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.
Molecular structure and free energy landscape for electron transport in the decahaem cytochrome MtrF
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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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