Team:Grenoble/Modeling/Signaling
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<td class="column1">Activation coefficient of Cya</td> | <td class="column1">Activation coefficient of Cya</td> | ||
<td class="column2">K<span class="indice">Cya</span> = 10<span class="exposant">-7</span>mol.L<span class="exposant">-1</span></td> | <td class="column2">K<span class="indice">Cya</span> = 10<span class="exposant">-7</span>mol.L<span class="exposant">-1</span></td> | ||
- | <td class="column3">The value K<span class="indice">AC</span> was set considering the maximum value of [AC]. Indeed if we consider the steady state and assume that <i>p<span class="indice">AC</span></i> is negligible compared to the other terms we have : <img src="" alt="" /> where h stands stands for the Hill function 0<h<1. We have then : . K<span class="indice">AC</span> should be in the same range as [AC]<span class="indice">max</span> not too high otherwise the gene would never be expressed and not too low otherwise the protein is always produced. We chose K<span class="indice">Cya</span> = 10<span class="exposant">-7</span>mol.L<span class="exposant">-1</span></td> | + | <td class="column3">The value K<span class="indice">AC</span> was set considering the maximum value of [AC]. Indeed if we consider the steady state and assume that <i>p<span class="indice">AC</span></i> is negligible compared to the other terms we have : <img src="" alt="" /> where h stands stands for the Hill function 0\<h\<1. We have then : . K<span class="indice">AC</span> should be in the same range as [AC]<span class="indice">max</span> not too high otherwise the gene would never be expressed and not too low otherwise the protein is always produced. We chose K<span class="indice">Cya</span> = 10<span class="exposant">-7</span>mol.L<span class="exposant">-1</span></td> |
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Revision as of 09:14, 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 |
|
Activation coefficient of Cya | KCya = 10-7mol.L-1 | The value KAC was set considering the maximum value of [AC]. Indeed if we consider the steady state and assume that pAC is negligible compared to the other terms we have : where h stands stands for the Hill function 0\ |
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.