QM/MM study of the binding of H2 to MoCu CO dehydrogenase: development and applications of improved H2 van der Waals parameters

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QM/MM study of the binding of H2 to MoCu CO dehydrogenase : development and applications of improved H2 van der Waals parameters. / Rovaletti, Anna; Greco, Claudio; Ryde, Ulf.

In: Journal of Molecular Modeling, Vol. 27, No. 3, 68, 2021.

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TY - JOUR

T1 - QM/MM study of the binding of H2 to MoCu CO dehydrogenase

T2 - development and applications of improved H2 van der Waals parameters

AU - Rovaletti, Anna

AU - Greco, Claudio

AU - Ryde, Ulf

PY - 2021

Y1 - 2021

N2 - The MoCu CO dehydrogenase enzyme not only transforms CO into CO2 but it can also oxidise H2. Even if its hydrogenase activity has been known for decades, a debate is ongoing on the most plausible mode for the binding of H2 to the enzyme active site and the hydrogen oxidation mechanism. In the present work, we provide a new perspective on the MoCu-CODH hydrogenase activity by improving the in silico description of the enzyme. Energy refinement—by means of the BigQM approach—was performed on the intermediates involved in the dihydrogen oxidation catalysis reported in our previously published work (Rovaletti, et al. “Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase.” Inorganics 7 (2019) 135). A suboptimal description of the H2–HN(backbone) interaction was observed when the van der Waals parameters described in previous literature for H2 were employed. Therefore, a new set of van der Waals parameters is developed here in order to better describe the hydrogen–backbone interaction. They give rise to improved binding modes of H2 in the active site of MoCu CO dehydrogenase. Implications of the resulting outcomes for a better understanding of hydrogen oxidation catalysis mechanisms are proposed and discussed.

AB - The MoCu CO dehydrogenase enzyme not only transforms CO into CO2 but it can also oxidise H2. Even if its hydrogenase activity has been known for decades, a debate is ongoing on the most plausible mode for the binding of H2 to the enzyme active site and the hydrogen oxidation mechanism. In the present work, we provide a new perspective on the MoCu-CODH hydrogenase activity by improving the in silico description of the enzyme. Energy refinement—by means of the BigQM approach—was performed on the intermediates involved in the dihydrogen oxidation catalysis reported in our previously published work (Rovaletti, et al. “Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase.” Inorganics 7 (2019) 135). A suboptimal description of the H2–HN(backbone) interaction was observed when the van der Waals parameters described in previous literature for H2 were employed. Therefore, a new set of van der Waals parameters is developed here in order to better describe the hydrogen–backbone interaction. They give rise to improved binding modes of H2 in the active site of MoCu CO dehydrogenase. Implications of the resulting outcomes for a better understanding of hydrogen oxidation catalysis mechanisms are proposed and discussed.

KW - BigQM approach

KW - Force field parametrization

KW - H oxidation

KW - Hydrogenases

KW - MoCu CO dehydrogenase

KW - QM/MM

U2 - 10.1007/s00894-020-04655-3

DO - 10.1007/s00894-020-04655-3

M3 - Article

C2 - 33538901

AN - SCOPUS:85100477177

VL - 27

JO - Journal of Molecular Modeling

JF - Journal of Molecular Modeling

SN - 1610-2940

IS - 3

M1 - 68

ER -