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Parameters for the educatETH E.coli system

In order to ensure that our simulation results match the biology as close as possible, we tried to find good estimates for the biological system parameters. To this end, we performed an extensive literature review. However, not all parameters were found in the literature, especially those which do not refer to vastly used proteins. Whenever this was the case, logical estimates were provided by our biologists based on empirical values.

Model Parameters

General parameters

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

Parameter Value Description Comments
dLacI 2.31e-3 [1/s] degradation of LacI Ref. [10]
  • 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

Parameter Value Description Comments
  • 0.1 - 1 [pM]
  • 800 [nM]
LacI repressor dissociation constant
  • Ref. [2]
  • Ref. [12]
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]
  • 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]

Hill cooperativity

Parameter Value Description Comments
  • 1
  • 2
LacI repressor Hill cooperativity
  • Ref. [5]
  • Ref. [12]
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]


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[10] Tuttle et al. "Model-Driven Designs of an Oscillating Gene Network", Biophys J 89(6):3873-3883, 2005
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[12] Basu S et al. "A synthetic multicellular system for programmed pattern formation", Nature 434:1130-1134, 2005