ETHZ/Parameters
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| - | + | To provide as realistic simulation results as possible and to find good estimates for the simulation parameters we performed an intensive literature review. However not all parameters could be found in the literature. Furthermore one has to take into account that biological parameters cannot be estimated to a very high precision. | |
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Revision as of 12:48, 13 October 2007
Overview
To provide as realistic simulation results as possible and to find good estimates for the simulation parameters we performed an intensive literature review. However not all parameters could be found in the literature. Furthermore one has to take into account that biological parameters cannot be estimated to a very high precision.
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 [1/s] | degradation of lacI | Ref. [10] | dtetR |
| degradation of tetR |
| |
| dluxR | 1e-3 - 1e-4 [1/s] | degradation of luxR | Ref: [6] | |||||
| dcI | 7e-4 [1/s] | degradation of cI | Ref. [7] | dp22cII | degradation of p22cII | |||
| dYFP | 6.3e-3 [1/min] | degradation of YFP | suppl. mat. to Ref. [8] corresponding to a half life of 110min | dGFP | 6.3e-3 [1/min] | degradation of GFP | in analogy to YFP | |
| dRFP | 6.3e-3 [1/min] | degradation of RFP | in analogy to YFP | dCFP | 6.3e-3 [1/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
