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Timer Plus Sumo
From 2013.igem.org
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0.43 times the strength of T7 [1] and Ptet is approximatly 2.79. [2]. | 0.43 times the strength of T7 [1] and Ptet is approximatly 2.79. [2]. | ||
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<b>Turnover rate Ulp</b> | <b>Turnover rate Ulp</b> | ||
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| + | The parameter kcUlp is the turnover rate. It can be calculated based on in vitro speci�cations [5]. It is | ||
| + | stated that one unit of Ulp1 cleaves 85% of 2 �μg of SUMO combined with GFP in 1 hr. This results in a kcUlp of around 3 | ||
| + | a<min>-1</sup> | ||
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| + | </p> | ||
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<br> | <br> | ||
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Revision as of 08:30, 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
Transcription rates of T7
For the T7 promoter a transcription rate of 50 bp/sec [2] is converted to per minute using an average
base pair length of 720 bp:
The promoter strengths of cI and Tet are taken as a factor of T7. PcI is found to be approximatly 0.43 times the strength of T7 [1] and Ptet is approximatly 2.79. [2].
Turnover rate Ulp
The parameter kcUlp is the turnover rate. It can be calculated based on in vitro speci�cations [5]. It is
stated that one unit of Ulp1 cleaves 85% of 2 �μg of SUMO combined with GFP in 1 hr. This results in a kcUlp of around 3
a
The parameters used in the specific model are depicted underneath.
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
