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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)