Team:KULeuven/Modeling

From 2008.igem.org

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{{:Team:KULeuven/Tools/Navigation_Bar}}
{{:Team:KULeuven/Tools/Navigation_Bar}}
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[[Image:kulbanner.jpg|960px]]
+
= Modeling =
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=Modeling=
+
* [https://static.igem.org/mediawiki/2008/1/19/Numbers.xls Numbers.xls]
-
 
+
-
* [[Image:Numbers.xls]]
+
* [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html Synthetic biology: Engineering Escherichia coli to see light]
* [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html Synthetic biology: Engineering Escherichia coli to see light]
-
==CellDesigner==
+
== CellDesigner ==
-
===[https://static.igem.org/mediawiki/2008/d/d9/Output_v2.zip Output] ===
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=== [https://static.igem.org/mediawiki/2008/d/d9/Output_v2.zip Output] ===
 +
 
 +
[[Image:output_v2.png|500px|center|Output]]
 +
 
 +
{| border="1"
 +
|+ Parameter values Output
 +
! Name !! Value !! Reference
 +
|-
 +
! Degradation
 +
|  ||
 +
|-
 +
| CFP (protein) || 1.05E-4 /s || [https://2007.igem.org/ETHZ/Parameters link]
 +
|-
 +
| CFP (mRNA) || 0.0023 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
 +
! Transcription Rate
 +
|-
 +
| CFP || OmpF dependent ||
 +
|-
 +
! Translation Rate
 +
|-
 +
| CFP || 0.167 /s || Based on effenciency RBS
 +
|}
-
[[Image:output_v2.png|400px|center|Output]]
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[[Image:Sim_output_1.png|500px|center|Output]]
 +
[[Image:Sim_output_2.png|500px|center|Output]]
 +
[[Image:Sim_output_3.png|500px|center|Output]]
===[https://static.igem.org/mediawiki/2008/4/47/Celldeath.zip Cell Death]===
===[https://static.igem.org/mediawiki/2008/4/47/Celldeath.zip Cell Death]===
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[[Image:celldeath.png|400px|center|Cell Death]]
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[[Image:celldeath.png|800px|center|Cell Death]]
{| border="1"
{| border="1"
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| LuxR (protein) || 0.0010 /s ||
| LuxR (protein) || 0.0010 /s ||
|-
|-
-
| LuxR (mRNA) || 0.00227 /s ||
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| LuxR (mRNA) || 0.00227 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
|-
|-
| CcdB (protein) || 7.7E-5 /s || [http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]
| CcdB (protein) || 7.7E-5 /s || [http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]
|-
|-
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| CcdB (mRNA)|| 0.00231 /s ||
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| CcdB (mRNA)|| 0.00231 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
|-
|-
-
| HSL || 1.02E-6/s ||
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| HSL || 1.02E-6/s || [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
|-
|-
! Dissociation Rate
! Dissociation Rate
|-
|-
-
| HSL-LuxR || 1E-6 M/L || verified estimate
+
| k<sub>a</sub> (HSL+LuxR) || 1E6 /s || chosen to be relatively (to the other rate constants) high and such that K<sub>d</sub> equals 1E-6  
 +
|-
 +
| k<sub>d</sub> (HSL+LuxR) || 1 /s ||
|-
|-
! Dissociation Constant
! Dissociation Constant
|-
|-
-
| Binding LuxR on LuxPromotor || 1E-9 M/L || [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=321501 link]
+
| HSL-LuxR || 1E-6 M/L || [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]
 +
|-
 +
| Binding LuxR on LuxPromotor || 1E-9 M/L || [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]
 +
|-
 +
! Transcription Rate
 +
|-
 +
| LuxR (constitutive promotor) || 0.025 mRNA/s || see sections on Constitutive Promotors & E. coli transcription Rates
 +
|-
 +
| CcdB (LuxR repressor) || k_1*K_m^n/(K_m^n + [LuxR]^n) = 0.025*1E-9/(1E-9^1+[LuxR]) ||
 +
|-
|}
|}
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[[Image:inverter_v4.png|400px|center|Inverter]]
[[Image:inverter_v4.png|400px|center|Inverter]]
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===[https://static.igem.org/mediawiki/2008/0/05/Memory.zip Memory]===
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{| border="1"
-
 
