This demo shows the conversion of the somewhat more complex receptor demo's reaction network, consisting of 29 species and 53 reactions, into input for the simple ODE-based simulator "odie."
For this demo, the moleculizer version of the receptor demo was modified so that alpha factor is introduced at the beginning of the simulation, instead of in the middle. The present version of the simple ODE-based simulator "odie" does not have the "event" capability that would enable doing so.
The first plot shows most of the "action" in this simulation: the nucleotide exchange reaction converts Gpa1 in its GDP-bound state into the GTP-bound state, resulting in the dissociation of Gpa1 from Ste4. This dissociation can be seen in the rapid fall of the green "four-one-GTP" trace, which gives the total population of all complexes in which Ste4 is bound to Gpa1:GTP.
The dissociation of Gpa1 from Ste4 allows the binding of Ste5, the scaffold protein, to Ste4; Gpa1 and Ste5 bind Ste4 competitively. The binding of Ste5 to Ste4 can be seen in the rise of the number of complexes containing Ste4:Ste5, illustrated in the purple "four-five" trace.
The second plot illustrates part of the simplified version of the nucleotide exchange reaction in this simulation. Simplified nucleotide exchange just swaps out GDP for GTP directly, instead of modifiying the affinities of Gpa1 for the two nucleotides and waiting for nucleotide-unbinding and nucleotide-binding reactions to accomplisht the swap.
One result of this simplified approach is the strict constant sum of the GTP and GDP-bound versions of Gpa1 seen here. The unbound form never appears at all, unlike the version of this simulation with the more-complex version of nucleotide exchange.
