Team:KULeuven/Model/Inverter

From 2008.igem.org

(Difference between revisions)
(Describing the system)
(Parameters)
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|-  
|-  
| d<sub>LuxI</sub>
| d<sub>LuxI</sub>
-
| 0.00231 s<sup>-1</sup>
+
| d<sub>LVA</sub> = 2.814E-4 s<sup>-1</sup>
-
|  
+
| LVA-tag reduces lifetime to 40 minutes
-
|  
+
| [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106306 link]
|-
|-
| d<sub>RNA_LuxI</sub>
| d<sub>RNA_LuxI</sub>
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|-
|-
| d<sub>LuxI_antimRNA</sub>
| d<sub>LuxI_antimRNA</sub>
-
| 0.00125 s<sup>-1</sup>
+
| 0.0045303737 s<sup>-1</sup>
-
|  
+
| estimate: because this RNA isn't translated, it degrades faster
|  
|  
|-
|-
| d<sub>LacI</sub>
| d<sub>LacI</sub>
-
| 0.00231 s<sup>-1</sup>
+
| d<sub>LVA</sub> = 2.814E-4 s<sup>-1</sup>
-
|  
+
| LVA-tag reduces lifetime to 40 minutes
-
| [http://www.biophysj.org/cgi/content/full/89/6/3873?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=89&firstpage=3873&resourcetype=HWCIT link]
+
| [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106306 link]
|-
|-
-
| d<sub>LacI</sub> (closed mRNA)
+
| d<sub>closed mRNA LacI</sub>
| 0.0046209812 s<sup>-1</sup>
| 0.0046209812 s<sup>-1</sup>
| estimate: because this mRNA isn't translated, it degrades faster  
| estimate: because this mRNA isn't translated, it degrades faster  
|  
|  
|-
|-
-
| d<sub>LacI</sub> (open mRNA)
+
| d<sub>open mRNA LacI</sub>
| 0.0023104906 s<sup>-1</sup>
| 0.0023104906 s<sup>-1</sup>
|  
|  
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
|-
|-
-
| d<sub>LacI_mRNA</sub> (open complex)
+
| d<sub>open mRNA LacI complex</sub>
| 0.0023104906 s<sup>-1</sup>
| 0.0023104906 s<sup>-1</sup>
|  
|  
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| d<sub>HSL</sub>
| d<sub>HSL</sub>
| 1.02E-6 s<sup>-1</sup>
| 1.02E-6 s<sup>-1</sup>
-
|  
+
| very stable in the medium, lifetime around 185h
| [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
| [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
|-
|-
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| Complex of LuxI mRNA with antisense mRNA
| Complex of LuxI mRNA with antisense mRNA
|  
|  
 +
|-
 +
! colspan="4" style="border-bottom: 1px solid #003E81;" | T7 Transcription
 +
|-
 +
| K<sub>T7</sub>
 +
| 421
 +
| dissociation constant, recalculated to remove units
 +
| [http://www.jbc.org/cgi/content/full/279/5/3239 link]
 +
|-
 +
| k<sub>max</sub>
 +
| 0.044 s<sup>-1</sup>
 +
| maximal T7 transcription rate
 +
| [http://www.jbc.org/cgi/content/full/279/5/3239 link]
|-
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
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|  
|  
|-
|-
-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Hill Cooperativity
+
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Repression
|-
|-
-
| K<sub>LuxI</sub>
+
| K<sub>LacI</sub> M
-
| 1.0E-10 s<sup>-1</sup>
+
| 1.0E-10 M<sup>-1</sup>
-
|  
+
| Dissociation constant
|  
|  
|-  
|-  
-
| n<sub>LuxI</sub>
+
| n<sub>LacI</sub>
| 2.0
| 2.0
-
|  
+
| Hill coefficient for LacI
-
|
+
| [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
-
|-
+
-
| k<sub>maxT7</sub>
+
-
| 0.044 s<sup>-1</sup>
+
-
|
+
-
| [http://www.jbc.org/cgi/content/full/279/5/3239#FIG2 link]
+
-
|-
+
-
| n<sub>T7</sub>
+
-
| 1
+
-
|
+
-
|
+
|-
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates
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| k<sub>LuxI</sub>
| k<sub>LuxI</sub>
| 0.167 s<sup>-1</sup>
| 0.167 s<sup>-1</sup>
-
| RBs is B0032 (efficiency 0.3)
+
| translation rate for B0032 RBS (0.3 relative efficiency)
|  
|  
|-
|-
| k<sub>LacI</sub>
| k<sub>LacI</sub>
| 0.167 s<sup>-1</sup>
| 0.167 s<sup>-1</sup>
-
| RBS is situated in the keylock
+
| estimate: RBS is situated in the keylock
|  
|  
|-
|-
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| K<sub>mRNA_LacI</sub>
| K<sub>mRNA_LacI</sub>
| 0.015
| 0.015
-
| equilibrium between open and closed mRNA LacI
+
| between closed and open LacI mRNA, experimental
-
|  
+
| [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
|-
|-
| K<sub>mRNA_LacI_Key</sub>
| K<sub>mRNA_LacI_Key</sub>
| 0.0212 /M
| 0.0212 /M
-
| equilibrium between closed mRNA LacI and complex of mRNA with keymRNA
+
| between closed LacI mRNA and key unlocked mRNA complex, experimental
-
|   
+
| [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]|   
 +
|-
 +
! colspan="4" style="border-bottom: 1px solid #003E81;" | Rate constants
 +
|-
 +
| k<sub>dis2</sub>
 +
| 100 s<sup>-1</sup>
 +
| derived from experimental values
 +
|
 +
|-
 +
| k<sub>complex2</sub>
 +
| 57 s<sup>-1</sup>
 +
| derived from experimental values
 +
|
|-
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Reaction Rates
! colspan="4" style="border-bottom: 1px solid #003E81;" | Reaction Rates

