Protein Control of Electron Transfer Rates via Polarization: Molecular Dynamics Studies of Rubredoxin

Abstract

The protein matrix of an electron transfer protein creates an electrostatic environment for its redox site, which influences its electron transfer properties. Our studies of Fe-S proteins indicate that the protein is highly polarized around the redox site. Here, measures of deviations of the environmental electrostatic potential from a simple linear dielectric polarization response to the magnitude of the charge are proposed. In addition, a decomposition of the potential is proposed here to describe the apparent deviations from linearity, in which it is divided into a "permanent" component that is independent of the redox site charge and a dielectric component that linearly responds or polarizes to the charge. The nonlinearity measures and the decomposition were calculated for Clostridium pasteurianum rubredoxin from molecular dynamics simulations. The potential in rubredoxin is greater than expected from linear response theory, which implies it is a better electron acceptor than a redox site analog in a solvent with a dielectric constant equivalent to that of the protein. In addition, the potential in rubredoxin is described well by a permanent potential plus a linear response component. This permanent potential allows the protein matrix to create a favorable driving force with a low activation barrier for accepting electrons. The results here also suggest that the reduction potential of rubredoxin is determined mainly by the backbone and not the side chains, and that the redox site charge of rubredoxin may help to direct its folding.

Factors influencing protein tyrosine nitration—structure-based predictive models

“…For the latter descriptor, no clear trends are observed in vivo (Figure 3A), although nitration is slightly favored for tyrosines when distance_to_backbone is greater than 5 Å (50 % nitrated), where they are more exposed, more accessible to nitrating species and better able to participate in protein-protein interactions. Somewhat more clear is that in vitro nitration (Figure 3B) is favored for tyrosines where distance_to_backbone is under 4 Å (57 % nitrated), which is consistent with a mechanistic role for charge transfer reactions [66,67], as might be expected for chemically-induced nitration.…”

Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition

“…The bond and angle force constants were obtained from resonance Raman spectra (29), the partial charges from density functional calculations (30), and the angles and dihedrals from those used in the refinement of the crystal structure (10). Other ferredoxin simulation studies have used the force constants from similar sources (31,32).…”

Dielectric relaxation in proteins: the computational perspective

“…One other study focused on deviations from LR in the protein rubredoxin (Dolan et al 2004). The deviations were found in a state very far from the protein's normal, functional state: they corresponded to a hypothetical zeroing of the protein's charges.…”