Identifying residues that cause pH-dependent reduction potentials

Abstract

The pH dependence of the reduction potential E° for a metalloprotein indicates that the protonation state of at least one residue near the redox site changes and may be important for its activity. The responsible residue is usually identified by site-specific mutagenesis, which may be time-consuming. Here, the titration of E° for Chromatium vinosum high-potential iron-sulfur protein is predicted to be in good agreement with experiment using density functional theory and Poisson-Boltzmann calculations if only the sole histidine undergoes changes in protonation. The implementation of this approach into CHARMMing, a user-friendly web-based portal, allows users to identify residues in other proteins causing similar pH dependence.

Figure 1

Ribbon drawing of Chromatium vinosum high-potential iron-sulfur protein, with the redox site and histi-dine in ball-and-stick.

Figure 2

pH dependence of the predicted (solid line), experimental data (solid circles), and best-fit to experiment (dashed line) reduction potentials of wt HiPIP (blue) and its H42Q (red) mutant.

Figure 3

Predicted with the pK_a of H42 equal to 6.3 (blue line), 4 (black line), and 7 (green dot-dashed) and experimental data (blue circles) for the reduction potential of wt HiPIP.