ETHZ/Parameters

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(Difference between revisions)
(→Parameters for the EducatETH <i>E. coli</i> system)
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Line 30: Line 30:
| c<sub>2</sub><sup>max</sup>
| c<sub>2</sub><sup>max</sup>
| 0.01 [mM/h]
| 0.01 [mM/h]
-
| max. transcription rate of luxR-activated promoter (per gene)
+
| max. transcription rate of LuxR-activated promoter (per gene)
| Estimate
| Estimate
|-
|-
Line 62: Line 62:
|  
|  
|-
|-
-
| d<sub>lacI</sub>
+
| d<sub>LacI</sub>
| 2.31e-3 [1/s]
| 2.31e-3 [1/s]
-
| degradation of lacI
+
| degradation of LacI
| Ref. [10]
| Ref. [10]
|
|
-
| d<sub>tetR</sub>
+
| d<sub>TetR</sub>
|  
|  
*1e-5 [1/s]
*1e-5 [1/s]
*2.31e-3 [1/s]
*2.31e-3 [1/s]
-
| degradation of tetR
+
| degradation of TetR
|  
|  
*Ref. [9]
*Ref. [9]
*Ref. [10]
*Ref. [10]
|-
|-
-
| d<sub>luxR</sub>
+
| d<sub>LuxR</sub>
| 1e-3 - 1e-4 [1/s]
| 1e-3 - 1e-4 [1/s]
-
| degradation of luxR
+
| degradation of LuxR
| Ref: [6]
| Ref: [6]
|
|
Line 86: Line 86:
|
|
|-
|-
-
| d<sub>cI</sub>
+
| d<sub>CI</sub>
| 7e-4 [1/s]
| 7e-4 [1/s]
-
| degradation of cI
+
| degradation of CI
| Ref. [7]
| Ref. [7]
|
|
-
| d<sub>p22cII</sub>
+
| d<sub>P22CII</sub>
|  
|  
-
| degradation of p22cII
+
| degradation of P22CII
|  
|  
|-
|-
Line 126: Line 126:
|  
|  
|-
|-
-
| K<sub>lacI</sub>
+
| K<sub>LacI</sub>
| 0.1 - 1 [pM]
| 0.1 - 1 [pM]
-
| lacI repressor dissociation constant
+
| LacI repressor dissociation constant
| Ref. [2]
| Ref. [2]
|
|
| K<sub>IPTG</sub>
| K<sub>IPTG</sub>
| 1.3 [&#181;M]
| 1.3 [&#181;M]
-
| IPTG-lacI repressor dissociation constant
+
| IPTG-LacI repressor dissociation constant
| Ref. [2]
| Ref. [2]
|-
|-
-
| K<sub>tetR</sub>
+
| K<sub>TetR</sub>
| 179 [pM]
| 179 [pM]
-
| tetR repressor dissociation constant
+
| TetR repressor dissociation constant
| Ref. [1]
| Ref. [1]
|
|
-
| K<sub>aTc</sub>
+
| K<sub>ATC</sub>
| 893 [pM]
| 893 [pM]
-
| aTc-tetR repressor dissociation constant
+
| ATC-TetR repressor dissociation constant
| Ref. [1]
| Ref. [1]
|-
|-
-
| K<sub>luxR</sub>
+
| K<sub>LuxR</sub>
| 55 - 520 [nM]
| 55 - 520 [nM]
-
| luxR activator dissociation constant
+
| LuxR activator dissociation constant
| Ref: [6]
| Ref: [6]
|
|
| K<sub>AHL</sub>
| K<sub>AHL</sub>