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|+ Parameter values Inverter
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[[Image:Memory.png|400px|center|Memory]]
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! Name !! Value !! Reference
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+
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===[https://static.igem.org/mediawiki/2008/7/72/Filter.zip Filter]===
+
-
 
+
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[[Image:ModelFilter.png|400px|center|Filter]]
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-
 
+
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===[https://static.igem.org/mediawiki/2008/8/8c/PulseGenerator.zip Pulse Generator]===
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-
 
+
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[[Image:PulseGenerator.png|400px|center|Pulse Generator]]
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-
 
+
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==Kinetic Constants==
+
-
 
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{| width=100% border="1" cellspacing="0"
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! colspan="3" | List of Kinetic Parameters
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-
|-valign="top"
+
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| rowspan="4" width=20% | Output
+
-
| transcription rate CFP
+
-
|
+
|-
|-
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| translation rate CFP
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! Degradation
-
|
+
|  ||  
|-
|-
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| degradation rate CFP (RNA)
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| LuxI (protein) || 0.00231 /s ||
-
|
+
|-
|-
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| degradation rate CFP (Protein)
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| LuxI (mRNA) || 0.0025 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
-
|
+
-
|-valign="top"
+
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| rowspan="12" | Memory
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| transcription rate P2_ogr
+
-
|
+
|-
|-
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| translation rate P2_ogr
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| LuxI (complex) || 0.00125 /s ||
-
|
+
|-
|-
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| degradation rate P2_ogr (RNA)
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| LacI (protein) || 0.00231 /s ||
-
|
+
|-
|-
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| degradation rate P2_ogr (Protein)
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| LacI (gesloten mRNA) || 0.0046209812 /s ||
-
|
+
|-
|-
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| transcription rate Psid
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| LacI (open mRNA) || 0.0023104906 /s ||
-
|
+
|-
|-
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| translation rate Psid
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| open mRNA LacI complex || 0.0023104906 /s ||
-
|
+
|-
|-
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| degradation rate Psid (RNA)
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| HSL || 1.02E-6 /s || [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
-
|
+
|-
|-
-
| degradation rate Rc II (Protein)
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! Dissociation Rate
-
|
+
|-
|-
-
| transcription rate P22
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! Transcription Rate
-
|
+
|-
|-
-
| translation rate P22
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| LacI || 0.0011 /s ||
-
|
+
|-
|-
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| degradation rate P22 (RNA)
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| LuxI || 0.0025 /s ||
-
|
+
|-
|-
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| degradation LuxI (Protein)
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| K_m || 1.0E-10 /s ||
-
|
+
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|-valign="top"
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| rowspan="9" | Filter
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| transcription rate Ribokey
+
-
|
+
|-
|-
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| degradation rate Ribokey (RNA)
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! Translation Rate
-
|
+
|-
|-
-
| transcription rate T7 polymerase
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| LuxI (RBS B0034) || 0.5 /s ||
-
|
+
|-
|-
-
| degradation rate P22 (RNA)
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| LacI (RBS ?) || 0.16667 /s ||  
-
|
+
|-
|-
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| association rate (Ribokey + T7 RNA)
+
! Equilibrium Constant
-
|
+
|-
|-
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| dissociation rate (Ribokey + T7 RNA)
+
| closed and open mRNA LacI || 0.015 ||
-
|
+
|-
|-
-
| degradation rate (Ribokey + T7 RNA)
+
| closed and complex mRNA LacI || 0.0212 /M ||
-
|
+
|-
|-
-
| translation rate T7 polymerase
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! Hill coëfficiënt
-
|
+
|-  
|-  
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| degradation rate pT7 polymerase (tag?)
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| n || 2 ||  
-
|
+
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|-valign="top"
+
-
| rowspan="12" | Invertor
+
-
| transcription rate C0061
+
-
|
+
|-
|-
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| translation rate C0061
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! Others
-
|
+
|-
|-
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| degradation rate C0061 (RNA)
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| LuxI --> HSL || 0.16 ||
-
|
+
|-
|-
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| degradation rate LuxI (Protein)
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| LuxI (mRNA) + anti sense <-> complex LuxI || 4.22E14 ||
-
|
+
|-
|-
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| reaction rate LuxI to HSL (??)
+
|  
-
|
+
|}
 +
 
