Calculations of the structure and spectra of the putative transient peroxide intermediates of peroxidases

Gilda H. Loew, Danni L. Harris, Michel Dupuis

Research output: Contribution to journalArticle

6 Citations (Scopus)

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 with the heme iron has been proposed as a key intermediate in this reaction, this intermediate is too transient to have thus far been definitively characterized. While electronic spectra attributed to it have been observed, in the absence of any addition information, it is not possible from these reported spectra alone to identify the transient species that give rise to them. Results of previous molecular dynamic (MD) simulations of a peroxide complex with cytochrome C peroxidase (CCP) indicated that peroxide does indeed form a stable complex with the heme unit and binds in a nonsymmetric end-on mode in which the oxygen atoms systematically exchange places as ligands for the heme iron. To further assess this mode of binding, ab initio quantum chemical methods have been used to determine the optimized geometry and stability of a peroxide complex with a model heme peroxidase. The results obtained provide confirmation of the important characteristics of this transient intermediate found in the previous MD simulations. Specifically, two equivalent stable minima were identified with a binding energy of about 10 kcal mole-1 in which the peroxide binds in an end-on mode with alternative oxygen atoms as the Fe ligand and a small energy barrier between them. To further explore evidence for this species, the semiempirical INDO/ROHF/CI quantum chemical method has been used to calculate its electronic spectra and the results were compared with the observed spectra for the transient species of horse radish peroxidase and a mutant of it. Comparison of the calculated spectra of the neutral (HOOH) and anionic (OOH-) form of the peroxide intermediate with the two experimental data, indicated that both had been observed, the anionic form in the wild type and the neutral form in the mutant horse radish peroxidase. Thus, these calculations, by providing the missing correspondence between species and spectra, have allowed the identification of the transient intermediate species in the pathway from the resting state to Compound I of peroxidases as the long proposed peroxide intermediate.

Original languageEnglish
Pages (from-to)497-505
Number of pages9
JournalJournal of Molecular Structure: THEOCHEM
Volume398-399
Publication statusPublished - Jun 30 1997

Fingerprint

Peroxidases
Peroxides
peroxides
Heme
Peroxidase
Raphanus
horses
Molecular Dynamics Simulation
electronic spectra
Molecular dynamics
oxygen atoms
Iron
Ligands
Cytochrome-c Peroxidase
Oxygen
molecular dynamics
Hemeproteins
iron
Reaction intermediates
Atoms

Keywords

  • Ab initio optimized structure
  • INDO calculated spectra
  • Peroxide-peroxidase heme complexes

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computational Theory and Mathematics
  • Atomic and Molecular Physics, and Optics

Cite this

Calculations of the structure and spectra of the putative transient peroxide intermediates of peroxidases. / Loew, Gilda H.; Harris, Danni L.; Dupuis, Michel.

In: Journal of Molecular Structure: THEOCHEM, Vol. 398-399, 30.06.1997, p. 497-505.

Research output: Contribution to journalArticle

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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 with the heme iron has been proposed as a key intermediate in this reaction, this intermediate is too transient to have thus far been definitively characterized. While electronic spectra attributed to it have been observed, in the absence of any addition information, it is not possible from these reported spectra alone to identify the transient species that give rise to them. Results of previous molecular dynamic (MD) simulations of a peroxide complex with cytochrome C peroxidase (CCP) indicated that peroxide does indeed form a stable complex with the heme unit and binds in a nonsymmetric end-on mode in which the oxygen atoms systematically exchange places as ligands for the heme iron. To further assess this mode of binding, ab initio quantum chemical methods have been used to determine the optimized geometry and stability of a peroxide complex with a model heme peroxidase. The results obtained provide confirmation of the important characteristics of this transient intermediate found in the previous MD simulations. Specifically, two equivalent stable minima were identified with a binding energy of about 10 kcal mole-1 in which the peroxide binds in an end-on mode with alternative oxygen atoms as the Fe ligand and a small energy barrier between them. To further explore evidence for this species, the semiempirical INDO/ROHF/CI quantum chemical method has been used to calculate its electronic spectra and the results were compared with the observed spectra for the transient species of horse radish peroxidase and a mutant of it. Comparison of the calculated spectra of the neutral (HOOH) and anionic (OOH-) form of the peroxide intermediate with the two experimental data, indicated that both had been observed, the anionic form in the wild type and the neutral form in the mutant horse radish peroxidase. Thus, these calculations, by providing the missing correspondence between species and spectra, have allowed the identification of the transient intermediate species in the pathway from the resting state to Compound I of peroxidases as the long proposed peroxide intermediate.",
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