Timer-SUMO-KillSwitch

From 2013.igem.org

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<h2 align="center">Parameters</h2>
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|'''Reference'''
|'''Reference'''
|-
|-
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| c<sub>a</sub>
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|a
|1020
|1020
|Translation rate per amino acid
|Translation rate per amino acid
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|min<sup>-1</sup>
|min<sup>-1</sup>
| [[Team:TUDelft/Modeling_References|[9]]]
| [[Team:TUDelft/Modeling_References|[9]]]
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|-
 
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| d<sub>PEP</sub>
 
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|6.3*10<sup>-3</sup>
 
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|Degradation rate of the peptide
 
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|min<sup>-1</sup>
 
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|Assumed the same as GFP
 
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| d<sub>PSU</sub>
| d<sub>PSU</sub>
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|Degradation rate of Ulp
|Degradation rate of Ulp
|min<sup>-1</sup>
|min<sup>-1</sup>
-
|Assumed the same as GFP
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|Assumed twice the rate of GFP
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|-
|l<sub>t7</sub>
|l<sub>t7</sub>
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|  -
|  -
|Assumption
|Assumption
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|-
 
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|l<sub>ci</sub>
 
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|0.002
 
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|Leakage factor of Pci
 
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|  -
 
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|Assumption
 
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|-
 
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|k<sub>tet</sub>
 
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|6
 
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|Dissociation constant of Ptet
 
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|#m
 
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|[[Team:TUDelft/Modeling_References|[10]]]
 
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|k<sub>ci</sub>
|k<sub>ci</sub>
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|[[Team:TUDelft/Modeling_References|[6]]]
|[[Team:TUDelft/Modeling_References|[6]]]
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|-
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|n<sub>ci</sub>
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|n<sub>tet</sub>
|3
|3
|Hills coefficient
|Hills coefficient
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|[[Team:TUDelft/Modeling_References|[11]]]
|[[Team:TUDelft/Modeling_References|[11]]]
|-
|-
-
|n<sub>tet</sub>
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|n<sub>ci</sub>
|3
|3
|Hills coefficient
|Hills coefficient
|  -
|  -
|[[Team:TUDelft/Modeling_References|[11]]]
|[[Team:TUDelft/Modeling_References|[11]]]
-
|-
 
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|s
 
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|0 or 1
 
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|Activation/Inactivation of T7 promoter
 
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|Binary
 
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|Assumption
 
|-
|-
|s<sub>ci</sub>
|s<sub>ci</sub>
|228
|228
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|Length of CI
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|Length of Ci
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|amino acids
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| amino acids
|[[Team:TUDelft/Modeling_References|[12]]]
|[[Team:TUDelft/Modeling_References|[12]]]
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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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<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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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


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