 +
===[https://static.igem.org/mediawiki/2008/0/05/Memory.zip Memory]===
 +
 
 +
[[Image:Memory.png|400px|center|Memory]]
 +
 
 +
{| border="1"
 +
|+ Parameter values Memory
 +
! Name !! Value !! Reference
|-
|-
-
| degradation rate HSL
+
! Degradation
-
|
+
|-
|-
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| transcription rate C0012
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| P2ogr (protein) || 0.002265 /s ||
-
|
+
|-
|-
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| degradation rate C0012 (RNA)
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| P2ogr (mRNA) || 0.002265 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
-
|
+
|-
|-
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| association rate (Ribokey + C0012 RNA)
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| P22CII (protein) || 0.002311 /s ||
-
|
+
|-
|-
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| dissociation rate (Ribokey + C0012 RNA)
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| P22CII (mRNA)|| 0,0022651 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
-
|
+
|-
|-
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| translation rate C0012 Lac
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| antimRNA_luxI  || 0.0045303/s ||  
-
|
+
|-
|-
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| degradation rate C0012 Lac (Protein)
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! Transcription rate
-
|
+
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|-valign="top"
+
-
| rowspan="12" | Cell Death
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-
| transcription rate LuxR
+
-
|
+
|-
|-
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| translation rate LuxR
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| P2ogr || 0.0125 || 
-
|
+
|-
|-
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| degradation rate LuxR (RNA)
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| P22CII || 0.0125 ||
-
|
+
|-
|-
-
| degradation rate LuxR (Protein)
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| AntimRNA || 0.0094 ||
-
|
+
|-
|-
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| association rate (HSL + LuxR)
+
! Dissociation Constant
-
|
+
|-
 +
| P2-ogr || 4.2156 M || [http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=P22+c2+repressor&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=258&resourcetype=HWCIT link]
 +
|-
 +
| R0053-P22CII || 0.1099 M ||
 +
|-
 +
! Hill coëfficiënt
 +
|-
 +
| n || 2 ||
 +
|-
 +
|}
 +
 
