KillSwitch

From 2013.igem.org

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<h2 align="center">Kill Switch</h2>
<h2 align="center">Kill Switch</h2>
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<br>
 
<p align="justify">
<p align="justify">
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The kill switch design is based on the expression of holin and antiholin. Holin is a protein that forms pores in cell membranes. Anti-holin binds to holin and inhibits it's action.  Once pores are formed by holin, lysozyme can access the periplasmic space and degrade the cell wall, causing cell lysis.  
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The kill switch design is based on the expression of holin and antiholin, Figure 1. Holin is a protein that forms pores in cell membranes. Anti-holin binds to holin and inhibits it's action.  Once pores are formed by holin, lysozyme can access the periplasmic space and degrade the cell wall, causing cell lysis.  
</p>
</p>
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<p align="justify">
<p align="justify">
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Kill switch constitutes a crucial part of our final system. It is activated after the production and release of the antimicrobial peptide. In that way, E.coli is killed and the safety of the system is ensured.
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Kill switch constitutes a crucial part of our final system. It is activated after the production and release of the antimicrobial peptide. In that way, the <i>E.colis</i> are killed and the safety of the system is ensured.
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</p>  
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<br>
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</p>
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<center>
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<img src="https://static.igem.org/mediawiki/2013/archive/5/5b/20130816105831!Kill_switch.png" >
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<p>Figure 1: Circuit of the kill switch</p></div>
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</center>
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<div style="margin-top:40px;margin-left:30px;margin-right:30px;float:left;display:inline-block;">   
<div style="margin-top:40px;margin-left:30px;margin-right:30px;float:left;display:inline-block;">   
<h2 align="center">Differential Equations</h2>
<h2 align="center">Differential Equations</h2>
<p align="justify">
<p align="justify">
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<p>
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The kill switch circuit can be represented by the following differential equations. </p>
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<br>
<br>
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</p>
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<center>
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<img src="https://static.igem.org/mediawiki/2013/5/5b/Kill_switch.png" width="600" >
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</center>
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<div style="margin-top:40px;margin-left:30px;margin-right:30px;float:left;display:inline-block;"> 
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<h2 align="center">Parameters</h2>
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</html>
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The used parameters are listed in Table 1. The dimer binding
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strengths are fitted on literature of Holin expression using the PcI promoter with and without antiholin
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[[Team:TUDelft/Modeling_References|[14]]].
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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>pconst</sub>
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|0.85
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|Transcription rate of Pconst
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|#m/min
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| Assumption
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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|[15]]]
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|-
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| d<sub>H</sub>
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|0.0348
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|Degradation rate of holin
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|M/min
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|  [[Team:TUDelft/Modeling_References|[17]]]
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|-
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| d<sub>H</sub>
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|0.0348
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|Degradation rate of Antiholin
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|M/min
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| [[Team:TUDelft/Modeling_References|[17]]]
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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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| k<sub>Atc,in</sub>
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|0.9
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| 
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| 
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|Assumption [[Team:TUDelft/Modeling_References|[11]]]
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|-
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| k<sub>Atc,out</sub>
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|0.05
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| 
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| 
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|Assumption [[Team:TUDelft/Modeling_References|[11]]]
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|-
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| k<sub>b,HAH</sub>
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|0.3*10<sup>-4</sup>
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|Backward rate
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|
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| [[Team:TUDelft/Modeling_References|[17]]]
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|-
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| k<sub>f,HAH</sub>
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|1.2*10<sup>-4</sup>
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|Forward rate
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|
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| [[Team:TUDelft/Modeling_References|[17]]]
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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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|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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|s<sub>H</sub>
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|219
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|Length of Holin
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|amino acids
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|
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|-
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|s<sub>AH</sub>
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|103
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|Length of Antiholin
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|amino acids
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|
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|-
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|}
</p>
</p>
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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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</html>
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The model is simulated upon activating. The lethal dosis of Holin is a 1000 molecules [[Team:TUDelft/Modeling_References|[17]]], which is shown in the graph as the horizontal line.
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<html>
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<br>
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<center>
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<img src="https://static.igem.org/mediawiki/2013/0/01/Kill.png" width="700">
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<p>Figure 2: Simulation Results</p></div>
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</center>
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<br>
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<h2 align="center">Discussion</h2>
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<p align="justify">
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As observed the dimer is formed, reducing the amount of antiholin. After 55 min the Holin level passes the 1000 molecules, so cell lysis would occur within an hour.
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</p>
</html>
</html>

Latest revision as of 07:57, 20 August 2013

Kill Switch

The kill switch design is based on the expression of holin and antiholin, Figure 1. Holin is a protein that forms pores in cell membranes. Anti-holin binds to holin and inhibits it's action. Once pores are formed by holin, lysozyme can access the periplasmic space and degrade the cell wall, causing cell lysis.

Kill switch constitutes a crucial part of our final system. It is activated after the production and release of the antimicrobial peptide. In that way, the E.colis are killed and the safety of the system is ensured.

Figure 1: Circuit of the kill switch

Differential Equations

The kill switch circuit can be represented by the following differential equations.


Parameters

The used parameters are listed in Table 1. The dimer binding strengths are fitted on literature of Holin expression using the PcI promoter with and without antiholin [14].


Parameter Value Description Units Reference
a 1020 Translation rate per amino acid min-1#a-1 [7]
cpconst 0.85 Transcription rate of Pconst #m/min Assumption
cptet 2.79 Maximum transcription rate of Ptet #m/min [15]
dH 0.0348 Degradation rate of holin M/min [17]
dH 0.0348 Degradation rate of Antiholin M/min [17]
dmRNA 0.231 Degradation rate of mRNA min-1 [8]
kAtc,in 0.9 Assumption [11]
kAtc,out 0.05 Assumption [11]
kb,HAH 0.3*10-4 Backward rate [17]
kf,HAH 1.2*10-4 Forward rate [17]
lptet 0.002 Leakage factor of Ptet - Assumption
ntet 3 Hills coefficient - [11]
sH 219 Length of Holin amino acids
sAH 103 Length of Antiholin amino acids

Results

The model is simulated upon activating. The lethal dosis of Holin is a 1000 molecules [17], which is shown in the graph as the horizontal line.


Figure 2: Simulation Results


Discussion

As observed the dimer is formed, reducing the amount of antiholin. After 55 min the Holin level passes the 1000 molecules, so cell lysis would occur within an hour.

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