Team:Paris Bettencourt/Modeling/Parameters

From 2011.igem.org

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<th>Parameter</th>
<th>Parameter</th>
<th>Description</th>
<th>Description</th>
-
<th>Value</th>
+
<th style="width:80px;">Value</th>
-
<th>Unit</th>
+
<th style="width:90px;">Unit </th>
<th>Reference</th>
<th>Reference</th>
</tr>
</tr>
<tr>
<tr>
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<td><img src='https://static.igem.org/mediawiki/2011/6/63/Beta_const.png' style='height:22px;' /></td>
+
<td><img src='https://static.igem.org/mediawiki/2011/9/98/Xconcentration.png' style='height:22px;' /></td>
 +
<td>Concentration of X</td>
 +
<td>NA</td>
 +
<td>molecules <br>per cell</td>
 +
<td>Notation convention</td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/c/c2/TX.png' style='height:22px;' /></td>
 +
<td>Delay due to protein X production and maturation</td>
 +
<td>NA</td>
 +
<td>s</td>
 +
<td>Notation convention</td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/6/63/Beta_const.png' style='height:28px;' /></td>
<td>Maximal production rate of pVeg promoter (constitutive)</td>
<td>Maximal production rate of pVeg promoter (constitutive)</td>
-
<td>???</td>
+
<td>0.02</td>
-
<td>molecules.s<sup>-1</sup> <br> or pops</td>
+
<td>molecules.s<sup>-1</sup> <br>or pops</td>
-
<td>Estimated</td>
+
<td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Promoter_strengths">justification</a></td>
</tr>
</tr>
<tr>
<tr>
-
<td><img src='https://static.igem.org/mediawiki/2011/d/d9/BetapLac.png' style='height:22px;' /></td>
+
<td><img src='https://static.igem.org/mediawiki/2011/d/d9/BetapLac.png' style='height:28px;' /></td>
-
<td>Maximal production rate of pLac promoter</td>
+
<td>Maximal production rate of pHyperSpank promoter</td>
<td>0.02</td>
<td>0.02</td>
-
<td>molecules.s<sup>-1</sup> or pops</td>
+
<td>molecules.s<sup>-1</sup> <br>or pops</td>
-
<td>Estimated</td>
+
<td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Promoter_strengths">justification</a></td>
</tr>
</tr>
<tr>
<tr>
-
<td><img src='https://static.igem.org/mediawiki/2011/5/5d/BetapT7.png' style='height:22px;' /></td>
+
<td><img src='https://static.igem.org/mediawiki/2011/5/5d/BetapT7.png' style='height:28px;' /></td>
<td>Maximal production rate of pT7 promoter</td>
<td>Maximal production rate of pT7 promoter</td>
<td>0.02</td>
<td>0.02</td>
-
<td>molecules.s<sup>-1</sup> or pops</td>
+
<td>molecules.s<sup>-1</sup> <br>or pops</td>
-
<td>Estimated</td>
+
<td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Promoter_strengths">justification</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/1/18/BetapComK.png' style='height:22px;' /></td>
 +
<td>Maximal production rate of pComK promoter</td>
 +
<td> 0.049</td>
 +
<td>molecules.s<sup>-1</sup> <br>or pops</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/6/68/BetapComS.png' style='height:22px;' /></td>
 +
<td>Maximal production rate of pComS promoter</td>
 +
<td>0.057</td>
 +
<td>molecules.s<sup>-1</sup> <br>or pops</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/b/bd/BetapComG.png' style='height:22px;' /></td>
 +
<td>Maximal production rate of pComG promoter</td>
 +
<td>0.02</td>
 +
<td>molecules.s<sup>-1</sup> <br>or pops</td>
 +
<td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Promoter_strengths">justification</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/f/fc/AlphaComK.png' style='height:22px;' /></td>
 +
<td>Basal production rate of pComK promoter</td>
 +
<td>0.0028</td>
 +
<td>molecules.s<sup>-1</sup> <br>or pops</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/f/fc/AlphaComG.png' style='height:22px;' /></td>
 +
<td>Basal production rate of pComG promoter</td>
 +
<td>0.028</td>
 +
<td>molecules.s<sup>-1</sup> <br>or pops</td>
 +
<td>Is roughly one order of magnitude higher than production rate of pComK<a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[4]</a></td>
</tr>
</tr>
<tr>
<tr>
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<td>Dissociation constant for IPTG to LacI</td>
<td>Dissociation constant for IPTG to LacI</td>
<td>1200</td>
<td>1200</td>
-
<td>molecules per cell</td>
+
<td>molecules <br>per cell</td>
<td><a href='https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1'>Aberdeen 2009 wiki</a></td>
<td><a href='https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1'>Aberdeen 2009 wiki</a></td>
</tr>
</tr>
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<td>Dissociation constant for LacI to LacO (pLac)</td>
<td>Dissociation constant for LacI to LacO (pLac)</td>
<td>700</td>
<td>700</td>
-
<td>molecules per cell</td>
+
<td>molecules <br>per cell</td>
<td><a href='https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1'>Aberdeen 2009 wiki</a></td>
<td><a href='https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1'>Aberdeen 2009 wiki</a></td>
</tr>
</tr>
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<td><img src='https://static.igem.org/mediawiki/2011/5/5d/KT7.png' style='height:22px;' /></td>
<td><img src='https://static.igem.org/mediawiki/2011/5/5d/KT7.png' style='height:22px;' /></td>
<td>Dissociation constant for T7 RNA polymerase to pT7</td>
<td>Dissociation constant for T7 RNA polymerase to pT7</td>
-
<td>3</td>
+
<td>10</td>
-
<td>molecules per cell</td>
+
<td>molecules <br>per cell</td>
-
<td>Estimated ADD EXPLANATION</td>
+
<td>We used the classic assumption 1nM=1 molecule per cell and <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[1]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/5/5b/KcomK.png' style='height:22px;' /></td>
 +
<td>Dissociation constant for ComK to pComK</td>
 +
<td>110</td>
 +
<td>molecules <br>per cell</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/a/a5/KcomS.png' style='height:22px;' /></td>
 +
<td>Dissociation constant for ComK to pComS</td>
 +
