Team:Grenoble/Modeling/Amplification/Sensitivity
From 2012.igem.org
Classic Odes Parameters
Explanation 1
- Arac and Ca:
- 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):
- 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.