Team:Grenoble/Modeling/Signaling
From 2012.igem.org
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Once the dipeptide molecule is fixed to the TAP receptor, it activates the phosphorylation of OmpR.</br> OmpR* (the phosphorylated form of OmpR) is the transcription factor that activates the gene expression of cya. | Once the dipeptide molecule is fixed to the TAP receptor, it activates the phosphorylation of OmpR.</br> OmpR* (the phosphorylated form of OmpR) is the transcription factor that activates the gene expression of cya. | ||
</br> | </br> | ||
- | If you need further details about the receptor design, you can check the | + | If you need further details about the receptor design, you can check the network section <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#10"> here</a>. |
</br> | </br> | ||
</br> | </br> |
Revision as of 07:09, 25 September 2012
Overview
The design of signaling module is given by the figure below:ODEs
Let’s begin by considering the cya gene activation by the transcription factor OmpR*. As it is a gene activation, the transcription rate is usually modelized by a hill function:Parameters
Here is the link to the parameters of the amplification module we sometimes refer to.Constants | Value | Derivation |
---|---|---|
Total quantity [OmprR]tot | 6.8*10-8mol.L-1 | The average number of OmpR molecules per cell is 80.769 ± 0.719 [2]. Knowing the cell volume (vc = 1.1*10-15L[3]) and the Avogadro number NA = 6.02*10-23mol.L-1, we deduce [OmpR]tot = 80/(NA*vc) = 6.8*10-8mol.L-1 |
Goldbeter-Koshland model constants | v = 80 L-1.min-1 V' = 7*10-8mol.L-1.min-1 K = 7*10-7mol.L-1 K' = 9*10-8mol.L-1 |
|
Hill Coefficient | n = 2 | We took a number greater than one to indicate positive cooperativity. |
References
- [1] Alejandra C.Ventura, Jacques-A. Sepulchre, Sofia D.Merajver. A Hidden Feedback in Signaling Cascades Is Revealed. PLOS Computational Biology, 2008, 4, 3, e1000041.
- [4] Michael D.Manson, Volker BlanK and Gabriele Brade. Peptide chemotaxis in E.Coli involves the Tap signal transducer and the dipeptide permease.Nature,15 May 1986,321,253-256.
- [5] Edith Gstrein-Reider and Manfred Schweiger, Institut fur Biochemie (nat. Fak.),UniversitAt Innsbruck, A-6020 Innsbruck, Austria. Regulation of adenylate cyclase in E. coli.