AQUEOUS SOLVATION OF A RUBREDOXIN REDOX SITE ANALOG - A MOLECULAR-DYNAMICS SIMULATION

A molecular dynamics simulation of Fe(SCH2CH3)4-, a redox site analog of the iron-sulfur protein rubredoxin, in aqueous solution has been performed. In this simulation, an average of 2.3 water molecules are able to penetrate the tetrahedral structure of the Fe-S site at an average distance of about 3.6 angstrom from the Fe, each with a hydrogen pointing toward the Fe. Moreover, the degree of penetration is determined by the C-S-Fe-S dihedral angles, since the CH2 group can block the approach to the Fe. In addition, there are about 4.4 water molecules near each sulfur with a preference for bifurcated hydrogen bonds to the sulfur. Rubredoxin provides a similar though less polar immediate environment for the Fe in that, although it excludes water from the Fe, it has two amide nitrogens at about the same distance from the Fe as the innermost waters, and each sulfur has three nearby amides, with two of the sulfurs having one N-H...S bond each and two of the sulfurs having two N-H...S bonds each. The protein also constrains the C-S-Fe-S dihedral angles, thus determining how close a polar group can approach, and these angles are different from those of [Fe(S2-o-xyl)2]-, the best synthetic analog for the redox site. In addition, analogs with the same C-Fe-S dihedral angles as the protein appear to have a substantially different electrostatic potential at the Fe than those with the same angles as [Fe(S2-o-xyl)2]-.