Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions

M. Dixit; S. Das; A. R. Mhashal; R. Eitan; D. T. Major

doi:10.1016/bs.mie.2016.05.046

Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions

M. Dixit, S. Das, A. R. Mhashal, R. Eitan, D. T. Major

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

12 Scopus citations

Abstract

This chapter aims to present some basic multiscale approaches available for enzyme simulations, and to point out practical details and pitfalls that are not often discussed in the literature, but can greatly influence the outcome of any in silico enzyme study. We cover principle methodological steps of multiscale studies of general enzyme reactions. This includes choice of starting structures, boundary conditions, potential energy surfaces, reaction coordinates, simulation methods, as well as the choice of method for the treatment of nuclear quantum effects. Together, these and additional steps are crucial for the success of enzyme-modeling projects and should be considered prior to embarking on multiscale modeling.

Original language	English
Title of host publication	Methods in Enzymology
Editors	Gregory A. Voth
Publisher	Academic Press Inc.
Pages	251-286
Number of pages	36
ISBN (Print)	9780128053478
DOIs	https://doi.org/10.1016/bs.mie.2016.05.046
State	Published - 2016

Publication series

Name	Methods in Enzymology
Volume	577
ISSN (Print)	0076-6879
ISSN (Electronic)	1557-7988

Bibliographical note

Publisher Copyright:
© 2016 Elsevier Inc.

Funding

This work has been supported by the Israel Science Foundation (Grant 1560/14) and the United States–Israel Binational Science Foundation (Grant #2012340).

Funders	Funder number
United States-Israel Binational Science Foundation	2012340
Israel Science Foundation	1560/14

Keywords

Enzyme modeling
Multiscale modeling
Nuclear quantum effect
Path-integral
Potential energy surface
Quantum mechanics-molecular mechanics

Access to Document

10.1016/bs.mie.2016.05.046

Cite this

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Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions

Abstract

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Bibliographical note

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Keywords

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