Team:TU-Delft/Timer-Sumo-KillSwitch
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Timer-SUMO-KillSwitch
The separate modules: Timer plus SUMO and Kill Switch are combined to form the complete model of the system: Timer - SUMO - Kill Switch. For the final model, the kill switch module is converted in such a way so as the holin and antiholin to be activated by the Pci promoter.
Figure 1: Circuit of the kill switch
Differential Equations
Parameters
Parameter | Value | Description | Units | Reference |
c_{a} | 1020 | Translation rate per amino acid | min^{-1}#_{a}^{-1} | [7] |
c_{T7} | 4.16 | Maximum transcription rate of T7 | #_{m}/min | [2] |
c_{ptet} | 2.79 | Maximum transcription rate of Ptet | #_{m}/min | [4] |
c_{pconst} | 0.5 | Transcription rate of Pconst | #m/min | Assumption |
c_{ci} | 1.79 | Maximum transcription rate of Pci | #_{m}/min | [3] |
d_{mRNA} | 0.231 | Degradation rate of mRNA | min^{-1} | [8] |
d_{H} | 0.0348 | Degradation rate of holin / Antiholin | M/min | [17] |
d_{TET} | 0.1386 | Degradation rate of TET | min^{-1} | [9] |
d_{CI} | 0.042 | Degradation rate of CI | min^{-1} | [9] |
k_{b,HAH} | 0.3*10^{-4} | Backward rate | [17] | |
k_{f,HAH} | 11.7*10^{-4} | Forward rate | [17] | |
d_{PEP} | 2.1*10^{-3} | Degradation rate of the peptide | min^{-1} | Assumed three times slower same as GFP |
d_{PSU} | 6.3*10^{-3} | Degradation rate of the peptide plus SUMO | min^{-1} | Assumed the same as GFP |
d_{Ulp} | 1.263*10^{-2} | Degradation rate of Ulp | min^{-1} | Assumed twice the rate of GFP |
l_{t7} | 0.002 | Leakage factor of T7 | - | Assumption |
l_{ptet} | 0.002 | Leakage factor of Ptet | - | Assumption |
l_{ci} | 0.002 | Leakage factor of Pci | - | Assumption |
k_{tet} | 6 | Dissociation constant of Ptet | #m | [10] |
k_{ci} | 20 | Dissociation constant of Pci | #m | [10] |
k_{cUlp} | 3 | Turnover rate of Ulp | min^{-1} | [6] |
n_{ci} | 3 | Hills coefficient | - | [11] |
n_{tet} | 3 | Hills coefficient | - | [11] |
s | 0 or 1 | Activation/Inactivation of T7 promoter | Binary | Assumption |
s_{ci} | 228 | Length of CI | amino acids | [12] |
s_{PSU} | 18 + 110 | Length of peptide plus SUMO | amino acids | [12] |
s_{TET} | 206 | Length of TET | amino acids | [13] |
s_{Ulp} | 233 | Length of Ulp1 | amino acids | [13] |
s_{H} | 219 | Length of Holin | amino acids | |
s_{AH} | 103 | Length of Antiholin | amino acids |
Results
In Figure 1 the results of the simulation are shown.Figure 1: Simulation Results
Conclusion/Discussion
In Figure 1 the behavior of the total circuit is seen, and the answers to the questions can be given:- How much peptides are produced by the circuit?
The total concentration is 18000 peptides per cell. - How much peptides are still uncleaved by the SUMO at the point of cell lysis?
The models shows that there is almost no SUMO-peptide uncleaved. - How many minutes does the cell lysis take from the point of induction?
After 165 minutes the Holin concentration passes 190 molecules per cell and cell lysis occurs.