Protein contributions to redox potentials of homologous rubredoxins: an energy minimization study.
The energetic contributions of the protein to the redox potential in an iron-sulfur protein are studied via energy minimization, comparing homologous rubredoxins from Clostridium pasteurianum, Desulfovibrio gigas, Desulfovibrio vulgaris, and Pyrococcus furiosus. The reduction reaction was divided into 1) the change in the redox site charge without allowing the protein to respond and 2) the relaxation of the protein in response to the new charge state, focusing on the latter. The energy minimizations predict structural relaxation near the redox site that agrees well with that in crystal structures of oxidized and reduced P. furiosus rubredoxin, but underpredicts it far from the redox site. However, the relaxation energies from the energy-minimized structures agree well with those from the crystal structures, because the polar groups near the redox site are the main determinants and the charged groups are all located at the surface and thus are screened dielectrically. Relaxation energies are necessary for good agreement with experimentally observed differences in reduction energies between C. pasteurianum and the other three rubredoxins. Overall, the relaxation energy is large (over 500 mV) from both the energy-minimized and the crystal structures. In addition, the range in the relaxation energy for the different rubredoxins is large (300 mV), because even though the structural perturbations of the polar groups are small, they are very near the redox site. Thus the relaxation energy is an important factor to consider in reduction energetics.
Swartz
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Department of Biochemistry and Biophysics, Washington State University, Pullman 99164-4660, USA.
Ichiye
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D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D055592:Biophysical Phenomena; D001703:Biophysics; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D012416:Rubredoxins / Q000737:chemistry*; D016415:Sequence Alignment; D013816:Thermodynamics
D001426:Bacterial Proteins; D012416:Rubredoxins