Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics

B. Ginovska, Simone Raugei, W. J. Shaw

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

Abstract

There is extensive interest in hydrogenases based on their ability to rapidly and efficiently interconvert H2 with protons and electrons, and their (typically) superior function relative to molecular mimics. Understanding the function of enzymes is one approach to implementing design features to make better catalysts and is an approach we have implemented in our work. In this review, we will discuss our efforts to develop design principles from enzymes, with specific focus on proton transport. We will also present computational studies of the mimics we have investigated with similar methodologies. We will discuss the mechanisms used by small scaffolds on molecular mimics which in many cases are surprisingly similar to those used by nature, while in other cases, computational analysis allowed us to reveal an unexpected role. Computational methods provide one of the best ways, and in some cases, the only way, to gain insight into the mechanistic details of enzymes. In this review, we illustrate the general computational strategy we used to study the proton pathway of [FeFe]-hydrogenase, and the similar strategy to investigate small molecules. We present the main results we obtained and how our computational work stimulated or worked in concert with experimental investigations. We also focus on estimation of errors and convergence of properties in the simulations. These studies demonstrate the powerful results that can be obtained by the close pairing of experimental and theoretical approaches.

Original languageEnglish
Title of host publicationComputational Approaches for Studying Enzyme Mechanism Part B
PublisherAcademic Press Inc
Pages73-101
Number of pages29
DOIs
Publication statusPublished - Jan 1 2016

Publication series

NameMethods in Enzymology
Volume578
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

Fingerprint

Hydrogenase
Molecular Dynamics Simulation
Molecular dynamics
Protons
Enzymes
Computational methods
Scaffolds
Electrons
Catalysts
Molecules

Keywords

  • Covariance analysis
  • Density-functional theory
  • Hydrogen bonding
  • Hydrogenase
  • Hydrogenase mimics
  • Metadynamics
  • Molecular dynamics
  • Proton transport

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Ginovska, B., Raugei, S., & Shaw, W. J. (2016). Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics. In Computational Approaches for Studying Enzyme Mechanism Part B (pp. 73-101). (Methods in Enzymology; Vol. 578). Academic Press Inc. https://doi.org/10.1016/bs.mie.2016.05.044

Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics. / Ginovska, B.; Raugei, Simone; Shaw, W. J.

Computational Approaches for Studying Enzyme Mechanism Part B. Academic Press Inc, 2016. p. 73-101 (Methods in Enzymology; Vol. 578).

Research output: Chapter in Book/Report/Conference proceedingChapter

Ginovska, B, Raugei, S & Shaw, WJ 2016, Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics. in Computational Approaches for Studying Enzyme Mechanism Part B. Methods in Enzymology, vol. 578, Academic Press Inc, pp. 73-101. https://doi.org/10.1016/bs.mie.2016.05.044
Ginovska B, Raugei S, Shaw WJ. Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics. In Computational Approaches for Studying Enzyme Mechanism Part B. Academic Press Inc. 2016. p. 73-101. (Methods in Enzymology). https://doi.org/10.1016/bs.mie.2016.05.044
Ginovska, B. ; Raugei, Simone ; Shaw, W. J. / Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics. Computational Approaches for Studying Enzyme Mechanism Part B. Academic Press Inc, 2016. pp. 73-101 (Methods in Enzymology).
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