Molecular Structure and Free Energy Landscape for Electron Transport in the Deca-Heme Cytochrome MtrF
Abstract
The free energy profile for electron flow through the bacterial deca-heme cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help validate the method and results, because differences in the profiles can be related to differences in the charged amino acids local to specific heme 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 force field dynamics and quantum chemical energy gap calculations, as well as quantum chemical computation of electronic coupling matrix elements.
- Authors:
- Publication Date:
- Research Org.:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1060120
- Report Number(s):
- PNNL-SA-88376
46203; KP1702030
- DOE Contract Number:
- AC05-76RL01830
- Resource Type:
- Journal Article
- Journal Name:
- Biochemical Society: Transactions, 40(6):1198-1203
- Additional Journal Information:
- Journal Name: Biochemical Society: Transactions, 40(6):1198-1203
- Country of Publication:
- United States
- Language:
- English
- Subject:
- Environmental Molecular Sciences Laboratory
Citation Formats
Breuer, Marian, Zarzycki, Piotr P, Shi, Liang, Clarke, Thomas, Edwards, Marcus, Butt, Julea N, Richardson, David J, Fredrickson, Jim K, Zachara, John M, Blumberger, Jochen, and Rosso, Kevin M. Molecular Structure and Free Energy Landscape for Electron Transport in the Deca-Heme Cytochrome MtrF. United States: N. p., 2012.
Web. doi:10.1042/BST20120139.
Breuer, Marian, Zarzycki, Piotr P, Shi, Liang, Clarke, Thomas, Edwards, Marcus, Butt, Julea N, Richardson, David J, Fredrickson, Jim K, Zachara, John M, Blumberger, Jochen, & Rosso, Kevin M. Molecular Structure and Free Energy Landscape for Electron Transport in the Deca-Heme Cytochrome MtrF. United States. https://doi.org/10.1042/BST20120139
Breuer, Marian, Zarzycki, Piotr P, Shi, Liang, Clarke, Thomas, Edwards, Marcus, Butt, Julea N, Richardson, David J, Fredrickson, Jim K, Zachara, John M, Blumberger, Jochen, and Rosso, Kevin M. 2012.
"Molecular Structure and Free Energy Landscape for Electron Transport in the Deca-Heme Cytochrome MtrF". United States. https://doi.org/10.1042/BST20120139.
@article{osti_1060120,
title = {Molecular Structure and Free Energy Landscape for Electron Transport in the Deca-Heme Cytochrome MtrF},
author = {Breuer, Marian and Zarzycki, Piotr P and Shi, Liang and Clarke, Thomas and Edwards, Marcus and Butt, Julea N and Richardson, David J and Fredrickson, Jim K and Zachara, John M and Blumberger, Jochen and Rosso, Kevin M},
abstractNote = {The free energy profile for electron flow through the bacterial deca-heme cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help validate the method and results, because differences in the profiles can be related to differences in the charged amino acids local to specific heme 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 force field dynamics and quantum chemical energy gap calculations, as well as quantum chemical computation of electronic coupling matrix elements.},
doi = {10.1042/BST20120139},
url = {https://www.osti.gov/biblio/1060120},
journal = {Biochemical Society: Transactions, 40(6):1198-1203},
number = ,
volume = ,
place = {United States},
year = {Sat Dec 01 00:00:00 EST 2012},
month = {Sat Dec 01 00:00:00 EST 2012}
}