Ahsan Mohd, Pindi Chinmai, Senapati Sanjib
Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
J Mol Graph Model. 2021 Jun;105:107894. doi: 10.1016/j.jmgm.2021.107894. Epub 2021 Mar 5.
Water can act as catalyst is perhaps the most intriguing property reported of this molecule in the last decade. However, despite being an integral part of many enzyme structures, the role of water in catalyzing enzymatic reactions remains sparsely studied. In a recent study, we have shown that the epoxide ring opening in aspartate proteases follows a two-step process involving water. In this work, we attempt to unravel the electronic basis of the co-catalytic role of water in the epoxide ring opening reaction by employing high-level quantum mechanical calculations at M06-2X/6-31+G(d,p) level of accuracy. Our computed electron density and its reduced gradient show that water anchor the reactant molecules through strong H-bond bridges. In addition, the strong ionizing power of water allows better charge delocalization to stabilize the transition states and oxyanion intermediate. Electrostatic analyses suggest greater charge transfer from the aspartates to the epoxide in the transition state, which is found to be exergonic in nature rendering a low-barrier reaction compared to a control system where water was omitted in the reaction field. This elucidated mechanism at electronic level could promote further research to search for the co-catalytic role of water in other enzymes.
水可以充当催化剂,这或许是过去十年间有关该分子报道的最引人入胜的特性。然而,尽管水是许多酶结构中不可或缺的一部分,但水在催化酶促反应中的作用仍鲜有研究。在最近的一项研究中,我们已经表明,天冬氨酸蛋白酶中的环氧开环反应遵循一个涉及水的两步过程。在这项工作中,我们试图通过在M06 - 2X/6 - 31 + G(d,p)精度水平上进行高水平量子力学计算,来揭示水在环氧开环反应中协同催化作用的电子基础。我们计算得到的电子密度及其降低梯度表明,水通过强氢键桥将反应物分子固定在一起。此外,水的强电离能力使电荷能更好地离域,从而稳定过渡态和氧阴离子中间体。静电分析表明,在过渡态中,从天冬氨酸到环氧化物有更大的电荷转移,与反应场中省略水的对照体系相比,该反应本质上是放能的,呈现出低势垒反应。这种在电子层面阐明机制可以推动进一步研究,以探寻水在其他酶中的协同催化作用。