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Team:TU-Delft/Timer-Sumo-KillSwitch
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<p>Figure 1: Circuit of the kill switch</p></div> | <p>Figure 1: Circuit of the kill switch</p></div> | ||
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<h2 align="center">Differential Equations</h2> | <h2 align="center">Differential Equations</h2> | ||
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Revision as of 10:54, 17 September 2013
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 |
| 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] |
| cpconst | 0.5 | Transcription rate of Pconst | #m/min | Assumption |
| cci | 1.79 | Maximum transcription rate of Pci | #m/min | [3] |
| dmRNA | 0.231 | Degradation rate of mRNA | min-1 | [8] |
| dH | 0.0348 | Degradation rate of holin / Antiholin | M/min | [17] |
| dTET | 0.1386 | Degradation rate of TET | min-1 | [9] |
| dCI | 0.042 | Degradation rate of CI | min-1 | [9] |
| kb,HAH | 0.3*10-4 | Backward rate | [17] | |
| kf,HAH | 11.7*10-4 | Forward rate | [17] | |
| dPEP | 2.1*10-3 | Degradation rate of the peptide | min-1 | Assumed three times slower 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 twice the rate of 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] |
| sH | 219 | Length of Holin | amino acids | |
| sAH | 103 | Length of Antiholin | amino acids |
Results
Figure 1: Simulation Results
