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Catalysts 2016, 6(6), 82; doi:10.3390/catal6060082

Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools

Department of Chemistry, University of California, Riverside, CA 92521, USA
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Author to whom correspondence should be addressed.
Academic Editor: David D. Boehr
Received: 12 April 2016 / Revised: 13 May 2016 / Accepted: 23 May 2016 / Published: 31 May 2016
(This article belongs to the Special Issue Enzyme Catalysis)
View Full-Text   |   Download PDF [8095 KB, uploaded 31 May 2016]   |  

Abstract

This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations. View Full-Text
Keywords: force field; calculation; energy; substrate binding force field; calculation; energy; substrate binding
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Chang, C.-E.A.; Huang, Y.-M.M.; Mueller, L.J.; You, W. Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools. Catalysts 2016, 6, 82.

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