| 0.09 - 1 [&#181;M]
| 0.09 - 1 [&#181;M]
-
| AHL-luxR activator dissociation constant
+
| AHL-LuxR activator dissociation constant
| Ref: [6]
| Ref: [6]
|-
|-
-
| K<sub>cI</sub>
+
| K<sub>CI</sub>
|
|
*8 [pM]
*8 [pM]
*50 [nM]
*50 [nM]
-
| cI repressor dissociation constant
+
| CI repressor dissociation constant
|
|
*Ref. [12]
*Ref. [12]
*starting with values of Ref. [6] and using Ref. [3]
*starting with values of Ref. [6] and using Ref. [3]
|
|
-
| K<sub>p22cII</sub>
+
| K<sub>P22CII</sub>
| 0.577 [&#181;M]
| 0.577 [&#181;M]
-
| p22cII repressor dissociation constant
+
| P22CII repressor dissociation constant
-
| Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match?
+
| Ref. [11]. Note that they use a protein CII and we have P22CII. Does that match?
|-
|-
|Hill cooperativity
|Hill cooperativity
Line 180: Line 180:
|
|
|-
|-
-
| n<sub>lacI</sub>
+
| n<sub>LacI</sub>
-
| 1
+
|  
-
| lacI repressor Hill cooperativity
+
* 1
-
| Ref. [5]
+
* 2
 +
| LacI repressor Hill cooperativity
 +
|  
 +
* Ref. [5]
 +
* Ref. [12]
|
|
| n<sub>IPTG</sub>
| n<sub>IPTG</sub>
| 2
| 2
-
| IPTG-lacI repressor Hill cooperativity
+
| IPTG-LacI repressor Hill cooperativity
| Ref. [5]
| Ref. [5]
|-
|-
-
| n<sub>tetR</sub>
+
| n<sub>TetR</sub>
| 3
| 3
-
| tetR repressor Hill cooperativity
+
| TetR repressor Hill cooperativity
| Ref. [3]
| Ref. [3]
|
|
-
| n<sub>aTc</sub>
+
| n<sub>ATC</sub>
| 2 (1.5-2.5)
| 2 (1.5-2.5)
-
| aTc-tetR repressor Hill cooperativity
+
| ATC-TetR repressor Hill cooperativity
|Ref. [3]
|Ref. [3]
|-
|-
-
| n<sub>luxR</sub>
+
| n<sub>LuxR</sub>
| 2
| 2
-
| luxR activator Hill cooperativity
+
| LuxR activator Hill cooperativity
| Ref: [6]
| Ref: [6]
|
|
| n<sub>AHL</sub>
| n<sub>AHL</sub>
| 1
| 1
-
| AHL-luxR activator Hill cooperativity
+
| AHL-LuxR activator Hill cooperativity
| Ref. [3]
| Ref. [3]
|-
|-
-
| n<sub>cI</sub>
+
| n<sub>CI</sub>
| 2
| 2
-
| cI repressor Hill cooperativity
+
| CI repressor Hill cooperativity
| Ref. [12]
| Ref. [12]
|
|
-
| n<sub>p22cII</sub>
+
| n<sub>P22CII</sub>
| 4
| 4
-
| p22cII repressor Hill cooperativity
+
| P22CII repressor Hill cooperativity
-
| Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match?
+
| Ref. [11]. Note that they use a protein CII and we have P22CII. Does that match?
|-
|-
|}
|}

