Timer Plus Sumo

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Timer Plus Sumo

In this section the system of Figure 1 is modeled. The structure of the timer has two repressing promoters (PcI and Ptet) and the input is the T7 promoter and the output is the protease Ulp-1. This Ulp-1 cleaves off the SUMO from the produced SUMO-peptide.

Figure 1: Circuit of the timer including sumo cleaving

Differential Equations

The above circuit can be represented by the following differential equations. We assume a binary behavior of the T7 promoter. In the presence of IPTG, the T7 promoter will be active. So, we make the assumption that the T7 is binary variable with two possible states: either active 1 or inactive 0.


Parameter Value Description Units Reference
ca 1020 Translation rate per amino acid min-1#a-1 [7]
cT7 4.16 Maximum transcription rate of T7 #m/min [2]
cptet 2.79 Maximum transcription rate of Ptet #m/min [4]
cci 1.79 Maximum transcription rate of Pci #m/min [3]
dmRNA 0.231 Degradation rate of mRNA min-1 [8]
dTET 0.1386 Degradation rate of TET min-1 [9]
dCI 0.042 Degradation rate of CI min-1 [9]
dPEP 6.3*10-3 Degradation rate of the peptide min-1 Assumed the same as GFP
dPSU 6.3*10-3 Degradation rate of the peptide plus SUMO min-1 Assumed the same as GFP
dUlp 1.263*10-2 Degradation rate of Ulp min-1 Assumed the same as GFP
lt7 0.002 Leakage factor of T7 - Assumption
lptet 0.002 Leakage factor of Ptet - Assumption
lci 0.002 Leakage factor of Pci - Assumption
ktet 6 Dissociation constant of Ptet #m [10]
kci 20 Dissociation constant of Pci #m [10]
kcUlp 3 Turnover rate of Ulp min-1 [6]
nci 3 Hills coefficient - [11]
ntet 3 Hills coefficient - [11]
s 0 or 1 Activation/Inactivation of T7 promoter Binary Assumption
sci 228 Length of CI amino acids [12]
sPSU 18 + 110 Length of peptide plus SUMO amino acids [12]
sTET 206 Length of TET amino acids [13]
sUlp 233 Length of Ulp1 amino acids [13]


TET and ULP must be set equal to zero (or a numerical equivalent). For CI the steady state value is assumed as a starting condition as this is expressed before activation.

Figure 2: Simulation Results