Model Constraints
Contents
Initial metabolite concentration
As eicosanoid levels were not detected above the limit of detection of the LC-MS/MS in experimental studies during homeostasis, the initial concentration of metabolites was assigned as zero. However, as this results in the ODE integrating to infinity, the initial metabolite concentration was set as a negligible level (10-28 mM) which was small enough that it would not contribute towards the metabolite concentrations in response to a stimulus, but large enough that it did not crash simulations.
Enzyme concentration
In this work the enzyme concentration is assumed constant for the duration of the simulation and is assumed to be the concentration of active enzyme. The value of this constraint is sampled from the log-normal distribution based upon multiple literature values.
Compartment volumes
The generic cell volume was set as 1 pL , based on the volume of a HeLa cell (3.7 pL) (Puck, Marcus et al. 1956). The extracellular volume was set to 1 nL per cell, based on the experimental conditions where approximately 1 million cells were cultured in 10 mL of media.
Transport Parameters
| Parameters | Value |
|---|---|
| ABC ΔG (kcal/mol) | -50000 |
| R Gas constant (J K-1 mol-1) | 8.314 |
| Temperature (K) | 310 |
| ATP (mM) | 0.00274 |
| ADP (mM) | 0.00134 |
