Timer-SUMO-KillSwitch

From 2013.igem.org

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<h2 align="center">Timer-SUMO-KillSwitch</h2>
<h2 align="center">Timer-SUMO-KillSwitch</h2>
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<p align="justify">The <a href="https://2013.igem.org/Timer_Plus_Sumo">Timer plus SUMO </a> and the <a href="https://2013.igem.org/KillSwitch">kill switch</a> are combined to form the complete model of the system: Timer - SUMO - Kill Switch.Specfically,the Kill Switch model is converted in such a way so as the holin and antiholin to be activated by the pci promoter.In that way, the final model is obtained.
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<p align="justify">The separate modules: <a href="https://2013.igem.org/Timer_Plus_Sumo">Timer plus SUMO </a> and <a href="https://2013.igem.org/KillSwitch">Kill Switch</a> 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.
</p>
</p>
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<h2 align="center">Differential Equations</h2>
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<center>
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<img src="https://static.igem.org/mediawiki/2013/8/87/Combined_equations.png" >
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</center>
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<h2 align="center">Parameters</h2>
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</html>
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<p>
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{| align="center" border="1"
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|'''Parameter'''
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|'''Value'''
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|'''Description'''
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|'''Units'''
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|'''Reference'''
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|-
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|a
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|1020
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|Translation rate per amino acid
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|min<sup>-1</sup>#<sub>a</sub><sup>-1</sup>
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| [[Team:TUDelft/Modeling_References|[7]]]
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|-
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| c<sub>T7</sub>
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|4.16
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|Maximum transcription rate of T7
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|#m/min
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| [[Team:TUDelft/Modeling_References|[2]]]
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|-
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| c<sub>ptet</sub>
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|2.79
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|Maximum transcription rate of Ptet
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|#m/min
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| [[Team:TUDelft/Modeling_References|[4]]]
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|-
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| c<sub>ci</sub>
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|1.79
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|Maximum transcription rate of Pci
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|#m/min
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| [[Team:TUDelft/Modeling_References|[3]]]
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|-
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| d<sub>mRNA</sub>
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|0.231
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|Degradation rate of mRNA
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|min<sup>-1</sup>
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| [[Team:TUDelft/Modeling_References|[8]]]
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|-
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| d<sub>TET</sub>
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|0.1386
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|Degradation rate of TET
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|min<sup>-1</sup>
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| [[Team:TUDelft/Modeling_References|[9]]]
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|-
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| d<sub>CI</sub>
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|0.042
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|Degradation rate of CI
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|min<sup>-1</sup>
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| [[Team:TUDelft/Modeling_References|[9]]]
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|-
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| d<sub>PSU</sub>
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|6.3*10<sup>-3</sup>
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|Degradation rate of the peptide plus SUMO
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|min<sup>-1</sup>
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|Assumed the same as GFP
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|-
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| d<sub>Ulp</sub>
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|1.263*10<sup>-2</sup>
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|Degradation rate of Ulp
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|min<sup>-1</sup>
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|Assumed twice the rate of GFP
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|-
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|l<sub>t7</sub>
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|0.002
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|Leakage factor of T7
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|  -
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|Assumption
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|-
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|l<sub>ptet</sub>
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|0.002
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|Leakage factor of Ptet
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|  -
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|Assumption
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|-
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|k<sub>ci</sub>
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|20
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|Dissociation constant of Pci
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|#m
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|[[Team:TUDelft/Modeling_References|[10]]]
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|-
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|k<sub>cUlp</sub>
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|3
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|Turnover rate of Ulp
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|min<sup>-1</sup>
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|[[Team:TUDelft/Modeling_References|[6]]]
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|-
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|n<sub>tet</sub>
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|3
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|Hills coefficient
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|  -
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|[[Team:TUDelft/Modeling_References|[11]]]
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|-
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|n<sub>ci</sub>
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|3
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|Hills coefficient
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|  -
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|[[Team:TUDelft/Modeling_References|[11]]]
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|-
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|s<sub>ci</sub>
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|228
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|Length of Ci
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| amino acids
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|[[Team:TUDelft/Modeling_References|[12]]]
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|-
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|s<sub>PSU</sub>
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|18 + 110
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|Length of peptide plus SUMO
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|amino acids
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|[[Team:TUDelft/Modeling_References|[12]]]
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|-
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|s<sub>TET</sub>
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|206
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|Length of TET
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|amino acids
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|[[Team:TUDelft/Modeling_References|[13]]]
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|-
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|s<sub>Ulp</sub>
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|233
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|Length of Ulp1
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|amino acids
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|[[Team:TUDelft/Modeling_References|[13]]]
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|-
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|}
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</p>
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<br>
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<html>
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<div style="margin-left:30px;margin-right:30px;float:left;display:inline-block;"> 
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<h2 align="center">Results</h2>
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<br>
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<center>
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<img src="https://static.igem.org/mediawiki/2013/f/f6/Combined_simulation.png" width="700">
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<p>Figure 1: Simulation Results</p></div>
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</center>
<br>
<br>
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</html>

Latest revision as of 07:52, 20 August 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.

Differential Equations

Parameters


Parameter Value Description Units Reference
a 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]
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
kci 20 Dissociation constant of Pci #m [10]
kcUlp 3 Turnover rate of Ulp min-1 [6]
ntet 3 Hills coefficient - [11]
nci 3 Hills coefficient - [11]
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]


Results


Figure 1: Simulation Results


Retrieved from "http://2013.igem.org/Timer-SUMO-KillSwitch"