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Title: Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

Abstract

Quantum mechanics/molecular mechanics ( QM / MM ) methods offer a very appealing option for the computational study of enzymatic reaction mechanisms, by separating the problem into two parts that can be treated with different computational methods. Hence, in a QM / MM formalism, the part of the system in which catalysis actually occurs and that involves the active site, substrates and directly participating amino acid residues is treated at an adequate quantum mechanical level to describe the chemistry taking place. For the remaining of the enzyme, which does not participate directly in the reaction, but that typically involves a much larger number of atoms, molecular mechanics is employed, traditionally through the application of a biomolecular force field. When applied with care, QM / MM methods can be used with great advantage in comparing, at a structural and energetic level, different mechanistic proposals, discarding mechanistic alternatives and proposing new mechanistic pathways that are consistent with the available experimental data. With time, diverse flavors within the QM / MM methods have emerged, differing in a variety of technical and conceptual aspects. Hence present alternatives differ between additive and subtractive QM / MM schemes, the type of boundary schemes, and the waymore » in which the electrostatic interactions between the two regions are accounted for. Also, single‐conformation QM / MM , multi‐ PES approaches, and QM / MM Molecular Dynamics coexist today, each type with its own advantages and limitations. This review focuses on the application of QM / MM methods in the study of enzymatic reaction mechanisms, briefly presenting also the most important technical aspects involved in these calculations. Particular attention is dedicated to the application of the single‐conformation QM / MM , multi‐ PES QM / MM studies, and QM / MM‐FEP methods and to the advantages and disadvantages of the different types of QM / MM . Recent breakthroughs are also introduced. A selection of hand‐picked examples is used to illustrate such features. WIREs Comput Mol Sci 2017, 7:e1281. doi: 10.1002/wcms.1281 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Structure and Mechanism > Reaction Mechanisms and Catalysis Electronic Structure Theory > Combined QM/MM Methods« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1]
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  1. Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1400800
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Wiley Interdisciplinary Reviews: Computational Molecular Science
Additional Journal Information:
Journal Name: Wiley Interdisciplinary Reviews: Computational Molecular Science Journal Volume: 7 Journal Issue: 2; Journal ID: ISSN 1759-0876
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United States
Language:
English