<td>100</td>
 +
<td>molecules <br>per cell</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/9/9b/Gamma_big_ComK.png' style='height:22px;' /></td>
 +
<td>ComK concentration for half maximal degradation</td>
 +
<td>500</td>
 +
<td>molecules <br>per cell</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/5/54/Gamma_big_ComS.png' style='height:22px;' /></td>
 +
<td>ComS concentration for half maximal degradation</td>
 +
<td>50</td>
 +
<td>molecules <br>per cell</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/6/64/NIPTG.png' style='height:22px;' /></td>
 +
<td>Hill coefficient for LacI/IPTG interaction</td>
 +
<td>2</td>
 +
<td>NA</td>
 +
<td><a href='https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1'>Aberdeen 2009 wiki</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/e/e0/NLacI.png' style='height:22px;' /></td>
 +
<td>Hill coefficient for LacI/pHyperSpank interaction</td>
 +
<td>2</td>
 +
<td>NA</td>
 +
<td><a href='https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1'>Aberdeen 2009 wiki</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/5/5d/NComK.png' style='height:22px;' /></td>
 +
<td>Hill coefficient for ComK/pComK and ComK/pComG (positive feedback) interaction</td>
 +
<td>2</td>
 +
<td>NA</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/e/ea/NComS.png' style='height:22px;' /></td>
 +
<td>Hill coefficient for ComK/pComS (negative feedback) interaction</td>
 +
<td>5</td>
 +
<td>NA</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
</tr>
</tr>
<tr>
<tr>
<td><img src='https://static.igem.org/mediawiki/2011/a/a3/Gamma_protein.png' style='height:22px;'  /></td>
<td><img src='https://static.igem.org/mediawiki/2011/a/a3/Gamma_protein.png' style='height:22px;'  /></td>
<td>Translation rate of proteins</td>
<td>Translation rate of proteins</td>
-
<td>1</td>
+
<td>0.9</td>
<td>s<sup>-1</sup></td>
<td>s<sup>-1</sup></td>
-
<td>Estimated ADD EXPLANATION</td>
+
<td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Protein_translation_rate_justification">justification</a></td>
</tr>
</tr>
<tr>
<tr>
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<td>s<sup>-1</sup></td>
<td>s<sup>-1</sup></td>
<td>Calculated with a 40 min generation time. See explanation</td>
<td>Calculated with a 40 min generation time. See explanation</td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/6/65/DeltaComK.png' style='height:22px;' /></td>
 +
<td>Unrepressed degradation rate of ComK</td>
 +
<td>1.4x10<sup>-3</sup></td>
 +
<td>s<sup>-1</sup></td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/d/de/DeltaComS.png' style='height:22px;' /></td>
 +
<td>Unrepressed degradation rate of ComS</td>
 +
<td>1.4x10<sup>-3</sup></td>
 +
<td>s<sup>-1</sup></td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
</tr>
</tr>
<tr>
<tr>
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<td>2.88x10<sup>-3</sup></td>
<td>2.88x10<sup>-3</sup></td>
<td>s<sup>-1</sup></td>
<td>s<sup>-1</sup></td>
-
<td>Uri Alon (To Be Confirmed)</td>
+
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[4]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/9/95/Delta_GFP.png' style='height:22px;' /></td>
 +
<td>Degradation rate of GFP</td>
 +
<td>10<sup>-4</sup></td>
 +
<td>s<sup>-1</sup></td>
 +
<td><a href="http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=105188&ver=2&hlid=56398">BioNumbers</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/1/1c/Delta_RFP.png' style='height:22px;' /></td>
 +
<td>Degradation rate of RFP</td>
 +
<td>10<sup>-4</sup></td>
 +
<td>s<sup>-1</sup></td>
 +
<td>Estimated equal to GFP degradation rate</td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/6/67/TCFP.png' style='height:22px;'/></td>
 +
<td>Delay due to CFP production and maturation</td>
 +
<td>360</td>
 +
<td>s</td>
 +
<td>Estimated equal to GFP delay (similar molecules)</td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/1/1e/TYFP.png' style='height:22px;'/></td>
 +
<td>Delay due to YFP production and maturation</td>
 +
<td>360</td>
 +
<td>s</td>
 +
<td>Estimated equal to GFP delay (similar molecules)</td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/e/eb/TComK.png' style='height:22px;'/></td>
 +
<td>Delay due to ComK production and maturation</td>
 +
<td>300</td>
 +
<td>s</td>
 +
<td>Arbitrary</td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/a/a7/TComS.png' style='height:22px;'/></td>
 +
<td>Delay due to ComS production and maturation</td>
 +
<td>300</td>
 +
<td>s</td>
 +
<td>Arbitrary</td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/a/a0/Trepress.png' style='height:22px;'/></td>
 +
<td>Delay for ComS repression by ComK</td>
 +
<td>714</td>
 +
<td>s</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/a/a8/TT7.png' style='height:22px;'/></td>
 +
<td>Delay due tT7 RNA polymerase production and maturation</td>
 +
<td>300</td>
 +
<td>s</td>
 +
<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[2]</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/f/f0/TGFP.png' style='height:22px;'/></td>
 +
<td>Delay due GFP production and maturation</td>
 +
<td>360</td>
 +
<td>s</td>
 +
<td><a href="http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=102972&ver=8">BioNumbers</a></td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/b/bc/TRFP.png' style='height:22px;'/></td>
 +
<td>Delay due RFP production and maturation</td>
 +
<td>360</td>
 +
<td>s</td>
 +
<td>Estimated equal to GFP delay (similar molecules)</td>
 +
</tr>
 +
<tr>
 +
<td><img src='https://static.igem.org/mediawiki/2011/9/9c/TmRNA.png' style='height:22px;' /></td>
 +
<td>Delay due to mRNA production</td>
 +
<td>30</td>
 +
<td>s</td>
 +
<td><a href="http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=104902&ver=5&hlid=58815 2kb">BioNumbers</a> with an approximation: all our contructs are around 1-2kb</td>
</tr>
</tr>
-
 
