Monte Carlo simulation and thermodynamic integration applied to protein charge transfer. Issue 11 (25th January 2020)

• Record Type: Journal Article
• Authors: Kaiser, Jan; Castellano, Mike; Gnandt, David; Koslowski, Thorsten
• Is Part Of: Journal of computational chemistry. Volume 41:Issue 11(2020)
• Page Start: 1105
• Page End: 1115
• Publication Date: 2020-01-25
• Subjects: Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.26155
• Languages: English
• ISSNs: 0192-8651

Abstract

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 . Abstract : Monte Carlo simulation and thermodynamic integration methods are used to address a model problem in free energy computations, electron transfer in proteins. Despite the simplicity of the approach, the data agree well with molecular dynamics, dielectric theory, and experiment.