Haiman2020 - Pyruvate Kinase Regulatory Model of Erythrocyte Glycolysis

Dynamic model utilizing mass action kinetics to elucidate network-level effects of allosteric regulation in erythrocyte metabolism. The pyruvate kinase regulatory model includes the glycolytic pathway, the Rapaport Leubering (R.L.) Shunt, hemoglobin-oxygen binding, and elementary reaction steps to represent the enzymatic mechanisms for Pyruvate Kinase (PYK). To demonstrate the sampling and ensemble handling capabilities of MASSpy, an eensemble modeling approach is utilized to assess the dynamics of pyruvate kinase regulation. For the ensemble modeling feature demonstration, a range of parameter sets are generated through Markov-chain Monte Carlo (MCMC) sampling to represent the biological variability across the ensemble of models. Transient dynamic behavior and model steady states are studied through dynamic simulation and analysis. All models associated with the ensemble-modeling example are found in the GitHub repository at (https://github.com/SBRG/MASSpy-publication), including iPython notebooks to construct all model variations presented in the publication.