Team:UANL Mty-Mexico/Modelling/Parameters

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Latest revision as of 17:18, 13 February 2012

Team: UANL_Mty-Mexico Team: UANL_Mty-Mexico

Modelling: Parameters

Parameters

Maximum transcription rates

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

Maximum Translation Rate

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

Dissociation Constants and Phosphorylation Rates

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
cI	O3 Binding (No cooperativity)	77.60592	O3 Binding (With cooperativity)	2.3542E-07	2	A,D
LasI-3-oxo-C12-HSL & LasR	0.011				1	C

Light-induced systems

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 Sensing

For 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

Degradation rates

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.

References

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.

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-             Modelling
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 Maximum transcription rates </span>
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 Maximum Translation Rate</span>
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 <span class="subtitle"><a name="Dissociation"></a>
 Dissociation Constants and Phosphorylation Rates</span>
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 <p>The OmpR phosphorylation is expressed through the following expressions adapted from Srividhya and Krishnaswamy, (2006), reference E:</p>
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 <p>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.</p>
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 <p>For 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.</p>
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 <p>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.</p>
 <p>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.</p>
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-   <li>Schuster, M, et al., (2004), Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR, Proc. NatL Acad. Sci. USA, Vol. 101, pp. 15833–15839. </li>
+   <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, AB, et al., (2005),  Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. Biosystems, pp. 178-87.</li>
+   <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, GK, et al., (1982), Quantitative model for gene regulation by A phage repressor, Proc. NatL Acad. Sci. USA, Vol. 79, pp. 1129-1133.</li>
+   <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 and Krishnaswamy, (2004), A simulation model of Escherichia coli osmoregulatory switch using E-CELL system, BMC Microbiology, 4:44</li>
+   <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, L, et al., (2001), The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli, PNAS, Vol. 98, No. 3, pp. 908-913.</li>
+   <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>
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      <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Quorum">Quorum Sensing</a></div>
      <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Degradation">Degradation rates</a></div>
+    <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#References">References</a></div>