Kinetic model of Central Metabolism

A kinetic model of glycolysis with serine activation is constructed from the literature data .

Description of the model

Schematic diagram of the model is given here. The dotted line represents activation(+) or inhibition(-) and the dashed arrow indicate Pentose Phosphate Pathway reactions not included in the model. Click on a reaction to have more information

Reactions

Details of the abbreviations for this model is listed here. Reactions of the model are listed below.

Glucose Transporter Hexokinase Pentose Phosphate Pathway Phosphoglucomutase UDPG-pyrophosphorylase Glycogen synthase Glycogen phosphorylase Hexose-6-phosphate isomerase Transketolase Phosphofructokinase type 1 Fructose 1,6 bisphosphate aldolase Adenylate kinase Dehydrogenase Triosephosphate isomerase Glyceraldehyde-3-phosphate dehydrogenase

3-phosphoglycerate kinase Phosphoglycerate dehydrogenase Phosphoserine amino-transferase Phosphoserine phosphatase 3-phosphoglycerate mutase Enolase Pyruvate kinase ATPase Lactate dehydrogenase Monocarboxylate (Lactate) transporter Mitocondrial pyruvate metabolism Glycine hydroxymethyltransferase Serine out Glycine out Nucleosid diphosphate kinase Pyrophosphate phosphohydrolase

Initial concentration of the metabolites can be found here

Model File

The SBML file of the model can be found [[[File:Baker_cancer_uncertainty.xml]|here]].

Notes

Necessary observation during model building and simulation is noted here.

Global parameters

The Vmax value in the paper "Modeling cancer glycolysis" is given in $U \times \text{(mg total cellular protein)}^{-1}$ unit . To homogenize the units it is then converted back to $\frac{mM}{min}$ by multiplying $U \times \text{(mg total cellular protein)}^{-1}$ with 65 as the HeLa cell was incubated in $65 \frac{\text{mg protein}}{\text{mL cell volume}}$.