Team:UANL Mty-Mexico/Modelling/Parameters

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             Modelling
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             Modelling: Parameters
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  <p><b>Parameters</b></p>
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<p><b>Maximum transcription rates </b></p>
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<span class="subtitle"><a name="Transcription"></a>
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Maximum transcription rates </span>
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         <p>Gene</p>
         <p>Gene</p>
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<p><b>Maximum Translation Rate</b></p>
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<span class="subtitle"><a name="Translation"></a>
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Maximum Translation Rate</span>
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         <p>Protein</p>
         <p>Protein</p>
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<p><b>Dissociation Constants and Phosphorylation Rates</b></p>
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<span class="subtitle"><a name="Dissociation"></a>
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Dissociation Constants and Phosphorylation Rates</span>
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         <p>Transcription factors/DNA-binding molecules</p>
         <p>Transcription factors/DNA-binding molecules</p>
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<p><b>Light-induced systems:</b></p>
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<div class="br2"></div><div class="br2"></div><div class="br2"></div>           
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          <a name="Light"></a>Light-induced systems
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<p>The OmpR phosphorylation is expressed through the following expressions adapted from Srividhya and Krishnaswamy, (2006), reference E:</p>
<p>The OmpR phosphorylation is expressed through the following expressions adapted from Srividhya and Krishnaswamy, (2006), reference E:</p>
<p>IMAGEN</p>
<p>IMAGEN</p>
<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>
<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><b>Quorum Sensing</b></p>
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<span class="subtitle"><a name="Quorum"></a>Quorum Sensing
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</span>
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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>
<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>Quorum sensing</p>
         <p>Quorum sensing</p>
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<p><b>Degradation rates</b></p>
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<span class="subtitle"><a name="Degradation"></a>
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Degradation rates </span>
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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>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>
<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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<p><b>References:</b></p>
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<p><br></p>
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<div class="br2"></div><div class="br2"></div><div class="br2"></div>           
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          <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>
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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>
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   <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>
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   <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>
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   <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>
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   <li>Srividhya and Krishnaswamy, (2004), A simulation model of Escherichia coli osmoregulatory switch using E-CELL system, BMC Microbiology, 4:44</li>
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   <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>
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   <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>
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   <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>
<p><br></p>
<p><br></p>
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     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/The_Code">The Code</a></div>
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     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Transcription">Transcription</a></div>
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     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism">Mechanism</a></div>
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     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Translation">Translation</a></div>
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     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Circuit">Genetic Circuit</a></div>
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     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Dissociation">Dissociation</a></div>
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     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Applications">Applications</a></div>
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     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Light">Light induction</a></div>
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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>
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    <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Degradation">Degradation rates</a></div>
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    <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#References">References</a></div>
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Latest revision as of 17:18, 13 February 2012

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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

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


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
  1. https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
  2. 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.
  3. 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.
  4. Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulation by A phage repressor. Proc Natl Acad Sci USA 79:1129-1133.
  5. Srividhya KV, Krishnaswamy S (2004) A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. BMC Microbiology 4:44.
  6. 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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