Concerted simulations reveal how peroxidase compound III formation results in cellular oscillations.

ABSTRACT: A major problem in mathematical modeling of the dynamics of complex biological systems is the frequent lack of knowledge of kinetic parameters. Here, we apply Brownian dynamics simulations, based on protein three-dimensional structures, to estimate a previously undetermined kinetic parameter, which is then used in biochemical network simulations. The peroxidase-oxidase reaction involves many elementary steps and displays oscillatory dynamics important for immune response. Brownian dynamics simulations were performed for three different peroxidases to estimate the rate constant for one of the elementary steps crucial for oscillations in the peroxidase-oxidase reaction, the association of superoxide with peroxidase. Computed second-order rate constants agree well with available experimental

SUBMITTER: Gabdoulline RR 

PROVIDER: S-EPMC1303318 | biostudies-literature | 2003 Sep

REPOSITORIES: biostudies-literature