Theoretical investigations of Ferredoxin I: The possible role of internal water molecules on the coupled electron proton transfer reaction

Abstract

The electron-coupled proton transfer reaction involving the [3Fe–4S] cluster in Ferredoxin I is studied by ab initio calculations and molecular dynamics simulations. The charge distributions of the [3Fe–4S] cluster are calculated with density functional theory (B3LYP) and used in the dynamics simulations. Structural differences between the oxidized and reduced clusters in the absence and presence of the protein are calculated to examine the hypothesis that an entatic state is involved in the reaction. The possible role of internal water molecules in the proton transfer process is explored. It is shown that water molecules are dynamically stable near the [3Fe–4S] cluster for tens of ps. Calculations for the native protein and a mutant D15N in which the Asp15 is replaced by a Glu15 are compared. It is found that water is less likely to escape from the region around the [3Fe–4S] cluster in the case of the D15N mutant than in the native protein. This finding could explain, in part, the lower proton transfer rate constant experimentally observed for the mutant if a water molecule were involved in transferring the proton from D15 to the [3Fe–4S] cluster.