ETHZ/Parameters

From 2007.igem.org

(Difference between revisions)
(→Model Parameters)
(→Model Parameters)
Line 57: Line 57:
|-
|-
| d<sub>lacI</sub>
| d<sub>lacI</sub>
-
| 2.31e-3 [per sec]
+
| 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 [pro sec]/2.31e-3 [per sec]
+
|  
 +
*1e-5 [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 [per sec]
+
| 1e-3 - 1e-4 [1/s]
| degradation of luxR
| degradation of luxR
| Ref: [6]
| Ref: [6]
Line 79: Line 81:
|-
|-
| d<sub>cI</sub>
| d<sub>cI</sub>
-
| 7e-4 [per sec]
+
| 7e-4 [1/s]
| degradation of cI
| degradation of cI
| Ref. [7]
| Ref. [7]
Line 89: Line 91:
|-
|-
| d<sub>YFP</sub>
| d<sub>YFP</sub>
-
| 6.3e-3 [per min]
+
| 6.3e-3 [1/min]
| degradation of YFP
| degradation of YFP
| suppl. mat. to Ref. [8] corresponding to a half life of 110min
| suppl. mat. to Ref. [8] corresponding to a half life of 110min
|
|
| d<sub>GFP</sub>
| d<sub>GFP</sub>
-
| 6.3e-3 [per min]
+
| 6.3e-3 [1/min]
| degradation of GFP
| degradation of GFP
| in analogy to YFP
| in analogy to YFP
|-
|-
| d<sub>RFP</sub>
| d<sub>RFP</sub>
-
| 6.3e-3 [per min]
+
| 6.3e-3 [1/min]
| degradation of RFP
| degradation of RFP
| in analogy to YFP
| in analogy to YFP
|
|
| d<sub>CFP</sub>
| d<sub>CFP</sub>
-
| 6.3e-3 [per min]
+
| 6.3e-3 [1/min]
| degradation of CFP
| degradation of CFP
| in analogy to YFP
| in analogy to YFP
Line 150: Line 152:
| 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>

Revision as of 12:37, 13 October 2007

Introduction

blabla


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 lacI repressor Hill cooperativity Ref. [5] 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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