Create and Simulate the Yeast Heterotrimeric G Protein Cycle

Overview

About the Example Model

This example uses the model described in Model of the Yeast Heterotrimeric G Protein Cycle.

This table shows the reactions used to model the G protein cycle and the corresponding rate parameters (rate constants) for each reaction. For reversible reactions, the forward rate parameter is listed first.

No.NameReaction1Rate Parameters
1Receptor-ligand interactionL + R <-> RLkRL, kRLm
2Heterotrimeric G protein formationGd + Gbg -> GkG1
3G protein activationRL + G -> Ga + Gbg + RLkGa
4Receptor synthesis and degradationR <-> nullkRdo, kRs
5Receptor-ligand degradationRL -> nullkRD1
6G protein inactivationGa -> GdkGd
1 Legend of species: L = ligand (alpha factor), R = alpha-factor receptor, Gd = inactive G-alpha-GDP, Gbg = free levels of G-beta:G-gamma complex, G = inactive Gbg:Gd complex, Ga = active G-alpha-GTP

About the Example

This example shows how to add an event to a model to trigger a time-based change. The event modifies the amount of ligand (L), thus modeling a delay in the addition of α-factor to the cell culture.

For information on events and how they are evaluated, see Event Object.

Opening the Example Model

Load the gprotein example project, which includes the variable m1, a model object:

sbioloadproject gprotein

The m1 model object appears in the MATLAB® Workspace.

Adding an Event to the Example Model

  1. Set the InitialAmount of species L (ligand) to be 0.0 when the simulation starts:

    speciesObj = sbioselect(m1, 'Type', 'species', 'Name', 'L');
    set(speciesObj, 'InitialAmount', 0);
    
  2. Add an event to the m1 model object. Configure the event to set the amount of species L (ligand) and to trigger when the simulation time equals 100:

    evt = addevent(m1, 'time >= 100', 'L = 6.022E17');

Simulating the Model

  1. Configure the simulation settings (configset object) for the m1 model object to log all states during the simulation:

    cs = getconfigset(m1);
    set(cs.RuntimeOptions, 'StatesToLog', 'all');
    
  2. Simulate the model:

    [t,x,names] = sbiosimulate(m1);
  3. Plot the results:

    plot(t,x)
    legend(names)
    xlabel('Time'); ylabel('Amount');title('All States')

    Notice that the species L amount increases when the event triggers at simulation time 100. The plot does not show the other species in the model due to the wide range in species amounts.

  4. To see plots of the species with smaller amounts, plot all species except the 5th (species L) and 7th (species Gbg).

    figure; plot(t, x(:, [1:4 6 8]))
    legend(names{[1:4 6 8]})
    xlabel('Time'); ylabel('Amount');title('States with Small Values')

    Notice the increase in the activation of G protein (species Ga, shown in red) after ligand (species L) is added at simulation time 100.

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