ETHZ/Simulations
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==== Allosteric regulation ==== | ==== Allosteric regulation ==== |
Revision as of 08:01, 13 September 2007
Contents |
Basic Model
Constitutively produced proteins
Learning system
Reporter system
System Equations
Constitutively produced proteins
Learning system
Reporter system
Allosteric regulation
Model Parameters
Parameter | Value | Description | Comments |
---|---|---|---|
aR | basic production of lacI | ||
aS | basic production of tetR | ||
aL | basic production of luxR | ||
aQ1 | basic production of cI | ||
aQ2 | basic production of p22cII | ||
aGFP | basic production of GFP | ||
aRFP | basic production of RFP | ||
dR | 0.06 | degradation of lacI | Ref. [4] |
dS | degradation of tetR | ||
dL | degradation of luxR | ||
dQ1 | degradation of cI | ||
dQ2 | degradation of p22cII | ||
dGFP | degradation of GFP | ||
dRFP | degradation of RFP | ||
kR | 0.22 [mM/h] | promoter strength (Promoter R0010) | |
kS | promoter strength (Promoter R0040) | ||
kL | promoter strength (Promoter R0062) | ||
kQ1 | 0.20 [mM/h] | promoter strength (Promoter R0051) | |
kQ2 | promoter strength (Promoter R0053) | ||
KR | 1.3e-3 - 2e-3 [mM/h] | lacI repressor dissociation constant | lower value is from Ref. [2], higher value is from Ref. [?] |
KIR | 1.5e-10 [mM/h] | IPTG-lacI repressor dissociation constant | |
KS | tetR repressor dissociation constant | ||
KIS | aTc-tetR repressor dissociation constant | ||
KL | luxR activator dissociation constant | ||
KIL | AHL-luxR activator dissociation constant | ||
KQ1 | 2e-3 [mM/h] | cI repressor dissociation constant | |
KQ2 | p22cII repressor dissociation constant | ||
nR | 1 | lacI repressor Hill cooperativity | |
nIR | 2 | IPTG-lacI repressor Hill cooperativity | |
nS | 3 | tetR repressor Hill cooperativity | Ref. [3] |
nIS | aTc-tetR repressor Hill cooperativity | ||
nL | 1 | luxR activator Hill cooperativity | Ref. [3] |
nIL | 1 | AHL-luxR activator Hill cooperativity | Ref. [3] |
nQ1 | 1.9 | cI repressor Hill cooperativity | |
nQ2 | p22cII repressor Hill cooperativity |
References
- A synthetic time-delay circuit in mammalian cells and mice (http://www.pnas.org/cgi/content/abstract/104/8/2643)
- Detailed map of a cis-regulatory input function (http://www.pnas.org/cgi/content/full/100/13/7702?ck=nck)
- Parameter Estimation for two synthetic gene networks (http://ieeexplore.ieee.org/iel5/9711/30654/01416417.pdf)
- Supplementary on-line information for "A Synthetic gene-metabolic oscillator" (no link)
Variable Mapping
Variable | Compound |
---|---|
R | lacI |
IR | IPTG |
S | tetR |
IS | aTc |
L | luxR |
IL | AHL |
Q1 | cI |
Q2 | p22cII |