Team:Paris Bettencourt/Modeling/Parameters

From 2011.igem.org

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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/2011/6/63/Beta_const.png' style='height:22px;' /></td>
<td>Maximal production rate of pVeg promoter (constitutive)</td>
<td>Maximal production rate of pVeg promoter (constitutive)</td>
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<td>???</td>
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<td>0.02</td>
<td>molecules.s<sup>-1</sup> <br>or pops</td>
<td>molecules.s<sup>-1</sup> <br>or pops</td>
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<td>Estimated</td>
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<td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Promoter_strengths">justification</a></td>
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<td>0.02</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>
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<td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Promoter_strengths">justification</a></td>
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<td>0.02</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>
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<td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Promoter_strengths">justification</a></td>
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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>
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<td>4.8</td>
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<td>10</td>
<td>molecules <br>per cell</td>
<td>molecules <br>per cell</td>
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<td>Estimated ADD EXPLANATION</td>
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<td>We used the classic assumption 1nM=1 molecule per cell and <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/tRNA_diffusion#references">[1]</a></td>
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<td>s<sup>-1</sup></td>
<td>s<sup>-1</sup></td>
<td>Uri Alon (To Be Confirmed)</td>
<td>Uri Alon (To Be Confirmed)</td>
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</tr>
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<tr>
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<td><img src='https://static.igem.org/mediawiki/2011/9/95/Delta_GFP.png' style='height:22px;' /></td>
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<td>Degradation rate of GFP</td>
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<td>10<sup>-4</sup></td>
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<td>s<sup>-1</sup></td>
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<td><a href="http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=105188&ver=2&hlid=56398">BioNumbers</a></td>
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<td><img src='https://static.igem.org/mediawiki/2011/1/1c/Delta_RFP.png' style='height:22px;' /></td>
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<td>Degradation rate of RFP</td>
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<td>10<sup>-4</sup></td>
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<td>s<sup>-1</sup></td>
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<td>Estimated equal to GFP degradation rate</td>
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<td>300</td>
<td>300</td>
<td>s</td>
<td>s</td>
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<td>http://mol-biol4masters.masters.grkraj.org/html/Prokaryotic_DNA_Replication13-T7_Phage_DNA_Replication.htm</td>
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<td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/tRNA_diffusion#references">[2]</a></td>
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<td><img src='https://static.igem.org/mediawiki/2011/f/f0/TGFP.png' style='height:22px;'/></td>
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<td>Delay due GFP production and maturation</td>
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<td>360</td>
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<td>s</td>
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<td><a href="http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=102972&ver=8">BioNumbers</a></td>
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</tr>
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<td><img src='https://static.igem.org/mediawiki/2011/b/bc/TRFP.png' style='height:22px;'/></td>
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<td>Delay due RFP production and maturation</td>
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<td>360</td>
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<td>s</td>
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<td>Estimated equal to GFP delay (similar molecules)</td>
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<td>30</td>
<td>30</td>
<td>s</td>
<td>s</td>
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<td>http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=104902&ver=5&hlid=58815 2kb/(50b/s) --> approximation: all our contructs are around 2kb</td>
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<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>
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</table>
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<div id="citation_box">
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<p id="references">References</p>
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<ol>
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<li><i>Cytoplasmic expression of a reporter gene by co-delivery of T7 RNA polymerase and T7 promoter sequence with cationic liposomes</i>,
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X Gao and L Huang, accessible <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC309671/pdf/nar00061-0090.pdf">here</a></li>
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<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>
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<ol>
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</div>
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<br/>
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Revision as of 11:38, 12 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 pLac 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
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]
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
Degradation rate of mRNA 2.88x10-3 s-1 Uri Alon (To Be Confirmed)
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 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

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