Metabolic Modeling

Computer modeling of metabolic kinetics

 

This page collects models of components/pathways of mammalian central metabolism for potential combination into large-scale models. The emphasis of this collection is in energy metabolism in muscle, including models of glycolysis/glycogenolysis, beta-oxidation, the tricarboxylic acid cycle, mitochondrial transporters, and oxidative phosphorylation. These models are constructed using the Matlab-based Biochemical Simulation Environment (BISEN) for modular construction of metabolic systems models. Using this environment, these models may be easily combined together. 

Glycolysis/glycogenolysis

The Vinnakota et al. (PMID:16617075) model includes the oxidation of glycogen to pyruvate and lactate. It also includes ATP hydrolysis, as well as the adenylate and creatine kinase reactions. (The model works well for resting conditions for skeletal muscle, but requires some structure changes to effectively simulate exercise conditions.)

Oxidative phosphorylation

The Bazil et al. 2016 model (PMID: 26910433) includes the components of the respiratory chain (Complex I, III, & IV) the F1F0 ATPase, ANT, and phosphate transporter, as well as K+/H+ exchange. The model also accounts for ROS production at Complexes I and III. The model is parameterized against data from rat cardiac mitochondria.

Tricarboxylic acid cycle

The Dasika et al. model includes pyruvate dehydrogenase and the enzymes of the TCA cycle, as well as the mono-, di-, and tricarboxylate exchangers. (The model is integrated with the Bazil et al. model of oxidative phosphorylation.)