Lankau Timm, Ken Hao Chun, Chang Hsiang Ming, Yu Chin Hui
Department of Chemistry, National Tsing Hua University, Hsinchu, 300044, Taiwan.
ACS Omega. 2022 Apr 6;7(15):12753-12764. doi: 10.1021/acsomega.1c07327. eCollection 2022 Apr 19.
A two-pronged computational approach was taken to study the promiscuity of the SAM-dependent methyl transferase AtHTMT1 from thale cress with several nucleophiles (Cl, Br, I, NCO, NCS). First, enzyme-free methyl transfer reactions were studied with M05/6-311+G(2d,p) DFT calculations and electrostatic continuum models (PCM/SMD) for various chemical environments. Second, QM/MM MD simulations with semiempirical Hamiltonians (PM7, PM6-D3, AM1, PM6-D3H4) and the AMBER 14SB force field were used to study the enzyme catalyzed reaction . The combination of the DFT and MD results shows that reactant desolvation generally accelerates the reaction, but it cannot explain the selectivity of the enzyme. The critical position of HO molecules at the reactive site favors the reaction of NCS over Cl and Br in agreement with experiments, but not observed in the quantum calculations for the cytosol. The addition of selected HO molecules to the N of NCS greatly increases its reactivity, while HO molecules attached to Cl slow the reaction. The partial solvation of the nucleophiles in the reactive pouch holds the key to understanding the reactivity of AtHTMT1.
采用了一种双管齐下的计算方法来研究拟南芥中依赖S-腺苷甲硫氨酸的甲基转移酶AtHTMT1与几种亲核试剂（Cl、Br、I、NCO、NCS）的混杂性。首先，使用M05/6-311+G(2d,p)密度泛函理论（DFT）计算和针对各种化学环境的静电连续介质模型（PCM/SMD）研究了无酶甲基转移反应。其次，使用具有半经验哈密顿量（PM7、PM6-D3、AM1、PM6-D3H4）和AMBER 14SB力场的量子力学/分子力学（QM/MM）分子动力学（MD）模拟来研究酶催化反应。DFT和MD结果的结合表明，反应物去溶剂化通常会加速反应，但无法解释酶的选择性。与实验结果一致，反应位点处HO分子的关键位置有利于NCS与Cl和Br的反应，但在细胞质的量子计算中未观察到。将选定的HO分子添加到NCS的N上会大大增加其反应性，而附着在Cl上的HO分子会减缓反应。亲核试剂在反应袋中的部分溶剂化是理解AtHTMT1反应性的关键。
