Team:KULeuven/Model/Inverter

From 2008.igem.org

(Difference between revisions)
(→Parameters)
(→Parameters)
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| very stable in the medium, lifetime around 185h
| 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]
-
|-
 
-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Dissociation Rates
 
-
|-
 
-
| K<sub>mRNA_LuxI:antisense_mRNA</sub>
 
-
| 4.22E14
 
-
| Complex of LuxI mRNA with antisense mRNA
 
-
|
 
|-
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | T7 Transcription
! colspan="4" style="border-bottom: 1px solid #003E81;" | T7 Transcription
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| [http://www.jbc.org/cgi/content/full/279/5/3239 link]
| [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;" | Key-Lock constants
|-
|-
-
| k<sub>mRNA_LacI</sub>
+
| K<sub>eq 1</sub>
-
| 0.0011 s<sup>-1</sup>
+
| 0,015 [M]
-
|  
+
| between closed and open T7 mRNA, experimental
-
|  
+
| [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
|-
|-
-
| k<sub>mRNA_LuxI</sub>
+
| K<sub>eq 2</sub>
-
| 0.0025 s<sup>-1</sup>
+
| 0.0212 [M]
-
|  
+
| between closed T7 mRNA and key unlocked mRNA complex, experimental
-
|  
+
| [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
 +
|-
 +
| k<sub>dis2</sub>
 +
| 100 s<sup>-1</sup>
 +
| derived from experimental values
 +
| [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
 +
|-
 +
| k<sub>complex2</sub>
 +
| 57 s<sup>-1</sup>
 +
| derived from experimental values
 +
| [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
 +
|-
 +
| k<sub>closed</sub>
 +
| 100 s<sup>-1</sup>
 +
| derived from experimental values
 +
| [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
 +
|-
 +
| k<sub>open</sub>
 +
| 1.5 s<sup>-1</sup>
 +
| derived from experimental values
 +
| [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
 +
|-
 +
| k<sub>translation</sub>
 +
| 0.167 s<sup>-1</sup>
 +
| lock defined translation rate for LacI
 +
| [http://partsregistry.org/Part:BBa_B0032 link]
|-
|-
-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Repression
+
! colspan="4" style="border-bottom: 1px solid #003E81;" | LacI repression
|-
|-
-
| K<sub>LacI</sub> M
+
| K<sub>LacI</sub>
| 1.0E-10 M<sup>-1</sup>
| 1.0E-10 M<sup>-1</sup>
| Dissociation constant
| Dissociation constant
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| [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
| [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
|-
|-
-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates
+
| k_trans_LacI
 +
| 0.0050 s<sup>-1</sup>
 +
| Estimated maximal transcription rate from R0011
 +
| [http://partsregistry.org/Part:BBa_R0011 link]
|-
|-
-
| k<sub>LuxI</sub>
+
! colspan="4" style="border-bottom: 1px solid #003E81;" | Antisense LuxI
-
| 0.167 s<sup>-1</sup>
+
-
| translation rate for B0032 RBS (0.3 relative efficiency)
+
-
|
+
|-
|-
-
| k<sub>LacI</sub>
+
| k_complex3
-
| 0.167 s<sup>-1</sup>
+
| 2.12 s<sup>-1</sup>
-
| estimate: RBS is situated in the keylock
+
| rate constant for formation of asRNA - LuxI mRNA duplex (CHANGE? ALSO KEY THEN)
-
|  
+
|
|-
|-
-
| k<sub>T7</sub>
+
| K<sub>mRNA_LuxI:antisense_mRNA</sub>
-
| 182 s<sup>-1</sup>
+
| 4.22E14
 +
| Complex of LuxI mRNA with antisense mRNA
|  
|  
-
|
 
-
|-
 
-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Equilibrium Constants
 
|-
|-
-
| K<sub>mRNA_LacI</sub>
+
| antisense leakiness
-
| 0.015
+
| 0.9 fwd vs 0.1 rev
-
| between closed and open LacI mRNA, experimental
+
| factor to reflect antisense competition with ribosomes
-
| [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
+
-
|-
+
-
| K<sub>mRNA_LacI_Key</sub>
+
-
| 0.0212 /M
+
-
| 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>
+
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates
-
| 57 s<sup>-1</sup>
+
-
| derived from experimental values
+
-
|  
+
|-
|-
-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Reaction Rates
+
| k<sub>transl LuxI</sub>
-
|-
+
| 0.167 s<sup>-1</sup>
-
| k<sub>LuxI:HSL</sub>
+
| translation rate for B0032 RBS (0.3 relative efficiency)
-
| 0.0167 s<sup>-1</sup>
+
|  
|  
-
| [http://www.pnas.org/content/93/18/9505.full.pdf+html link V<sub>max</sub>]
+
|-
 +
| k<sub>transl LacI</sub>
 +
| 0.167 s<sup>-1</sup>
 +
| lock defined translation rate for LacI
 +
| [http://partsregistry.org/Part:BBa_B0032 link]
|}
|}

Revision as of 10:14, 28 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 link link
dRNA_LuxI 0.0025 s-1 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 link 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 link
dopen mRNA LacI complex 0.0023104906 s-1 link
dHSL 1.02E-6 s-1 very stable in the medium, lifetime around 185h link
T7 Transcription
KT7 421 dissociation constant, recalculated to remove units link
kmax 0.044 s-1 maximal T7 transcription rate link
Key-Lock constants
Keq 1 0,015 [M] between closed and open T7 mRNA, experimental link
Keq 2 0.0212 [M] between closed T7 mRNA and key unlocked mRNA complex, experimental link
kdis2 100 s-1 derived from experimental values link
kcomplex2 57 s-1 derived from experimental values link
kclosed 100 s-1 derived from experimental values link
kopen 1.5 s-1 derived from experimental values link
ktranslation 0.167 s-1 lock defined translation rate for LacI link
LacI repression
KLacI 1.0E-10 M-1 Dissociation constant
nLacI 2.0 Hill coefficient for LacI link
k_trans_LacI 0.0050 s-1 Estimated maximal transcription rate from R0011 link
Antisense LuxI
k_complex3 2.12 s-1 rate constant for formation of asRNA - LuxI mRNA duplex (CHANGE? ALSO KEY THEN)
KmRNA_LuxI:antisense_mRNA 4.22E14 Complex of LuxI mRNA with antisense mRNA
antisense leakiness 0.9 fwd vs 0.1 rev factor to reflect antisense competition with ribosomes
Translation Rates
ktransl LuxI 0.167 s-1 translation rate for B0032 RBS (0.3 relative efficiency)
ktransl LacI 0.167 s-1 lock defined translation rate for LacI link

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
Retrieved from "http://2008.igem.org/Team:KULeuven/Model/Inverter"