 +
===[https://static.igem.org/mediawiki/2008/8/8b/Filter_Final.zip Filter]===
 +
 
 +
[[Image:FilterCellD.png|800px|center|filter]]
 +
 
 +
{| border="1"
 +
|+ Parameter values Filter
 +
! Name !! Value !! Reference
 +
|-
 +
! Degradation
 +
|  ||
 +
|-
 +
| pT7_tag(protein) || 0.00155/s ||
 +
|-
 +
| mRNA_RIBOKEY (RNA) || 0.00462 /s ||[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
|-
|-
-
| dissociation rate (HSL + LuxR)
+
|gesloten_mRNA_T7 (RNA) || 0.00462 /s ||[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
-
|
+
|-
|-
-
| degradation rate HSL, LuxR complex
+
|open_mRNA_T7 (RNA) ||0.00231 / s||[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
-
|
+
|-
|-
-
| reaction (HSL + lactonase -> hydroxy acid)
+
|open_mRNA_T7_complex (RNA) || 0.00231 /s||[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
-
|
+
|-
|-
-
| transcription rate ccdb
+
! Equilibrium Constant
-
|
+
|-
|-
-
| translation rate ccdb
+
| closed and open mRNA || 0,015||  
-
|
+
|-
|-
-
| degradation ccdb (RNA)
+
| closed and key complex mRNA || 0.0212 /M ||
-
|
+
|-
|-
-
| degradation ccdb (Protein)
+
! Transcription Rate
-
|
+
|-
|-
-
|-valign="top"
+
| mRNA_RIBOKEY || Input dependent ||
-
| rowspan="2" | Pulse Generator
+
-
|
+
-
|
+
|-
|-
-
|
+
|mRNA_T7 || 0,0011 mRNA/s ||
-
|
+
|}
|}
 +
 +
===[https://static.igem.org/mediawiki/2008/8/8c/PulseGenerator.zip Pulse Generator]===
 +
 +
[[Image:PulseGenerator.png|400px|center|Pulse Generator]]
 +
 +
===Constant Lactonase production===
 +
 +
===[https://static.igem.org/mediawiki/2008/c/c0/FilterLactonaseCelldeathInverter.zip Partial Model]===
 +
 +
[[Image:Model.png|950px|center|Model]]
 +
 +
==Kinetic Constants==
===ETHZ list of parameters===
===ETHZ list of parameters===
-
* [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters ETHZ list of parameters]
+
* [https://2007.igem.org/ETHZ/Parameters ETHZ list of parameters]
===mRNA decay===
===mRNA decay===
*[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays]
*[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays]
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*[http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i11/pdf/bi0158472.pdf Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence]
*[http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i11/pdf/bi0158472.pdf Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence]
*[http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP data T7 team Tsinghua 2007]
*[http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP data T7 team Tsinghua 2007]
 +
*[http://www.jbc.org/cgi/reprint/281/47/35677 Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase]
===LacI - LuxI===
===LacI - LuxI===
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*[http://bioinformatics.oxfordjournals.org/cgi/content/full/21/11/2722#E11 Noise-induced cooperative behavior in a multicell system]
*[http://bioinformatics.oxfordjournals.org/cgi/content/full/21/11/2722#E11 Noise-induced cooperative behavior in a multicell system]
-
===HSL decay===
+
*[http://www.pnas.org/content/93/18/9505 LuxI kinetics]
 +
 
 +
===HSL stuff===
*[http://aem.asm.org/cgi/content/abstract/71/3/1291 Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils] Fig 6: half-life 185 h ==> decay rate 1.02 * 10^-6 s^-1 ==> 0.00889 nM/h
*[http://aem.asm.org/cgi/content/abstract/71/3/1291 Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils] Fig 6: half-life 185 h ==> decay rate 1.02 * 10^-6 s^-1 ==> 0.00889 nM/h
 +
 +
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D0X9-9&_user=877992&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000047079&_version=1&_urlVersion=0&_userid=877992&md5=36d07f326b2c2e55c4de05a1ab426e09 Kinetics of the AHL Regulatory System in a Model Biofilm System]
 +
 +
*[http://www.pnas.org/content/96/8/4360.full HSL lactone synthesis kinetics by a LuxI-related enzyme]
 +
 +
*[http://www.jbc.org/cgi/content/full/279/14/13645#TBL2 Lactonase mediated HSL degradation (hydrolysis)]
===OmpR, OmpF===
===OmpR, OmpF===
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===Psid met P2ogr promotor===
===Psid met P2ogr promotor===
-
*[http://parts.mit.edu/igem07/index.php/Cambridge/Amplifier_project Cambridge amplifier project, combinatie van verschillende promotoren met verschillende activatoren, experimenteel amplification factor bepaald met GFP reporter]
+
*[https://2007.igem.org/Cambridge/Amplifier_project Cambridge amplifier project, combinatie van verschillende promotoren met verschillende activatoren, experimenteel amplification factor bepaald met GFP reporter]
 +
 
