Superoxide dismutases (SOD) are vital enzymes for disproportionation of superoxide molecules in mammals. Despite the high similarity between the Mn-SOD and Fe-SOD, they are inactive if the metals in the active sites are exchanged. Here, we use DFT, QM/MM and Monte Carlo sampling to optimize the crystal structure and to calculate the mid-point potential for the native and substituted Mn/Fe-SOD. The optimized DFT and QM/MM structures of the Mn-SOD show a major conformational change for the conserved TYR34 compared to the X-ray structure. These changes reduce the distance between TYR34 and Mn ion to 2.59 Å, which yields a lower reduction potential for the Mn. On contrary, there is no significant difference between optimized and crystal structures in the Fe-SOD. The calculated E m values starting from the DFT structures of the active sites show similar pattern, in good agreement with those observed experimentally. However, the calculated E m values starting with the QM/MM structures that include the whole protein are significantly higher due to the desolvation penalty. In addition, the pK a values for the water ligand in the reduced state Mn(II) and Fe(II) were calculated. The water pK a in Mn-SOD is higher than that in Fe-SOD by 3.5 pH units, which is similar to the shift measured experimentally. Finally, we investigated the role of HIS30 and the effect of its protonation state on the E m values.
Keywords: DFT; Midpoint potential; Monte Carlo; QM/MM; Superoxide dismutase.