Kumar Devesh, Hirao Hajime, de Visser Sam P, Zheng Jingjing, Wang Dongqi, Thiel Walter, Shaik Sason
Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
J Phys Chem B. 2005 Oct 27;109(42):19946-51. doi: 10.1021/jp054754h.
Density functional theory (DFT) is applied to the dark section of the catalytic cycle of the enzyme cytochrome P450, namely, the formation of the active species, Compound I (Cpd I), from the ferric-hydroperoxide species (Cpd 0) by a protonation-assisted mechanism. The chosen 96-atom model includes the key functionalities deduced from experiment: Asp(251), Thr(252), Glu(366), and the water channels that relay the protons. The DFT model calculations show that (a) Cpd I is not formed spontaneously from Cpd 0 by direct protonation, nor is the process very exothermic. The process is virtually thermoneutral and involves a significant barrier such that formation of Cpd I is not facile on this route. (b) Along the protonation pathway, there exists an intermediate, a protonated Cpd 0, which is a potent oxidant since it is a ferric complex of water oxide. Preliminary quantum mechanical/molecular mechanical calculations confirm that Cpd 0 and Cpd I are of similar energy for the chosen model and that protonated Cpd 0 may exist as an unstable intermediate. The paper also addresses the essential role of Thr(252) as a hydrogen-bond acceptor (in accord with mutation studies of the OH group to OMe).
密度泛函理论（DFT）应用于细胞色素P450酶催化循环的暗反应部分，即通过质子化辅助机制从铁过氧化氢物种（化合物0，Cpd 0）形成活性物种化合物I（Cpd I）。所选择的96原子模型包含从实验中推导出来的关键官能团：天冬氨酸（251）、苏氨酸（252）、谷氨酸（366）以及传递质子的水通道。DFT模型计算表明：（a）Cpd I不会通过直接质子化从Cpd 0自发形成，该过程也不是非常放热。该过程实际上是热中性的，并且涉及一个显著的势垒，使得在这条途径上Cpd I的形成并不容易。（b）沿着质子化途径，存在一种中间体，即质子化的Cpd 0，它是一种强氧化剂，因为它是水合氧化铁的铁配合物。初步的量子力学/分子力学计算证实，对于所选择的模型，Cpd 0和Cpd I具有相似的能量，并且质子化的Cpd 0可能作为一种不稳定的中间体存在。本文还阐述了苏氨酸（252）作为氢键受体的重要作用（这与将羟基突变为甲氧基的研究结果一致）。
