This is a simulation of a larger part of the alpha pathway, including both the G-protein coupled receptor complex and the scaffolding complex, which is the site of the main part of the signal-transducing kinase cascade.
This simulation involves 34,485 species and 70,558 reactions. Because it takes somewhat longer to run than the other demos, it and the "scaffold-basal" simulations are in a separate make target; "make long" in the demo directory.
The first plot shows the main activity of the G-protein-coupled receptor complex, which is the subject of several of the other demos. This demo uses the "more sophisticated" version of the nucleotide exchange reaction involving Gpa1 and the hyrdolysis reaction of Sst2 on Gpa1, as illustrated in the the receptor-nx-sst2 demo.
One difference between this and the dedicated receptor demos is the presence of Ste20, the kinase that starts the signal-transducing kinase cascade.
In this simulation, binding between Ste4 and Gpa1 obstructs binding Ste20 as well as binding to Ste5. Hence, in the first plot, we see that the species containing a Ste4-Ste20 binding rise sharply after the introduction of alpha factor and subsequent unbinding of Gpa1 (in its GTP-bound state) from Ste4.
Ste20 is responsible for phosphorylating Ste11, the first of the kinases in the cascade that is bound to the scaffolding protein Ste5. The phosphorylation action of Ste20 on Ste11 occurs only as a unary reaction in species of complexes containing the "enabling" Ste20:Ste4:Ste5:Ste11 subcomplex. The presence of species containing this subcomplex is shown in another plot.
The profile of the nucleotide exchange reaction is more or less the same as before, except that equilibrium levels are different.
This simulation has the membrane-spanning receptor protein Ste2 bound to Ste4, rather than to Gpa1 itself, as in the "receptor-structure" demo. The nucleotide exchange reaction is therefore "enabled" by the Ste2:Ste4:Gpa1 subcomplex.
The last plot shows the kinase cascade. The initial step in the cascade is the phosphorylation of Ste11 by Ste20, which happens as a unary reaction in all species of complexes containing the subcomplex Ste20:Ste4:Ste5:Ste11, and in which Ste20 is ATP-bound and Ste11 presents an appropriate free phosphorylation site. The total population of all species containing this "enabling" subcomplex is shown by the light green "20-11-enabling" trace. It rises sharply after alpha factor is introduced at time 2.0.
Species of complexes containing Ste11 that has been activated by being phosphorylated by Ste20 is shown in the red "Ste11-p" trace.
Ste7 is the next kinase in the kinase cascade. It is activated by being phosphorylated by Ste11. This reaction happens only in complexes that contain the subcomplex Ste7:Ste5:Ste11. Complexes containing activated Ste7 are shown in the dark green "Ste7-active" trace.
Fus3 is the last kinase in the cascade. It is phosphorylated at two sites by Ste7. When fully phosphorylated, Fus3's affinity for the scaffolding protein Ste5 is reduced, and Fus3 dissociates from the scaffolding complex. The purple "active-Fus3" trace shows Fus3 that is fully phosphorylated and has already dissociated from the scaffolding complex.
Fus3 also "back-phosphorylates" Ste7 in a negative feedback. Again, this reaction happens only when Ste7 and Fus3 are both bound to Ste5. When phosphorylated by Fus3, the upstream kinase Ste7's phosphorylation of Fus3 is completely blocked. The complexes containing Ste7 that is phosphorylated at the inhibitory site targeted by Fus3 is shown in the blue "Ste7-inhib" trace.
