Imported:YPM/Model Process page for 2008 01 24 15h08m33s (Receptor/G protein model)

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This model was extracted on 2008/01/24. The full model documentation is available here (a zip file of the documentation is also available). The unmodified bngl file is available here.

In order to limit the scope of the model, we removed the following reaction sections from the model file:


We also removed all reactions and declarations related to Dig1, Dig2, Far1, Fus3, Kss1, Msg5, Ptp, Ste11, Ste12, Ste20 Ste50 and Ste7.

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

Because the model no longer included Fus3, we simplified Sst2 degradation to include only constitutive degradation (not Fus3-mediated degradation.

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.

We selected only one observable, the amount of Ste5 associated with Ste4 (i.e., membrane associated Ste5): begin observables

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) \
end observables