 +
*[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=178405 P<sub>sid</sub> promotor with different activators]
===Constitutive promoters===
===Constitutive promoters===
-
*Estimated transcription rate for J23105:[http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters]
+
*Estimated transcription rate for J23105:[https://2007.igem.org/title=ETHZ/Parameters]
*Scale other transcription rate with table in parts registry.
*Scale other transcription rate with table in parts registry.
* Estimate the rate of transcription from a constitutive promotor family member.
* Estimate the rate of transcription from a constitutive promotor family member.
-
[[Image:Const_pro_strength.png|center|400px]]
+
[[Image:Const_pro_strength.png|center|400px|thumb|Estimates for the rate of transcription from the constitutive promotor family members. X is the GFP fluorescence in arbitrary units according to the Registry. Y is the number of mRNA's produced per second from that promotor]]
===E. coli transcription rates===
===E. coli transcription rates===
[http://www.fasebj.org/cgi/content/summary/20/10/1721 Paper about the calculated transcription rates for every E.coli ORF] <br>
[http://www.fasebj.org/cgi/content/summary/20/10/1721 Paper about the calculated transcription rates for every E.coli ORF] <br>
[http://users.path.ox.ac.uk/~pcook/data/catalogs.html Tables with the calculated transcription rates for every E.coli ORF]
[http://users.path.ox.ac.uk/~pcook/data/catalogs.html Tables with the calculated transcription rates for every E.coli ORF]

Latest revision as of 15:17, 22 July 2008

Result:

To have a dropdown for your own team copy over all of the content below. It might be needed to adjust a thing or two. Comments have been added throughout the code what must be changed.

Inspirational websites:

  • [http://javascript-array.com/scripts/simple_drop_down_menu/ Most basic dropdown menu, with no submenu's]
  • [http://jquery.com/ The javascript library used to add effects and optimise the dropdown]
  • [http://www.tyssendesign.com.au/articles/css/centering-a-dropdown-menu/ How to center a ul list effectively]

The dropdown has been created and developed by the KULeuven team. 

<html>

<style type="text/css">
#content {z-index:4;}
#ddwrapper * {z-index:8 !important;}

div#ddwrapper {
	margin:0;
	padding:0;
	height:28px;
	width:945px;				/* change to adjust imperfections in width */
}
div#ddnav {
	margin:0 auto;				/* needed to center the dropdown */
	padding:0;
	top:5px;
	/* width: 965px */
	visibility:hidden;			/* dropdown is hidden until properly initalised by javascript */
}
div#ddtoggle {
	margin:0;
	position:fixed;
	right:2px;
	top:15px;
	height:10px;
	width:10px;
	z-index:100;
}

#ddnav ul {
	display:table-row;			/* works only for firefox, later adjusted by javascript for IE */
	margin:0 auto;
	padding:0;
}
#ddnav ul li {
	display:table-cell;			/* works only for firefox, later adjusted by javascript for IE */
	list-style:none;
	margin:0;
	padding:0 !important;
	border-right:1px solid #FFF;		/* creates illusion of spacing between tabs */
}
#ddnav ul li:last-child{border-right:none;}
#ddnav a{
	display:block;
	margin:0;
	padding:4px 14px;			/* play with dimensions for size of tabs */
	background-color:#075A90;		/* background color for tabs */
	color:#FFF !important;			/* font color for text in tabs */
	text-align:center;			/* aligning for text in tabs */
	text-decoration:none !important;
	font:bold 10pt Trebuchet MS;		/* font properties for text in tabs */
	outline:0;
}
#ddnav ul li a:hover {background-color:#99CCFF;}/* background color for tabs on mouseover */
#ddnav li a:active {outline:none;}		/* remove standard dotted border for links when clicked (IE) */
#ddnav li a:focus {-moz-outline-style:none;}	/* remove standard dotted border for links when clicked (FF) */
#ddnav div {
	display:none;
	position:absolute;
	width:9em;
	background-color:#000;			/* bug solution, do not change ! */
	border:1px solid #5970B2;		/* border color for dropdown menus */
	opacity:0.9;				/* transparancy of the dropdown menus (FF) */
	filter:alpha(opacity=90);		/* transparancy of the dropdown menus (IE) */
}
#ddnav div a {
	display:block;
	padding:5px 10px;			/* play with dimensions of block element in dropdown menus */
	position:relative;
	font:normal 8pt arial;			/* font properties for text in dropdown menus */
	text-align:left;			/* aligning of text in dropdown menus */
	cursor:pointer;
}
#ddnav div a:hover, #ddnav span a:hover {color:#000 !important;}	/* text color on mouseover */
#ddnav span div {
	position:relative;
	border:none;
	border-bottom:2px groove #5970B2;	/* separator for submenus, groove does not work in FF */
	opacity:1.0;				/* avoid stacking transparancy for submenus (FF) */
	filter:alpha(opacity=100);		/* avoid stacking transparancy for submenus (IE) */
}

