Team:KULeuven/Model/Inverter
From 2008.igem.org
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| d<sub>LuxI</sub> | | d<sub>LuxI</sub> | ||
- | | | + | | 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. | + | | 0.0045303737 s<sup>-1</sup> |
- | | | + | | estimate: because this RNA isn't translated, it degrades faster |
| | | | ||
|- | |- | ||
| d<sub>LacI</sub> | | d<sub>LacI</sub> | ||
- | | | + | | d<sub>LVA</sub> = 2.814E-4 s<sup>-1</sup> |
- | | | + | | LVA-tag reduces lifetime to 40 minutes |
- | | [http:// | + | | [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106306 link] |
|- | |- | ||
- | | d<sub>LacI</sub> | + | | 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> | + | | 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> | + | | 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;" | | + | ! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Repression |
|- | |- | ||
- | | K<sub> | + | | K<sub>LacI</sub> M |
- | | 1.0E-10 | + | | 1.0E-10 M<sup>-1</sup> |
- | | | + | | Dissociation constant |
| | | | ||
|- | |- | ||
- | | n<sub> | + | | n<sub>LacI</sub> |
| 2.0 | | 2.0 | ||
- | | | + | | Hill coefficient for LacI |
- | + | | [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] | |
- | + | ||
- | + | ||
- | + | ||
- | + | ||
- | | [http:// | + | |
- | + | ||
- | + | ||
- | + | ||
- | + | ||
- | + | ||
|- | |- | ||
! 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> | ||
- | | | + | | 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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|- | |- | ||
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| K<sub>mRNA_LacI</sub> | | K<sub>mRNA_LacI</sub> | ||
| 0.015 | | 0.015 | ||
- | | | + | | 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 | ||
- | | | + | | 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
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
ODE's
Parameters
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)
Matlab (SBML file)
Remark: not yet up to date to latest (final) version
Simulations
Remark: simulation is not from latest version.