Rubredoxin Function: Redox Behavior from Electrostatics.

Abstract

Continuum electrostatic theory was applied to compute redox potentials of rubredoxin (Rd) proteins. We used multiple side chain conformers of Rd crystal structures, optimized geometries of salt bridges, mutated residues, and residues in the neighborhood of the iron-sulfur complex (FeS complex) self-consistently for given solvent pH and redox potential. The following contributions to Rd redox potentials are discussed: side chain conformations, H-bond geometries of the FeS complex, dielectric environment, charged residues, and salt bridges. We considered 15 different Rd's (of different species/strains and mutants) with available crystal structures whose redox potentials vary between -86 mV and +31 mV. The computed redox potentials deviated by less than 16 mV, root-mean-square deviation (RMSD), from measured values. The amide H-bond geometry is considered to be crucial for the variation of Rd redox potentials. To test this assumption, we considered 14 mutant Rd's for which we modeled the structures based on Rd from WT Clostridium pasterianum (Cp) leaving the amide H-bond geometry of the FeS complex invariant. Here, we obtained an RMSD of only 14 mV with measured values demonstrating that the amide H bond geometries cannot be a major factor determining Rd redox potentials. We analyzed the factors determining the Rd redox potentials of a mesophilic and a thermophilic Rd differing by nearly 90 mV. We found that half of the difference is due to sequence and half is due to backbone variations. Albeit salt-bridge networks vary considerably between these two Rd's and are considered to be responsible for differences in thermostability, their overall influence on Rd redox potentials is small.