</table>
</table>
 +
 +
<div id="citation_box">
 +
<p id="references">References</p>
 +
<ol>
 +
<li><i>Cytoplasmic expression of a reporter gene by co-delivery of T7 RNA polymerase and T7 promoter sequence with cationic liposomes</i>,
 +
X Gao and L Huang, accessible <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC309671/pdf/nar00061-0090.pdf">here</a></li>
 +
<li><i>Molecular Biology for Masters</i> by Dr. G. R. Kantharaj, accessible <a href="http://mol-biol4masters.masters.grkraj.org/html/Prokaryotic_DNA_Replication13-T7_Phage_DNA_Replication.htm">here</a></li>
 +
<li><i>An excitable gene regulatory circuit induces transient cellular differentiation</i>,
 +
Süel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB, Nature. 2006 Mar 23;440(7083):545-50.</li>
 +
<li><i>Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits</i>,
 +
Çağatay, Tolga and Turcotte, Marc and Elowitz, Michael B. and Garcia-Ojalvo, Jordi and Süel, Gürol M, Cell, 2009 139 (3). pp. (Supplementary Data) </li>
 +
<li><i>An Introduction to Systems Biology: Design Principles of Biological Circuits</i>, Uri Alon</li>
 +
<ol>
 +
</div>
 +
<br/>
 +
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Latest revision as of 20:39, 21 September 2011

