Timer Plus Sumo

From 2013.igem.org

(Difference between revisions)
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|1020
|1020
|Translation rate per amino acid
|Translation rate per amino acid
-
|min<sup>-1</sup>#a<sup>-1</sup>
+
|min<sup>-1</sup>#<sub>a</sub><sup>-1</sup>
-
| [[Team:TUDelft/Modeling_References|[1]]]
+
| [[Team:TUDelft/Modeling_References|[7]]]
|-
|-
-
| c<sub>pTet</sub>
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| c<sub>T7</sub>
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|1.5e-7
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|4.16
-
|maximum transcription rate (M/min)
+
|Maximum transcription rate of T7
 +
|#<sub>m</sub>/min
| [[Team:TUDelft/Modeling_References|[2]]]
| [[Team:TUDelft/Modeling_References|[2]]]
|-
|-
-
| c<sub>p&lambda;</sub>
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| c<sub>ptet;</sub>
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|1.5e-7
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|2.79
-
|maximum transcription rate (M/min)
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|Maximum transcription rate of Ptet
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| estimate
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|#<sub>m</sub>/min
 +
| [[Team:TUDelft/Modeling_References|[4]]]
|-
|-
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| K<sub>50</sub><sup>IPTG</sup>
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| c<sub>ci;</sub>
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|1.3e-6
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|1.79
-
|dissociation constant (M)
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|Maximum transcription rate of Pci
 +
|#<sub>m</sub>/min
| [[Team:TUDelft/Modeling_References|[3]]]
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
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| K<sub>50</sub><sup>LacI</sup>
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| d<sub>mRNA;</sub>
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|800e-9
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|0.231
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|dissociation constant (M)
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|Degradation rate of mRNA
-
| [[Team:TUDelft/Modeling_References|[3]]]
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|min<sup>-1</sup>
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|-
+
| [[Team:TUDelft/Modeling_References|[8]]]
-
| K<sub>50</sub><sup>TetR</sup>
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-
|179e-12
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-
|dissociation constant (M)
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-
| [[Team:TUDelft/Modeling_References|[3]]]
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-
|-
+
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| K<sub>50</sub><sup>CI</sup>
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-
|8e-12
+
-
|dissociation constant (M)
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-
| [[Team:TUDelft/Modeling_References|[3]]]
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-
|-
+
-
| n<sub>IPTG</sub>
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|2
+
-
| Hills coefficient
+
-
| [[Team:TUDelft/Modeling_References|[3]]]
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-
|-
+
-
| n<sub>LacI</sub>
+
-
|2
+
-
| Hills coefficient
+
-
| [[Team:TUDelft/Modeling_References|[3]]]
+
-
|-
+
-
| n<sub>TetR</sub>
+
-
|3
+
-
| Hills coefficient
+
-
| [[Team:TUDelft/Modeling_References|[3]]]
+
-
|-
+
-
| n<sub>CI</sub>
+
-
|2
+
-
| Hills coefficient
+
-
| [[Team:TUDelft/Modeling_References|[3]]]
+
-
|-
+
-
| d<sub>LacI</sub>
+
-
| 0.1386
+
-
| degradation rate (M/min)
+
-
| [[Team:TUDelft/Modeling_References|[3]]]
+
-
|-
+
-
| d<sub>TetR</sub>
+
-
| 0.1386
+
-
| degradation rate (M/min)
+
-
| [[Team:TUDelft/Modeling_References|[3]]]
+
-
|-
+
-
| d<sub>CI</sub>
+
-
| 0.042
+
-
| degradation rate (M/min)
+
-
| [[Team:TUDelft/Modeling_References|[3]]]
+
-
|-
+
-
| d<sub>RFP</sub>
+
-
| 6.3e-3
+
-
| degradation rate (M/min)
+
-
| [[Team:TUDelft/Modeling_References|[3]]]
+
-
|-
+
-
| d<sub>GFP</sub>
+
-
| 6.3e-3
+
-
| degradation rate (M/min)
+
-
| [[Team:TUDelft/Modeling_References|[3]]]
+
-
|-
+
-
| d<sub>mRNA</sub>
+
-
| 0.029
+
-
| degradation rate (M/min)
+
-
| [[Team:TUDelft/Modeling_References|[4]]]
+
-
|-
+
-
| &alpha;
+
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| 16 - 57
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-
| translation rate (translations/min/mRNA), depends on growth rate (a default value of 30 is used)
+
-
| [[Team:TUDelft/Modeling_References|[5]]]
+
|-
|-
-
| k<sub>IPTG</sub>
+
| d<sub>TET;</sub>
-
| 0.92
+
|0.1386
-
| rate constant for IPTG diffusion into cell
+
|Degradation rate of TET
-
| [[Team:TUDelft/Modeling_References|[6]]]
+
|min<sup>-1</sup>
 +
| [[Team:TUDelft/Modeling_References|[8]]]
|-
|-
 +
|}
|}
</p>
</p>

Revision as of 09:04, 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 [8]


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