Density functional and electrostatic calculations of manganese superoxide dismutase active site complexes in protein environments

Density functional and electrostatic methods have been applied to calculate active site geometries and the redox potential of manganese superoxide dis mutase (MnSOD). The initial active site clusters were built up by including only first-shell side chain ligands and then augmented by second-shell lig ands. The density functional optimized Mn-ligand bond lengths for the reduc ed complexes in general compared fairly well with protein crystallography d ata; however, large deviations for calculated Mn-OH distances were found fo r the oxidized active site clusters. Our calculations suggest that this dev iation can be attributed to the redox heterogeneity of the oxidized protein in X-ray crystallography studies. The redox potential was calculated by tr eating the protein environment and the solvent bulk by a semimacroscopic el ectrostatic model. The protein structures were taken from the Thermus therm ophilus enzyme. The calculated coupled redox potentials converge toward exp erimental values with increasing size of the active site cluster models, an d the final calculated value was +0.06 V, compared to experimental values o f +0.26 V determined for Bacillus stearothermophilus and +0.31 V in Escheri chia coli enzymes. Using an energy decomposition scheme, the effects of the second-shell ligands and the protein and reaction fields have been analyze d.