Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: Changes in structure and electrostatic potential duringredox reactions

Abstract

Molecular dynamics simulations of Clostridium pasteurianum rubredoxin in the oxidized and reduced forms have been performed. Good agreement between both forms and crystal data has been obtained (rms deviation of backbone atoms of 1.06 and 1.42 A, respectively), which was due in part to the use of explicit solvent and counterions. The reduced form exhibits an unexpected structural change: the redox site becomes much more solvent-accessible, so that water enters a channel between the surface and the site, but with little actual structural rearrangement (the rms deviation of backbone atoms between the oxidized and reduced is 0.77 A). The increase in solvent accessibility is also seen, although to a much lesser extent, between the oxidized and reduced crystal structures of Pyrococcus furiosus rubredoxin, but no high resolution crystal or nuclear magnetic resonance solution data exist for reduced C. pasteurianum rubredoxin. The electrostatic potential at the iron site and fluctuations in the potential, which contribute to both the redox and electron transfer properties, have also been evaluated for both the oxidized and the reduced simulations. These results show that the backbone plays a significant role (62-70 kcal/mol/e) and the polar side chains contribute relatively little (0-4 kcal/mol/e) to the absolute electrostatic potential at the iron of rubredoxin for both forms. However, both groups contribute significantly to the change in redox state by becoming more polarized and more densely packed around the redox site upon reduction. Furthermore, these results show that the solvent becomes much more polarized in the reduced form than in the oxidized form, even excluding the penetrating water. Finally, the simulation indicates that the contribution of the charged side chains to the electrostatic potential is largely canceled by that of the counterions.

The de novo design of a rubredoxin‐like fe site

“…Indeed, one of the factors that may attribute to the stability of the Fe(II1) center is that the protein matrix shields the center from solvent. In the crystal structure of the oxidized form of rubredoxin from C. pasteurianum (Watenpaugh et al, 1979(Watenpaugh et al, , 1980Yelle et al, 1995), the nearest water molecule is 7.1 8, from the metal center, and only two waters molecules are within 8 A. Furthermore, the crystal structure of rubredoxin from Pyrococcus furiosus also reveals that the Fe(II1) center is inaccessible to solvent.…”

Mutation of the surface valine residues 8 and 44 in the rubredoxin from Clostridium pasteurianum : solvent access versus structural changes as determinants of reversible potential

“…A pseudo-twofold axis is perpendicular to the page, passing though the Fe atom term for iron-sulfur proteins [5][6][7][8]. Quantitative estimates of the Fe III -S covalency in three Rds and in a model anion, [Fe{o-C 6 H 4 (CH 2 S) 2 } 2 ] -, have been made from the intensities of sulfur K-edge X-ray absorption spectra [9].…”

“…Possible access of solvent water to the iron site in Rd Cp has been examined theoretically [6,7]. As part of that work, it was predicted that conversion of V44 to A in Rd Cp would shift the reversible potential by c40 mV, bringing it close to that of the protein from Desulfovibrio gigas which features A in the equivalent position.…”

“…Consequently, increased solvent accessibility should induce a positive shift in potential. Of course, significant changes in protein structure near the active site may also impose an environment of higher polarity [6][7][8].…”

“…Ichiye and co-workers [6,7] and Scott and co-workers [13] have drawn attention to two classes of Rd proteins from bacterial sources. The potentials of class I (Chlorobium limicola f. sp.…”