Structural origins of redox potentials in Fe-S proteins: electrostatic potentials of crystal structures

Abstract

Redox potentials often differ dramatically for homologous proteins that have identical redox centers. For two types of iron-sulfur proteins, the rubredoxins and the high-potential iron-sulfur proteins (HiPIPs), no structural explanations for these differences have been found. We calculated the classical electrostatic potential at the redox site using static crystal structures of four rubredoxins and four HiPIPs to identify important structural determinants of their redox potentials. The contributions from just the backbone and polar side chains are shown to explain major features of the experimental redox potentials. For instance, in the rubredoxins, the presence of Val 44 versus Ala 44 causes a backbone shift that explains a approximately 50 mV lower redox potential in one of the four rubredoxins. This result is consistent with experimental redox potentials of five additional rubredoxins with known sequence. Also, we attribute the unusually lower redox potentials of two of the HiPIPs studied to a less positive electrostatic environment around their redox sites. Finally, molecular dynamics simulations of solvent around static rubredoxin crystal structures indicate that water alone is a major factor in dampening the contribution of charged side chains, in accord with experiments showing that mutations of surface charges produce relatively little effect on redox potentials.

Rubredoxins Involved in Alkane Oxidation

“…Correlation of specific positions with the presence or absence of AlkG1-type Rds in particular alkane-degrading strains shows that the three AlkG2-type Rds from organisms that only contain AlkG2-type Rds have a valine at position 44, while all AlkG2-type Rds from organisms that also contain AlkG1-type Rds have an alanine at this position. Swartz and coworkers have found that the identity of this residue correlates with the redox potential; V44 Rds have reduction potentials that are about Ϫ50 mV while A44 Rds have values around 0 mV (38). This was substantiated by Eidsness and coworkers, who have shown that replacement of A44 by V in the P. furiosus Rd reduces the redox potential by 95 mV while the reverse replacement in the C. pasteurianum Rd results in an 86-mV increase (8).…”

Electrostatics of Proteins: Principles, Models and Applications

“…However, Warshel and coworkers have shown by using the PDLD model [116,117] that the evaluation of redox potentials must take into account the protein permanent dipoles, and the penetration of water molecules. The role of the protein permanent dipoles has been most clearly established in subsequent studies of iron-sulfur proteins [118,119]. Another interesting factor is the effect of ionized groups on redox potentials.…”

Mutation of the surface valine residues 8 and 44 in the rubredoxin from Clostridium pasteurianum : solvent access versus structural changes as determinants of reversible potential

“…A pseudo-twofold axis is perpendicular to the page, passing though the Fe atom term for iron-sulfur proteins [5][6][7][8]. Quantitative estimates of the Fe III -S covalency in three Rds and in a model anion, [Fe{o-C 6 H 4 (CH 2 S) 2 } 2 ] -, have been made from the intensities of sulfur K-edge X-ray absorption spectra [9].…”

“…Possible access of solvent water to the iron site in Rd Cp has been examined theoretically [6,7]. As part of that work, it was predicted that conversion of V44 to A in Rd Cp would shift the reversible potential by c40 mV, bringing it close to that of the protein from Desulfovibrio gigas which features A in the equivalent position.…”