Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin
Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin
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DOI：
10.1021/acs.biochem.7b00016
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发表时间：
2017-03-14
期刊：
影响因子：
2.9
通讯作者：
Cui, Qang
中科院分区：
文献类型：
--
作者：
Lu, Xiya;Ovchinnikov, Victor;Cui, Qang
使用DFTB3/CHARMM模拟和增强采样技术的组合分析了肌球蛋白运动域ATP水解的机制。马达结构域被建模为动力冲程前状态、严格状态后状态，以及基于严格状态后与封闭核苷酸结合口袋的混合体。发现ATP水解活性取决于附近水分子的位置，并且极性残基网络有助于水解过程中的质子转移和电荷重新分配。将观察到的水解接力途径与相应的自由能谱进行比较，可以建立ATP在动力冲程前状态下的水解机制的详细模型，并提出了在不同构象状态下调节水解活性的因素。在前强力冲程状态下，可剪切的p - γ - o - 3ss键在反应早期断裂。质子通过活性位点残基从裂解水转移到γ -磷酸是动力学瓶颈的重要组成部分；几种具有不同质子转移路线的水解途径被发现具有相似的自由能垒，这表明水解机制具有显著程度的可塑性。在强力冲程前状态和封闭后严格模型下的水解比较表明，优化活性位点以外的残基以实现静电稳定和预组织可能对酶的设计很重要。
The mechanism of ATP hydrolysis in the myosin motor domain is analyzed using a combination of DFTB3/CHARMM simulations and enhanced sampling techniques. The motor domain is modeled in the pre-powerstroke state, in the post-rigor state, and as a hybrid based on the post-rigor state with a closed nucleotide-binding pocket. The ATP hydrolysis activity is found to depend on the positioning of nearby water molecules, and a network of polar residues facilitates proton transfer and charge redistribution during hydrolysis. Comparison of the observed hydrolysis Relay pathways and the corresponding free energy profiles leads to detailed models for the mechanism of ATP hydrolysis in the pre-powerstroke state and proposes factors that regulate the hydrolysis activity in different conformational states. In the pre-powerstroke state, the scissile P-gamma-O-3 ss bond breaks early in the reaction. Proton transfer from the lytic water to the gamma-phosphate through active site residues is an important part of the kinetic bottleneck; several hydrolysis pathways that feature distinct proton transfer routes are found to have similar free energy barriers, suggesting a significant degree of plasticity in the hydrolysis mechanism. Comparison of hydrolysis in the pre-powerstroke state and the closed post-rigor model suggests that optimization of residues beyond the active site for electrostatic stabilization and preorganization is likely important to enzyme design.