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Team:UPO-Sevilla/Modeling/Signaling
From 2010.igem.org
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:
The main parts simulated are:
- Plant cell wall lingand, FecA-PrhA binding
- Activation of FecR induced by FecA-PrhA
- Activation of FecA, induced by the activation of FecR
- Transcription of
- Translation of
- Generation of L_aspartate induced by AAL
- Diffusion of L_aspartate through the cell wall
Reactions
The reaction equations, 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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