Revision as of 12:26, 23 October 2007

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Parameters for the EducatETH E. coli system

In order to provide as realistic simulation results as possible, and to find good estimates for the simulation parameters, we performed an intensive literature review. However, not all parameters could be found in the literature. Furthermore, one has to take into account that biological parameters cannot be estimated to a very high precision.


Model Parameters

Parameter Value Description Comments Parameter Value Description Comments
c1max 0.01 [mM/h] max. transcription rate of constitutive promoter (per gene) promoter no. J23105; Estimate c2max 0.01 [mM/h] max. transcription rate of LuxR-activated promoter (per gene) Estimate
lhi 25 high-copy plasmid number Estimate llo 5 low-copy plasmid number Estimate
a 1% basic production levels Estimate
Degradation constants
dLacI 2.31e-3 [1/s] degradation of LacI Ref. [10] dTetR
  • 1e-5 [1/s]
  • 2.31e-3 [1/s]
degradation of TetR
  • Ref. [9]
  • Ref. [10]
dLuxR 1e-3 - 1e-4 [1/s] degradation of LuxR Ref: [6]
dCI 7e-4 [1/s] degradation of CI Ref. [7] dP22CII degradation of P22CII
dYFP 6.3e-3 [1/min] degradation of YFP suppl. mat. to Ref. [8] corresponding to a half life of 110min dGFP 6.3e-3 [1/min] degradation of GFP in analogy to YFP
dRFP 6.3e-3 [1/min] degradation of RFP in analogy to YFP dCFP 6.3e-3 [1/min] degradation of CFP in analogy to YFP
Dissociation constants
KLacI 0.1 - 1 [pM] LacI repressor dissociation constant Ref. [2] KIPTG 1.3 [µM] IPTG-LacI repressor dissociation constant Ref. [2]
KTetR 179 [pM] TetR repressor dissociation constant Ref. [1] KATC 893 [pM] ATC-TetR repressor dissociation constant Ref. [1]
KLuxR 55 - 520 [nM] LuxR activator dissociation constant Ref: [6] KAHL 0.09 - 1 [µM] AHL-LuxR activator dissociation constant Ref: [6]
KCI
  • 8 [pM]
  • 50 [nM]
CI repressor dissociation constant
  • Ref. [12]
  • starting with values of Ref. [6] and using Ref. [3]
KP22CII 0.577 [µM] P22CII repressor dissociation constant Ref. [11]. Note that they use a protein CII and we have P22CII. Does that match?
Hill cooperativity
nLacI
  • 1
  • 2
LacI repressor Hill cooperativity
  • Ref. [5]
  • Ref. [12]
nIPTG 2 IPTG-LacI repressor Hill cooperativity Ref. [5]
nTetR 3 TetR repressor Hill cooperativity Ref. [3] nATC 2 (1.5-2.5) ATC-TetR repressor Hill cooperativity Ref. [3]
nLuxR 2 LuxR activator Hill cooperativity Ref: [6] nAHL 1 AHL-LuxR activator Hill cooperativity Ref. [3]
nCI 2 CI repressor Hill cooperativity Ref. [12] nP22CII 4 P22CII repressor Hill cooperativity Ref. [11]. Note that they use a protein CII and we have P22CII. Does that match?


References

[http://www.pnas.org/cgi/content/abstract/104/8/2643 [1] Weber W et al.] "A synthetic time-delay circuit in mammalian cells and mice", P Natl Acad Sci USA 104(8):2643-2648, 2007
[http://www.pnas.org/cgi/content/full/100/13/7702?ck=nck [2] Setty Y et al.] "Detailed map of a cis-regulatory input function", P Natl Acad Sci USA 100(13):7702-7707, 2003
[http://ieeexplore.ieee.org/iel5/9711/30654/01416417.pdf [3] Braun D et al.] "Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005
[http://www.nature.com/nature/journal/v435/n7038/suppinfo/nature03508.html [4] Fung E et al.] "A synthetic gene--metabolic oscillator", Nature 435:118-122, 2005 (supplementary material)
[http://dx.doi.org/10.1016/j.jbiotec.2005.08.030 [5] Iadevaia S and Mantzais NV] "Genetic network driven control of PHBV copolymer composition", J Biotechnol 122(1):99-121, 2006
[http://dx.doi.org/10.1016/j.biosystems.2005.04.006 [6] Goryachev AB et al.] "Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004
[http://www.genetics.org/cgi/content/abstract/149/4/1633 [7] Arkin A et al.] "Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-Infected Escherichia coli cells", Genetics 149: 1633-1648, 1998
[http://download.cell.com/supplementarydata/cell/107/6/739/DC1/index.htm [8] Colman-Lerner A et al.] "Yeast Cbk1 and Mob2 Activate Daughter-Specific Genetic Programs to Induce Asymmetric Cell Fates", Cell 107(6): 739-750, 2001 (supplementary material)
[http://www.nature.com/nature/journal/v405/n6786/abs/405590a0.html [9] Becskei A and Serrano L] "Engineering stability in gene networks by autoregulation", Nature 405: 590-593, 2000
[http://www.biophysj.org/cgi/content/full/89/6/3873?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=89&firstpage=3873&resourcetype=HWCIT [10] Tuttle et al.] "Model-Driven Designs of an Oscillating Gene Network", Biophys J 89(6):3873-3883, 2005
[http://www.pnas.org/cgi/reprint/99/2/679 [11] McMillen LM et al.] "Synchronizing genetic relaxation oscillators by intercell signaling", P Natl Acad Sci USA 99(2):679-684, 2002
[http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html [12] Basu S et al.] "A synthetic multicellular system for programmed pattern formation", Nature 434:1130-1134, 2005

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