Enzymatic reactions are complex chemical processes taking place in complex dynamic environments. Theoretical characterization of these reactions requires the determination of the reaction coordinate and the transition state ensemble. This is not an easy task because many degrees of freedom may be involved in principle. We present recent efforts to find good enzymatic reaction coordinates and the implications of these findings in the interpretation of enzymatic efficiency. In particular, we analyze different strategies based on the use of minimum free energy paths and direct localization of the dividing surface on multidimensional free energy surfaces. Another strategy is based on the generation of reactive trajectories, using the transition path sampling method, from which transition state configurations can be harvested. Most of the applications carried out until now coincide to stress the change in the nature of the reaction coordinate, in terms of the participation of the chemical and environmental degrees of freedom, as the reaction advances. The degrees of freedom of the chemical system are dominant at the transition state while environmental participation can be more important at early or late stages of the process. WIREs Comput Mol Sci 2018, 8:e1329. doi: 10.1002/wcms.1329

中文翻译：

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酶催化反应的反应坐标和过渡态

酶促反应是在复杂的动态环境中发生的复杂化学过程。这些反应的理论表征需要确定反应坐标和过渡态整体。这不是一件容易的事，因为原则上可能涉及许多自由度。我们目前正在努力寻找良好的酶促反应坐标，以及这些发现在酶解效率解释中的意义。特别地，我们基于最小自由能路径的使用和多维自由能表面上分割面的直接定位来分析不同的策略。另一种策略是基于使用过渡路径采样方法的反应性轨迹的生成，可以从中获取过渡状态配置。迄今为止进行的大多数应用都一致地强调了随着反应的进行，就化学和环境自由度的参与而言，反应坐标的性质发生了变化。化学系统的自由度在过渡状态占主导地位，而环境参与在该过程的早期或后期可能更为重要。电线计算科学2018，8：e1329。doi：10.1002 / wcms.1329