ETHZ/Parameters

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= Parameters for the educatETH <i>E.coli</i> system =
<p>
<p>
-
blabla
+
In order to ensure that our simulation results match the biology as close as possible, we tried to find good estimates for the biological system parameters. To this end, we performed an extensive literature review. However, not all parameters were found in the literature, especially those which do not refer to vastly used proteins. Whenever this was the case, logical estimates were provided by our biologists based on empirical values.
</p><br>
</p><br>
== Model Parameters ==
== Model Parameters ==
-
{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
+
 
-
! Parameter                         
+
=== General parameters ===
-
! Value
+
{| class="wikitable" width="100%" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
-
! Description
+
!width="10%"| Parameter                         
-
! Comments
+
!width="10%"| Value
-
!
+
!width="20%"| Description
-
! Parameter                       
+
!width="60%"| Comments
-
! Value
+
-
! Description
+
-
! Comments
+
|-
|-
| c<sub>1</sub><sup>max</sup>
| c<sub>1</sub><sup>max</sup>
Line 21: Line 104:
| max. transcription rate of constitutive promoter (per gene)
| max. transcription rate of constitutive promoter (per gene)
| promoter no. J23105; Estimate
| promoter no. J23105; Estimate
-
|
+
|-
| 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 31: Line 114:
| high-copy plasmid number
| high-copy plasmid number
| Estimate
| Estimate
-
|
+
|-
| l<sup>lo</sup>
| l<sup>lo</sup>
| 5
| 5
Line 41: Line 124:
| basic production levels
| basic production levels
| Estimate
| Estimate
-
|
 
-
|
 
-
|
 
-
|
 
-
|
 
|-
|-
-
| Degradation constants  
+
|}
-
|
+
 
-
|  
+
=== Degradation constants ===
-
|  
+
{| class="wikitable" width="100%" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
-
|  
+
!width="10%"| Parameter                       
-
|
+
!width="10%"| Value
-
|
+
!width="20%"| Description
-
|
+
!width="60%"| Comments
|-
|-
-
| 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]
+
-
| degradation of tetR
+
|  
|  
-
Ref. [9]
+
*1e-5 [1/s]
-
Ref. [10]
+
*2.31e-3 [1/s]
 +
| degradation of TetR
 +
|
 +
*Ref. [9]
 +
*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]
-
|
 
-
|
 
-
|
 
-
|
 
-
|
 
|-
|-
-
| 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]
-
|
+
|-
-
| d<sub>p22cII</sub>
+
| d<sub>P22CII</sub>
|  
|  
-
| degradation of p22cII
+
| degradation of P22CII
|  
|  
|-
|-
| 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
|-
|-
-
| Dissociation constants
+
|}
-
|  
+
 
-
|  
+
=== Dissociation constants ===
-
|  
+
 
-
|
+
{| class="wikitable" width="100%" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
-
|  
+
!width="10%"| Parameter                       
-
|  
+
!width="10%"| Value
 +
!width="20%"| Description
 +
!width="60%"| Comments
 +
|-
 +
| K<sub>LacI</sub>
|  
|  
 +
* 0.1 - 1 [pM]
 +
* 800 [nM]
 +
| LacI repressor dissociation constant
|  
|  
 +
* Ref. [2]
 +
* Ref. [12]
|-
|-
-
| K<sub>lacI</sub>
 
-
| 0.1 - 1 [pM]
 
-
| lacI repressor dissociation constant
 
-
| 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]
|-
|-
-
|Hill cooperativity
+
|}
-
|
+
 
-
|
+
=== Hill cooperativity ===
-
|
+
{| class="wikitable" width="100%" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
-
|
+
!width="10%"| Parameter                       
-
|
+
!width="10%"| Value
-
|
+
!width="20%"| Description
-
|
+
!width="60%"| Comments
-
|
+
|-
 +
| n<sub>LacI</sub>
 +
|  
 +
* 1
 +
* 2
 +
| LacI repressor Hill cooperativity
 +
|
 +
* Ref. [5]
 +
* Ref. [12]
|-
|-
-
| n<sub>lacI</sub>
 
-
| 1
 
-
| lacI repressor Hill cooperativity
 
-
| Ref. [5]
 
-
|
 
| 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]
|-
|-
|}
|}

Latest revision as of 14:27, 26 October 2007

ETHZ banner.png

 


Parameters for the educatETH E.coli system

In order to ensure that our simulation results match the biology as close as possible, we tried to find good estimates for the biological system parameters. To this end, we performed an extensive literature review. However, not all parameters were found in the literature, especially those which do not refer to vastly used proteins. Whenever this was the case, logical estimates were provided by our biologists based on empirical values.


Model Parameters

General parameters

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

Parameter Value Description Comments
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

Parameter Value Description Comments
KLacI
  • 0.1 - 1 [pM]
  • 800 [nM]
LacI repressor dissociation constant
  • Ref. [2]
  • Ref. [12]
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]

Hill cooperativity

Parameter Value Description Comments
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]


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
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