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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:
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 |
Simulations
The following figure shows the typical evolution of the output of the system (the generated chemoattractant) againts the inputs (the wall cells ligand and the FecA-PrhA components on the outer membrane)
https://static.igem.org/mediawiki/2010/9/9f/UPOSimulation.png
Analysis
Sensibility
Simbiology allows to compute the sensibility of the system against the different parameters.
The following figure
This analysis is referred to the steady-state of the system. Some parameters do not affect the final steady-state number of molecules, but on the other hand affects the velocity of the system in the transition. This can be seen in the following
Temporal evolution
Sponsors
