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Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods.

Dong, Geng LU and Ryde, Ulf LU (2016) In Journal of Biological Inorganic Chemistry 21(3). p.383-394
Abstract
The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the... (More)
The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SIa, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14-51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Biological Inorganic Chemistry
volume
21
issue
3
pages
383 - 394
publisher
Springer
external identifiers
  • pmid:26940957
  • scopus:84960115057
  • wos:000375415300009
ISSN
1432-1327
DOI
10.1007/s00775-016-1348-9
language
English
LU publication?
yes
id
700d7f9d-1438-4f89-a3a7-fc30471da202 (old id 8856298)
date added to LUP
2016-03-21 10:23:03
date last changed
2017-06-18 03:03:22
@article{700d7f9d-1438-4f89-a3a7-fc30471da202,
  abstract     = {The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SIa, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14-51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein.},
  author       = {Dong, Geng and Ryde, Ulf},
  issn         = {1432-1327},
  language     = {eng},
  month        = {03},
  number       = {3},
  pages        = {383--394},
  publisher    = {Springer},
  series       = {Journal of Biological Inorganic Chemistry},
  title        = {Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods.},
  url          = {http://dx.doi.org/10.1007/s00775-016-1348-9},
  volume       = {21},
  year         = {2016},
}