ETHZ/Parameters
From 2007.igem.org
(→Model Parameters) |
(→Model Parameters) |
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| Ref. [2] | | Ref. [2] | ||
| | | | ||
| - | | K<sub> | + | | K<sub>IPTG</sub> |
| 1.3 [µM] | | 1.3 [µM] | ||
| IPTG-lacI repressor dissociation constant | | IPTG-lacI repressor dissociation constant | ||
| Ref. [2] | | Ref. [2] | ||
|- | |- | ||
| - | | K<sub> | + | | K<sub>tetR</sub> |
| 179 [pM] | | 179 [pM] | ||
| tetR repressor dissociation constant | | tetR repressor dissociation constant | ||
| Ref. [1] | | Ref. [1] | ||
| | | | ||
| - | | K<sub> | + | | K<sub>aTc</sub> |
| 893 [pM] | | 893 [pM] | ||
| aTc-tetR repressor dissociation constant | | aTc-tetR repressor dissociation constant | ||
| Ref. [1] | | Ref. [1] | ||
|- | |- | ||
| - | | K<sub> | + | | K<sub>luxR</sub> |
| 55 - 520 [nM] | | 55 - 520 [nM] | ||
| luxR activator dissociation constant | | luxR activator dissociation constant | ||
| Ref: [6] | | Ref: [6] | ||
| | | | ||
| - | | K<sub> | + | | K<sub>AHL</sub> |
| 0.09 - 1 [µM] | | 0.09 - 1 [µM] | ||
| AHL-luxR activator dissociation constant | | AHL-luxR activator dissociation constant | ||
| Ref: [6] | | Ref: [6] | ||
|- | |- | ||
| - | | K<sub> | + | | K<sub>cI</sub> |
| | | | ||
* 8 [pM] | * 8 [pM] | ||
| Line 157: | Line 157: | ||
* starting with values of Ref. [6] and using Ref. [3] | * starting with values of Ref. [6] and using Ref. [3] | ||
| | | | ||
| - | | K<sub> | + | | K<sub>p22cII</sub> |
| 0.577 [µM] | | 0.577 [µM] | ||
| p22cII repressor dissociation constant | | p22cII repressor dissociation constant | ||
| Line 172: | Line 172: | ||
| | | | ||
|- | |- | ||
| - | | n<sub> | + | | n<sub>lacI</sub> |
| 1 | | 1 | ||
| lacI repressor Hill cooperativity | | lacI repressor Hill cooperativity | ||
| Ref. [5] | | Ref. [5] | ||
| | | | ||
| - | | n<sub> | + | | n<sub>IPTG</sub> |
| 2 | | 2 | ||
| IPTG-lacI repressor Hill cooperativity | | IPTG-lacI repressor Hill cooperativity | ||
| Ref. [5] | | Ref. [5] | ||
|- | |- | ||
| - | | n<sub> | + | | n<sub>tetR</sub> |
| 3 | | 3 | ||
| tetR repressor Hill cooperativity | | tetR repressor Hill cooperativity | ||
| Ref. [3] | | Ref. [3] | ||
| | | | ||
| - | | n<sub> | + | | n<sub>aTc</sub> |
| 2 (1.5-2.5) | | 2 (1.5-2.5) | ||
| aTc-tetR repressor Hill cooperativity | | aTc-tetR repressor Hill cooperativity | ||
|Ref. [3] | |Ref. [3] | ||
|- | |- | ||
| - | | n<sub> | + | | n<sub>luxR</sub> |
| 2 | | 2 | ||
| luxR activator Hill cooperativity | | luxR activator Hill cooperativity | ||
| Ref: [6] | | Ref: [6] | ||
| | | | ||
| - | | n<sub> | + | | n<sub>AHL</sub> |
| 1 | | 1 | ||
| AHL-luxR activator Hill cooperativity | | AHL-luxR activator Hill cooperativity | ||
| Ref. [3] | | Ref. [3] | ||
|- | |- | ||
| - | | n<sub> | + | | n<sub>cI</sub> |
| 2 | | 2 | ||
| cI repressor Hill cooperativity | | cI repressor Hill cooperativity | ||
| Ref. [12] | | Ref. [12] | ||
| | | | ||
| - | | n<sub> | + | | n<sub>p22cII</sub> |
| 4 | | 4 | ||
| p22cII repressor Hill cooperativity | | p22cII repressor Hill cooperativity | ||
Revision as of 12:32, 13 October 2007
Introduction
blabla
Model Parameters
| Parameter | Value | Description | Comments | Parameter | Value | Description | Comments | |
|---|---|---|---|---|---|---|---|---|
| c1max | 0.01 [mM/h] | max. transcription rate of constitutive promoter (per gene) | promoter no. J23105; Estimate | c2max | 0.01 [mM/h] | max. transcription rate of luxR-activated promoter (per gene) | Estimate | |
| lhi | 25 | high-copy plasmid number | Estimate | llo | 5 | low-copy plasmid number | Estimate | |
| a | 1% | basic production levels | Estimate | |||||
| Degradation constants | ||||||||
| dlacI | 2.31e-3 [per sec] | degradation of lacI | Ref. [10] | dtetR | 1e-5 [pro sec]/2.31e-3 [per sec] | degradation of tetR |
Ref. [9] Ref. [10] | |
| dluxR | 1e-3 - 1e-4 [per sec] | degradation of luxR | Ref: [6] | |||||
