Team:USTC Software/detail
From 2010.igem.org
Modeling Details of Repressilator
Key points of this modeling are:
- LacI protein tends to form LacI dimer, which tends to form LacI tetramer further.
- Only LacI tetramer binds with pLacI gene and thus repressing expression of its downstream genes.
- TetR protein only forms dimer.
- Only tetR dimer binds with pTet gene and thus repressing expression of its downstream genes.
- One IPTG molecule binds with one LacI tetramer to form complex IPTG:LacI4.
- cIlam protein only forms dimer.
- Only cIlam dimer binds with pcIlam gene and thus repressing expression of its downstream genes.
An overview of species list is provided:
where each species with its specific identifier has its own meaning:
- 0:E_coli: E.Coli cell;
- 1:IPTG: IPTG in flask;
- 2:DNA: initial transformed plasmids;
- 3:IPTG: IPTG in E.Coli due to diffusion;
- 4:RNA: mRNA of tetR;
- 5:RNA: mRNA of lacI;
- 6:RNA: mRNA of cIlam;
- 7:tetR154: tetR protein;
- 8:lacI153: lacI protein;
- 9:cIlam156: lacI protein;
- 10:(tetR154)2: tetR dimer;
- 11:(lacI153)2: lacI dimer;
- 12:(cIlam156)2: cIlam dimer;
- 13:DNA;(tetR154)2: complex of tetR dimer binding to pTet gene of plasmid DNA;
- 14:(lacI153)4; lacI tetramer;
- 15:DNA;(cIlam156)2: complex of cIlam dimer binding to pCI gene of plasmid DNA;
- 16:DNA;(cIlam156)2;(tetR154)2: complex of plasmid of DNA with both pCI and pTet genes bound with cIlam dimer and tetR dimer;
- 17:DNA;(lacI153)4: complex of LacI tetramer binding to pLacI gene plasmid DNA;
- 18:DNA;(lacI153)4;(tetR154)2: complex of plasmid DNA with both pLacI and pTet genes bound with LacI tetramer and tetR dimer, respectively;
- 19:IPTG;(lacI153)4: complex of LacI tetramer binding to pLacI gene of plasmid DNA;
- 20:DNA;(cIlam156)2;(lacI153)4: complex of plasmid DNA with both pCI and placI genes bound with cIlam dimer and lacI tetramer, respectively;
- 21:DNA;(cIlam156)2;(lacI153)4;(tetR154)2: complex of plasmid DNA with both pCI, placI and pTet genes bound with cIlam dimer, lacI tetramer and tetR dimer, respectively;
Since there are 153 reactions in total, we only provide a screenshot (we strongly recommend users to run our example to learn more details about automatic modeling):
Moreover, parameters of our modeling network are provided below:
- Initial time: 0 s
- Initial volumes:
- Chemostat 0.1 l
- E_coli 4.4247e-006 l
- Initial concentrations:
- 0:E_coli 1.05e-013 mol/l
- 1:IPTG 0.001 mol/l
- 2:DNA 2.4e-009 mol/l
- 3:IPTG 0 mol/l
- 4:RNA 0 mol/l
- 5:RNA 0 mol/l
- 6:RNA 0 mol/l
- 7:tetR154 0 mol/l
- 8:lacI153 0 mol/l
- 9:cIlam156 0 mol/l
- 10:(tetR154)2 0 mol/l
- 11:(lacI153)2 0 mol/l
- 12:(cIlam156)2 0 mol/l
- 13:DNA;(tetR154)2 0 mol/l
- 14:(lacI153)4 0 mol/l
- 15:DNA;(cIlam156)2 0 mol/l
- 16:DNA;(cIlam156)2;(tetR154)2 0 mol/l
- 17:DNA;(lacI153)4 0 mol/l
- 18:DNA;(lacI153)4;(tetR154)2 0 mol/l
- 19:IPTG;(lacI153)4 0 mol/l
- 20:DNA;(cIlam156)2;(lacI153)4 0 mol/l
- 21:DNA;(cIlam156)2;(lacI153)4;(tetR154)2 0 mol/l
- Initial values of global quantities:
- ts 0
- te 40000
- s 0.001
- t 0
- Reaction parameters:
- reproduction of Ecoli cell
- kgr 0.000192 1/s
- maxc 1.66e-012 mol/l
- dilution of species in chemostat
- k1 0.00017 1/s
- diffusion of IPTG molecule
- k_diff 0.014 ?
- dilution_2 of species in E.coli
- kgr 0.000192 1/s
- maxc 1.66e-012 mol/l
- transcription
- k_tc 0.5 1/s
- replication of reverse pSB1A3
- kgr 0.003 1/s
- repression of reverse pSB1A3 replication
- kgr -0.003 ?
- maxc 4.746e-007 ?
- translation
- k_tl 0.1 1/s
- degradation of mRNAs
- k1 0.0048 1/s
- tetR-tetR dimerization
- kon 1.79e+011 l/(mol*s)
- degradation of proteins in E.coli
- k1 0.0023 1/s
- Laci-Laci dimerization
- kon 1.25e+007 l/(mol*s)
- cI (lambda)-cI (lambda) dimerization
- kon 1.79e+011 l/(mol*s)
- binding reverse-ptetR:tetR2
- kon 1e+008 l/(mol*s)
- LacI2-LacI2 dimerization
- kon 1e+014 l/(mol*s)
- binding reverse-pcI (lambda):cI2 (lambda)
- kon 1e+009 l/(mol*s)
- binding reverse-placI:lacI4
- kon 4e+011 l/(mol*s)
- IPTG:lacI4 binding
- kon 154000 l/(mol*s)