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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 (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
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
external identifiers
  • wos:000354260000023
  • scopus:84928984220
ISSN
1521-3773
DOI
10.1002/anie.201501737
language
English
LU publication?
yes
id
57b6f94f-7a5e-404f-aa97-139760e1c69f (old id 7422846)
date added to LUP
2015-06-26 09:25:27
date last changed
2017-09-24 04:14:13
@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},
  keyword      = {[Fe] hydrogenase,hydrogen activation,molecular mechanics,multiscale,modeling,quantum mechanics},
  language     = {eng},
  number       = {21},
  pages        = {6246--6250},
  publisher    = {John Wiley & Sons},
  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},
  volume       = {54},
  year         = {2015},
}