Team:KULeuven/Model/Inverter
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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 | 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 |
LuxI catalysis | |||
kcat | 0.0166666667 s-1 | Estimated to be about 90% of Vmax in LB medium. | 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 | 0.00416 s-1 | derived from experimental values | link |
kcomplex2 | 0.00237 s-1 | derived from experimental values | link |
kclosed | 500 s-1 | derived from experimental values | link |
kopen | 7.5 s-1 | derived from experimental values | link |
LacI repression | |||
KLacI | 1.0E-10 M-1 | Dissociation constant | |
nLacI | 2.0 | Hill coefficient for LacI | link |
k_trans_LacI | 0.0025 s-1 | Estimated maximal transcription rate from R0011 | link |
Antisense LuxI | |||
k_complex3 | 0.00237 s-1 | rate constant for formation of asRNA - LuxI mRNA duplex | |
KmRNA_LuxI:antisense_mRNA | 4.22E14 | Complex of LuxI mRNA with antisense mRNA | |
Translation Rates | |||
ktransl LuxI | 0.167 s-1 | translation rate for B0032 RBS (0.3 relative efficiency) | link |
ktransl LacI | 0.167 s-1 | lock defined translation rate for LacI |
Models
CellDesigner (SBML file)
Matlab (SBML file)
Simulations
Remark: simulation is not from latest version.