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Monte Carlo simulation and thermodynamic integration applied to protein charge transfer
Author(s) -
Kaiser Jan,
Castellano Mike,
Gnandt David,
Koslowski Thorsten
Publication year - 2020
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.26155
Subject(s) - monte carlo method , ferredoxin , desulfovibrio vulgaris , statistical physics , thermodynamic integration , electron transfer , molecular dynamics , chemistry , monte carlo molecular modeling , dynamic monte carlo method , quantum monte carlo , physics , poisson–boltzmann equation , computational chemistry , markov chain monte carlo , quantum mechanics , mathematics , ion , biochemistry , biology , statistics , bacteria , genetics , enzyme
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 .