Timer Plus Sumo

From 2013.igem.org

(Difference between revisions)
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| [[Team:TUDelft/Modeling_References|[3]]]
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
-
| d<sub>mRNA;</sub>
+
| d<sub>mRNA</sub>
|0.231
|0.231
|Degradation rate of mRNA
|Degradation rate of mRNA
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| [[Team:TUDelft/Modeling_References|[8]]]
| [[Team:TUDelft/Modeling_References|[8]]]
|-
|-
-
| d<sub>TET;</sub>
+
| d<sub>TET</sub>
|0.1386
|0.1386
|Degradation rate of TET
|Degradation rate of TET
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| [[Team:TUDelft/Modeling_References|[9]]]
| [[Team:TUDelft/Modeling_References|[9]]]
|-
|-
-
| d<sub>CI;</sub>
+
| d<sub>CI</sub>
|0.042
|0.042
|Degradation rate of CI
|Degradation rate of CI
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| [[Team:TUDelft/Modeling_References|[9]]]
| [[Team:TUDelft/Modeling_References|[9]]]
|-
|-
-
| d<sub>PEP;</sub>
+
| d<sub>PEP</sub>
|6.3*10<sup>-3</sup>  
|6.3*10<sup>-3</sup>  
|Degradation rate of the peptide
|Degradation rate of the peptide
|min<sup>-1</sup>
|min<sup>-1</sup>
 +
|Assumed the same as GFP
 +
|-
 +
| d<sub>PSU</sub>
 +
|6.3*10<sup>-3</sup>
 +
|Degradation rate of the peptide plus SUMO
 +
|min<sup>-1</sup>
 +
|Assumed the same as GFP
 +
|-
 +
| d<sub>Ulp</sub>
 +
|1.263*10<sup>-2</sup>
 +
|Degradation rate of Ulp
 +
|min<sup>-1</sup>
 +
|Assumed the same as GFP
 +
|-
 +
|l<sub>t7</sub>
 +
|0.002
 +
|Leakage factor of T7
 +
|-
|Assumption
|Assumption
|-
|-
 +
|l<sub>ptet</sub>
 +
|0.002
 +
|Leakage factor of Ptet
 +
|-
 +
|Assumption
 +
|-
 +
|l<sub>ci</sub>
 +
|0.002
 +
|Leakage factor of Pci
 +
|-
 +
|Assumption
 +
|-
 +
|k<sub>tet</sub>
 +
|6
 +
|Dissociation constant of Ptet
 +
|#<sub>min</sub>
 +
|[[Team:TUDelft/Modeling_References|[10]]]
 +
|-
 +
|k<sub>ci</sub>
 +
|20
 +
|Dissociation constant of Pci
 +
|#<sub>min</sub>
 +
|[[Team:TUDelft/Modeling_References|[10]]]
 +
|-
 +
|k<sub>cUlp</sub>
 +
|3
 +
|Turnover rate of Ulp
 +
|min<sup>-1</sup>
 +
|[[Team:TUDelft/Modeling_References|[6]]]
 +
|-
 +
|n<sub>ci</sub>
 +
|3
 +
|Hills coefficient
 +
|-
 +
|[[Team:TUDelft/Modeling_References|[11]]]
 +
|-
 +
|n<sub>tet</sub>
 +
|3
 +
|Hills coefficient
 +
|--
 +
|[[Team:TUDelft/Modeling_References|[11]]]
 +
|-
 +
|}
|}
</p>
</p>

Revision as of 09:17, 16 August 2013

Timer Plus Sumo


In this section the system of Figure 1 is modeled. The structure of the timer is very similar version of the timer compared to the construct of iGEM TU Delft team 2009. Here the input is changed to a T7 promoter and the output to Ulp-1. Furthermore, the Ulp-1 cleaves off the SUMO from the peptide combined with the SUMO.


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.


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]
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 #min [10]
kci 20 Dissociation constant of Pci #min [10]
kcUlp 3 Turnover rate of Ulp min-1 [6]
nci 3 Hills coefficient
[11]
ntet 3 Hills coefficient
[11]


Simulation


Initial Conditions

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.

Results

Figure 2: Simulation Results


Retrieved from "http://2013.igem.org/Timer_Plus_Sumo"