Bound Flavin–Cytochrome Model of Extracellular Electron Transfer in Shewanella oneidensis: Analysis by Free Energy Molecular Dynamics Simulations

Flavins are known to enhance extracellular electron transfer (EET) in Shewanella oneidensis MR-1 bacteria, which reduce electron acceptors through outer-membrane (OM) cytochromes c. Free-shuttle and bound-redox cofactor mechanisms were proposed to explain this enhancement, but recent electrochemical...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2016-06, Vol.120 (25), p.5617-5624
Main Authors: Hong, Gongyi, Pachter, Ruth
Format: Article
Language:English
Subjects:
Bacteria
Binding
Binding energy
Binding Sites
Computer simulation
Cytochromes c - chemistry
Cytochromes c - metabolism
Electrode potentials
Electron transfer
Electron Transport
Electrons
Flavins - chemistry
Flavins - metabolism
Free energy
Hydrogen Bonding
Molecular dynamics
Molecular Dynamics Simulation
Oxidation-Reduction
Protein Binding
Riboflavin - chemistry
Riboflavin - metabolism
Shewanella - metabolism
Static Electricity
Thermodynamics
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Summary:Flavins are known to enhance extracellular electron transfer (EET) in Shewanella oneidensis MR-1 bacteria, which reduce electron acceptors through outer-membrane (OM) cytochromes c. Free-shuttle and bound-redox cofactor mechanisms were proposed to explain this enhancement, but recent electrochemical reports favor a flavin-bound model, proposing two one-electron reductions of flavin, namely, oxidized (Ox) to semiquinone (Sq) and semiquinone to hydroquinone (Hq), at anodic and cathodic conditions, respectively. In this work, to provide a mechanistic understanding of riboflavin (RF) binding at the multiheme OM cytochrome OmcA, we explored binding configurations at hemes 2, 5, 7, and 10. Subsequently, on the basis of molecular dynamics (MD) simulations, binding free energies and redox potential shifts upon RF binding for the Ox/Sq and Sq/Hq reductions were analyzed. Our results demonstrated an upshift in the Ox/Sq and a downshift in the Sq/Hq redox potentials, consistent with a bound RF–OmcA model. Furthermore, binding free energy MD simulations indicated an RF binding preference at heme 7. MD simulations of the OmcA–MtrC complex interfacing at hemes 5 revealed a small interprotein redox potential difference with an electron transfer rate of 107–108/s.
ISSN:1520-6106
1520-5207
DOI:10.1021/acs.jpcb.6b03851