Putative reaction mechanism of nitrogenase after dissociation of a sulfide ligand
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/95420c1d-96a4-4e60-b25e-ca363c8d166e
- author
- Cao, Lili LU and Ryde, Ulf LU
- organization
- publishing date
- 2020-09-01
- 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}}, }