Theoretical Study on Redox Potential Control of Iron-Sulfur Cluster by Hydrogen Bonds: A Possibility of Redox Potential Programming

Abstract

The effect of hydrogen bonds around the active site of Anabaena [2Fe-2S] ferredoxin (Fd) on a vertical ionization potential of the reduced state (IP(red)) is examined based on the density functional theory (DFT) calculations. The results indicate that a single hydrogen bond increases the relative stability of the reduced state, and shifts IP(red) to a reductive side by 0.31–0.33 eV, regardless of the attached sulfur atoms. In addition, the IP(red) value can be changed by the number of hydrogen bonds around the active site. The results also suggest that the redox potential of [2Fe-2S] Fd is controlled by the number of hydrogen bonds because IP(red) is considered to be a major factor in the redox potential. Furthermore, there is a possibility that the redox potentials of artificial iron-sulfur clusters can be finely controlled by the number of the hydrogen bonds attached to the sulfur atoms of the cluster.

Characterization of the Geometrical and Electronic Structures of the Active Site and Its Effects on the Surrounding Environment in Reduced High-Potential Iron–Sulfur Proteins Investigated by the Density Functional Theory Approach

“…Note that it is generally difficult to discuss the contribution only to hydrogen bonding because the electrostatic potential of the surrounding amino acids also affects the S atomic charges. However, previous work has considered that the hydrogen bonding affects the S atomic charges in Fe–S clusters. , Thus, the hydrogen bonding of the [4Fe–4S] cluster with sulfur is expected to control the interactions taking place within the cluster. Previous DFT calculations of the model [4Fe–4S] complexes showed that the difference of 0.1–0.2 Å in the Fe–S distance and the existence or nonexistence of hydrogen bonds affect their spin states .…”

Characterization of Methyl- and Acetyl-Ni Intermediates in Acetyl CoA Synthase Formed during Anaerobic CO2 and CO Fixation

“…With the possibility of spin delocalization ruled out, broken symmetry (BS) DFT calculations on the low-spin as well as a high-spin (triplet) calculation were performed using a ∼300 atom model (Figure S7) of the Ni p (II)–Me species, A Me ( 4′ ) (Figure e–g and Tables S5–S7) to better understand the potential electronic configurations and structures in question. DFT and TD-DFT have been successfully employed in prior investigations to describe the electronic and geometric structures of ACS and other biological Fe–S clusters. ,− Both BS-low-spin and high-spin ground states converged to approximately square planar geometries. The low-spin configuration was lower in energy (∼8.8 kcal mol –1 ) and showed better agreement with the experimental data.…”

Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic Aromatoleum aromaticum EbN1 T

“…A. aromaticum EbN1 T has a small number of enzymes using FAD as a cosubstrate. Instead, it uses ferredoxin (13 enzymes) with its wide range of redox potentials ( 55 ), particularly in the degradation pathways of aromatic compounds. Moreover, A. aromaticum EbN1 T possesses several enzymes that transfer electrons between NAD, NADP, ferredoxin, flavodoxin, ETFs, and ubiquinol, which enable a wide flexibility of metabolic pathways.…”