Influence of protein flexibility on the redox potential of rubredoxin: Energy minimization studies

Abstract

A theoretical investigation of the protein contribution to the redox potential of the iron-sulfur protein rubredoxin is presented. Structures of the oxidized and reduced forms of the protein were obtained by energy minimizing the oxidized crystal structure of Clostridium pasteurianum rubredoxin with appropriate charges and parameters. By including 102 crystal waters, structures close to the original crystal structure were obtained (rms difference of 1.16 A), even with extensive minimization, thus allowing accurate calculations of comparative energies. Our calculations indicate an energy change of about -60 kcal/mol (2.58 eV) in the protein alone upon reduction. This energy change was due to both the change in charge of the redox site and the subsequent relaxation of the protein. An energy minimization procedure for the relaxation gives rms differences between the oxidized and reduced states of about 0.2 A. The changes were small and occurred in both the backbone and sidechain mainly near the Fe-S center but contributed about -16 kcal/mol (0.69 eV) to the total protein contribution. Although the neglect of certain effects such as electronic polarization may make the relaxation energies calculated an upper limit, the results indicate that protein relaxation contributes substantially to the redox potential.