Prediction of Reorganization Free Energies for Biological Electron Transfer: A Comparative Study of Ru-Modified Cytochromes and a 4-Helix Bundle Protein

Abstract

The acceleration of electron transfer (ET) rates in redox proteins relative to aqueous solutes can be attributed to the protein's ability to reduce the nuclear response or reorganization upon ET, while maintaining sufficiently high electronic coupling. Quantitative predictions of reorganization free energy remain a challenge, both experimentally and computationally. Using density functional calculations and molecular dynamics simulation with an electronically polarizable force field, we report reorganization free energies for intraprotein ET in four heme-containing ET proteins that differ in their protein fold, hydrophilicity, and solvent accessibility of the electron-accepting group. The reorganization free energies for ET from the heme cofactors of cytochrome c and b(5) to solvent exposed Ru-complexes docked to histidine residues at the surface of these proteins fall within a narrow range of 1.2-1.3 eV. Reorganization free energy is significantly lowered in a designed 4-helix bundle protein where both redox active cofactors are protected from the solvent. For all ET reactions investigated, the major components of reorganization are the solvent and the protein, with the solvent contributing close to or more than 50% of the total. In three out of four proteins, the protein reorganization free energy can be viewed as a collective effect including many residues, each of which contributing a small fraction. These results have important implications for the design of artificial electron transport proteins. They suggest that reorganization free energy may in general not be effectively controlled by single point mutations, but to a large extent by the degree of solvent exposure of the ionizable cofactors.

Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases

“…It is often assumed or observed that the solvent dominates the outer-sphere RE, 15,18 although this not the case for all proteins. 105 In our case, for which there is no change in the net charge of the protein, the solvent contribution to the RE is rather small. Many residues contribute to the protein term, all providing rather small contributions.…”

“…Our simulations show that this is a reasonable assumption, as can be seen in Figure 6. The parameters  and  Finally, the reorganisation energy can also be calculated directly from  2 2RT , 15,105 which gives 124 and 114 kJ/mol for the OR and RO simulations, respectively. Some further understanding of the RE can be obtained by dividing the results from Eqn.…”

“…Similar effects have been observed for other proteins. 105 To check the accuracy of the fixed ESP-charge model of the QM systems, we also tested to calculate the RE by EE. The results of those calculations are also collected in Table 6.…”

Electron flow in multiheme bacterial cytochromes is a balancing act between heme electronic interaction and redox potentials

“…The classical MD simulations were carried out with the the AMBER03 protein force field (36) together with the TIP3P water model (37). Force field parameters for the heme cofactors were taken from earlier work (32,38,39).…”

The relationship between redox enzyme activity and electrochemical potential—cellular and mechanistic implications from protein film electrochemistry

“…But QM/MM approaches that model intramolecular electron transfer in a manner that parallels Marcus theory may prove valuable in moving to this goal. [71][72][73] …”