Team:UPO-Sevilla/Modeling/Signaling

From 2010.igem.org

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<p>
<p>
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The main parts simulated are:
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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):
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</p>
<ol>
<ol>
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<li>Plant cell wall lingand, FecA-PrhA binding</li>
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<li> Generation of L_aspartate induced by AAL</li>
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<li> Diffusion of L_aspartate through the cell wall</li>
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<li> Transcription of the aspA, promoted by FecI_a (active)</li>
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<li> Translation of aspA</li>
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<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>
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<li> Activation of FecA, induced by the activation of FecR</li>
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<li> Plant cell wall lingand, FecA-PrhA binding</li>
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<li> Transcription of </li>
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<li> Translation of </li>
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<li>Generation of L_aspartate induced by AAL</li>
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<li>Diffusion of L_aspartate through the cell wall</li>
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The reaction equations, and the reactions rates associated are summarized in the following table:
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The reaction equations for the previous parts, and the reactions rates associated, are summarized in the following table:
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</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:

Simbiology model

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):

  1. Generation of L_aspartate induced by AAL
  2. Diffusion of L_aspartate through the cell wall
  3. Transcription of the aspA, promoted by FecI_a (active)
  4. Translation of aspA
  5. Activation of FecI, induced by the activation of FecR
  6. Activation of FecR induced by FecA-PrhA
  7. 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:

#ReactionReactionRateActive
1ecoli.ammonia + ecoli.fumarate + ecoli.AAL <-> ecoli.L_aspartate + ecoli.AALk1*ecoli.ammonia*ecoli.fumarate*ecoli.AAL - k2*ecoli.L_aspartate*ecoli.AALtrue
2ecoli.L_aspartate <-> medium.L_aspartatekWallDiffusion*ecoli.L_aspartate - kWallDiffusionBack*medium.L_aspartatetrue
3ecoli.DNAaspA + ecoli.FecI_a -> ecoli.ARNm_aspA + ecoli.DNAaspA + ecoli.FecI_akTranscript*ecoli.DNAaspA*ecoli.FecI_atrue
4ecoli.ARNm_aspA -> ecoli.AAL + ecoli.ARNm_aspAkTranslation*ecoli.ARNm_aspAtrue
5ecoli.FecR_a + ecoli.FecI <-> ecoli.FecI_a + ecoli.FecR_akFecIActivation*ecoli.FecR_a*ecoli.FecI - kFecIDeactivation*ecoli.FecI_a*ecoli.FecR_atrue
6ecoli.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
7plant_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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