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Putative reaction mechanism of nitrogenase after dissociation of a sulfide ligand

Cao, Lili LU and Ryde, Ulf LU orcid (2020) In Journal of Catalysis 391. p.247-259
Abstract
We have investigated the implications of the recent crystallographic findings that the m2-bridging S2B sulfide ligand may reversibly dissociate from the active-site FeMo cluster of nitrogenase. We show with combined quantum mechanical and molecular mechanical (QM/MM) calculations that once S2B has dis- sociated, N2 may bind in that position and can be protonated to two NH3 groups by thermodynamically favourable steps. The substrate forms hydrogen bonds with two protein ligands, Gln-191 and His-195. For all steps, we have studied three possible protonation states of His-195 (protonated on either ND1, NE2 or both). We find that the thermodynamically favoured path involves an end-on NNH2 structure, a mixed side-on/end-on H2NNH structure, a... (More)
We have investigated the implications of the recent crystallographic findings that the m2-bridging S2B sulfide ligand may reversibly dissociate from the active-site FeMo cluster of nitrogenase. We show with combined quantum mechanical and molecular mechanical (QM/MM) calculations that once S2B has dis- sociated, N2 may bind in that position and can be protonated to two NH3 groups by thermodynamically favourable steps. The substrate forms hydrogen bonds with two protein ligands, Gln-191 and His-195. For all steps, we have studied three possible protonation states of His-195 (protonated on either ND1, NE2 or both). We find that the thermodynamically favoured path involves an end-on NNH2 structure, a mixed side-on/end-on H2NNH structure, a side-on H2NNH2 structure, a bridging NH2 structure and a bridging NH3 structure. In all cases, His-195 seems to be protonated on the NE2 atom. Dissociation of the NH3 pro- duct is often unfavourable and requires either further reduction or protonation of the cluster or rebinding of S2B. In conclusion, our calculations show that dissociation of S2B gives rise to a natural binding and reaction site for nitrogenase, between the Fe2 and Fe6 atoms, which can support an alternating reaction mechanism with favourable energetics. (Less)
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author
and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Nitrogenase, QM/MM, S2B dissociation, Nitrogen fixation, Alternating or distal reaction mechanism
in
Journal of Catalysis
volume
391
pages
13 pages
publisher
Elsevier
external identifiers
  • scopus:85090838787
ISSN
1090-2694
DOI
10.1016/j.jcat.2020.08.028
language
English
LU publication?
yes
id
95420c1d-96a4-4e60-b25e-ca363c8d166e
date added to LUP
2020-09-26 10:43:06
date last changed
2023-04-10 20:43:26
@article{95420c1d-96a4-4e60-b25e-ca363c8d166e,
  abstract     = {{We have investigated the implications of the recent crystallographic findings that the m2-bridging S2B sulfide ligand may reversibly dissociate from the active-site FeMo cluster of nitrogenase. We show with combined quantum mechanical and molecular mechanical (QM/MM) calculations that once S2B has dis- sociated, N2 may bind in that position and can be protonated to two NH3 groups by thermodynamically favourable steps. The substrate forms hydrogen bonds with two protein ligands, Gln-191 and His-195. For all steps, we have studied three possible protonation states of His-195 (protonated on either ND1, NE2 or both). We find that the thermodynamically favoured path involves an end-on NNH2 structure, a mixed side-on/end-on H2NNH structure, a side-on H2NNH2 structure, a bridging NH2 structure and a bridging NH3 structure. In all cases, His-195 seems to be protonated on the NE2 atom. Dissociation of the NH3 pro- duct is often unfavourable and requires either further reduction or protonation of the cluster or rebinding of S2B. In conclusion, our calculations show that dissociation of S2B gives rise to a natural binding and reaction site for nitrogenase, between the Fe2 and Fe6 atoms, which can support an alternating reaction mechanism with favourable energetics.}},
  author       = {{Cao, Lili and Ryde, Ulf}},
  issn         = {{1090-2694}},
  keywords     = {{Nitrogenase; QM/MM; S2B dissociation; Nitrogen fixation; Alternating or distal reaction mechanism}},
  language     = {{eng}},
  month        = {{09}},
  pages        = {{247--259}},
  publisher    = {{Elsevier}},
  series       = {{Journal of Catalysis}},
  title        = {{Putative reaction mechanism of nitrogenase after dissociation of a sulfide ligand}},
  url          = {{https://lup.lub.lu.se/search/files/84188317/n2ase_rotation_268.pdf}},
  doi          = {{10.1016/j.jcat.2020.08.028}},
  volume       = {{391}},
  year         = {{2020}},
}