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Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods

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Abstract

The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SIa, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14–51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein.

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Acknowledgments

This investigation has been supported by grants from the Swedish research council (project 2014-5540), the China Scholarship Council, and COST through Action CM1305 (ECOSTBio). The computations were performed on computer resources provided by the Swedish National Infrastructure for Computing (SNIC) at Lunarc at Lund University.

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  1. Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, 221 00, Lund, Sweden

    Geng Dong & Ulf Ryde

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  1. Geng Dong
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Correspondence to Ulf Ryde.

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Dong, G., Ryde, U. Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods. J Biol Inorg Chem 21, 383–394 (2016). https://doi.org/10.1007/s00775-016-1348-9

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