Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
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DOI：
10.1073/pnas.1111252108
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发表时间：
2011-08-23
影响因子：
11.1
通讯作者：
Warshel, Arieh
中科院分区：
文献类型：
--
作者：
Adamczyk, Andrew J.;Cao, Jie;Warshel, Arieh
酶催化是由于构象波动的建议，以前已经通过间接的考虑。然而，最近的工作集中在相关运动的情况下，有组件对不同的构象区域，其人口可以操纵突变。特别是，最近的一项工作声称提供了直接的实验证据，动力学的贡献，催化二氢叶酸还原酶，其中阻止相关的构象坐标与抑制运动向闭塞的构象。目前的工作利用计算机模拟来阐明实验观察到的效果的真正的分子基础。我们首先再现突变后催化作用的测量变化趋势（假设这是突变引起的“动态敲除”的结果）。该分析通过计算相应激活势垒的变化来执行，而不需要调用动力学效应。然后，我们生成的酶的催化景观，并证明在构象空间的运动并不能帮助驱动催化。我们还讨论了灵活性和构象动力学在催化中的作用，再次证明它们的作用是可以忽略不计的，催化的最大贡献来自静电预组织。最后，我们指出，在反应势面的变化修改重组自由能（其中包括熵效应），这种变化的表面也改变相应的运动。然而，这种运动从来不是催化的原因，而只是反应势面形状的反映。
The proposal that enzymatic catalysis is due to conformational fluctuations has been previously promoted by means of indirect considerations. However, recent works have focused on cases where the relevant motions have components toward distinct conformational regions, whose population could be manipulated by mutations. In particular, a recent work has claimed to provide direct experimental evidence for a dynamical contribution to catalysis in dihydrofolate reductase, where blocking a relevant conformational coordinate was related to the suppression of the motion toward the occluded conformation. The present work utilizes computer simulations to elucidate the true molecular basis for the experimentally observed effect. We start by reproducing the trend in the measured change in catalysis upon mutations (which was assumed to arise as a result of a "dynamical knockout" caused by the mutations). This analysis is performed by calculating the change in the corresponding activation barriers without the need to invoke dynamical effects. We then generate the catalytic landscape of the enzyme and demonstrate that motions in the conformational space do not help drive catalysis. We also discuss the role of flexibility and conformational dynamics in catalysis, once again demonstrating that their role is negligible and that the largest contribution to catalysis arises from electrostatic preorganization. Finally, we point out that the changes in the reaction potential surface modify the reorganization free energy (which includes entropic effects), and such changes in the surface also alter the corresponding motion. However, this motion is never the reason for catalysis, but rather simply a reflection of the shape of the reaction potential surface.