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:

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)

@@ Line 44: / Line 44: @@
 [[Image:USTCS_graph2.JPG|600px|thumb|center]]
+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)

Team:USTC Software/detail

From 2010.igem.org

Latest revision as of 17:54, 27 October 2010

Modeling Details of Repressilator