Here we discuss current trends in the simulations of enzymatic reactions focusing on phosphate catalysis. The mechanistic details of the proton transfers coupled to the phosphate cleavage is one of the key challenges in QM/MM calculations of these and other enzyme catalyzed reactions. The lack of experimental information offers both an opportunity for computations as well as often unresolved controversies. We discuss the example of small GTPases including the important human Ras protein. The high dimensionality and chemical complexity of these reactions demand carefully chosen computational techniques both in terms of the underlying quantum chemical theory and the sampling of the conformational ensemble. We also point out the important role of Mg2+ ions, and recent advances in their transient involvement in the catalytic mechanisms.

中文翻译：

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运动中的阳离子：QM / MM研究H +和Mg2 +离子在酶反应中的动态和静电作用。

在这里，我们讨论着重于磷酸盐催化的酶促反应模拟中的当前趋势。质子转移与磷酸盐裂解偶联的机械细节是这些以及其他酶催化反应的QM / MM计算中的关键挑战之一。缺乏实验信息既提供了计算的机会，也常常带来未解决的争议。我们讨论了包括重要的人类Ras蛋白在内的小GTP酶的例子。这些反应的高维数和化学复杂性需要根据基础的量子化学理论和构象集合的采样精心选择的计算技术。我们还指出了Mg2 +离子的重要作用，以及它们在催化机制中的短暂参与的最新进展。