甲烷浓度的活性位点。乙烷和丙烷羟基化反应的进一步研究表明，较高的烷烃浓度有利于所有三种小烷烃的羟基化反应。因此，对于最小的烷烃，甲烷，至少需要三个分子，而对于较大的乙烷，需要两个分子来迫使一个乙烷更接近Cpd I。最后，对于丙烷，第二个分子是有帮助的，但不是绝对必要的;对于这个分子，PFDA可能足以使丙烷接近Cpd I以进行有效氧化。因此，我们建议，高烷烃压力应有助于小烷烃羟基化的P450的方式成反比的烷烃的大小。
Recent experimental studies show that usage of perfluoro decanoic acid (PFDA), as a dummy substrate, can elicit P450BM3 to perform hydroxylation of small alkanes, such as methane (ref.) and propane (ref. and ref.). To comprehend the mechanism whereby PFDA operates to potentiate P450BM3 to catalyze the hydroxylation of small alkanes, we used molecular dynamics (MD) and hybrid quantum mechanical / molecular mechanical (QM/MM) calculations. The MD results show that without the PFDA, methane escapes the active site, while the presence of PFDA can potentially induce a productive Cpd I-Methane juxtaposition for rapid oxidation. Nevertheless, when only a single methane molecule is present near the PFDA, it still escapes the pocket within less than a nanosecond. However, when three methane molecules are present in the pocket, they alternate quasi-periodically such that at all times (within 10 ns), a molecule of methane is always present in the proximity of Cpd I in a reactive conformation. Our results further demonstrate that the PFDA does not exert any electrostatic catalysis, whether the PFDA is in the protonated or deprotonated forms. Taken together, we conclude that methane hydroxylation requires, in addition to PFDA, a high partial pressure of methane that will cause a high methane concentration in the active site. Further study of ethane and propane hydroxylations demonstrates that higher alkane concentration is helpful for all the three small alkanes. Thus for the smallest alkane, methane, at least three molecules are necessary whereas for the larger ethane, two molecules are needed to force one ethane to be closer to Cpd I. Finally, for propane a second molecule is helpful but not absolutely necessary; for this molecule the PFDA may well be sufficient to keep propane close to Cpd I for efficient oxidation. We therefore propose that high alkane pressure should assist small alkane hydroxylation by P450 in a manner inversely proportional to the size of the alkanes.