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Hydrogen bonding catalysis by water in epoxide ring opening reaction.
Ahsan, Mohd; Pindi, Chinmai; Senapati, Sanjib.
Affiliation
  • Ahsan M; Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
  • Pindi C; Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
  • Senapati S; Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India. Electronic address: sanjibs@iitm.ac.in.
J Mol Graph Model ; 105: 107894, 2021 06.
Article in En | MEDLINE | ID: mdl-33725641
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Water / Epoxy Compounds Language: En Journal: J Mol Graph Model Journal subject: BIOLOGIA MOLECULAR Year: 2021 Document type: Article Affiliation country: India Country of publication: United States

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Water / Epoxy Compounds Language: En Journal: J Mol Graph Model Journal subject: BIOLOGIA MOLECULAR Year: 2021 Document type: Article Affiliation country: India Country of publication: United States