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Contents

Modeling

  • [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html Synthetic biology: Engineering Escherichia coli to see light]

CellDesigner

Output

Output
Parameter values Output
Name Value Reference
Degradation
CFP (protein) 1.05E-4 /s link
CFP (mRNA) 0.0023 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
Transcription Rate
CFP OmpF dependent
Translation Rate
CFP 0.167 /s Based on effenciency RBS
Output
Output
Output

Cell Death

Cell Death
Parameter values Cell Death
Name Value Reference
Degradation
LuxR (protein) 0.0010 /s
LuxR (mRNA) 0.00227 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
CcdB (protein) 7.7E-5 /s [http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]
CcdB (mRNA) 0.00231 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
HSL 1.02E-6/s [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
Dissociation Rate
ka (HSL+LuxR) 1E6 /s chosen to be relatively (to the other rate constants) high and such that Kd equals 1E-6
kd (HSL+LuxR) 1 /s
Dissociation Constant
HSL-LuxR 1E-6 M/L [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]
Binding LuxR on LuxPromotor 1E-9 M/L [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]
Transcription Rate
LuxR (constitutive promotor) 0.025 mRNA/s see sections on Constitutive Promotors & E. coli transcription Rates
CcdB (LuxR repressor) k_1*K_m^n/(K_m^n + [LuxR]^n) = 0.025*1E-9/(1E-9^1+[LuxR])

Inverter

Inverter
Parameter values Inverter
Name Value Reference
Degradation
LuxI (protein) 0.00231 /s
LuxI (mRNA) 0.0025 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
LuxI (complex) 0.00125 /s
LacI (protein) 0.00231 /s
LacI (gesloten mRNA) 0.0046209812 /s
LacI (open mRNA) 0.0023104906 /s
open mRNA LacI complex 0.0023104906 /s
HSL 1.02E-6 /s [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
Dissociation Rate
Transcription Rate
LacI 0.0011 /s
LuxI 0.0025 /s
K_m 1.0E-10 /s
Translation Rate
LuxI (RBS B0034) 0.5 /s
LacI (RBS ?) 0.16667 /s
Equilibrium Constant
closed and open mRNA LacI 0.015
closed and complex mRNA LacI 0.0212 /M
Hill coëfficiënt
n 2
Others
LuxI --> HSL 0.16
LuxI (mRNA) + anti sense <-> complex LuxI 4.22E14

Memory

Memory
Parameter values Memory
Name Value Reference
Degradation
P2ogr (protein) 0.002265 /s
P2ogr (mRNA) 0.002265 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
P22CII (protein) 0.002311 /s
P22CII (mRNA) 0,0022651 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
antimRNA_luxI 0.0045303/s
Transcription rate
P2ogr 0.0125
P22CII 0.0125
AntimRNA 0.0094
Dissociation Constant
P2-ogr 4.2156 M [http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=P22+c2+repressor&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=258&resourcetype=HWCIT link]
R0053-P22CII 0.1099 M
Hill coëfficiënt
n 2

Filter

filter
Parameter values Filter
Name Value Reference
Degradation
pT7_tag(protein) 0.00155/s
mRNA_RIBOKEY (RNA) 0.00462 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
gesloten_mRNA_T7 (RNA) 0.00462 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
open_mRNA_T7 (RNA) 0.00231 / s[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
open_mRNA_T7_complex (RNA) 0.00231 /s[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
Equilibrium Constant
closed and open mRNA 0,015
closed and key complex mRNA 0.0212 /M
Transcription Rate
mRNA_RIBOKEY Input dependent
mRNA_T7 0,0011 mRNA/s

