An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes

Proteins
K FukushimaM Sakurai

Abstract

In this study, we explored the general relationship between the three-dimensional (3D) structures of enzymes and their electronic wave functions. Furthermore, we developed a method for the prediction of their functionally important sites. For this purpose, we first performed linear-scaling molecular orbital calculations for 112 nonredundant, non-homologous enzymes with known structure and function. In consequence, we showed that the canonical molecular orbitals (MOs) of the enzymes could be classified into three groups according to the degree of electron delocalization: highly localized orbitals (Group A), highly delocalized orbitals whose electrons are distributed over almost the whole molecule (Group B), and moderately delocalized orbitals (Group C). The MOs belonging to Group A are located near the HOMO-LUMO band gap, and thereby include the frontier orbitals of a given enzyme. We inferred that the MOs of Group B play a role in stabilizing the 3D structure of the enzyme, while those of Group C contribute to constructing the covalent bond framework of the enzyme. Next, we investigated whether the frontier orbitals of enzymes could be used for identifying their potential functional sites. As a result, we found that the frontie...Continue Reading

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Citations

May 8, 2014·Journal of Chemical Theory and Computation·Timothy J GieseDarrin M York
Aug 25, 2015·Journal of Biomolecular Structure & Dynamics·Umadevi Palanivel, Senthilkumar Lakshmipathi
Jan 10, 2017·Journal of Chemical Theory and Computation·Maria Karelina, Heather J Kulik
Jun 22, 2018·Molecular Informatics·Christoph Sotriffer
Sep 4, 2018·Physical Chemistry Chemical Physics : PCCP·Chang-Liang SunLin-Wang Wang
Jan 22, 2020·Journal of Computational Chemistry·Igor Barden GrilloGerd Bruno Rocha
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Oct 23, 2020·Journal of Molecular Modeling·Julio Daniel Carvalho MaiaGerd Bruno Rocha
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Sep 11, 2012·Journal of Chemical Theory and Computation·Julio Daniel Carvalho MaiaGerd B Rocha
Jan 3, 2020·Journal of Chemical Information and Modeling·Igor Barden GrilloGerd Bruno Rocha

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