This demo shows the effect of using a more sophisticated model of nucleotide exchange and of including Sst2 in the simulation.
The more-sophisticated model of the nucleotide exchange reaction does not just "swap-out" GTP for GDP in Gpa1. Rather, the conformational change in the receptor complex just causes the relative binding strengths of Gpa1 for GTP and GDP to change. Then separate nucleotide binding and unbinding reactions must do the swap.
Sst2 acts to assist the reversion of the GTP-bound form of Gpa1 back to its GDP-bound state. This reaction that "assists" the hydrolysis reaction carried out by Gpa1 itself requires a special reaction generator of its own, delivered in the nucleotide exchange module.
Neither of these improvements makes a substantial qualitative difference in the simulation. But note that, unlike the version of the receptor complex using the simpler form of nucleotide exchange, one does see some difference between the four-one-GDP trace and the four-one-total trace: there is now some Gpa1 that is bound to neither GTP nor GDP.
Here is the mix of complexes containing Gpa1-GTP and Gpa1-GDP; it is different from the corresponding plot with the simplified nucleotide-exchange reaction in that there is now some Gpa1 that is bound to neither GTP nor GDP.
