Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.
J Phys Chem B. 2010 Aug 19;114(32):10594-600. doi: 10.1021/jp102785s.
Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics and free energy simulations are performed to study the process of the deacylation reaction catalyzed by kumamolisin-As, a serine-carboxyl peptidase, and to elucidate the catalytic mechanism. The results given here suggest that Asp-164 acts as a general acid/base catalyst not only for the acylation reaction but also for the deacylation reaction. It is shown that the electrostatic oxyanion hole interactions may be less effective in transition state stabilization for the kumamolisin-As catalyzed reaction compared to the general acid/base mechanism involving the proton transfer from or to Asp-164. The dynamic substrate-assisted catalysis (DSAC) involving His at the P1 site of the substrate is found to be less important for the deacylation reaction than for the acylation reaction in the kumamolisin-As catalyzed reaction. The proton transfer processes during the enzyme-catalyzed process are examined and their role in the catalysis is discussed.
本文运用量子力学/分子力学（QM/MM）分子动力学和自由能模拟方法，研究了枯草溶菌素 As（一种丝氨酸羧肽酶）催化的脱酰反应过程，阐明了其催化机制。结果表明，Asp164 不仅作为酰化反应的通用酸碱催化剂，也作为脱酰反应的通用酸碱催化剂。实验结果表明，与涉及质子从 Asp164 转移到或转移到 Asp164 的质子转移的通用酸碱机制相比，静电缺电子空穴相互作用在枯草溶菌素 As 催化反应的过渡态稳定化中可能效果较差。在枯草溶菌素 As 催化的反应中，与酰化反应相比，发现位于底物 P1 位的 His 参与的动态底物辅助催化（DSAC）在脱酰反应中不太重要。本文还考察了酶催化过程中的质子转移过程及其在催化中的作用。
