An Experimentally Based Model of the Peroxidase-NADH Biochemical Oscillator: An Enzyme-Mediated Chemical switch

The development of a chemically realistic model of the peroxidase-NADH biochemical oscillator is described, characterized, and compared with experiments. The selection of each reaction and rate constant in the model is chemically justified, and derived only from studies published by others, or our own laboratory data. Peroxidase and the modifier methylene blue are included in the model, along with correct incorporation of oxygen mass transport. No dimensionless or abstract variables were employed, and no specific attempt was made to include any principle of nonlinear dynamics commonly regarded as responsible for oscillations, such as autocatalysis, autoinhibition, or delayed feedback. Eight steps form the basis of a complete oscillation in the model, beginning with species initially present in experiments, and proceeding to a process dominated by the interconversion of native peroxidase (Per³⁺) and Compound III (Cp III). Four additional steps relate directly to the conditions under which actual experiments were performed. Simulated numerical output is shown for all dynamical chemical species in a standard model. Results are similar to experimental data for oxygen, NADH, Per³⁺, and Cp III. It is demonstrated in the model that oxygen growth and decay hinge on the reactivity of the superoxide radical (O₂^•-). Two reactions operate as a chemical switch where Cp III serves as a regulatory intermediate. Oxidation of Per³⁺ to Cp III by reaction with O₂^•- occurs until Per³⁺ is depleted. Superoxide disproportion then becomes rate-limiting. The reaction rate of NAD• (a radical of nicotinamide adenine dinucleotide) with oxygen decreases for a short time. This allows NAD* to begin a cascade reaction to reduce Cp III back to Per³⁺, which produces additional NAD• to rapidly consume remaining oxygen, replenish Per³⁺, and initiate a new oscillation.