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Team:Grenoble/Modeling/Amplification/Sensitivity
From 2012.igem.org
Classic Odes Parameters
| Parameter Name | Value | Unit | Source |
|---|---|---|---|
| AraC synthesis rate vmAraC | 12*10-8 | mol.L-1.min-1 | Yes [1] and explanation 1 |
| Ca synthesis rate vmAraC | 2*10-9 | mol.L-1.min-1 | No, explanation 2 |
| AraC threshold KAraC | 0.3*10-6 | mol.L-1 | No, explanation 3 |
| Ca threshold KCa (for (CRP-cAMP) activation) | 0.6*10-6 | mol.L-1 | No, explanation 3 |
| Ca threshold K'Ca (for AraC* activation) | 0.6*10-6 | mol.L-1 | No, explanation 3 |
| Dissociation constant of cAMP and CRP Kc | 10-5 | mol.L-1 | Yes [2] |
| Dissociation of arabinose with AraC Kc1 | 2*10-13 | mol.L-1 | Yes [3] |
| Degradation rate of AraC αAraC | 6*10-3 | min-1 | Yes [1] |
| Degradation rate of Ca αCa | 6*10-3 | min-1 | No, explanation 4 |
| Degradation/exports rate of cAMP αcAMP | 2.1 | min-1 | Yes [4] |
| Arabinose concentration | 10-6 | mol.L-1 | Chosen by the team |
Explanation 1
- Arac and Ca:
where
Avogadro number and
is E. coli volume. Thus, we have 
. Then, we get the value of 
.
For the adenylate cyclase, but we assumed that there is less adenylate cyclase in the cell than Arac. Indeed, when there is too much cAMP is inhibits the production of the adenylate cyclase (see reference [6]).
- CRP:
Explanation 2
We don’t know the value of the synthesis rate of adenylate cyclase, but we assume that there is less adenylate cyclase, because if there is a huge amont of adenylate cyclase, there will too much cAMP, and then cAMP will repress the adenylate cyclase production (see reference [6]). For the basal production, we make the same assumption as for Arac.Explanation 3
- Activations by (CRP-cAMP):
when [cAMP] increases. Thus, in this case we could be sure that the concentration of (CRP-cAMP) wouldn’t exceed 10-6 mol/L.
In addition, when [cAMP]≤10-6 mol/L, we also know that because of the value of [CRP], [(CRP-cAMP)] wouldn’t exceed this threshold.
- Activation by Arac*:
Explanation 4
Inspired from Arac. By discussing with the biologists we concluded that Ca is also a stable protein.Explanation 5
By discussing with the biologists, we assumed that there is around 10 times more cAMP out of the cell than inside the cell.Explanation 6
In the reference [6], we have kcat=100 min-1 in vitro. However, by discussing with the biologists, we assumed that in vivo this value was higher.
Quorum sensing parameters
Explanation 1
We assumed that they wouldn’t be glued together, but not too far at the same time.Explanation 2
We work above the threshold, because we want to know the speed of the diffusion when we have a detection.References
- [1] Bionumbers. http://bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=arac&org=
- [2] Purification of and properties of the cyclic adenosine 2' ,5'-monophosphate receptor which mediates cyclic adenosine 3',5'-monophosphate dependent gene transcription in E. Coli. W.B. Aderson, A. B. Schneider, M. Emmer, R.L. Perlman, and I. Pasta
- [3] AraC protein, regulation of the L-arabinose operon inEscherichiacoli, and the light switch mechanism of AraC action. Robert Schleif Biology Department, Johns Hopkins University, Baltimore, MD, USA.
- [4] Epstein et Hesse 1975.
- [5] Transcriptional regulation shapes the organization of genes on bacterial chromosomes.Sarath Chandra Janga, Heladia Salgado, Augustino Martinez. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699516/
- [6] Regulation of adenylate cyclase in E. coli. Edith Gstrein-Reider and Manfred Schweiger, Institut fur Biochemie (nat. Fak.), UniversitAt Innsbruck, A-6020 Innsbruck, Austria.
- [7] Purification and characterization of adenylate cyclase from E. coli K12. Yang and Epstein 1983.
- [8] Solubility and diffusion coefficient of adenosine 3’ :5’ – monophosphate. Martin Dworkin and Kenneth H. Keller, 1976.
