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Team:UPO-Sevilla/Modeling/Signaling
From 2010.igem.org
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| - | + | For the level of detail considered, the main parts simulated are the following (the number correspond to the equations listed in the table in the next section): | |
</p> | </p> | ||
<ol> | <ol> | ||
| - | <li> | + | <li> Generation of L_aspartate induced by AAL</li> |
| + | <li> Diffusion of L_aspartate through the cell wall</li> | ||
| + | <li> Transcription of the aspA, promoted by FecI_a (active)</li> | ||
| + | <li> Translation of aspA</li> | ||
| + | <li> Activation of FecI, induced by the activation of FecR</li> | ||
<li> Activation of FecR induced by FecA-PrhA </li> | <li> Activation of FecR induced by FecA-PrhA </li> | ||
| - | <li> | + | <li> Plant cell wall lingand, FecA-PrhA binding</li> |
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| - | The reaction equations, and the reactions rates associated are summarized in the following table: | + | The reaction equations for the previous parts, and the reactions rates associated, are summarized in the following table: |
</p> | </p> | ||
Revision as of 10:39, 26 October 2010
The signaling circuit
The signaling circuit 3 described in the Circuit Section has been modeled using Matlab Simbiology desktop. The following diagram shows the different parts of the model we have simulated:
For the level of detail considered, the main parts simulated are the following (the number correspond to the equations listed in the table in the next section):
- Generation of L_aspartate induced by AAL
- Diffusion of L_aspartate through the cell wall
- Transcription of the aspA, promoted by FecI_a (active)
- Translation of aspA
- Activation of FecI, induced by the activation of FecR
- Activation of FecR induced by FecA-PrhA
- Plant cell wall lingand, FecA-PrhA binding
Reactions
The reaction equations for the previous parts, and the reactions rates associated, are summarized in the following table:
| # | Reaction | ReactionRate | Active |
|---|---|---|---|
| 1 | ecoli.ammonia + ecoli.fumarate + ecoli.AAL <-> ecoli.L_aspartate + ecoli.AAL | k1*ecoli.ammonia*ecoli.fumarate*ecoli.AAL - k2*ecoli.L_aspartate*ecoli.AAL | true |
| 2 | ecoli.L_aspartate <-> medium.L_aspartate | kWallDiffusion*ecoli.L_aspartate - kWallDiffusionBack*medium.L_aspartate | true |
| 3 | ecoli.DNAaspA + ecoli.FecI_a -> ecoli.ARNm_aspA + ecoli.DNAaspA + ecoli.FecI_a | kTranscript*ecoli.DNAaspA*ecoli.FecI_a | true |
| 4 | ecoli.ARNm_aspA -> ecoli.AAL + ecoli.ARNm_aspA | kTranslation*ecoli.ARNm_aspA | true |
| 5 | ecoli.FecR_a + ecoli.FecI <-> ecoli.FecI_a + ecoli.FecR_a | kFecIActivation*ecoli.FecR_a*ecoli.FecI - kFecIDeactivation*ecoli.FecI_a*ecoli.FecR_a | true |
| 6 | ecoli.FecR + ecoli.[ligand:FecA-PrhA] <-> ecoli.FecR_a + ecoli.[ligand:FecA-PrhA] | kFecRActivation*ecoli.FecR*ecoli.[ligand:FecA-PrhA] - kFecRDeactivation*ecoli.FecR_a*ecoli.[ligand:FecA-PrhA] | true |
| 7 | plant_cell_wall.ligand + ecoli.[FecA-PrhA] <-> ecoli.[ligand:FecA-PrhA] | kCellBinding*plant_cell_wall.ligand*ecoli.[FecA-PrhA] - kCellUnbinding*ecoli.[ligand:FecA-PrhA] | true |
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