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Team:UPO-Sevilla/Project/Improving Flip Flop/Modeling/Introduction
From 2011.igem.org
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<h2>Introduction</h2> | <h2>Introduction</h2> | ||
| - | <p> | + | <p>We have also modeled the improving flip-flop. This models is an extension of the <a href="/Team:UPO-Sevilla/Project/Basic_Flip_Flop/Modeling/Basic_Bistable">Basic Flip-Flop model</a>. The main reactions at that model were:.</p> |
| - | <p> | + | <p><strong>TRANSCRIPTION:</strong> <i>RNAp + Promoter → RNAp + Promoter + mRNA</i></p> |
| - | <p> | + | <p>The mRNA production is described using Michaelis-Menten kinetics.</p> |
| - | <p> | + | <p><strong>TRANSLATION:</strong><i> mRNA + Ribosomes → mRNA + Ribosomes + Repressor</i></p> |
| - | <p> | + | <p>The Repressor production is also modeled using Michaelis-Menten kinetics.</p> |
| - | + | <p><strong>REPRESSION:</strong> <i>Promoter + n · Repressor → Promoter_Repressor<sub>n</sub></i></p> | |
| - | + | ||
| - | <p><strong>REPRESSION:</strong> Promoter + n · Repressor → Promoter_Repressor<sub>n</sub></p> | + | |
<p>Finally we use a Hill kinetics model for the transcription inhibition, which offers an approximation to the cooperative action.</p> | <p>Finally we use a Hill kinetics model for the transcription inhibition, which offers an approximation to the cooperative action.</p> | ||
| - | <p> | + | <p>In the new model, we have to include the new reactions involved in the Improving Flip-Flop. These are:</p> |
| - | <p><strong>PROTEOLYSIS: </strong> Protease + Repressor 1 → Protease</p> | + | <p><strong>PROTEOLYSIS: </strong> <i>Protease + Repressor 1 → Protease</i></p> |
<p>We will consider a mass action rate law, where the protein will be digested according to the protease concentration.</p> | <p>We will consider a mass action rate law, where the protein will be digested according to the protease concentration.</p> | ||
| - | <p><strong>IHNIBITION of TRANSLATION: </strong> asRNA + mRNA → RNA complex</p> | + | <p><strong>IHNIBITION of TRANSLATION: </strong><i> asRNA + mRNA → RNA complex</i></p> |
<p>We assume a mass action rate law again. | <p>We assume a mass action rate law again. | ||
</p> | </p> | ||
| - | + | ||
<h2>Diagram</h2> | <h2>Diagram</h2> | ||
| + | |||
| + | <p>These two new effects may enhance the robustness of the toggle switch. We will analyze their effects by implementing the model in Simbiology. The following diagram shows all the species and reactions of the model:</p> | ||
<div class="center"> | <div class="center"> | ||
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<p>Here we can see all the species involved in the new model for the bistable.</p> | <p>Here we can see all the species involved in the new model for the bistable.</p> | ||
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| + | <p>The model can be downloaded here:</p> | ||
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| + | <a href="https://static.igem.org/mediawiki/2011/a/a1/Improved_Bistable.sbproj.zip" title="Improving Flip-Flop"><img style="margin: 0em 0em 1em 0em" class="imgcenter" width="200px" src="https://static.igem.org/mediawiki/2011/9/97/UPOSevillaDownloadIcon.png" title="Download Improving Flip-Flop"></a> | ||
| + | |||
| + | <p>In the <a href="/Team:UPO-Sevilla/Project/Improving_Flip_Flop/Modeling/Equations">next section</a>, we describe in detail the equations of the model</p> | ||
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</div> | </div> | ||
Revision as of 15:07, 21 September 2011
Modeling
Introduction
We have also modeled the improving flip-flop. This models is an extension of the Basic Flip-Flop model. The main reactions at that model were:.
TRANSCRIPTION: RNAp + Promoter → RNAp + Promoter + mRNA
The mRNA production is described using Michaelis-Menten kinetics.
TRANSLATION: mRNA + Ribosomes → mRNA + Ribosomes + Repressor
The Repressor production is also modeled using Michaelis-Menten kinetics.
REPRESSION: Promoter + n · Repressor → Promoter_Repressorn
Finally we use a Hill kinetics model for the transcription inhibition, which offers an approximation to the cooperative action.
In the new model, we have to include the new reactions involved in the Improving Flip-Flop. These are:
PROTEOLYSIS: Protease + Repressor 1 → Protease
We will consider a mass action rate law, where the protein will be digested according to the protease concentration.
IHNIBITION of TRANSLATION: asRNA + mRNA → RNA complex
We assume a mass action rate law again.
Diagram
These two new effects may enhance the robustness of the toggle switch. We will analyze their effects by implementing the model in Simbiology. The following diagram shows all the species and reactions of the model:
Here we can see all the species involved in the new model for the bistable.
The model can be downloaded here:
In the next section, we describe in detail the equations of the model
Sponsors
