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Ramp function approximations of Michaelis-Menten functions in biochemical dynamical systems

In 2019, Adams, Ehlting, and Edwards developed a four-variable system of ordinary differential equations modelling phenylalanine metabolism in plants according to Michaelis-Menten kinetics. Analysis of the model suggested that when a series of reactions known as the Shikimate Ester Loop (SEL) is included, phenylalanine flux into primary metabolic pathways is prioritized over flux into secondary metabolic pathways when the availability of shikimate, a phenylalanine precursor, is low. Adams et al. called this mechanism of metabolic regulation the Precursor Shutoff Valve (PSV). Here, we attempt to simplify Adams and colleagues’ model by reducing the system to three variables and replacing the Michaelis-Menten terms with piecewise-defined approximations we call ramp functions. We examine equilibria and stability in this simplified model, and show that PSV-type regulation is still present in the version with the SEL. Then, we define a class of systems structurally similar to the simplified Adams model called biochemical ramp systems. We study the properties of the Jacobian matrices of these systems and then explore equilibria and stability in systems of n ≥ 2 variables. Finally, we make several suggestions regarding future work on biochemical ramp systems. / Graduate

Identiferoai:union.ndltd.org:uvic.ca/oai:dspace.library.uvic.ca:1828/12485
Date22 December 2020
CreatorsDore-Hall, Skye
ContributorsEdwards, Roderick
Source SetsUniversity of Victoria
LanguageEnglish, English
Detected LanguageEnglish
TypeThesis
Formatapplication/pdf
RightsAvailable to the World Wide Web

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