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Biomolecules 2013, 3(3), 662-702; doi:10.3390/biom3030662

Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions

1
Laboratory of Structural Chemistry and Biology and HAS-ELTE Protein Modeling Group, Eötvös Loránd University, Pázmány Péter St. 1A, Budapest H-1117, Hungary
2
Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Gellért tér 4, Budapest H-1111, Hungary
*
Author to whom correspondence should be addressed.
Received: 6 August 2013 / Revised: 17 September 2013 / Accepted: 19 September 2013 / Published: 23 September 2013
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications)

Abstract

Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods.
Keywords: enzyme; reaction; mechanism; model; quantum mechanics; QM/MM enzyme; reaction; mechanism; model; quantum mechanics; QM/MM
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This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Náray-Szabó, G.; Oláh, J.; Krámos, B. Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions. Biomolecules 2013, 3, 662-702.

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