Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Delhi-NCR, 201314, India.
Center for Informatics, Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Delhi-NCR, 201314, India.
目前对酶活性的理论认识高度依赖于反应活化能的确定，这通常使用计算要求高的量子力学计算来计算。随着越来越多的生物工程技术使用产生过多相同酶的变体，目前迫切需要一种快速准确的方法来研究酶的相对效率。在这里，我们使用天然形式的分支酸变位酶和几种变体（R90A、R90G 和 R90K/C88S）为例，提出沿反应轴的酶的局部电场 (LEF) 作为酶活性的描述符。该研究显示了计算的酶 EF 与所有复合物的酶活性之间的直接相关性。Michaelis 复合物和过渡态类似物 (TSA) 的 MD 模拟显示由于酶促 EF 对 TSA 的稳定力。在存在沿反应轴取向的外部电场 (EEF) 的情况下，QM/MM 和仅 QM 的 DFT 计算表明，电场可以与 TS 的偶极矩相互作用，从而使其稳定，从而降低活化能。
The current theoretical perception of enzymatic activity is highly reliant on the determination of the activation energy of the reactions, which is often calculated using computationally demanding quantum mechanical calculations. With the ever-increasing use of bioengineering techniques that produce too many variants of the same enzyme, a fast and accurate way to study the relative efficiency of enzymes is currently in high demand. Here, we propose the local electric field (LEF) of the enzyme along the reaction axis as a descriptor for the enzymatic activity using the example of chorismate mutase in its native form and several variants (R90A, R90G, and R90K/C88S). The study shows a direct correlation between the calculated enzymatic EF and the enzymatic activity for all the complexes. MD simulations of the Michaelis complex and the transition state analog (TSA) show a stabilizing force on the TSA due to the enzymatic EF. QM/MM and QM-only DFT calculations in the presence of an external electric field (EEF) oriented along the reaction axis show that the electric field can interact with the dipole moment of the TS, thereby stabilizing it and thus lowering the activation energy.
