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Create Model of Receptor-Ligand Kinetics

This example shows how to create and simulate a simple model of receptor-ligand kinetics using theSimBiology Model BuilderandSimBiology Model Analyzerapps.

In this model, ligandLand receptorRspecies form receptor-ligand complexes through reversible binding reactions. These reactions are defined using mass action kinetics by d C d t = k f ⋅ L ⋅ R − k r ⋅ C , wherekfandkrare forward and reverse rate constants.L,R, andCare the concentrations of the ligand, receptor, and receptor-ligand complex, respectively.

Open Model Builder App

Click theSimBiology Model Buildericon on theAppstab or entersimBiologyModelBuilderat the command line.

Build Model

  1. On theHometab of the app, selectModel>Create New Blank Model. Enterm1as the name for the model. The app creates an empty compartmentunnamedand displays the compartment on theDiagramtab.

  2. Drag and drop three species blocksand one reaction blockinto the compartment. Optionally, you can rename the species and compartment by double-clicking the default names. For instance, changeunnamedtocell.

  3. To connect the species to the reaction, press and hold theCtrlkey (on Windows®and Linux®) or theOptionkey (on macOS), click the species block, and drag the line.

  4. Click the reaction block to see its properties in theProperty Editorpane. Set the following parameters.

    • SelectReversible>true.

    • In theStatestable, update the values ofLto5andRto10. Set the units of theL,R, andCspecies tonanomole/liter.

    • Set the value of the forward rate parameterkfto0.05. Set the unit toliter/nanomole/hour.

    • Set the value of the reverse rate parameterkrto0.1with the unit1/hour.

Simulate Model

  1. On theHometab, click theModel Analyzericon to open theSimBiology Model Analyzer应用程序。

  2. In theModel Analyzerapp, selectProgram>Simulate Modelon theHometab. TheProgram1tab opens.

  3. In theSimulationstep of the program, set theStop Timeto 20 seconds because the model reaches a saturated state after that. ClickRunfrom theHometab.

  4. Running the program plots the results in thePlot1tab. The plot shows the simulated responses in different colors. The program stores the simulationresultsin theLastRunfolder of the program.

See Also

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