This repository contains mathematical models, model analysis scripts, biochemical data, and data analysis scrips, all relating to the manuscript entitled "Co-substrate pools can constrain and regulate pathway fluxes in cell metabolism".
In this work, we modelled metabolic pathways (i.e. enzyme reaction pathways) to analyse the effect of co-substrate cycling on reaction and pathway fluxes. Part of this analysis was done analytically, solving systems equations, while part of it was done through simulation of pathway dynamics. The analytical study is mostly given in the supplemental text to the manuscript (available on ). The simulation part is exemplified in two python scripts provided here.
To support the model findings on co-substrate pools acting as a possible limitation on reaction fluxes, we analysed measured and FBA-derived flux data collated previously. Specifcially, we used data on enzyme kinetics and levels as collated (and based on the BRENDA database) and proteomics-based measurements. When comparing flux levels against co-substrate pool sizes, we used the matching, measured pool-sizes. All the data used in this analysis is provided here, along with scripts for plotting and data analysis.
Enjoy!