Journal Article

Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations

Ohnishi, Yusuke, Takano, Yu, Nakayoshi, Tomoki, Kondo, Hiroko X., Tanaka, Hideaki, Kurisu, Genji

2022

Overview

“Plant-type” ferredoxins (Fds) in the thylakoid membranes of plants, algae, and cyanobacteria possess a single [2Fe-2S] cluster in active sites and mediate light-induced electron transfer from Photosystem I reaction centers to various Fd-dependent enzymes. Structural knowledge of plant-type Fds is relatively limited to static structures, and the detailed behavior of oxidized and reduced Fds has not been fully elucidated. It is important that the investigations of the effects of active-center reduction on the structures and dynamics for elucidating electron-transfer mechanisms. In this study, model systems of oxidized and reduced Fds were constructed from the high-resolution crystal structure of Chlamydomonas reinhardtii Fd1, and three 200 ns molecular dynamics simulations were performed for each system. The force field parameters of the oxidized and reduced active centers were independently obtained using quantum chemical calculations. There were no substantial differences in the global conformations of the oxidized and reduced forms. In contrast, active-center reduction affected the hydrogen-bond network and compactness of the surrounding residues, leading to the increased flexibility of the side chain of Phe61, which is essential for the interaction between Fd and the target protein. These computational results will provide insight into the electron-transfer mechanisms in the Fds.

• Publisher: MDPI AG,MDPI
• Subject: Algae / Amino acids / Crystal structure / Cyanobacteria / Cyanobacteria - metabolism / Cytochrome / Electron Transport / Ferredoxins - metabolism / Hydrogen bonds / Molecular Dynamics Simulation / Oxidation-Reduction / Plants - metabolism / Proteins / Simulation / Sulfur