Revision as of 15:00, 27 August 2008

  dock/undock dropdown  

Pictogram inverter.png

Contents

Invertimer

Position in the system

The invertimer subsystem receives its input from the filter, T7. The invertimer's function is to produce HSL when no input is present, so a low T7 input gives rise to a high HSL output and vice versa. The production of HSL means that the cell will start a timer that eventually will be used in the celldeath-subsystem to produce ccdB. In this way the cell will die off if no desease remains present.

Describing the system

see also: Project:Invertimer

Inverter BioBrick.jpg

ODE's

Parameters

Parameter values (Inverter)
Name Value Comments Reference
Degradation Rates
dLuxI dLVA = 2.814E-4 s-1 LVA-tag reduces lifetime to 40 minutes [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106306 link]
dRNA_LuxI 0.0025 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dLuxI_antimRNA 0.0045303737 s-1 estimate: because this RNA isn't translated, it degrades faster
dLacI dLVA = 2.814E-4 s-1 LVA-tag reduces lifetime to 40 minutes [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106306 link]
dclosed mRNA LacI 0.0046209812 s-1 estimate: because this mRNA isn't translated, it degrades faster
dopen mRNA LacI 0.0023104906 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dopen mRNA LacI complex 0.0023104906 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dHSL 1.02E-6 s-1 very stable in the medium, lifetime around 185h [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
Dissociation Rates
KmRNA_LuxI:antisense_mRNA 4.22E14 Complex of LuxI mRNA with antisense mRNA
T7 Transcription
KT7 421 dissociation constant, recalculated to remove units [http://www.jbc.org/cgi/content/full/279/5/3239 link]
kmax 0.044 s-1 maximal T7 transcription rate [http://www.jbc.org/cgi/content/full/279/5/3239 link]
Transcription Rates
kmRNA_LacI 0.0011 s-1
kmRNA_LuxI 0.0025 s-1
Transcription Repression
KLacI M 1.0E-10 M-1 Dissociation constant
nLacI 2.0 Hill coefficient for LacI [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
Translation Rates
kLuxI 0.167 s-1 translation rate for B0032 RBS (0.3 relative efficiency)
kLacI 0.167 s-1 estimate: RBS is situated in the keylock
kT7 182 s-1
Equilibrium Constants
KmRNA_LacI 0.015 between closed and open LacI mRNA, experimental [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
KmRNA_LacI_Key 0.0212 /M between closed LacI mRNA and key unlocked mRNA complex, experimental
Rate constants
kdis2 100 s-1 derived from experimental values
kcomplex2 57 s-1 derived from experimental values
Reaction Rates
kLuxI:HSL 0.0167 s-1 [http://www.pnas.org/content/93/18/9505.full.pdf+html link Vmax]

Models

CellDesigner (SBML file)

Inverter

Matlab (SBML file)

Remark: not yet up to date to latest (final) version

Inverter

Simulations

Remark: simulation is not from latest version.

filter

Sensitivity Analysis

Sens Inverter.png