Computational study of redox active centres of blue copper proteins: a computational DFT study
Matěj Pavelka, Jaroslav V. Burda · Molecular Physics · 2008
Active sites of blue copper proteins in both reduced and oxidized states were studied at the Density Functional Theory (DFT) level. Two families of these redox sites were examined: the Type A centres with methionine ligand as fourth residue and the Type B with glutamine residue. Constrained and full optimizations were performed on the protein data bank structures in vacuo and in implicit solvent model simulating protein and water environments. It was found that the redox sites do not possess optimum geometries regardless of the oxidation state. The axial Cu-ligand bond elongates/shortens in the fully optimized Cu(I)/Cu(II) complexes. The reduced centres have a tendency to decrease the coordination number, while a trend to form four ‘equivalent’ bonds is preferred in the oxidized centres. Comparison of the full and constrained optimizations also revealed that the A centres exhibit lower relaxation energies. In the constrained structures, a higher ionization potential was predicted for the A centres when compared with the B centres regardless of the influence of environment. The calculated relative difference of the redox potentials between various A and B centres is in good agreement with the experimental data. In the fully optimized complexes, the redox properties are dependent on the environment but usually higher IP for the B centres is predicted. Partial charges, MOs, and spin density distributions (obtained by natural population analysis) were analysed together with calculated electron paramagnetic resonance (EPR) spectra for deeper understanding of the results obtained.