Département de chimie moléculaire

Superoxide reductase is a mononuclear iron enzyme involved in superoxide radical detoxification in some bacteria. Its catalytic mechanism is assocd. with the remarkable formation of a ferric hydroperoxide (Fe3+-OOH) intermediate, which is specifically protonated on its proximal oxygen to generate the reaction product, H2O2. Here, we present a computational study of the protonation mechanism of the Fe3+-OOH intermediate, at different levels of theory. This was performed on the whole system (solvated protein) using well-tempered metadynamics at the QM/MM (B3LYP/AmberFF99SB) level. Enabled by the development of a new set of force field parameters for the active site, a conformational MM study of the Fe3+-OOH species gave insights into its solvation pattern, in addn. to generating the two starting conformations for the ab initio metadynamics setup. Two different protonation mechanisms for the Fe3+-OOH intermediate were found depending on the starting structure. Whereas a possible mechanism involves at 1st the protonation of the hydroperoxide ligand and then dissocn. of H2O2, the most probable one starts with an unexpected dissocn. of the HOO- ligand from the iron, followed by its protonation. This favored reactivity was specifically linked to the influence of both the nearby conserved Lys-48 residue and the microsolvatation on the charge distribution of the oxygens of the HOO- ligand. These data highlight the crucial role of the whole environment, solvent, and protein, to describe accurately this 2nd protonation step in superoxide reductase. This was clearly not possible with smaller models unable to reproduce correctly the mechanistically determinant charge distribution. [on SciFinder(R)]