Literature DB >> 33725641

Hydrogen bonding catalysis by water in epoxide ring opening reaction.

Mohd Ahsan1, Chinmai Pindi1, Sanjib Senapati2.   

Abstract

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.
Copyright © 2021 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Aspartate protease; Epoxide ring opening; Quantum calculations; Water H-bond catalysis

Year:  2021        PMID: 33725641     DOI: 10.1016/j.jmgm.2021.107894

Source DB:  PubMed          Journal:  J Mol Graph Model        ISSN: 1093-3263            Impact factor:   2.518


  1 in total

1.  Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes.

Authors:  Yanhui Zheng; Weizhu Yan; Chao Dou; Dan Zhou; Yunying Chen; Ying Jin; Lulu Yang; Xiaotao Zeng; Wei Cheng
Journal:  MedComm (2020)       Date:  2022-01-10
  1 in total

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