Imported:YPM/Model Process page for 2008 01 24 15h08m33s (Receptor/G protein model)
In order to limit the scope of the model, we removed the following reaction sections from the model file:
We simplified Ste2 internalization, because it's not clear whether there is any benefit to modeling the interactions of the Yck proteins with Ste2. Instead, we allowed pheromone-bound Ste2 internalized at rate of 1.7e-3 (half time of 7 minutes), and free Ste2 to be internalized at a rate of 2.9e-4 (corresponding to a half-time of 40 min). We also removed the reactions and declarations related to Yck. The Ste2 internalizations were thus changed to:
Ste2(Pheromone_site) + Cell -> \ Cell \ kinternalization_Ste2 DeleteMolecules
Ste2(Pheromone_site!1).Pheromone(Ste2_site!1) -> \ Pheromone(Ste2_site) \ kinternalization_PheromoneSte2 DeleteMolecules
No reactions remained involving phosphorylation, so we removed the all Non-specific_dephosphorylation reactions.
Finally, to prevent depletion of pheromone due to binding of pheromone to the receptor, we made the pheromone concentration constant using the seed species $Pheromone(Ste2_site) Pheromone_tot_conc (the '$' means that the concentration is fixed). We did this because pheromone is extracellular, and is thus in a much larger volume that Ste2, so binding of pheromone to Ste2 should not significantly affect the concentration of free pheromone, whereas it should affect the concentration of Ste2.
Species Ste5_at_membrane Ste4(Ste5_site!1).Ste5(Ste5_site,Ste4_site!1) \ Ste4(Ste5_site!1).Ste5(Ste5_site!2,Ste4_site!1).Ste5(Ste5_site!2,Ste4_site) \ Ste4(Ste5_site!1).Ste5(Ste5_site!2,Ste4_site!1).Ste5(Ste5_site!2,Ste4_site) \ Ste4(Ste5_site!1).Ste5(Ste5_site!2,Ste4_site!1).Ste5(Ste5_site!2,Ste4_site!+) end observables