Reduction-Induced Structural and Motional Changes of Plant-Type Ferredoxin Using Molecular Dynamics and Umbrella Sampling Simulations

Plant-type ferredoxin (Fd) is a metalloprotein that contains a [2Fe–2S] cluster as its active center and plays an important role in electron transfer in photosynthesis. In this study, to investigate the effects of the redox-state conversions of Fd on its structures and motions, 5-μs long-time molecular dynamics (MD) simulations were performed on both the oxidized and reduced forms of Anabaena PCC7119 Fds. Although the overall geometrical properties of the oxidized and reduced forms were virtually identical, there were differences in local structure and motion. In particular, the C-terminal region of the reduced form was allowed to have more conformations than that of the oxidized form. Furthermore, the free-energy profile of the flip of the peptide bond linking Cys46 and Ser47 (conversion from “CO-in” to “CO-out” conformations) with the Fd reduction was obtained using 14.6-μs umbrella sampling simulation. It was estimated that the “CO-out” conformation was substantially more stable than “CO-in” conformation and that the activation free energy of the peptide-bond flip was very low. The dynamical structural information obtained in this study on plant-type Fds is expected to contribute to the elucidations of Fd functions.