Team:Aberdeen Scotland/parameters

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University of Aberdeen iGEM 2009

Internal Dynamics Parameters

When modeling any process, it is essential to use parameters which reflect reality, otherwise the model will not give accurate predictions. Thus we spend a considerable time researching, analysing and estimating parameters so that our model will reflect real life behaviour as accuratly as possible.

Parameter Description Value Unit Reference
Rate of production of HSL from LuxI 0.45 1/s [1]
HSL Rate of diffusion of HSL in/out of the cell 0.4 1/s [1]
IPTG Rate of diffusion of IPTG in/out of the cell 0.014 1/s [3]
pproduction Number of plasmids 10 medium plasmid number; decided within the team
platch Number of plasmids 10 medium plasmid number; decided within the team
plysis Number of plasmids 10 medium plasmid number; decided within the team
panti-lysis Number of plasmids 10 medium plasmid number; decided within the team
pQS Number of plasmids 10 medium plasmid number; decided within the team
max_production Maximal production rate of lux box promoter 0.44 pops [1]
min_production Minimal production rate of lux box promoter 0.013 pops estimated
latch Maximal production rate of latch promoter 0.28 pops nick
lysis Maximal production rate of lysis promoter 0.0426 pops nick
anti-lysis Maximal production rate of anti-lysis promoter 0.0066 pops nick
QS Maximal production rate of QS promoter 0.018 pops nick
KLacI Dissociation constant for LacI to LacO 700 m see explanation</td> </tr>

<tr> <td>KLacI-IPTG</td> <td>Dissociation constant for IPTG to LacI </td> <td>1200</td> <td>m</td> <td>see explanation</td> </tr>

<tr> <td>KTetR</td> <td>Dissociation constant for TetR to TetO </td> <td>7000</td> <td>m</td> <td>see explanation</td> </tr>

<tr> <td>KcI</td> <td>Dissociation constant for cI to operon </td> <td>7000</td> <td>m</td> <td>see explanation</td> </tr>

<tr> <td>KP</td> <td>Dissociation constant for P to lux box </td> <td>700</td> <td>m</td> <td>see explanation</td> </tr>

<tr> <td>nLacI</td> <td>Hill coefficient </td> <td>2</td> <td></td> <td>[10]</td> </tr>

<tr> <td>ncI</td> <td>Hill coefficient </td> <td>2</td> <td></td> <td>[11]</td> </tr>

<tr> <td>nTetR</td> <td>Hill coefficient </td> <td>3</td> <td></td> <td>1</td> </tr>

<tr> <td>nP</td> <td>Hill coefficient </td> <td>2</td> <td></td> <td>[1]</td> </tr>

<tr> <td><img src="Alpha.gif">mRNA</td> <td>Degradation of mRNA</td> <td>0.00288</td> <td>1/s</td> <td>[2]</td> </tr>

<tr> <td><img src="Alpha.gif">X</td> <td>Degradation of X</td> <td>0.00000802</td> <td>1/s</td> <td>[5]</td> </tr>

<tr> <td><img src="Alpha.gif">Y</td> <td>Degradation of Y</td> <td>0.00000802</td> <td>1/s</td> <td>[5]</td> </tr>

<tr> <td><img src="Alpha.gif">λ-CI</td> <td>Degradation of lambda CI</td> <td>0.002888</td> <td>1/s</td> <td>[5]</td> </tr>


<tr> <td><img src="Alpha.gif">LacI</td> <td>Degradation of LacI</td> <td>0.001155</td> <td>1/s</td> <td>[8]</td> </tr>

<tr> <td><img src="Alpha.gif">TetR</td> <td>Degradation of TetR</td> <td>0.00288811</td> <td>1/s</td> <td>tagged; half-life of 4 min</td> </tr>

<tr> <td><img src="Alpha.gif">Holin</td> <td>Degradation of Holin</td> <td>0.0002</td> <td>1/s</td> <td>estmated; half-life of an hour</td> </tr>

<tr> <td><img src="Alpha.gif">Endolysin</td> <td>Degradation of Endolysin</td> <td>0.0002</td> <td>1/s</td> <td>estimated; half-life of an hour</td> </tr>

<tr> <td><img src="Alpha.gif">Antiholin</td> <td>Degradation of Antiholin</td> <td>0.0002</td> <td>1/s</td> <td>estimated; half-life of an hour</td> </tr>


<tr> <td><img src="Alpha.gif">LuxI</td> <td>Degradation of LuxI</td> <td>0.002888</td> <td>1/s</td> <td>tagged; half-life of 4 min</td> </tr>

<tr> <td><img src="Alpha.gif">LuxR</td> <td>Degradation of LuxR</td> <td>0.0002</td> <td>1/s</td> <td>[1]</td> </tr>

<tr> <td><img src="Alpha.gif">HSL</td> <td>Degradation of HSL</td> <td>0.00016667</td> <td>1</td> <td>[8]; value for AHL</td> </tr>

<tr> <td><img src="Gamma.gif">Protein</td> <td>Translation rate of Protein</td> <td>0.1</td> <td>1/s</td> <td>[2]</td> </tr>


<tr> <td><img src="K.gif">P</td> <td>Rate of formation of the HSL-LuxI complex</td> <td>0.00010</td> <td>1/ms</td> <td>[1]</td> </tr>

<tr> <td><img src="K.gif">-P</td> <td>Rate of dissociation of the HSL-LuxI complex</td> <td>0.003</td> <td>1/s</td> <td>[1]</td> </tr>


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References

[1] Goryachev, A.B., D.J. Toh and T. Lee. “System analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constant.” BioSystems 2006: 83, 178-187.

[2] Alon, Uri. “An Introduction to Systems Biology Design Principles of Biological Circiuts.” London: Chapman & Hall/CRC, 2007.

[3] Kepes, A., 1960, “Etudes cinetiques sur la galactoside-permease D'Escherichia coli. Biochim.” Biophys. Acta 40, 70-84.

[4] Canton, B. and Anna Labno. “Part: BBa_F2620.” BioBrick Registry. 13th August 2009. <http://partsregistry.org/Part:BBa_F2620>

[5] Andersen JB, Sternberg C, Poulsen LK, Bjorn SP, Givskov M, Molin S. “New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria.” Appl Environ Microbiol. 1998 Jun; 64(6):2240-6.

[6] Elowitz MB, Leibler S.; “A synthetic oscillatory network of transcriptional regulators.” Nature 2000 Jan; 403(6767):335-8.;

[7] BCCS-Bristol 2008. “Modelling Parameters” iGEM wiki. 13th August 2009. <https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters>

[8] Subhayu Basu; “A synthetic multicellular system for programmed pattern formation.” Nature April 2005: 434, 1130-1134

[9] KULeuven 2008. “Cell Death”iGEM wiki. 13th August 2009. <https://2008.igem.org/Team:KULeuven/Model/CellDeath>

[10] ETHZ 2007. “Engineering” iGem wiki. 13th August 2009. <http://parts.mit.edu/igem07/index.php/ETHZ/Engineering>

[11] Bintu, Lacramioara, Terence Hwa. “Transcriptional regulation by the numbers: applications.” Current Opinion in Genetics & Development 2005, 15:125–135.

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