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Multiscale Modeling of the Active Site of [Fe] Hydrogenase: The H-2 Binding Site in Open and Closed Protein Conformations

Hedegard, Erik Donovan ; Kongsted, Jacob and Ryde, Ulf LU orcid (2015) In Angewandte Chemie (International edition) 54(21). p.6246-6250
Abstract
A series of QM/MM optimizations of the full protein of [Fe] hydrogenase were performed. The FeGP cofactor has been optimized in the water-bound resting state (1), with a side-on bound dihydrogen (2), or as a hydride intermediate (3). For inclusion of H4MPT in the closed structure, advanced multiscale modeling appears to be necessary, especially to obtain reliable distances between CH-H4MPT+ and the dihydrogen (H-2) or hydride (H-) ligand in the FeGP cofactor. Inclusion of the full protein is further important for the relative energies of the two intermediates 2 and 3. We finally find that hydride transfer from 3 has a significantly higher barrier than found in previous studies neglecting the full protein environment.
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author
; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
[Fe] hydrogenase, hydrogen activation, molecular mechanics, multiscale, modeling, quantum mechanics
in
Angewandte Chemie (International edition)
volume
54
issue
21
pages
6246 - 6250
publisher
John Wiley & Sons Inc.
external identifiers
  • wos:000354260000023
  • pmid:25867218
  • scopus:84928984220
ISSN
1521-3773
DOI
10.1002/anie.201501737
language
English
LU publication?
yes
additional info
The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)
id
57b6f94f-7a5e-404f-aa97-139760e1c69f (old id 7422846)
date added to LUP
2016-04-01 14:56:03
date last changed
2023-03-28 06:52:44
@article{57b6f94f-7a5e-404f-aa97-139760e1c69f,
  abstract     = {{A series of QM/MM optimizations of the full protein of [Fe] hydrogenase were performed. The FeGP cofactor has been optimized in the water-bound resting state (1), with a side-on bound dihydrogen (2), or as a hydride intermediate (3). For inclusion of H4MPT in the closed structure, advanced multiscale modeling appears to be necessary, especially to obtain reliable distances between CH-H4MPT+ and the dihydrogen (H-2) or hydride (H-) ligand in the FeGP cofactor. Inclusion of the full protein is further important for the relative energies of the two intermediates 2 and 3. We finally find that hydride transfer from 3 has a significantly higher barrier than found in previous studies neglecting the full protein environment.}},
  author       = {{Hedegard, Erik Donovan and Kongsted, Jacob and Ryde, Ulf}},
  issn         = {{1521-3773}},
  keywords     = {{[Fe] hydrogenase; hydrogen activation; molecular mechanics; multiscale; modeling; quantum mechanics}},
  language     = {{eng}},
  number       = {{21}},
  pages        = {{6246--6250}},
  publisher    = {{John Wiley & Sons Inc.}},
  series       = {{Angewandte Chemie (International edition)}},
  title        = {{Multiscale Modeling of the Active Site of [Fe] Hydrogenase: The H-2 Binding Site in Open and Closed Protein Conformations}},
  url          = {{http://dx.doi.org/10.1002/anie.201501737}},
  doi          = {{10.1002/anie.201501737}},
  volume       = {{54}},
  year         = {{2015}},
}