Superoxide Dismutase Catalytic Reaction Mechanism

In view of the importance of scavenging free radicals from the organism, superoxide dismutases have attented a worldwide interest. Specially, the unique structural feature of the nickel superoxide dismutase has attracted great interest to many scientists since the structure was characterized recently. In recent years, many theoretical and experimental studies on the reaction catalyzed by superoxide dismutases have been reported.Although the EPR, XAS spectroscopic and theoretical investigations of superoxide dismutases have reported, the mechanism of catalysis and of electron transfer still are unresolved completely. The density functional theory is employed to investigate the disproportionation of superoxide radical anions and electron transfer by CuZnSOD and NiSOD in this paper.The main results are as follows:The disproportionation of superoxide radical anions catalyzed by copper-zinc superoxide dismutase was investigated in detail using density functional theory. The structures of each stationary point and the transition states were located so that the reaction pathways were determined. The results indicate that the reactions proceed by two steps both for the oxidized process of superoxide radical anion and the reduced one. The catalytic process of the reaction begins from the nucleophilic attack of O₂^·- on Cu2+ in the active site forming a complex. Secondly, the radical O₂^·- is bonded to the central copper ion and the group of His61 is dissociated from the active site via a transition state. Finally, the imidazolate bridge broken in the former step is reformed and the oxygen molecule is released.The reaction (2) involves CuZnSOD with the superoxide radical anion in the reductive reaction. The reaction steps are similar to the reaction (1). The difference between reactoin (1) and (2) is that the Cu- NεHis61 bond is intact during the reaction (2). The electron on copper has delocalized to the oxygen to form a stable hydrogen peroxide so that the electron transfer is achieved. The catalyzer CuZnSOD keeps unchanged during the whole catalyzing process.The Gibbs free energy curves of the whole reaction solvents are gained. As for as the relative free energies are concerned, the barriers of the reacton in diethyl ether were lower than that in water solvent and gas phase. The solvation effect on the reaction was also discussed and the electrostatic contribution was the main part of the total solvation energy. We also calculated the rate for the control step of the half-reaction (2) is 2.7×109 M^-1s^-1 in diethyl ether (6.0×1010 M^-1s^-1 for water). It follows that our calculated result is in very good agreement with the experimental value (2.0×109 M^-1s^-1 ).The disproportionation of superoxide radical anions catalyzed by nickel superoxide dismutase was investigated in detail using density functional theory. The structures of each stationary point and the transition states were located so that the reaction pathways were determined. The results indicated that the reactions proceeded by two steps both for the oxidized process of superoxide radical anion and the reduced one. In the first half-reaction, the first catalytic process of the reaction begins from the nucleophilic attack of O2·- on Ni3+ in the active site forming a complex. Secondly, the radical O2·- is bonded to the central nickel ion and the group of His1 is dissociated from the nickel ion via a transition state and this step is basically in concert. Finally, the imidazolate is broken in the reductive NiSOD and the oxygen molecule is released.In the second half-reaction, the Ni2+-SOD was oxidated by the superoxide radical anion by electron transfer at first. Then the superoxide radical anion accepted an proton and formed a stable hydrogen peroxide. At last, the imidazolate broken in the former step is reformed and the hydrogen peroxide is released.The hydrogen bond was considered in the reactive process and the barriers were reduced by intramolecular hydrogen bond in the whole reaction. The hydrogen-bonding interaction was strong between the (Arg)-H and (Cys)-O. The hydrogen-bonding interaction was also strong between the (Glu17)-CO2- and (His1)N-H units. We believe that the hydrogen bond energy is one of the main parts of the total energy. Electron transfer was explain by natural bond orbital (NBO) analysis. It confirmed that the electron transfer occured the inner-sphere between the subtrate and the nickel ion in the whole redox reaction. In addition, the singlet-triplet energy gap was also discussed. The spin contamination may be result in the inaccuracy of the singlet-triplet energy gapΔunr,ST from unrestricted calculations. The triplet energies were lower than singlet energies, so the triplet states were more stable than singlet states for state 1-3 invovled in the first half-reaction.