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Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase

Söderhjelm, Pär LU and Ryde, Ulf LU orcid (2006) In Journal of molecular structure. Theochem 770(1-3). p.199-219
Abstract
[NiFe] hydrogenases catalyse the reaction H2 <-> 2H(+) + 2e(-). Several states of the enzyme have been observed by spectroscopic methods. Among these, the two most oxidized states, called the unready Ni-A and Ni-SU states, have been especially intriguing, because they take a much longer time to activate than the corresponding ready Ni-B and Ni-SI states. It has recently been suggested that the unready states actually contain a (hydro)peroxide bridge between the Ni and Fe ions, in contrast to the hydroxide bridge in the ready states. In this paper, we use quantum refinement (crystallographic refinement, in which the molecular mechanics [MM] calculations, normally employed to supplement the crystallographic data, are replace by more... (More)
[NiFe] hydrogenases catalyse the reaction H2 <-> 2H(+) + 2e(-). Several states of the enzyme have been observed by spectroscopic methods. Among these, the two most oxidized states, called the unready Ni-A and Ni-SU states, have been especially intriguing, because they take a much longer time to activate than the corresponding ready Ni-B and Ni-SI states. It has recently been suggested that the unready states actually contain a (hydro)peroxide bridge between the Ni and Fe ions, in contrast to the hydroxide bridge in the ready states. In this paper, we use quantum refinement (crystallographic refinement, in which the molecular mechanics [MM] calculations, normally employed to supplement the crystallographic data, are replace by more accurate quantum mechanics [QM] calculations), combined QM/MM calculations, and accurate energy estimates to study the nature of a recent oxidised crystal structure of [NiFe] hydrogenase from Desulfovibrio fructosovorans. We show that the structure contains a mixture of several states in the active site. The experimental data is best explained by structures with a hydroxide bridge but with two of the cysteine ligands (one bridging and one terminal) partly oxidised. When the terminal Cys-543 ligand is oxidised, the sulphur occupies an alternative position, observed in several crystal structures. The Glu-25 residue, that forms a hydrogen bond to this sulphur, also changes position. A peroxide ligand may exist as a minor component in the crystal and the suggested structure is supported by the calculations. We suggest that oxidised states are slow-equilibrium mixtures of structures with a peroxide bound and structures with oxidised Cys residues, and that the former can be activated by replacement of the protonated peroxide with a H-2 or CO ligand, as has been observed in electrochemical experiments. (c) 2006 Elsevier B.V. All rights reserved. (Less)
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author
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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
QM/MM methods, [NiFe] hydrogenase, crystallographic refinement, solvation energy
in
Journal of molecular structure. Theochem
volume
770
issue
1-3
pages
199 - 219
publisher
Elsevier
external identifiers
  • wos:000241243900031
  • scopus:33748460267
ISSN
0166-1280
DOI
10.1016/j.theochem.2006.06.008
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
0977bef8-cbba-4443-9536-5054ee0e0d42 (old id 387930)
date added to LUP
2016-04-01 16:35:13
date last changed
2020-11-24 02:46:20
@article{0977bef8-cbba-4443-9536-5054ee0e0d42,
  abstract     = {[NiFe] hydrogenases catalyse the reaction H2 &lt;-&gt; 2H(+) + 2e(-). Several states of the enzyme have been observed by spectroscopic methods. Among these, the two most oxidized states, called the unready Ni-A and Ni-SU states, have been especially intriguing, because they take a much longer time to activate than the corresponding ready Ni-B and Ni-SI states. It has recently been suggested that the unready states actually contain a (hydro)peroxide bridge between the Ni and Fe ions, in contrast to the hydroxide bridge in the ready states. In this paper, we use quantum refinement (crystallographic refinement, in which the molecular mechanics [MM] calculations, normally employed to supplement the crystallographic data, are replace by more accurate quantum mechanics [QM] calculations), combined QM/MM calculations, and accurate energy estimates to study the nature of a recent oxidised crystal structure of [NiFe] hydrogenase from Desulfovibrio fructosovorans. We show that the structure contains a mixture of several states in the active site. The experimental data is best explained by structures with a hydroxide bridge but with two of the cysteine ligands (one bridging and one terminal) partly oxidised. When the terminal Cys-543 ligand is oxidised, the sulphur occupies an alternative position, observed in several crystal structures. The Glu-25 residue, that forms a hydrogen bond to this sulphur, also changes position. A peroxide ligand may exist as a minor component in the crystal and the suggested structure is supported by the calculations. We suggest that oxidised states are slow-equilibrium mixtures of structures with a peroxide bound and structures with oxidised Cys residues, and that the former can be activated by replacement of the protonated peroxide with a H-2 or CO ligand, as has been observed in electrochemical experiments. (c) 2006 Elsevier B.V. All rights reserved.},
  author       = {Söderhjelm, Pär and Ryde, Ulf},
  issn         = {0166-1280},
  language     = {eng},
  number       = {1-3},
  pages        = {199--219},
  publisher    = {Elsevier},
  series       = {Journal of molecular structure. Theochem},
  title        = {Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase},
  url          = {http://dx.doi.org/10.1016/j.theochem.2006.06.008},
  doi          = {10.1016/j.theochem.2006.06.008},
  volume       = {770},
  year         = {2006},
}