| dcI | 7e-4 [per sec] | degradation of cI | Ref. [7] | dp22cII | degradation of p22cII | |||
| dYFP | 6.3e-3 [per min] | degradation of YFP | suppl. mat. to Ref. [8] corresponding to a half life of 110min | dGFP | 6.3e-3 [per min] | degradation of GFP | in analogy to YFP | |
| dRFP | 6.3e-3 [per min] | degradation of RFP | in analogy to YFP | dCFP | 6.3e-3 [per min] | degradation of CFP | in analogy to YFP | |
| Dissociation constants | ||||||||
| KlacI | 0.1 - 1 [pM] | lacI repressor dissociation constant | Ref. [2] | KIPTG | 1.3 [µM] | IPTG-lacI repressor dissociation constant | Ref. [2] | |
| KtetR | 179 [pM] | tetR repressor dissociation constant | Ref. [1] | KaTc | 893 [pM] | aTc-tetR repressor dissociation constant | Ref. [1] | |
| KluxR | 55 - 520 [nM] | luxR activator dissociation constant | Ref: [6] | KAHL | 0.09 - 1 [µM] | AHL-luxR activator dissociation constant | Ref: [6] | |
| KcI |
| cI repressor dissociation constant |
| Kp22cII | 0.577 [µM] | p22cII repressor dissociation constant | Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match? | |
| Hill cooperativity | ||||||||
| nlacI | 1 | lacI repressor Hill cooperativity | Ref. [5] | nIPTG | 2 | IPTG-lacI repressor Hill cooperativity | Ref. [5] | |
| ntetR | 3 | tetR repressor Hill cooperativity | Ref. [3] | naTc | 2 (1.5-2.5) | aTc-tetR repressor Hill cooperativity | Ref. [3] | |
| nluxR | 2 | luxR activator Hill cooperativity | Ref: [6] | nAHL | 1 | AHL-luxR activator Hill cooperativity | Ref. [3] | |
| ncI | 2 | cI repressor Hill cooperativity | Ref. [12] | np22cII | 4 | p22cII repressor Hill cooperativity | Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match? |
References
[http://www.pnas.org/cgi/content/abstract/104/8/2643 [1] Weber W et al.] "A synthetic time-delay circuit in mammalian cells and mice", P Natl Acad Sci USA 104(8):2643-2648, 2007
[http://www.pnas.org/cgi/content/full/100/13/7702?ck=nck [2] Setty Y et al.] "Detailed map of a cis-regulatory input function", P Natl Acad Sci USA 100(13):7702-7707, 2003
[http://ieeexplore.ieee.org/iel5/9711/30654/01416417.pdf [3] Braun D et al.] "Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005
[http://www.nature.com/nature/journal/v435/n7038/suppinfo/nature03508.html [4] Fung E et al.] "A synthetic gene--metabolic oscillator", Nature 435:118-122, 2005 (supplementary material)
[http://dx.doi.org/10.1016/j.jbiotec.2005.08.030 [5] Iadevaia S and Mantzais NV] "Genetic network driven control of PHBV copolymer composition", J Biotechnol 122(1):99-121, 2006
[http://dx.doi.org/10.1016/j.biosystems.2005.04.006 [6] Goryachev AB et al.] "Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004
[http://www.genetics.org/cgi/content/abstract/149/4/1633 [7] Arkin A et al.] "Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-Infected Escherichia coli cells", Genetics 149: 1633-1648, 1998
[http://download.cell.com/supplementarydata/cell/107/6/739/DC1/index.htm [8] Colman-Lerner A et al.] "Yeast Cbk1 and Mob2 Activate Daughter-Specific Genetic Programs to Induce Asymmetric Cell Fates", Cell 107(6): 739-750, 2001 (supplementary material)
[http://www.nature.com/nature/journal/v405/n6786/abs/405590a0.html [9] Becskei A and Serrano L] "Engineering stability in gene networks by autoregulation", Nature 405: 590-593, 2000
[http://www.biophysj.org/cgi/content/full/89/6/3873?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=89&firstpage=3873&resourcetype=HWCIT [10] Tuttle et al.] "Model-Driven Designs of an Oscillating Gene Network", Biophys J 89(6):3873-3883, 2005
[http://www.pnas.org/cgi/reprint/99/2/679 [11] McMillen LM et al.] "Synchronizing genetic relaxation oscillators by intercell signaling", P Natl Acad Sci USA 99(2):679-684, 2002
[http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html [12] Basu S et al.] "A synthetic multicellular system for programmed pattern formation", Nature 434:1130-1134, 2005
