Investigation of Ion Binding in Chlorite Dismutases
by Means of Molecular Dynamics Simulations
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Abstract
Chlorite
dismutases are prokaryotic heme <i>b</i> oxidoreductases
that convert chlorite to chloride and dioxygen. It has been postulated
that during turnover hypochlorite is formed transiently, which might
be responsible for the observed irreversible inactivation of these
iron proteins. The only charged distal residue in the heme cavity
is a conserved and mobile arginine, but its role in catalysis and
inactivation is not fully understood. In the present study, the pentameric
chlorite dismutase (Cld) from the bacterium <i>Candidatus Nitrospira
defluvii</i> was probed for binding of the low spin ligand cyanide,
the substrate chlorite, and the intermediate hypochlorite. Simulations
were performed with the enzyme in the ferrous, ferric, and compound
I state. Additionally, the variant R173A was studied. We report the
parametrization for the GROMOS force field of the anions ClO<sup>–</sup>, ClO<sub>2</sub><sup>–</sup>, ClO<sub>3</sub><sup>–</sup>, and ClO<sub>4</sub><sup>–</sup> and describe spontaneous
binding, unbinding, and rebinding events of chlorite and hypochlorite,
as well as the dynamics of the conformations of Arg173 during simulations.
The findings suggest that (i) chlorite binding to ferric NdCld occurs
spontaneously and (ii) that Arg173 is important for recognition and
to impair hypochlorite leakage from the reaction sphere. The simulation
data is discussed in comparison with experimental data on catalysis
and inhibition of chlorite dismutase