The free energy profile for electron flow through the bacterial decahaem cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help to validate the method and results, because differences in the profiles can be related to differences in the charged amino acids local to specific haem groups. First estimates of reorganization free energies λ yield a range consistent with expectations for partially solvent-exposed cofactors, and reveal an activation energy range surmountable for electron flow. Future work will aim at increasing the accuracy of λ with polarizable forcefield dynamics and quantum chemical energy gap calculations, as well as quantum chemical computation of electronic coupling matrix elements.
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December 2012
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Conference Article|
November 21 2012
Molecular structure and free energy landscape for electron transport in the decahaem cytochrome MtrF
Marian Breuer;
Marian Breuer
*Condensed Matter and Materials Physics, Department of Physics and Astronomy, Faculty of Mathematical and Physical Sciences, University College London, Gower Street, London WC1E 6BT, U.K.
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Piotr Zarzycki;
Piotr Zarzycki
†Institute of Physical Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka, 01-224 Warsaw, Poland
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Liang Shi;
Liang Shi
‡Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, U.S.A.
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Thomas A. Clarke;
Thomas A. Clarke
§University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
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Marcus J. Edwards;
Marcus J. Edwards
§University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
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Julea N. Butt;
Julea N. Butt
§University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
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David J. Richardson;
David J. Richardson
§University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
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James K. Fredrickson;
James K. Fredrickson
‡Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, U.S.A.
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John M. Zachara;
John M. Zachara
‡Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, U.S.A.
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Jochen Blumberger;
Jochen Blumberger
*Condensed Matter and Materials Physics, Department of Physics and Astronomy, Faculty of Mathematical and Physical Sciences, University College London, Gower Street, London WC1E 6BT, U.K.
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Kevin M. Rosso
Kevin M. Rosso
1
‡Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, U.S.A.
1To whom correspondence should be addressed (emailkevin.rosso@pnnl.gov).
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Publisher: Portland Press Ltd
Received:
June 01 2012
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© 2012 The Authors Journal
2012
Biochem Soc Trans (2012) 40 (6): 1198–1203.
Article history
Received:
June 01 2012
Citation
Marian Breuer, Piotr Zarzycki, Liang Shi, Thomas A. Clarke, Marcus J. Edwards, Julea N. Butt, David J. Richardson, James K. Fredrickson, John M. Zachara, Jochen Blumberger, Kevin M. Rosso; Molecular structure and free energy landscape for electron transport in the decahaem cytochrome MtrF. Biochem Soc Trans 1 December 2012; 40 (6): 1198–1203. doi: https://doi.org/10.1042/BST20120139
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