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    Multiscale Simulation Reveals Multiple Pathways for H2 and O2 Transport in a [NiFe]-Hydrogenase
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    † Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
    ‡ Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
    [email protected]; [email protected]
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    Journal of the American Chemical Society

    Cite this: J. Am. Chem. Soc. 2011, 133, 10, 3548–3556
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    https://doi.org/10.1021/ja109712q
    Published February 22, 2011
    Copyright © 2011 American Chemical Society
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    Abstract

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    Hydrogenases are enzymes that catalyze the reversible conversion of hydrogen molecules to protons and electrons. The mechanism by which the gas molecules reach the active site is important for understanding the function of the enzyme and may play a role in the selectivity for hydrogen over inhibitor molecules. Here, we develop a general multiscale molecular simulation approach for the calculation of diffusion rates and determination of pathways by which substrate or inhibitor gases can reach the protein active site. Combining kinetic data from both equilibrium simulations and enhanced sampling, we construct a master equation describing the movement of gas molecules within the enzyme. We find that the time-dependent gas population of the active site can be fit to the same phenomenological rate law used to interpret experiments, with corresponding diffusion rates in very good agreement with experimental data. However, in contrast to the conventional picture, in which the gases follow a well-defined hydrophobic tunnel, we find that there is a diverse network of accessible pathways by which the gas molecules can reach the active site. The previously identified tunnel accounts for only about 60% of the total flux. Our results suggest that the dramatic decrease in the diffusion rate for mutations involving the residue Val74 could be in part due to the narrowing of the passage Val74−Arg476, immediately adjacent to the binding site, explaining why mutations of Leu122 had only a negligible effect in experiment. Our method is not specific to the [NiFe]-hydrogenase and should be generally applicable to the transport of small molecules in proteins.

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    Details of the MD simulation protocols and of the determination of CO poses, a graph showing the percentage of gas molecules inside the protein versus time, a table summarizing the number of CO poses for each mutant, and the full refs 13 and 14. This material is available free of charge via the Internet at http://pubs.acs.org.

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    This article is cited by 68 publications.

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    Journal of the American Chemical Society

    Cite this: J. Am. Chem. Soc. 2011, 133, 10, 3548–3556
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ja109712q
    Published February 22, 2011
    Copyright © 2011 American Chemical Society
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