Department of Chemistry (Seeley G. Mudd 418), University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089, USA.
Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):14115-20. doi: 10.1073/pnas.1111252108. Epub 2011 Aug 10.
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.
先前曾通过间接考虑来提出酶催化是由于构象波动的观点。然而,最近的研究工作集中在相关运动具有朝向不同构象区域的分量的情况下,其种群可以通过突变来操纵。特别是,最近的一项工作声称提供了直接的实验证据,证明二氢叶酸还原酶中的催化动力学贡献,其中阻断相关构象坐标与阻止朝向闭塞构象的运动有关。本工作利用计算机模拟阐明了实验观察到的效应的真实分子基础。我们首先通过计算相应的激活势垒变化来再现实验测量的突变对催化作用的变化趋势(该变化被认为是由于突变引起的“动力学敲除”所致)。该分析不需要调用动力学效应即可完成。然后,我们生成酶的催化景观,并证明构象空间中的运动无助于驱动催化。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可以忽略不计,对催化作用的最大贡献来自静电预组织。最后,我们指出反应势能表面的变化改变了重组自由能(包括熵效应),表面的这种变化也改变了相应的运动。然而,这种运动绝不是催化的原因,而仅仅是反应势能表面的形状的反映。