Pulse Generator

Pulse Generator

Constant Lactonase production

Partial Model

Model

Kinetic Constants

ETHZ list of parameters

mRNA decay

  • [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays]

T7 RNAP

  • [http://www.jbc.org/cgi/reprint/267/4/2640 Initiation of Transcription by T7 RNA Polymerase at Its Natural Promoters]
  • [http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i11/pdf/bi0158472.pdf Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence]
  • [http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP data T7 team Tsinghua 2007]
  • [http://www.jbc.org/cgi/reprint/281/47/35677 Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase]

LacI - LuxI

  • [http://www.tam.cornell.edu/tam/cms/manage/upload/Strogatz_20coupled_repressilators_PNAS.pdf Coupled repressilators]
  • [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]

LuxI, LuxR, mRNALuxI, mRNALuxR decay

  • [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/11/2722#E11 Noise-induced cooperative behavior in a multicell system]
  • [http://www.pnas.org/content/93/18/9505 LuxI kinetics]

HSL stuff

  • [http://aem.asm.org/cgi/content/abstract/71/3/1291 Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils] Fig 6: half-life 185 h ==> decay rate 1.02 * 10^-6 s^-1 ==> 0.00889 nM/h
  • [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D0X9-9&_user=877992&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000047079&_version=1&_urlVersion=0&_userid=877992&md5=36d07f326b2c2e55c4de05a1ab426e09 Kinetics of the AHL Regulatory System in a Model Biofilm System]
  • [http://www.pnas.org/content/96/8/4360.full HSL lactone synthesis kinetics by a LuxI-related enzyme]
  • [http://www.jbc.org/cgi/content/full/279/14/13645#TBL2 Lactonase mediated HSL degradation (hydrolysis)]

OmpR, OmpF

  • [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=543474&blobtype=pdf A simulation model of Escherichia coli osmoregulatory switch using E-CELL system] (Relevance: High), bekijk pg.11/13
  • [http://www.jbc.org/cgi/reprint/281/25/17114 Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR] (Relevance: Medium)
  • [http://jb.oxfordjournals.org/cgi/reprint/111/6/707.pdf Transmembrane Signal Transduction and Osmoregulation in Escherichia coli: Functional Importance of the Transmembrane Regions of Membrane-Located Protein Kinase, EnvZ] (Relevance:?), geen toegang tenzij account
  • [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=209999 DNA-Binding Properties of the Transcription Activator (OmpR) for the Upstream Sequences of ompF in Escherichia coli Are Altered by envZ Mutations and Medium Osmolarity] (Relevance: Low)
  • [http://jb.asm.org/cgi/reprint/176/5/1309 A Distant Upstream Site Involved in the Negative Regulation of the Escherichia coli ompF Gene] (Relevance: ?), voor repressor regulatie van OmpF door OmpR
  • [http://jb.asm.org/cgi/reprint/176/16/5005.pdf micF Antisense RNA Has a Major Role in Osmoregulation of OmpF in Escherichia coli] (Relevance: Low), invloed 'Antisense RNA' op OmpF regulatie, hmm...

Psid met P2ogr promotor

  • [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=178405 Psid promotor with different activators]

Constitutive promoters

  • Estimated transcription rate for J23105:[1]
  • Scale other transcription rate with table in parts registry.
  • Estimate the rate of transcription from a constitutive promotor family member.
Estimates for the rate of transcription from the constitutive promotor family members. X is the GFP fluorescence in arbitrary units according to the Registry. Y is the number of mRNA's produced per second from that promotor

E. coli transcription rates

[http://www.fasebj.org/cgi/content/summary/20/10/1721 Paper about the calculated transcription rates for every E.coli ORF]
[http://users.path.ox.ac.uk/~pcook/data/catalogs.html Tables with the calculated transcription rates for every E.coli ORF]

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