Team:ETH Zurich/Modeling/Switch Circuit

From 2008.igem.org

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Revision as of 15:57, 27 October 2008

Contents

Switch Circuit

Detailed Model

diffusion of IPTG

60

diffusion of tet

Diffusion tet.JPG

binding of tetR to LacI-promotor and LacIIs-promotor

Binding tetR to LacI.JPG

binding of LacI and LacIIs to GFP-promotor

Binding LacIIs to Pgfp.JPG
Binding LacI to Pgfp.JPG

binding of tet to tetR

Binding tet to tetR.JPG

binding of IPTG to LacI

Binding IPTG to LacI.JPG

transcription and translation of LacI

Transcription of LacI.JPG
Translation of LacI.JPG

transcription and translation of LacIIs

Transcription of LacIIs.JPG
Translation of LacIIs.JPG

transcription and translation of tetR

Transcription of tetR.JPG
Translation of tetR.JPG

transcription and translation of GFP

Transcription of gfp.JPG
Translation of gfp.JPG

dimerization of tetR

Dimerization of tetR.JPG

dimerization and tetramerization of LacI and LacIIs

Dimerization of LacI.JPG
Dimerization of LacIIs.JPG
Tetramerization of LacI.JPG
Tetramerization of LacIIs.JPG

Implementation

The model of the switch circuit has been implemented using the Simbiology Toolbox in MATLAB.

For the sake of simplicity, the effects of dimerization and dimerization/tetramerization of tetR and LacI/LacIIs have been neglected. So we did with the additional steps involving the RNApolymerase in the transcription of proteins and the ribosomes in the translation of proteins.

diagram view of the model

Simulation

Results and Discussion

Parameters

In this section you can find all the parameters used in the simulation.

The table's caption
# Parameter name Value Reference
1 k_assoc(IPTG_LacI) 5.0 X
2 k_tr(LacIs) 2.0 X
3 k_tr(LacI) 2.0 X
4 k_tr(gfp) 2.0 X
5 k_tl(tetR) Cell 2 X
6 4 Cell 2 X
7 4 Cell 2 X
8 4 Cell 2 X
9 4 Cell 2 X
10 4 Cell 2 X
11 4 Cell 2 X
12 4 Cell 2 X
13 4 Cell 2 X
14 4 Cell 2 X
15 4 Cell 2 X
16 4 Cell 2 X
17 4 Cell 2 X
18 4 Cell 2 X
19 4 Cell 2 X
20 4 Cell 2 X
21 4 Cell 2 X
22 4 Cell 2 X
23 4 Cell 2 X
24 4 Cell 2 X
25 4 Cell 2 X
26 4 Cell 2 X
27 4 Cell 2 X
28 4 Cell 2 X
29 4 Cell 2 X
30 4 Cell 2 X
31 4 Cell 2 X
32 4 Cell 2 X
33 4 Cell 2 X
34 4 Cell 2 X
35 4 Cell 2 X
36 4 Cell 2 X
37 4 Cell 2 X
38 4 Cell 2 X
39 4 Cell 2 X

References

Retrieved from "http://2008.igem.org/Team:ETH_Zurich/Modeling/Switch_Circuit"