The "open" (Aopen) and "closed" (Aclosed) A-clusters of the acteyl-CoA synthase (ACS) enzyme from Moorella thermoacetica have been studied using a combined quantum mechanical (QM)/molecular mechanical (MM) approach. Geometry optimizations of the oxidized, one- and two-electron reduced Aopen state have been carried out for the fully solvated ACS enzyme, and the CO ligand has been modeled in the reduced models. Using a combination of both αopen and αclosed protein scaffolds and the positions of metal atoms in these structures, we have been able to piece together critical parts of the catalytic cycle of ACS. We have replaced the unidentified exogenous ligand in the crystal structure with CO using both a square planar and tetrahedral proximal Ni atom. A one-electron reduced A-cluster that is characterized by a proximal Ni atom in a tetrahedral coordination pattern observed in both the Aopen (lower occupancy proximal Ni) and Aclosed (proximal Zn atom) geometries with three cysteine thiolates and a modeled CO ligand demonstrates excellent agreement with the crystal structure atomic positions, particularly with the displacement of the side chain ring of Phe512 which appears to serve as a structural gate for ligand binding. The QM/MM optimized geometry of the A-cluster of ACS with an uncoordinated, oxidized proximal nickel atom in a square planar geometry demonstrates poor agreement with the atomic coordinates taken from the crystal structure. Based on these calculations, we conclude that the square planar proximal nickel coordination that has been captured in the Aopen structure does not correspond to the ligand-free, oxidized [Fe4S4]2+ - Nip2+ - Nid2+ state. Overall, these computations shed further light on the mechanistic details of protein conformational changes and electronic transitions involved in the ACS catalytic cycle.

中文翻译：

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QM/MM 计算揭示了乙酰辅酶 A 合成酶催化中心的细节。

已使用组合的量子力学 (QM)/分子力学 (MM) 方法研究了来自热乙酸摩尔氏菌的乙酰辅酶 A 合酶 (ACS) 的“开放”(Aopen) 和“封闭”(Aclosed) A 簇。已经对完全溶剂化的 ACS 酶进行了氧化的、一电子和二电子还原的 Aopen 状态的几何优化，并且已经在还原模型中对 CO 配体进行了建模。结合使用 αopen 和 αclosed 蛋白质支架以及金属原子在这些结构中的位置，我们已经能够拼凑出 ACS 催化循环的关键部分。我们使用正方形平面和四面体近端 Ni 原子用 CO 替换了晶体结构中未识别的外源配体。在具有三个半胱氨酸硫醇盐和模型化 CO 配体的 Aopen（低占有率近端 Ni）和 Aclosed（近端 Zn 原子）几何形状中观察到的单电子还原 A 簇，其特征在于四面体配位模式中的近端 Ni 原子证明与晶体结构原子位置非常一致，特别是与 Phe512 的侧链环的位移，这似乎作为配体结合的结构门。ACS 的 A 簇的 QM/MM 优化几何结构在方形平面几何结构中具有未配位的氧化近端镍原子，表明与从晶体结构中获取的原子坐标的一致性较差。基于这些计算，我们得出结论，在 Aopen 结构中捕获的方形平面近端镍配位不对应于无配体、氧化的 [Fe4S4]2+ - Nip2+ - Nid2+ 状态。总体而言，这些计算进一步揭示了 ACS 催化循环中涉及的蛋白质构象变化和电子跃迁的机制细节。