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Team:KULeuven/Model/Inverter
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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.
Sensitivity Analysis
