A QM/MM study of proton transport pathways in a [NiFe] hydrogenase

Authors

  • Ignacio Fdez. Galván,

    Corresponding author
    1. Laboratoire de Dynamique Moléculaire, IBS (Institut de Biologie Structurale — Jean-Pierre Ebel), CEA, CNRS, Université Joseph Fourier, F-38027 Grenoble, France
    • Química Física, Universidad de Extremadura, Avda. de Elvas s/n, 06071 Badajoz, Spain
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  • Anne Volbeda,

    1. Laboratoire de Cristallographie et Cristallogenèse des Protéines, IBS (Institut de Biologie Structurale — Jean-Pierre Ebel), CEA, CNRS, Université Joseph Fourier, F-38027 Grenoble, France
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  • Juan C. Fontecilla-Camps,

    1. Laboratoire de Cristallographie et Cristallogenèse des Protéines, IBS (Institut de Biologie Structurale — Jean-Pierre Ebel), CEA, CNRS, Université Joseph Fourier, F-38027 Grenoble, France
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  • Martin J. Field

    1. Laboratoire de Dynamique Moléculaire, IBS (Institut de Biologie Structurale — Jean-Pierre Ebel), CEA, CNRS, Université Joseph Fourier, F-38027 Grenoble, France
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Abstract

A theoretical QM/MM study of the [NiFe] hydrogenase from Desulfovibrio fructosovorans has been performed to investigate possible routes of proton transfer between the active site and the protein surface. We obtained the minimum energy paths, with a modified version of the nudged elastic band method, for a set of proposed pathways. The calculations were carried out for the crystallographic structure and for several structures of the protein obtained from a molecular dynamics simulation. The results show one of the studied pathways to be preferred for transport from the active site to the surface, but the preference is not so strong when transport occurs in the opposite direction. Proteins 2008. © 2008 Wiley-Liss, Inc.

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