Structure of a Model Transient Peroxide Intermediate of Peroxidases by ab Initio Methods

Abstract

Peroxidases are oxidative metabolizing heme proteins that require hydrogen peroxide to be transformed to the catalytically active, compound I, species from the ferric resting state. Although a peroxide complex has been proposed as a key intermediate in this reaction, this intermediate is too transient to have thus far been definitively characterized. Results of previous molecular dynamics (MD) simulations of a peroxide complex with cytochrome C peroxidase (CCP) indicated that peroxide forms a stable complex and binds in a nonsymmetric, end-on mode in which the oxygen atoms systematically exchange places as ligands for the iron. These results provided support for a plausible pathway from the peroxide complex to compound I, involving the participation of nearby histidine and arginine residues. To further explore the reliability of this bonding description, we report here, for the first time, the use of ab initio methods to determine the optimized geometry and stability of a peroxide complex with a model heme peroxidase. Two stable minima were identified, with binding energies of 9.7 kcal/mol. In both of these complexes, the peroxide binds in an end-on mode but with alternative oxygen atoms as the Fe ligand. No minimum corresponding to a bridged structure could be found. The two end-on minima are connected by a low-energy ridge. These results provide confirmation of three mechanistically important characteristics found in the previous 300 K MD simulations of a peroxidase−HOOH complex: (i) formation of a stable peroxide complex, (ii) binding of peroxide in an asymmetric end-on mode, and (iii) dynamic interchange between the oxygen atoms that bind to the Fe, implying a small energy barrier between them.