Tutorial

Start the Simmune Modeler.

Click "New..." in the Model menu and save the model as "Ecad". (The modeler application will add a .dbf file ending.)

View of the empty model.

Click "Molecule" on the second menu bar to switch to the Molecule Tab.

Click "New".

Click "Add Component".

Resize the component to 40x80.

Back on the Molecule main Tab click in the Molecule graph window outside of the molecule component to deselect it.

Now, you can set the properties of the molecule. Set the name to "Ecad", select "Protein" as Type, select "Membrane Associated" and "Receptor" as Category. The diffusion coefficient should take a default value of 0.01 square microns / second -- which is within the estimated range of values for E-cadherin.

Click the component to select it for editing. It should appear highlighted.Click "Add Binding Site" to add a binding site. Select the component again and add a 2nd binding site.

Select the Binding sites in the Molecule Composition tree view and assign names "Trans Interface" and "Cis Interface" to the binding sites 1 and 2.

Select the component and change the location to "Outside-membrane".

Click "Save" to save the molecule.

Click "Complex" on the second menu bar to switch to the Complex Species Tab.

Simmune automatically created a complex species "Ecad". Double click the icon to select the species for editing.

Click "New" in the Relations field to the right.

Keep "Create/Edit Complex" and click "go".

Now, the window for editing complex properties should be visible.

The state of both binding sites should be "Unbound". We will use this as the basal unbound single-molecular version of the Ecad complex species and call this complex "Ecad_unbound". Click "Save" and then "Back" to return to the Complex species window.

Repeat steps 16 to 18. Right-click on the binding sites and change their states to "Don't Care" Call this complex "Ecad_all". Click "Save" and then "Back" to return to the Complex species window.

Now, we will define reactions for Ecad: Click on "New" in the Relations field to the right and then select "Create/Edit Association (Current Complex As "Component")". Click "Go".

We will create the trans-association of Ecad.

Double-clicking the "Species: Ecad" entry on the left selects the binding partner.

Double-clicking the complex symbols in the "Complex Interaction" graph allows us to rotate the two single-molecular complexes to let them face each other with their trans binding site (this step is optional).

Now, draw a line between the two '1' labeled binding sites.

Since we had not defined this interaction at the molecular level the modeler application will prompt us to confirm the creation of a molecular level interaction which is the prerequisite for defining the specifics of a complex-complex interaction. Click "Yes" in the Confirmation Dialog.

Click "Define Result Complex Species" in the lower right corner of the window to switch to the complex species definition window showing both binding partners.

Move one of the two complexes so they make contact via binding sites "1". Type "Ecad trans-dimer" as Short Name and click "Save and Back".

The Result Complex now shows "Ecad_trans_dimer" as Species Name. We could define a descriptive (but rather long) complex name such as "Ecad_trans_dimer_cis_unbnd" or, as we do in this example, let the software set a default name by simply clicking "Save Complex".

Note

We don't have to specify explicitly that the trans binding sites are unbound before the assocation. The modeler will set the state of the involved binding sites to "Unbound" and will ensure that the source complexes are represented in the database.We can avoid cluttering the lists of complexes in the modeler with complexes that were only created to specify reaction rules by unchecking the "Display in Complex List" checkboxes in the panels that show the source and result complex properties.

Choose a name for the association (e.g. "Trans Association") and define the rate (here: 90000). Important: select "trans-binding"! Click "Save" and then "Back".

The Complex window should now look like this:

Click on "New" in the Relations field to the right and then select "Create/Edit Association (Current Complex As "Component")". Click "Go". Then double-click the Species: Ecad entry in the list on the left to select the binding partner. We want to make cis interactions depend on prior trans association so we set Binding site 1: Trans Interface to "Bound" for both, Complex 1 and Complex 2. To set the state tags double-click them in the tree view listing the molecules, the components and states, or right-click on the graphical representation of the tag.

Flip the rigth binding partner and draw a line between the binding sites '2'. Click "Yes" in the dialog. Then click "Define Result Complex Species" in the lower right corner of the window.

Move one of the binding partners to bring the complexes into contact at sites '2'. Type a Short Name, e.g. Ecad cis-dimer (optional). Click "Save and Back".

