Two local minima for structures of [4Fe–4S] clusters obtained with density functional theory methods
Jafari, Sonia ; Ryde, Ulf LU
and Irani, Mehdi
LU
(2023)
In Scientific Reports
13(1).
- Abstract
[4Fe–4S] clusters are essential cofactors in many proteins involved in biological redox-active processes. Density functional theory (DFT) methods are widely used to study these clusters. Previous investigations have indicated that there exist two local minima for these clusters in proteins. We perform a detailed study of these minima in five proteins and two oxidation states, using combined quantum mechanical and molecular mechanical (QM/MM) methods. We show that one local minimum (L state) has longer Fe–Fe distances than the other (S state), and that the L state is more stable for all cases studied. We also show that some DFT methods may only obtain the L state, while others may obtain both states. Our work provides new insights into... (More)
[4Fe–4S] clusters are essential cofactors in many proteins involved in biological redox-active processes. Density functional theory (DFT) methods are widely used to study these clusters. Previous investigations have indicated that there exist two local minima for these clusters in proteins. We perform a detailed study of these minima in five proteins and two oxidation states, using combined quantum mechanical and molecular mechanical (QM/MM) methods. We show that one local minimum (L state) has longer Fe–Fe distances than the other (S state), and that the L state is more stable for all cases studied. We also show that some DFT methods may only obtain the L state, while others may obtain both states. Our work provides new insights into the structural diversity and stability of [4Fe–4S] clusters in proteins, and highlights the importance of reliable DFT methods and geometry optimization. We recommend r2SCAN for optimizing [4Fe-4S] clusters in proteins, which gives the most accurate structures for the five proteins studied.
(Less)
- author
- Jafari, Sonia
; Ryde, Ulf
LU
and Irani, Mehdi
LU
- organization
- publishing date
- 2023
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Scientific Reports
- volume
- 13
- issue
- 1
- article number
- 10832
- publisher
- Nature Publishing Group
- external identifiers
-
- pmid:37402767
- scopus:85164026358
- ISSN
- 2045-2322
- DOI
- 10.1038/s41598-023-37755-0
- language
- English
- LU publication?
- yes
- id
- 18005947-9cff-4444-aa76-aca6f854f3e9
- date added to LUP
- 2023-08-28 13:21:08
- date last changed
- 2024-04-20 02:04:36
@article{18005947-9cff-4444-aa76-aca6f854f3e9,
abstract = {{<p>[4Fe–4S] clusters are essential cofactors in many proteins involved in biological redox-active processes. Density functional theory (DFT) methods are widely used to study these clusters. Previous investigations have indicated that there exist two local minima for these clusters in proteins. We perform a detailed study of these minima in five proteins and two oxidation states, using combined quantum mechanical and molecular mechanical (QM/MM) methods. We show that one local minimum (L state) has longer Fe–Fe distances than the other (S state), and that the L state is more stable for all cases studied. We also show that some DFT methods may only obtain the L state, while others may obtain both states. Our work provides new insights into the structural diversity and stability of [4Fe–4S] clusters in proteins, and highlights the importance of reliable DFT methods and geometry optimization. We recommend r<sup>2</sup>SCAN for optimizing [4Fe-4S] clusters in proteins, which gives the most accurate structures for the five proteins studied.</p>}},
author = {{Jafari, Sonia and Ryde, Ulf and Irani, Mehdi}},
issn = {{2045-2322}},
language = {{eng}},
number = {{1}},
publisher = {{Nature Publishing Group}},
series = {{Scientific Reports}},
title = {{Two local minima for structures of [4Fe–4S] clusters obtained with density functional theory methods}},
url = {{http://dx.doi.org/10.1038/s41598-023-37755-0}},
doi = {{10.1038/s41598-023-37755-0}},
volume = {{13}},
year = {{2023}},
}