Team:USTC Software/detail

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{{Team:USTC_Software/Header}}
{{Team:USTC_Software/Header}}
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=Details=
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=Modeling Details of Repressilator=
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<br/>
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Key points of this modeling are:
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* LacI protein tends to form LacI dimer, which tends to form LacI tetramer further.
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* Only LacI tetramer binds with pLacI gene and thus repressing expression of its downstream genes.
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* TetR protein only forms dimer.
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* Only tetR dimer binds with pTet gene and thus repressing expression of its downstream genes.
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* One IPTG molecule binds with one LacI tetramer to form complex IPTG:LacI4.
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* cIlam protein only forms dimer.
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* Only cIlam dimer binds with pcIlam gene and thus repressing expression of its downstream genes.
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<br/>
An overview of species list is provided:  
An overview of species list is provided:  
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<br/>
[[Image:USTCS_graph1.JPG|600px|thumb|center]]
[[Image:USTCS_graph1.JPG|600px|thumb|center]]
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<br/>
where each species with its specific identifier has its own meaning:
where each species with its specific identifier has its own meaning:
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<br/>
*0:E_coli: E.Coli cell;
*0:E_coli: E.Coli cell;
*1:IPTG: IPTG in flask;
*1:IPTG: IPTG in flask;
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[[Image:USTCS_graph2.JPG|600px|thumb|center]]
[[Image:USTCS_graph2.JPG|600px|thumb|center]]
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Moreover, parameters of our modeling network are provided below:
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*Initial time: 0 s
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*Initial volumes:
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*Chemostat 0.1 l
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*E_coli 4.4247e-006 l
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*Initial concentrations:
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*0:E_coli 1.05e-013 mol/l
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*1:IPTG 0.001 mol/l
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*2:DNA 2.4e-009 mol/l
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*3:IPTG 0 mol/l
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*4:RNA 0 mol/l
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*5:RNA 0 mol/l
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*6:RNA 0 mol/l
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*7:tetR154 0 mol/l
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*8:lacI153 0 mol/l
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*9:cIlam156 0 mol/l
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*10:(tetR154)2 0 mol/l
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*11:(lacI153)2 0 mol/l
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*12:(cIlam156)2 0 mol/l
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*13:DNA;(tetR154)2 0 mol/l
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*14:(lacI153)4 0 mol/l
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*15:DNA;(cIlam156)2 0 mol/l
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*16:DNA;(cIlam156)2;(tetR154)2 0 mol/l
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*17:DNA;(lacI153)4 0 mol/l
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*18:DNA;(lacI153)4;(tetR154)2 0 mol/l
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*19:IPTG;(lacI153)4 0 mol/l
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*20:DNA;(cIlam156)2;(lacI153)4 0 mol/l
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*21:DNA;(cIlam156)2;(lacI153)4;(tetR154)2 0 mol/l
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*Initial values of global quantities:
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*ts 0
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*te 40000
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*s 0.001
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*t 0
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*Reaction parameters:
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*reproduction of Ecoli cell
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**  kgr 0.000192 1/s
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**  maxc 1.66e-012 mol/l
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*dilution of species in chemostat
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**  k1 0.00017 1/s
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*diffusion of IPTG molecule
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**  k_diff 0.014 ?
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*dilution_2 of species in E.coli
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**  kgr 0.000192 1/s
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**  maxc 1.66e-012 mol/l
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*transcription
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**  k_tc 0.5 1/s
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*replication of reverse pSB1A3
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**  kgr 0.003 1/s
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*repression of reverse pSB1A3 replication
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**  kgr -0.003 ?
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**  maxc 4.746e-007 ?
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*translation
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**  k_tl 0.1 1/s
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*degradation of mRNAs
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**  k1 0.0048 1/s
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*tetR-tetR dimerization
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**  kon 1.79e+011 l/(mol*s)
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*degradation of proteins in E.coli
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**  k1 0.0023 1/s
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*Laci-Laci dimerization
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**  kon 1.25e+007 l/(mol*s)
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*cI (lambda)-cI (lambda) dimerization
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**  kon 1.79e+011 l/(mol*s)
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*binding reverse-ptetR:tetR2
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**  kon 1e+008 l/(mol*s)
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*LacI2-LacI2 dimerization
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**  kon 1e+014 l/(mol*s)
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*binding reverse-pcI (lambda):cI2 (lambda)
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**  kon 1e+009 l/(mol*s)
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*binding reverse-placI:lacI4
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**  kon 4e+011 l/(mol*s)
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*IPTG:lacI4 binding
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**  kon 154000 l/(mol*s)

Latest revision as of 17:54, 27 October 2010

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:

USTCS graph1.JPG


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):

USTCS graph2.JPG

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)
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