Team:ETH Zurich/Modeling/Switch Circuit

From 2008.igem.org

Revision as of 17:34, 27 October 2008 by Nico (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

Switch Circuit

Detailed Model

diffusion of IPTG

diffusion of tet

binding of tetR to LacI-promotor and LacIIs-promotor

binding of LacI and LacIIs to GFP-promotor

binding of tet to tetR

binding of IPTG to LacI

transcription and translation of LacI

transcription and translation of LacIIs

transcription and translation of tetR

transcription and translation of GFP

dimerization of tetR

dimerization and tetramerization of LacI and LacIIs

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_assoc(LacI)	5.0	X
3	k_assoc(LacIs)	5.0	X
4	k_assoc(tet)	5.0	X
5	k_assoc(tetR)	5.0	X
6	k_dec(IPTG)	0.005	X
7	k_dec(IPTG_ext)	Cell 2	X
8	k_dec(LacI)	Cell 2	X
9	k_dec(LacIs)	Cell 2	X
10	k_dec(gfp)	Cell 2	X
11	k_dec(mRNA_LacI)	Cell 2	X
12	k_dec(mRNA_LacIs)	Cell 2	X
13	k_dec(mRNA_gfp)	Cell 2	X
14	k_dec(mRNA_tetR)	Cell 2	X
15	k_dec(tet)	Cell 2	X
16	k_dec(tetR)	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