Challenges in computational studies of enzyme structure, function and dynamics

Alexandra T.P. Carvalho; Alexandre Barrozo; Dvir Doron; Alexandra Vardi Kilshtain; Dan Thomas Major; Shina Caroline Lynn Kamerlin

doi:10.1016/j.jmgm.2014.09.003

Challenges in computational studies of enzyme structure, function and dynamics

Alexandra T.P. Carvalho, Alexandre Barrozo, Dvir Doron, Alexandra Vardi Kilshtain, Dan Thomas Major, Shina Caroline Lynn Kamerlin

Department of Chemistry

Research output: Contribution to journal › Article › peer-review

53 Scopus citations

Abstract

In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.

Original language	English
Pages (from-to)	62-79
Number of pages	18
Journal	Journal of Molecular Graphics and Modelling
Volume	54
DOIs	https://doi.org/10.1016/j.jmgm.2014.09.003
State	Published - Nov 2014

Bibliographical note

Publisher Copyright:
© 2014, Elsevier Inc. All rights reserved.

Funding

The European Research Council has provided financial support under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement n° 306474. The authors also thank the Swedish Research Council (Vetenskapsrådet, 2010-5026) for an assistant professorship to SCLK as well as the US-Israel BSF (grant #2007256) and Israel Science Foundation (grant #1560/14) to DTM.

Funders	Funder number
US-Israel BSF	2007256
Seventh Framework Programme
European Commission	306474
Israel Science Foundation	1560/14
Vetenskapsrådet	2010-5026
Seventh Framework Programme

Keywords

Computational enzymology
Conformational sampling
Free energy simulations
QM/MM
Reaction coordinates

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10.1016/j.jmgm.2014.09.003

Cite this

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abstract = "In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.",

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AU - Major, Dan Thomas

AU - Kamerlin, Shina Caroline Lynn

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Challenges in computational studies of enzyme structure, function and dynamics

Abstract

Bibliographical note

Funding

Keywords

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