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Simulate Biological Variability of the Yeast G Protein Cycle Using the Wild-Type and Mutant Strains

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 apply a variant to a model that contains a parameter value for a G protein cycle in a wild-type strain. The variant represents a parameter value for a G protein cycle in a mutant strain. Thus, when you simulate the model without applying the variant, you see results for the wild type strain, and when you simulate the model with the variant, you see results for the mutant strain.

About the Variant Created in This Example

The value of the parameter kGd is 0.11 for the wild-type strain and 0.004 for the mutant strain. To represent the mutant strain, store an alternate value of 0.004 for the kGd parameter in a variant. Then apply this variant when simulating the model.

For information on variants, see Variant 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.

Applying an Alternate Parameter Value Using a Variant

  1. Add a variant to the m1 model object:

    v1 = addvariant(m1, 'mutant_strain');
  2. Add content to the variant object v1. Specifically, add a parameter kGd with a value of 0.004:

    addcontent(v1, {'parameter', 'kGd', 'Value', 0.004});

Simulating the Model With and Without the Variant

  1. Simulate the model of the wild-type strain, that is by not applying the variant:

    [t,x,names] = sbiosimulate(m1);
    
  2. Plot the results of the wild-type strain (no variant):

    plot(t,x)
    legend(names)
    xlabel('Time'); ylabel('Amount'); title('Wild Type')

  3. Simulate the model of the mutant strain by applying the variant:

    [t,x,names] = sbiosimulate(m1, v1);
  4. Plot the results of the mutant strain (variant):

    figure; plot(t,x)
    legend(names)
    xlabel('Time'); ylabel('Amount'); title('Mutant')

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