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From 2010.igem.org

Modeling Details of Toggle Switch

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 and one aTc molecule binds with one tetR dimer to form complex aTc:TetR2.

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 and GFP;
• 5:RNA: mRNA of LacI;
• 6:tetR154: tetR protein;
• 7:GFP12923: GFP;
• 8:lacI153: LacI protein;
• 9:(tetR154)2: tetR dimer;
• 10:(lacI153)2: LacI dimer;
• 11:DNA;(tetR154)2: complex of tetR dimer binding to pTet gene of plasmid DNA;
• 12:(lacI153)4: LacI tetramer;
• 13:DNA;(lacI153)4: complex of LacI tetramer binding to pLacI gene of plasmid DNA;
• 14:DNA;(lacI153)4;(tetR154)2: complex of plasmid DNA with both pLacI and pTet genes bound with LacI tetramer and tetR dimer, respectively;
• 15:IPTG;(lacI153)4: complex of IPTG binding with LacI tetramer;

Since there are 65 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 (we spend much efforts on tuning parameters) based on papers and estimates together:

• Initial time: 0 s
• Initial volumes:
  • Flask： 0.4 l
  • E_coli： 1.6856e-012 l

• Initial concentrations:
  • 0:E_coli： 1e-020 mol/l
  • 1:IPTG： 0 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:tetR154: 0 mol/l
  • 7:GFP12923: 0 mol/l
  • 8:lacI153: 0 mol/l
  • 9:(tetR154)2: 0 mol/l
  • 10:(lacI153)2: 0 mol/l
  • 11:DNA;(tetR154)2: 0 mol/l
  • 12:(lacI153)4: 0 mol/l
  • 13:DNA;(lacI153)4: 0 mol/l
  • 14:DNA;(lacI153)4;(tetR154)2: 0 mol/l
  • 15:IPTG;(lacI153)4: 0 mol/l

• Reaction parameters:
  • reproduction of Ecoli cell
    • growth constant: 0.000192 1/s
    • maximum concentration: 1.66e-012 mol/l
  • diffusion of IPTG molecule
    • diffusion constant: 0.014 1/s
  • transcription
    • transcription rate of pTet/pLacI: 0.5 1/s
  • replication of reverse pSB3C5
    • replication constant: 0.003 1/s
  • repression of reverse pSB3C5 replication
    • max concentration of pSB3C5: 2.847e-008 mol/l
  • translation
    • translation rate: 0.1 1/s
  • degradation of mRNAs
    • degradation of mRNA molecules: 0.0048 1/s
  • degradation of proteins in E.coli_3
    • degradation rate of proteins: 0.0023 1/s
  • Laci-Laci dimerization
    • kon: 1.25e+007 l/(mol*s)
    • koff: 10 1/s
  • binding forward-ptetR:tetR2
    • kon: 1e+008 l/(mol*s)
    • koff: 0.001 1/s
  • tetR-tetR dimerization_2
    • kon: 4e+011 1/(mol*s)
    • koff: 10 1/s
  • LacI2-LacI2 dimerization
    • kon: 1e+014 l/(mol*s)
    • koff: 10 1/s
  • binding reverse-placI:lacI4
    • kon: 4e+011 l/(mol*s)
    • koff: 0.04 1/s
  • IPTG:lacI4 binding
    • kon: 154000 l/(mol*s)
    • koff: 0.2 1/s