Modeling the Ligand Effect on the Structure of CYP 450 Within the Density Functional Theory
Modeling the Ligand Effect on the Structure of CYP 450 Within the Density Functional Theory
复制标题
在密度泛函理论中模拟配体对 CYP 450 结构的影响
DOI：
10.1021/acs.jpca.2c01783
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Garashchuk, Sophya
中科院分区：
文献类型：
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作者：
Dutra, Matthew;McElhenney, Shannon;Manley, Olivia;Makris, Tom;Rassolov, Vitaly;Garashchuk, Sophya
对P450结构的进一步理解与仿生催化剂和抑制剂的开发有关，用于控制CH键活化，这是合成化学的一个突出挑战。受野生型（WT）OleT P450脱羧酶相对于半胱氨酸口袋突变体形式（A369 P）的2.18 π的异常短的Fe-S键的实验发现的启发，提出了捕获硫醇盐轴向配体对铁-硫距离的影响的计算模型。考虑到计算效率和简化分析，该模型将酶的簇表示（40-110个原子，取决于血红素和配体截断水平）与电子结构（ES）的密度泛函理论（DFT）描述相结合，并根据实验数据进行校准。优化的Fe-S距离显示低自旋态和高自旋态之间的差异为0.25 μ m，与OleT WT和突变体形式的晶体结构一致。我们推测，这种差异是由于包装的配体，突变体是笨重的，由于丙氨酸到脯氨酸的替代，这意味着它被排除在积极有利的低自旋最低，因为空间限制。纯自旋状态对的存在和交叉的低/高自旋状态的酶模型是指示单参考ES方法在这样的系统中的局限性，并强调使用适当的状态时，建模的氢原子转移（HAT）反应催化的OleT的意义。与此同时，在一个基于DFT的42个原子的小模型中正确表征了短和长Fe-S键，为HAT步骤的量子动力学建模铺平了道路，该步骤启动了OleT脱羧反应。
An improved understanding of the P450 structure is relevant to the development of biomimetic catalysts and inhibitors for controlled CH-bond activation, an outstanding challenge of synthetic chemistry. Motivated by the experimental findings of an unusually short Fe–S bond of 2.18 Å for the wild-type (WT) OleT P450 decarboxylase relative to a cysteine pocket mutant form (A369P), a computational model that captures the effect of the thiolate axial ligand on the iron–sulfur distance is presented. With the computational efficiency and streamlined analysis in mind, this model combines a cluster representation of the enzyme─40–110 atoms, depending on the heme and ligand truncation level─with a density functional theory (DFT) description of the electronic structure (ES) and is calibrated against the experimental data. The optimized Fe–S distances show a difference of 0.25 Å between the low and high spin states, in agreement with the crystallographic structures of the OleT WT and mutant forms. We speculate that this difference is attributable to the packing of the ligand; the mutant is bulkier due to an alanine-to-proline replacement, meaning that it is excluded from the energetically favored low-spin minimum because of steric constraints. The presence of pure spin-state pairs and the intersection of the low/high spin states for the enzyme model is indicative of the limitations of single-reference ES methods in such systems and emphasizes the significance of using the proper state when modeling the hydrogen atom transfer (HAT) reaction catalyzed by OleT. At the same time, the correct characterization of both the short and long Fe–S bonds within a small DFT-based model of 42 atoms paves the way for quantum dynamics modeling of the HAT step, which initiates the OleT decarboxylation reaction.