Team:UANL Mty-Mexico/Modelling/Parameters
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- | Modelling | + | Modelling: Parameters |
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- | References | + | <a name="References"></a>References |
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<ol> | <ol> | ||
<li><a href="https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters">https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters</a></li> | <li><a href="https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters">https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters</a></li> | ||
- | <li>Schuster | + | <li>Schuster M, Urbanowski L, Greenberg EP (2004) Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR. <i>Proc Natl Acad Sci USA</i> <b>101</b>:15833–15839. </li> |
- | <li>Goryachev | + | <li>Goryachev AB, Toh DJ, Lee T (2005) Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. <i>Biosystems</i> <b>83</b>:178-87.</li> |
- | <li>Ackers | + | <li>Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulation by A phage repressor. <i>Proc Natl Acad Sci USA</i> <b>79</b>:1129-1133.</li> |
- | <li>Srividhya | + | <li>Srividhya KV, Krishnaswamy S (2004) A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. <i>BMC Microbiology</i> <b>4</b>:44.</li> |
- | <li>Qin | + | <li>Qin L, Yoshida T, Inouye M (2001) The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in <i>Escherichia coli</i>. <i>Proc Natl Acad Sci USA</i><b> 98</b>:908-913.</li> |
</ol> | </ol> | ||
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Latest revision as of 17:18, 13 February 2012
![banner-main](https://static.igem.org/mediawiki/igem.org/3/38/Notebook-3.jpg)
Gene |
Maximum Transcription Rate (molecules min.1) |
Source |
Red Photoreceptor |
1.879194631 |
A |
ompR |
5.857740586 |
A |
mnt |
14.58333333 |
A |
tetR |
6.363636364 |
A |
cI |
5.6 |
A |
lacI |
3.723404255 |
A |
cI434 |
6.278026906 |
A |
lasI |
1.20E-01 |
B |
lasR |
2.88E-01 |
B |
GFP |
5.533596838 |
A |
SBFP2 |
5.833333333 |
A |
CFP |
5.511811024 |
A |
YFP |
5.511811024 |
A |
RFP |
5.809128631 |
A |
Protein |
Maximum Translation Rate (molecules min.1) |
Source |
Red Photoreceptor |
3.22147651 |
A |
OmpR |
10.041841 |
A |
Mnt |
25 |
A |
TetR |
10.90909091 |
A |
cI |
9.6 |
A |
LacI |
6.382978723 |
A |
cI434 |
10.76233184 |
A |
LasI |
9.60E-01 |
B |
LasR |
9.60E-01 |
B |
GFP |
9.486166008 |
A |
SBFP2 |
10 |
A |
CFP |
9.448818898 |
A |
YFP |
9.448818898 |
A |
RFP |
9.958506224 |
A |
Transcription factors/DNA-binding molecules |
||||||
Protein |
Dissociation constant (nM) |
Hill coefficient |
Source |
|||
CcaR-Phosphate |
N/A |
|
A |
|||
OmpR-pompC |
31.4 |
|
A |
|||
Mnt |
50 |
1 |
A |
|||
TetR |
0.179 |
3 |
A |
|||
LacI |
800 |
2 |
A |
|||
cI434 |
40 |
2 |
A |
|||
cI |
O2 Binding (No cooperativity) |
77.60592 |
O2 Binding (With cooperativity) |
1.7599E-08 |
2 |
A,D |
O3 Binding (No cooperativity) |
77.60592 |
O3 Binding (With cooperativity) |
2.3542E-07 |
A,D |
||
LasI-3-oxo-C12-HSL & LasR |
0.011 |
1 |
C |
The OmpR phosphorylation is expressed through the following expressions adapted from Srividhya and Krishnaswamy, (2006), reference E:
IMAGEN
OmpR-P dephosphorylation rate (from Qin, L, et al., 2001, reference F): 17 min when red light is present / 56 min when far-red light is present.
Quorum SensingFor simplicity just the parameters of the LasI/LasR quorum sensing system are shown, because they are supposed to be equivalent according to the used general Quorum Sensing model.
Quorum sensing |
||
Parameter |
Constant |
Source |
Transcription of lasI |
1.20E-01 molecules min.1 |
C |
Translation of lasI |
9.60E-01 molecules min.1 |
C |
Degradation of lasI mRNA |
3.60E-01 min.1 |
C |
Degradation of LasI |
3.00E-03 min.1 |
C |
Transcription of lasR |
2.88E-01 molecules min.1 |
C |
Translation of lasR |
9.60E-01 molecules min.1 |
C |
Degradation of lasR mRNA |
3.60E-01 min.1 |
C |
Degradation of LasR |
1.20E-02 min.1 |
C |
Enzymatic activity LasI |
27 min.1 |
C |
Autoinductor diffusibility |
2.40E+01 min.1 |
C |
Binding between LasR/3-oxo-C12-HSL |
6.00E-03 molecules min.1 |
C |
Dissociation of LasR/3-oxo-C12-HSL |
1.80E-01 min.1 |
C |
Dimerization LasR/3-oxo-C12-HSL |
1.80E-03 molecules min.1 |
C |
Dissociation of the dimer |
6.00E-01 min.1 |
C |
Following the recommendations of team Peking 2009, we set all mRNAs half-lives to 4.4 min and, supposing that all regulatory and reporter gene would have an LVG tag attached, all protein half-lives were set to 40 min, with the exception of phosphorylated OmpR, whose case is exposed on the last sections.
Considering a cell division rate of 30 min, then, the degradation rates for mRNA are: 1/4.4 + 1/30 min, and the protein degradation rates are: 1/40 + 1/30 min.
- https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
- Schuster M, Urbanowski L, Greenberg EP (2004) Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR. Proc Natl Acad Sci USA 101:15833–15839.
- Goryachev AB, Toh DJ, Lee T (2005) Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. Biosystems 83:178-87.
- Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulation by A phage repressor. Proc Natl Acad Sci USA 79:1129-1133.
- Srividhya KV, Krishnaswamy S (2004) A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. BMC Microbiology 4:44.
- Qin L, Yoshida T, Inouye M (2001) The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli. Proc Natl Acad Sci USA 98:908-913.