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The use of eq 20 for the ionized protein model is not fully justifiable since such a continuum model is not expected to properly present this system. This reflects the fact that the contribution of the ionized groups in region 2 is compensated for by the solvent in regions 3-5. This effect is not captured by the oversimplified model of Figure 3 and eq 19. In fact, we feel that the actual distance dependence of A in a given donor-acceptor pair should be determined by realistic calculations rather than by eq 20. Moreover, most biological donor-acceptor pairs involve complementary surface charges that neutralize each other. The corresponding distance dependence is not expected to be the same as the one evaluated here for two identical cytochromes.
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4 estimated the reorganization energy by defining a reaction coordinate along the vector that connected the crystal structures of the reduced and oxidized cytochromes. Of course, the use of this effective coordinate is not identical to rigorous free energy perturbation calculations.
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62 This relatively small λ is of some relevance since in this case it was possible to estimate λ by a systematic variation of the thermodynamic driving force and since the donor and acceptor are kept at constant distance.
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