Antoniou Dimitri, Schwartz Steven D
Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Blvd., Tucson, Arizona 85721, United States.
J Phys Chem B. 2020 Oct 29;124(43):9483-9489. doi: 10.1021/acs.jpcb.0c05725. Epub 2020 Oct 16.
We have analyzed the reaction catalyzed by formate dehydrogenase using transition path sampling. This system has recently received experimental attention using infrared spectroscopy and heavy-enzyme studies. Some of the experimental results point to the possible importance of protein motions that are coupled to the chemical step. We found that the residue Val123 that lies behind the nicotinamide ring occasionally comes into van der Waals contact with the acceptor and that in all reactive trajectories, the barrier-crossing event is preceded by this contact, meaning that the motion of Val123 is part of the reaction coordinate. Experimental results have been interpreted with a two-dimensional formula for the chemical rate, which cannot capture effects such as the one we describe.
我们使用过渡路径采样分析了甲酸脱氢酶催化的反应。最近，该系统通过红外光谱和重酶研究受到了实验关注。一些实验结果表明与化学步骤耦合的蛋白质运动可能具有重要性。我们发现位于烟酰胺环后方的缬氨酸残基123偶尔会与受体形成范德华接触，并且在所有反应轨迹中，跨越势垒的事件之前都有这种接触，这意味着缬氨酸残基123的运动是反应坐标的一部分。实验结果已用化学速率的二维公式进行了解释，但该公式无法捕捉我们所描述的这类效应。
