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Parameters for the EducatETH E. coli system

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	1e-5 [1/s] 2.31e-3 [1/s]	degradation of tetR	Ref. [9] Ref. [10]
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	8 [pM] 50 [nM]	cI repressor dissociation constant	Ref. [12] starting with values of Ref. [6] and using Ref. [3]		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