Jiang, X;
Futera, Z;
Blumberger, J;
(2019)
Ergodicity-Breaking in Thermal Biological Electron Transfer? Cytochrome C Revisited.
The Journal of Physical Chemistry B
, 123
(35)
pp. 7588-7598.
10.1021/acs.jpcb.9b05253.
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Abstract
It was recently suggested that certain redox proteins operate in an ergodicity-breaking regime to facilitate biological electron transfer (ET). A signature for this is a large variance reorganization free energy (several electronvolts) but a significantly smaller Stokes reorganization free energy due to incomplete protein relaxation on the time scale of the ET event. Here we investigate whether this picture holds for oxidation of cytochrome c in aqueous solution, at various levels of theory including classical molecular dynamics with two additive and one electronically polarizable force field, and QM/MM calculations with the QM region treated by full electrostatic DFT embedding and by the perturbed matrix method. Sampling the protein and energy gap dynamics over more than 250 ns, we find no evidence for ergodicity-breaking effects. In particular, the inclusion of electronic polarizability of the heme group at QM/MM levels did not induce nonergodic effects, contrary to previous reports by Matyushov et al. The well-known problem of overestimation of reorganization free energies with additive force fields is cured when the protein and solvent are treated as electronically polarizable. Ergodicity-breaking effects may occur in other redox proteins, and our results suggest that long simulations, ideally on the ET time scale, with electronically polarizable force fields are required to obtain strong numerical evidence for them.
Type: | Article |
---|---|
Title: | Ergodicity-Breaking in Thermal Biological Electron Transfer? Cytochrome C Revisited |
Location: | United States |
Open access status: | An open access version is available from UCL Discovery |
DOI: | 10.1021/acs.jpcb.9b05253 |
Publisher version: | https://doi.org/10.1021/acs.jpcb.9b05253 |
Language: | English |
Additional information: | This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions. |
Keywords: | Polarizability, Free energy, Molecular mechanics, Chemical calculations, Computational chemistry |
UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Physics and Astronomy |
URI: | https://discovery.ucl.ac.uk/id/eprint/10080653 |
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