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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 LU and Ryde, Ulf LU (2021) In Journal of Molecular Modeling 27(3).
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... (More)

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.

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author
; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
BigQM approach, Force field parametrization, H oxidation, Hydrogenases, MoCu CO dehydrogenase, QM/MM
in
Journal of Molecular Modeling
volume
27
issue
3
article number
68
publisher
Springer
external identifiers
  • pmid:33538901
  • scopus:85100477177
ISSN
1610-2940
DOI
10.1007/s00894-020-04655-3
language
English
LU publication?
yes
id
ac1a5704-8f3c-49ce-9f39-09bc34bc1eb9
date added to LUP
2021-02-16 14:10:51
date last changed
2021-06-16 05:53:08
@article{ac1a5704-8f3c-49ce-9f39-09bc34bc1eb9,
  abstract     = {<p>The MoCu CO dehydrogenase enzyme not only transforms CO into CO<sub>2</sub> but it can also oxidise H<sub>2</sub>. Even if its hydrogenase activity has been known for decades, a debate is ongoing on the most plausible mode for the binding of H<sub>2</sub> 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 H<sub>2</sub>–HN(backbone) interaction was observed when the van der Waals parameters described in previous literature for H<sub>2</sub> 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 H<sub>2</sub> 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.</p>},
  author       = {Rovaletti, Anna and Greco, Claudio and Ryde, Ulf},
  issn         = {1610-2940},
  language     = {eng},
  number       = {3},
  publisher    = {Springer},
  series       = {Journal of Molecular Modeling},
  title        = {QM/MM study of the binding of H<sub>2</sub> to MoCu CO dehydrogenase : development and applications of improved H<sub>2</sub> van der Waals parameters},
  url          = {http://dx.doi.org/10.1007/s00894-020-04655-3},
  doi          = {10.1007/s00894-020-04655-3},
  volume       = {27},
  year         = {2021},
}