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Empirical Valence Bond Simulations of Organophosphate Hydrolysis : Theory and Practice

Purg, Miha and Kamerlin, Shina Caroline Lynn LU orcid (2018) In Methods in Enzymology 607. p.3-51
Abstract

Recent years have seen an explosion of interest in understanding the mechanisms of phosphate ester hydrolysis in biological systems, using a range of computational approaches, each with different advantages and limitations. In this contribution, we present the empirical valence bond (EVB) approach as a powerful tool for modeling biochemical reactivity, using the example of organophosphate hydrolysis by diisopropyl fluorophosphatase as our model reaction. We walk the reader through the protocol for setting up and performing EVB simulations, as well as key technical considerations that need to be taken into account. Finally, we provide examples of the applications of the EVB approach to understanding different experimental observables.

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author
and
publishing date
type
Chapter in Book/Report/Conference proceeding
publication status
published
keywords
Computer Simulation, Cryoelectron Microscopy/instrumentation, Crystallography, X-Ray/instrumentation, Hydrolysis, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular/instrumentation, Organophosphates/metabolism, Phosphoric Triester Hydrolases/chemistry, Protein Structure, Tertiary, Thermodynamics
host publication
Phosphatases
series title
Methods in Enzymology
editor
Allen, Karen N.
volume
607
pages
49 pages
external identifiers
  • scopus:85051482004
  • pmid:30149862
ISSN
0076-6879
ISBN
978-0-12-813881-6
DOI
10.1016/bs.mie.2018.06.007
language
English
LU publication?
no
additional info
© 2018 Elsevier Inc. All rights reserved.
id
b5ee8ab9-b2e6-4fe3-b88d-62f85ac0d8eb
date added to LUP
2025-01-11 21:03:08
date last changed
2025-01-18 03:18:30
@inbook{b5ee8ab9-b2e6-4fe3-b88d-62f85ac0d8eb,
  abstract     = {{<p>Recent years have seen an explosion of interest in understanding the mechanisms of phosphate ester hydrolysis in biological systems, using a range of computational approaches, each with different advantages and limitations. In this contribution, we present the empirical valence bond (EVB) approach as a powerful tool for modeling biochemical reactivity, using the example of organophosphate hydrolysis by diisopropyl fluorophosphatase as our model reaction. We walk the reader through the protocol for setting up and performing EVB simulations, as well as key technical considerations that need to be taken into account. Finally, we provide examples of the applications of the EVB approach to understanding different experimental observables.</p>}},
  author       = {{Purg, Miha and Kamerlin, Shina Caroline Lynn}},
  booktitle    = {{Phosphatases}},
  editor       = {{Allen, Karen N.}},
  isbn         = {{978-0-12-813881-6}},
  issn         = {{0076-6879}},
  keywords     = {{Computer Simulation; Cryoelectron Microscopy/instrumentation; Crystallography, X-Ray/instrumentation; Hydrolysis; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular/instrumentation; Organophosphates/metabolism; Phosphoric Triester Hydrolases/chemistry; Protein Structure, Tertiary; Thermodynamics}},
  language     = {{eng}},
  pages        = {{3--51}},
  series       = {{Methods in Enzymology}},
  title        = {{Empirical Valence Bond Simulations of Organophosphate Hydrolysis : Theory and Practice}},
  url          = {{http://dx.doi.org/10.1016/bs.mie.2018.06.007}},
  doi          = {{10.1016/bs.mie.2018.06.007}},
  volume       = {{607}},
  year         = {{2018}},
}