(72f) Network Motifs and Mechanisms for Oscillatory Dynamics of Biochemical Networks

We formulate and examine detailed  mechanisms for a number of enzyme and  biochemical oscillatory/signalling networks with the aim of uncovering critical subnetworks that generate the excitable/bistable/oscillatory dynamics. Such core models of the specified nonlinear dynamics are often referred to as network motifs. Our method of finding the motifs is based on a theory of stability of chemical networks known as the stoichiometric network analysis. Given that the mechanism is formulated in terms of mass action kinetics, the instabilities of steady states are linked to topological features of the (sub)network diagrams.  This approach enables a classification of biochemical networks.  Based on our experimental  observations we examine in vitro enzyme reactions including  the glucose–glucose oxidase– catalase–hydrogen peroxide reaction, the urea–urease reaction and glucose–glucose oxidase–ferricyanide reactions. Topology of the core oscillatory subnetworks are compared against one another as well as against other enzyme reactions known to oscillate, such as oxidase–peroxidase reaction. We also examine some in vivo enzyme systems of biological importance including the mitogen-activated protease kinase (MAPK) and systems determining circa- and ultradian cycles in photosythesizing microbes.