Citation Formats

Sousa, Sérgio Filipe, Ribeiro, António J. M., Neves, Rui P. P., Brás, Natércia F., Cerqueira, Nuno M. F. S. A., Fernandes, Pedro A., and Ramos, Maria João. Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms. United States: N. p., 2016. Web. doi:10.1002/wcms.1281.
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Sousa, Sérgio Filipe, Ribeiro, António J. M., Neves, Rui P. P., Brás, Natércia F., Cerqueira, Nuno M. F. S. A., Fernandes, Pedro A., & Ramos, Maria João. Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms. United States. https://doi.org/10.1002/wcms.1281
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Sousa, Sérgio Filipe, Ribeiro, António J. M., Neves, Rui P. P., Brás, Natércia F., Cerqueira, Nuno M. F. S. A., Fernandes, Pedro A., and Ramos, Maria João. Thu . "Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms". United States. https://doi.org/10.1002/wcms.1281.
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@article{osti_1400800,
title = {Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms},
author = {Sousa, Sérgio Filipe and Ribeiro, António J. M. and Neves, Rui P. P. and Brás, Natércia F. and Cerqueira, Nuno M. F. S. A. and Fernandes, Pedro A. and Ramos, Maria João},
abstractNote = {Quantum mechanics/molecular mechanics ( QM / MM ) methods offer a very appealing option for the computational study of enzymatic reaction mechanisms, by separating the problem into two parts that can be treated with different computational methods. Hence, in a QM / MM formalism, the part of the system in which catalysis actually occurs and that involves the active site, substrates and directly participating amino acid residues is treated at an adequate quantum mechanical level to describe the chemistry taking place. For the remaining of the enzyme, which does not participate directly in the reaction, but that typically involves a much larger number of atoms, molecular mechanics is employed, traditionally through the application of a biomolecular force field. When applied with care, QM / MM methods can be used with great advantage in comparing, at a structural and energetic level, different mechanistic proposals, discarding mechanistic alternatives and proposing new mechanistic pathways that are consistent with the available experimental data. With time, diverse flavors within the QM / MM methods have emerged, differing in a variety of technical and conceptual aspects. Hence present alternatives differ between additive and subtractive QM / MM schemes, the type of boundary schemes, and the way in which the electrostatic interactions between the two regions are accounted for. Also, single‐conformation QM / MM , multi‐ PES approaches, and QM / MM Molecular Dynamics coexist today, each type with its own advantages and limitations. This review focuses on the application of QM / MM methods in the study of enzymatic reaction mechanisms, briefly presenting also the most important technical aspects involved in these calculations. Particular attention is dedicated to the application of the single‐conformation QM / MM , multi‐ PES QM / MM studies, and QM / MM‐FEP methods and to the advantages and disadvantages of the different types of QM / MM . Recent breakthroughs are also introduced. A selection of hand‐picked examples is used to illustrate such features. WIREs Comput Mol Sci 2017, 7:e1281. doi: 10.1002/wcms.1281 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Structure and Mechanism > Reaction Mechanisms and Catalysis Electronic Structure Theory > Combined QM/MM Methods},
doi = {10.1002/wcms.1281},
journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
number = 2,
volume = 7,
place = {United States},
year = {Thu Sep 01 00:00:00 EDT 2016},
month = {Thu Sep 01 00:00:00 EDT 2016}
}
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The Catalytic Mechanism of HIV-1 Integrase for DNA 3′-End Processing Established by QM/MM Calculations
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Catalytic Mechanism of the Arylsulfatase Promiscuous Enzyme from Pseudomonas Aeruginosa
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The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase
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Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds
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Unraveling the Base Excision Repair Mechanism of Human DNA Glycosylase
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Farnesyltransferase: Theoretical studies on peptide substrate entrance—thiol or thiolate coordination?
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Computational Analysis of Methyl Transfer Reactions in Dengue Virus Methyltransferase
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Resolving the complex role of enzyme conformational dynamics in catalytic function
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A density functional theory investigation on the formation mechanisms of DNA interstrand crosslinks induced by chloroethylnitrosoureas
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Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics
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The role of quantum chemistry in the elucidation of the elementary mechanisms of catalytic processes: from atoms, to surfaces, to enzymes
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Mechanism of tungsten-dependent acetylene hydratase from quantum chemical calculations
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Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase
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Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover
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Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations
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Biochemical Characterization of the HIV-1 Integrase 3‘-Processing Activity and Its Inhibition by Phosphorothioate Oligonucleotides †
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Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations
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Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease
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Making and Breaking Nucleic Acids: Two-Mg2+-Ion Catalysis and Substrate Specificity
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Comparison of QM-Only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene Hydratase
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Development of Polyphenols as HIV-1 Integrase Inhibitors: a Summary and Perspective
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Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations
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The Accuracy of Density Functional Theory in the Description of Cation−π and π–Hydrogen Bond Interactions
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QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human β-HexosaminidaseA
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New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models
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Establishing the Catalytic Mechanism of Human Pancreatic α-Amylase with QM/MM Methods
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Accurate QM/MM Free Energy Calculations of Enzyme Reactions:  Methylation by Catechol O -Methyltransferase
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The Catalytic Mechanism of RNA Polymerase II
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A View at the Millennium:  the Efficiency of Enzymatic Catalysis
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  • DOI: 10.1002/prot.21219

Classical Polarization in Hybrid QM/MM Methods
journal, May 2006

  • Illingworth, Christopher J. R.; Gooding, Stuart R.; Winn, Peter J.
  • The Journal of Physical Chemistry A, Vol. 110, Issue 20
  • DOI: 10.1021/jp046944i

Farnesyltransferase—New Insights into the Zinc-Coordination Sphere Paradigm: Evidence for a Carboxylate-Shift Mechanism
journal, January 2005

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