Understanding intramolecular electron transfer in ferredoxin: A molecular dynamics study

An important question about electron-transfer proteins is how the environment of the redox site created by the protein's matrix affects their electron-transfer properties. Here, we investigate intramolecular electron transfer in the [4Fe-4S] ferredoxins, which are a class of iron-sulfur electron-transfer proteins found in numerous electron transport chains, including the photosynthetic pathway. These proteins are characterized by having two [4Fe-4S] clusters, often but not always with the same reduction potential, and by the pseudo-2-fold symmetry of the protein backbone. The nuclear polarization is calculated from molecular dynamics simulations of Clostridrium acidiurici ferredoxin, with a total of 6 ns of simulation, and is then used to calculate free energy reaction curves. In addition, we present here a new method, referred to as the Gaussian parabola method, for obtaining the reaction energy DeltaGdegrees and the reorganization energy lambda from the mean and fluctuations of the polarization, which is based on the linear response of a system with Gaussian fluctuations. For ferredoxin, the calculated outer sphere lambda is small (<200 meV) and is consistent with the lack of temperature dependence in experimental measurements of rates for this protein; however, the rate calculated from the calculated lambda is consistent with experimental values if the inner sphere lambda is large. The calculations also indicate that the contribution of the protein lambda is smaller than that of the solvent, which implies that the protein enhances the rate of electron transfer by providing an environment that has a low reorganization energy.