Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy.
J Chem Inf Model. 2024 May 13;64(9):3953-3958. doi: 10.1021/acs.jcim.4c00475. Epub 2024 Apr 12.
The rate constants of enzyme-catalyzed reactions () are often approximated from the barrier height of the reactive step. We introduce an enhanced sampling QM/MM approach that directly calculates the kinetics of enzymatic reactions, without introducing the transition-state theory assumptions, and takes into account the dynamical equilibrium between the reactive and non-reactive conformations of the enzyme/substrate complex. Our computed values are in order-of-magnitude agreement with the experimental data for two representative enzymatic reactions.
酶催化反应的速率常数（）通常可以通过反应步骤的势垒高度来近似。我们引入了一种增强采样的QM/MM 方法，可以直接计算酶促反应的动力学，而无需引入过渡态理论假设，并考虑酶/底物复合物的反应和非反应构象之间的动力平衡。我们计算得到的 值与两个代表性酶促反应的实验数据在数量级上是一致的。
