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Monte Carlo simulation and thermodynamic integration applied to protein charge transfer.

Authors
  • Kaiser, Jan1
  • Castellano, Mike1
  • Gnandt, David1
  • Koslowski, Thorsten1
  • 1 Institut für Physikalische Chemie, Universität Freiburg, Freiburg im Breisgau, Germany. , (Germany)
Type
Published Article
Journal
Journal of Computational Chemistry
Publisher
Wiley (John Wiley & Sons)
Publication Date
Apr 30, 2020
Volume
41
Issue
11
Pages
1105–1115
Identifiers
DOI: 10.1002/jcc.26155
PMID: 31981372
Source
Medline
Language
English
License
Unknown

Abstract

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. © 2020 Wiley Periodicals, Inc.

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