Team IGEM Paris 2011

Parameters

Parameter Description Value Unit Reference
Concentration of X NA molecules
per cell		 Notation convention
Delay due to protein X production and maturation NA s Notation convention
Maximal production rate of pVeg promoter (constitutive) 0.02 molecules.s-1
or pops		 Estimated, see the justification
Maximal production rate of pHyperSpank promoter 0.02 molecules.s-1
or pops		 Estimated, see the justification
Maximal production rate of pT7 promoter 0.02 molecules.s-1
or pops		 Estimated, see the justification
Maximal production rate of pComK promoter 0.049 molecules.s-1
or pops		 [3]
Maximal production rate of pComS promoter 0.057 molecules.s-1
or pops		 [3]
Maximal production rate of pComG promoter 0.02 molecules.s-1
or pops		 Estimated, see the justification
Basal production rate of pComK promoter 0.0028 molecules.s-1
or pops		 [3]
Basal production rate of pComG promoter 0.028 molecules.s-1
or pops		 Is roughly one order of magnitude higher than production rate of pComK[4]
Dissociation constant for IPTG to LacI 1200 molecules
per cell		 Aberdeen 2009 wiki
Dissociation constant for LacI to LacO (pLac) 700 molecules
per cell		 Aberdeen 2009 wiki
Dissociation constant for T7 RNA polymerase to pT7 10 molecules
per cell		 We used the classic assumption 1nM=1 molecule per cell and [1]
Dissociation constant for ComK to pComK 110 molecules
per cell		 [3]
Dissociation constant for ComK to pComS 100 molecules
per cell		 [3]
ComK concentration for half maximal degradation 500 molecules
per cell		 [3]
ComS concentration for half maximal degradation 50 molecules
per cell		 [3]
Hill coefficient for LacI/IPTG interaction 2 NA Aberdeen 2009 wiki
Hill coefficient for LacI/pHyperSpank interaction 2 NA Aberdeen 2009 wiki
Hill coefficient for ComK/pComK and ComK/pComG (positive feedback) interaction 2 NA [3]
Hill coefficient for ComK/pComS (negative feedback) interaction 5 NA [3]
Translation rate of proteins 0.9 s-1 Estimated, see the justification
Dilution rate in exponential phase 2.88x10-4 s-1 Calculated with a 40 min generation time. See explanation
Unrepressed degradation rate of ComK 1.4x10-3 s-1 [3]
Unrepressed degradation rate of ComS 1.4x10-3 s-1 [3]
Degradation rate of mRNA 2.88x10-3 s-1 [4]
Degradation rate of GFP 10-4 s-1 BioNumbers
Degradation rate of RFP 10-4 s-1 Estimated equal to GFP degradation rate
Delay due to CFP production and maturation 360 s Estimated equal to GFP delay (similar molecules)
Delay due to YFP production and maturation 360 s Estimated equal to GFP delay (similar molecules)
Delay due to ComK production and maturation 300 s Arbitrary
Delay due to ComS production and maturation 300 s Arbitrary
Delay for ComS repression by ComK 714 s [3]
Delay due tT7 RNA polymerase production and maturation 300 s [2]
Delay due GFP production and maturation 360 s BioNumbers
Delay due RFP production and maturation 360 s Estimated equal to GFP delay (similar molecules)
Delay due to mRNA production 30 s BioNumbers with an approximation: all our contructs are around 1-2kb

References

  1. Cytoplasmic expression of a reporter gene by co-delivery of T7 RNA polymerase and T7 promoter sequence with cationic liposomes, X Gao and L Huang, accessible here
  2. Molecular Biology for Masters by Dr. G. R. Kantharaj, accessible here
  3. An excitable gene regulatory circuit induces transient cellular differentiation, Süel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB, Nature. 2006 Mar 23;440(7083):545-50.
  4. Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits, Çağatay, Tolga and Turcotte, Marc and Elowitz, Michael B. and Garcia-Ojalvo, Jordi and Süel, Gürol M, Cell, 2009 139 (3). pp. (Supplementary Data)
  5. An Introduction to Systems Biology: Design Principles of Biological Circuits, Uri Alon

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