Monte Carlo simulation and thermodynamic integration applied to protein charge transfer.
Journal
Journal of computational chemistry
ISSN: 1096-987X
Titre abrégé: J Comput Chem
Pays: United States
ID NLM: 9878362
Informations de publication
Date de publication:
30 04 2020
30 04 2020
Historique:
received:
28
10
2019
revised:
29
12
2019
accepted:
02
01
2020
pubmed:
26
1
2020
medline:
27
5
2021
entrez:
26
1
2020
Statut:
ppublish
Résumé
We introduce a combination of Monte Carlo simulation and thermodynamic integration methods to address a model problem in free energy computations, electron transfer in proteins. The feasibility of this approach is tested using the ferredoxin protein from Clostridium acidurici. The results are compared to numerical solutions of the Poisson-Boltzmann equation and data from recent molecular dynamics simulations on charge transfer in a protein complex, the NrfHA nitrite reductase of Desulfovibrio vulgaris. Despite the conceptual and computational simplicity of the Monte Carlo approach, the data agree well with those obtained by other methods. A link to experiments is established via the cytochrome subunit of the bacterial photosynthetic reaction center of Rhodopseudomonas viridis.
Substances chimiques
Cytochromes
0
Ferredoxins
0
Photosynthetic Reaction Center Complex Proteins
0
Nitrite Reductases
EC 1.7.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1105-1115Informations de copyright
© 2020 Wiley Periodicals, Inc.
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