Mechanochemical coupling in myosin: A theoretical analysis with molecular dynamics and combined QM/MM reaction path calculations
Mechanochemical coupling in myosin: A theoretical analysis with molecular dynamics and combined QM/MM reaction path calculations
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DOI：
10.1021/jp0371783
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发表时间：
2004-03-11
影响因子：
3.3
通讯作者：
Cui, Q
中科院分区：
文献类型：
--
作者：
Li, GH;Cui, Q
为了阐明肌球蛋白ATP水解的详细机制，采用经典力场和反应路径分析，采用结合量子力学和分子力学（QM/MM）势的分子动力学进行。虽然QM/MM反应路径分析的准确性有限，由于缺乏广泛的构象采样，目前的工作表明，明智的能量更接近实验测量比以前的计算研究，可以获得蛋白质环境中，一旦包括。在这里研究的两个关联机制，涉及保守的残基，丝氨酸236，作为质子中继基团的途径被发现有一个较低的限速屏障。然而，它也表明，如果O-2 γ得到质子化，没有调用任何质子中继的机制只有一个略高的障碍，因此也可能有助于，特别是在突变体，如Ser 236 A。通过对两种不同的马达结构域构象进行计算，结果表明，肌球蛋白中的机械化学偶联主要受开关I和开关II区域中的几个残基（如Arg 238、Gly 457和Glu 459）的调节。特别是，当Arg 238和Glu 459之间的盐桥如在马达结构域的预水解构象中那样断裂时，ATP水解在能量上是非常不利的。在这种构象中，Arg 238更接近ATP，因此在水解产物上稳定ATP状态。此外，在没有盐桥的情况下，活性位点中的水结构不再稳定以有利于γ-磷酸盐的在线亲核攻击。从目前的工作的结果有一般的影响，其他分子马达，涉及ATP水解，如驱动蛋白，F-1-ATP酶和Ca 2 +-ATP酶，虽然更强大的结论，有关水解机制需要更详细的模拟，考虑蛋白质的波动和其他可能的质子化状态的ATP和水解产物。
To elucidate the detailed mechanism of ATP hydrolysis in myosin, molecular dynamics employing classical force field and reaction path analyses employing a combined quantum mechanical and molecular mechanical (QM/MM) potential were carried out. Although the QM/MM reaction path analyses have limited accuracy due to the lack of extensive conformational sampling, the present work showed that sensible energetics much closer to experimental measurements than previous computational studies can be obtained once the protein environment is included. In the two associative mechanisms studied here, the pathway that involves the conserved residue, Ser 236, as the proton relay group was found to have a lower rate-limiting barrier. However, it was also shown that if O-2gamma gets protonated, the mechanism without invoking any proton relay has only a slightly higher barrier and therefore may also contribute, especially in mutants such as Ser 236A. By performing calculations for two different motor domain conformations, it was shown that the mechanochemical coupling in myosin is mainly regulated by several residues in the switch I and switch II regions, such as Arg 238, Gly 457, and Glu 459. In particular, when the salt bridge between Arg 238 and Glu 459 is broken as in the prehydrolysis conformation of the motor domain, ATP hydrolysis is highly unfavorable energetically. In this conformation, Arg 238 is closer to ATP and therefore stabilizes the ATP state over the hydrolysis products. Moreover, without the salt bridge, the water structure in the active site is no longer stabilized to favor the in-line nucleophilic attack of the gamma-phosphate. The results from the current work have general implications to other molecular motors that involve ATP hydrolysis, such as kinesin, F-1-ATPase and Ca2+-ATPase, although more robust conclusions concerning the hydrolysis mechanism require more elaborate simulations that consider protein fluctuations and other possible protonation states of ATP and the hydrolysis products.