Combined QM/MM and Monte Carlo study for redox leveling in Mn and Fe superoxide dismutase

Abstract

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.