Now, we will define how the ligated receptor recruits the G protein complex. Start by double-clicking the Ligand.Receptor complex species in the list on the left.

Click 'New' under 'Relations' and select 'Create/Edit Association'.

On the Association page, double-click the complex species consisting of Galpha and Gbetagamma to select it as a binding partner for the ligated receptor. Note that we are specifying here that only the Ligand-bound Receptor can bind to the complex consisting of both molecules, Galpha and Gbetagamma. So, even though the interaction is between the Receptor and Galpha, the association requires the involvement of the two bimolecular complexes. Situations such as this are the reason why associations are defined at the complex level in Simmune, as opposed to the molecule level.

Now, to specify that the receptor only recruits the on-activated Galpha.Gbetagamma complex (with Galpha in the GDP state) please set the GTP feature on Galpha to 'off'.

Draw a line between the intracellular binding site of the receptor and the free site on Galpha. Confirm the creation of a new binding site interaction.

Define the result complex.

Set the association rate (1.0e4) and (optionally) a name for the association. Note that this on-rate is quite low, compared to the other rates we defined so far. The reason is that it - implicitly - takes into account that the reaction partners have to diffuse within the membrane to find each other. And since both partners are sizeable complexes, this diffusion-limited association will be rather slow (more precisely: will happen rather infrequently). Click 'Save'.

...and go back to the complex page with the properties of the ligated receptor.

The file "G_protein_5.8.dbf" represents the model as it should be at this stage of the tutorial.

Click 'Clear' to obtain an empty complex page.

We have specified how the ligated receptor recruits the G protein complex. To define how the receptor releases the Galpha again, we don't want to just invert the association and define a release of Galpha.Gbetagamma from the receptor because this would only apply to exactly this complex structure: The ligated receptor bound to the Galpha.Gbetagamma. A complex that had lost its Ligand or Gbetagamma would not be covered and would (without additional dissociation specifications covering it) not decay.

We will therefore define the dissociation of Galpha from the Receptor and do this in a way that ensures that the specification applies as well to larger complexes containing these two molecules.

First, we have to build the Galpha.Receptor complex species. Click 'New' under 'Complexes' on the left.

This will allow you to sequentially add the molecules that will build the complex species.

First, double-click the Receptor molecule...

...and flip it to make its binding sites face to the right.

Then, double-click the Galpha molecule to make it appear alongside the receptor.

Bring the two molecules together with the appropriate binding sites. Note that the Modeler accepted the binding of the binding sites without prompting you for a confirmation with regard to the creation of a new interaction. The reason is that we already defined the interaction possibility between the involved binding sites when specifying the association between the ligated receptor and the G (alpha-betagamma) protein complex.

Create a dissociation for the Galpha.Receptor complex species.

Break the binding between the Receptor and Galpha.

The dissociation rate will depend on the state of Galpha since the receptor will recruit Galpha in its GDP state and quickly release Galpha(GTP). To first define the fast release of Galpha(GTP), set the GTP feature of Galpha in the Galpha.Receptor complex to 'on', define a fast off-rate (10 per second) and (optionally) a name for the dissociation. Click 'Save' (important!!).

Next, to define the longer life-span of the Galpha(GDP state).Receptor complex set the GTP feature of Galpha in the Galpha.Receptor complex to 'off', define a slower off-rate (0.01 per second) and click 'Save'.

Make sure to specify this as a new dissociation since you would otherwise overwrite the previous one.

Go back to the complex page (currently showing the Galpha.Receptor species).

The file "G_protein_5.19.dbf" represents the model as it should be at this stage of the tutorial.