Modelling glycogen: structure, metabolism, and enzyme mechanistic

The spatio-temporal model that allows investigating the structure of glycogen in three dimensions . The model is based on a stochastic process that simulates the key enzymatic steps. The model is designed to track the position of all glucose units in time together with the activities of the enzymatic reactions. The four main reactions involved in synthesis and degradation (catalysed by Glycogen Synthase - GYS, Glycogen Branching Enzyme - GBE, Glycogen Phosphorylase – GLP - and Glycogen Debranching Enzyme - GDE) are simulated using a Gillespie algorithm. The approach of generating the structure is similar to simple polymer models, such as self-excluded random walk, with the difference that the successive monomers follow the same direction (a branch) and the randomisation takes place when generating a new branch.