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

Research output: Contribution to journalArticle

Abstract

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.

Details

Authors
Organisations
External organisations
  • University of Milano-Bicocca
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Theoretical Chemistry

Keywords

  • BigQM approach, Force field parametrization, H oxidation, Hydrogenases, MoCu CO dehydrogenase, QM/MM
Original languageEnglish
Article number68
JournalJournal of Molecular Modeling
Volume27
Issue number3
Publication statusPublished - 2021
Publication categoryResearch
Peer-reviewedYes