Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-4098, USA.
Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5699-704. doi: 10.1073/pnas.1117060109. Epub 2012 Mar 26.
Despite growing evidence suggesting the importance of enzyme conformational dynamics (ECD) in catalysis, a consensus on how precisely ECD influences the chemical step and reaction rates is yet to be reached. Here, we characterize ECD in Cyclophilin A, a well-studied peptidyl-prolyl cis-trans isomerase, using normal and accelerated, atomistic molecular dynamics simulations. Kinetics and free energy landscape of the isomerization reaction in solution and enzyme are explored in unconstrained simulations by allowing significantly lower torsional barriers, but in no way compromising the atomistic description of the system or the explicit solvent. We reveal that the reaction dynamics is intricately coupled to enzymatic motions that span multiple timescales and the enzyme modes are selected based on the energy barrier of the chemical step. We show that Kramers' rate theory can be used to present a clear rationale of how ECD affects the reaction dynamics and catalytic rates. The effects of ECD can be incorporated into the effective diffusion coefficient, which we estimate to be about ten times slower in enzyme than in solution. ECD thereby alters the preexponential factor, effectively impeding the rate enhancement. From our analyses, the trend observed for lower torsional barriers can be extrapolated to actual isomerization barriers, allowing successful prediction of the speedup in rates in the presence of CypA, which is in notable agreement with experimental estimates. Our results further reaffirm transition state stabilization as the main effect in enhancing chemical rates and provide a unified view of ECD's role in catalysis from an atomistic perspective.
尽管越来越多的证据表明酶构象动力学（ECD）在催化中具有重要性，但如何准确地确定 ECD 影响化学步骤和反应速率仍未达成共识。在这里，我们使用正常和加速的原子分子动力学模拟来描述亲环素 A（一种研究得很好的肽基脯氨酰顺反异构酶）中的 ECD。在无约束模拟中，通过允许显著降低扭转势垒，探索了溶液中和酶中的异构化反应的动力学和自由能景观，但不以任何方式影响系统的原子描述或明确的溶剂。我们揭示了反应动力学与酶运动紧密耦合，酶运动跨越多个时间尺度，并且根据化学步骤的能量势垒来选择酶模式。我们表明，克拉默斯速率理论可用于清晰地说明 ECD 如何影响反应动力学和催化速率。ECD 的影响可以包含在有效扩散系数中，我们估计在酶中的扩散系数比在溶液中慢约十倍。因此，ECD 改变了指数前因子，有效地阻碍了速率的提高。从我们的分析中，可以将观察到的较低扭转势垒的趋势外推到实际的异构化势垒，从而成功预测 CypA 存在时速率的提高，这与实验估计非常吻合。我们的结果进一步证实了过渡态稳定化是提高化学速率的主要效应，并从原子角度提供了 ECD 在催化中作用的统一观点。
