This is a demo of our earliest model of the alpha pathway g-protein-coupled receptor complex, consisting of the receptor molecule Ste2, together with the g-protein complex of Gpa1, Ste4, and Ste18.
Recall that binding of alpha factor to Ste2 causes a conformational change in the complex of Ste2, Ste4 and Gpa1 such that Gpa1 changes from its GTP-bound form into its GDP-bound form. The GDP-bound form of Gpa1 tends to dissociate from Ste4 rapidly, allowing the scaffolding protein Ste5 to bind to Ste4.
This is the most informative of the plots:
In this plot, the red "four-one-total" trace of all species containing Ste4 and Gpa1 coincides with the dark green trace labeled "four-one-GTP." In this simulation Gpa1 is always bound to either GTP or GDP. You can see by looking at the blue "four-one-GTP" trace of all species containing Ste4 and Gpa1 with Gpa1 bound to GTP, essentially none of this GTP-bound Gpa1 remains bound to Ste4; hence the coincidence of the red and dark green traces.
The interesting action happens at time 2.0, when alpha factor is introduced. The unbinding of Gpa1 from Ste4 is seen in how the dark-green trace falls at this time. The binding of Ste5 to Ste4 permitted by Gpa1's abandoning Ste4 is seen in the rise of the purple "four-five" trace of all species of complexes containing Ste4 and Ste5 bound together.
The next plot shows the overall economy of the two forms of Gpa1. This plot is interesting because of how it compares with the corresponding plot in the structurally different "receptor-structure" simulation.