Type an Assoc Name (e.g. Cis Association) and set the rate to 9000. Important: select "cis-binding" so that this association can happen between two Ecad complexes located in the same membrane.

Save all complexes in this window and click "Save" and then "Back".

The complex window should now look like this. Now, we define intra-complex reactions that form or dissolve bonds within existing complexes.

Click Relations->New and then "Create/Edit Association".Double-click "Species: Ecad" in the left hand list of all Complexes to set a binding partner for the Ecad in the Complex Interaction graph field. Rotate both complexes to make them 'face' each other at binding site 1. Draw an interaction between the two "1" sites. The software realizes that the sites can bind to each other and sets a Result complex. For this binding to be an association within an existing complex, both partners must be bound via their 'cis' sites to other molecules on their respective membranes (otherwise they would not be able to be part of a common complex without being directly bound through their trans sites) so we can leave all State tags at "Don't care" for the binding partners. Save all complexes, then (important!!) select "trans-binding" and "Intra Complex". As a name for the association we can choose something as "Intra-Complex Trans Association". Set a rate of 100. The unit that was automatically chosen is 'per second' since this association is rather a transformation than a real association. Click "Save" and then "Back".

Similarly, we define an "Intra-Complex Cis Association". Click "Save" and then "Back".

Finally, we define the dissociations in the system. Select the Ecad trans-dimer species by double-clicking it.

Click Relations->New and then "Create/Edit Dissociation".

In the Complex to Decay field below the complex graph click "Select Complex" and click the complex being offered. Click OK.

Under "Select the Binding Site to Split" select (the only) "Binding Site Interaction 1". Click "Split".

Specify a name, e.g "Trans Dissociation", a rate (1) and click trans-binding. Click "Save" and then "Back".

Similarly, define an "Intra-Complex Trans Dissociation" -- but with the "Intra Complex" checkbox set and with a lower decay rate (0.01) reflecting the greater stability (longer lifespan) of bindings that are embedded into larger complexes.Save and then "Back.

Click "Clear" in the Complex Species window. Then, select the complex species "Ecad cis-dimer" by double-clicking "Species: Ecad cis-dimer" in the list to the left.

Click Relations->New and then "Create/Edit Dissociation", then "Go".

In the Complex to Decay field below the complex graph click "Select Complex" and select the complex with the state of the "Trans" binding sites set to "Don't Care" (denoted by a dotted outline). Click OK.

Under "Select the Binding Site to Split" select the only binding site interaction. Click "Split". Then, specify a name, e.g "Cis Dissociation", a rate (1) and click cis-binding. Click "Save" and then "Back". Similarly, define an "Intra-Complex Cis Dissociation" -- but with the "Intra Complex" checkbox set and with a lower decay rate (0.01) reflecting the greater stability (longer lifespan) of bindings that are embedded into larger complexes. Save and then "Back.

The model is ready for simulation. We could now additionally define complexes with properties we are particularly interested in, for instance a complex representing a true Trimer

Click "Clear" in the Complex Species window. Then click "New" above the list of complexes. The software will show the list of molecules that are available for complex building (just one: Ecad). Double-click the "Ecad" molecule three times. You may need to move the scroll wheel over the Complex Species graph to zoom out so you can see all three molecules.

Build a trimer by rotating, flipping and moving the molecules, bringing them into contact at the adequate binding sites. Double-click a molecule to select it for rotation/flipping. Moving the mouse over the empty space in the graph you can move the entire scene. Define a name (e.g. "Trimer") and click "Save".

Click Relation->New and then "Create/Edit Complex". Click "Go".

Now, make sure the unbound binding sites have the tag "Unbound". Set a name -- for instance "True Trimer". Click "Save" and then "Back".

To create a pattern that will represent all complexes containing trimers, Click Relation->New and then "Create/Edit Complex". Click "Go". Set the status of the unbound binding sites to "Don't care". Set a name (e.g. "All_Trimers") and click "Save and then "Back".

To see an overview of the model click "Model" on the second menu bar. You can double-click the entries to jump to the definition of a particular complex or reaction.