Use of QM/DMD as a Multiscale Approach to Modeling Metalloenzymes

Enzymes are complex biomolecules capable of performing unique catalysis under physiological conditions at neutral temperature and pH. However, the architecture of enzymatic catalysis is often a combination of the quantum influence of the immediate active site, as well as the electrostatic and config...

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Bibliographic Details
Published inMethods in enzymology Vol. 577; p. 319
Main Authors Gallup, N M, Alexandrova, A N
Format Journal Article
LanguageEnglish
Published United States 2016
Subjects
Animals
Biocatalysis
Catalytic Domain
Enzymes - chemistry
Enzymes - metabolism
Humans
Metalloproteins - chemistry
Metalloproteins - metabolism
Molecular Dynamics Simulation
Quantum Theory
Static Electricity
QM/MM
DFT
Catalysis
Metalloenzyme
Multiscale
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Summary:Enzymes are complex biomolecules capable of performing unique catalysis under physiological conditions at neutral temperature and pH. However, the architecture of enzymatic catalysis is often a combination of the quantum influence of the immediate active site, as well as the electrostatic and configurational influences of amino acids surrounding the active site. As a result of this cooperation between baseline chemical reactivity and electrostatic assistance, it has become important to model enzymes using multiscale methods that take advantage of treating the active site with quantum mechanical methods, while approximately treating the surrounding protein using cheaper, classically driven force-field molecular mechanics methods. Here we describe the use of a multiscale engine which utilizes a combination of density functional theory with discrete molecular dynamics (dubbed QM/DMD) to aid in the characterization of metalloenzymes.
ISSN:1557-7988
DOI:10.1016/bs.mie.2016.05.018