Team:Paris Bettencourt/Modeling/Parameters

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Team IGEM Paris 2011

Parameters

Parameter Description Value Unit Reference
Concentration of X NA molecules
per cell		 Notation convention
Delay due to protein X production and maturation NA s Notation convention
Maximal production rate of pVeg promoter (constitutive) 0.02 molecules.s-1
or pops		 Estimated, see the justification
Maximal production rate of pHyperSpank promoter 0.02 molecules.s-1
or pops		 Estimated, see the justification
Maximal production rate of pT7 promoter 0.02 molecules.s-1
or pops		 Estimated, see the justification
Maximal production rate of pComK promoter 0.049 molecules.s-1
or pops		 [3]
Maximal production rate of pComS promoter 0.057 molecules.s-1
or pops		 [3]
Maximal production rate of pComG promoter 0.02 molecules.s-1
or pops		 Estimated, see the justification
Basal production rate of pComK promoter 0.0028 molecules.s-1
or pops		 [3]
Basal production rate of pComG promoter 0.028 molecules.s-1
or pops		 Is roughly one order of magnitude higher than production rate of pComK[4]
Dissociation constant for IPTG to LacI 1200 molecules
per cell		 Aberdeen 2009 wiki
Dissociation constant for LacI to LacO (pLac) 700 molecules
per cell		 Aberdeen 2009 wiki
Dissociation constant for T7 RNA polymerase to pT7 10 molecules
per cell		 We used the classic assumption 1nM=1 molecule per cell and [1]
Dissociation constant for ComK to pComK 110 molecules
per cell		 [3]
Dissociation constant for ComK to pComS 100 molecules
per cell		 [3]
ComK concentration for half maximal degradation 500 molecules
per cell		 [3]
ComS concentration for half maximal degradation 50 molecules
per cell		 [3]
Hill coefficient for LacI/IPTG interaction 2 NA Aberdeen 2009 wiki
Hill coefficient for LacI/pHyperSpank interaction 2 NA Aberdeen 2009 wiki
Hill coefficient for ComK/pComK and ComK/pComG (positive feedback) interaction 2 NA [3]
Hill coefficient for ComK/pComS (negative feedback) interaction 5 NA [3]
Translation rate of proteins 0.9 s-1 Estimated, see the justification
Dilution rate in exponential phase 2.88x10-4 s-1 Calculated with a 40 min generation time. See explanation
Unrepressed degradation rate of ComK 1.4x10-3 s-1 [3]
Unrepressed degradation rate of ComS 1.4x10-3 s-1 [3]
Degradation rate of mRNA 2.88x10-3 s-1 [4]
Degradation rate of GFP 10-4 s-1 BioNumbers
Degradation rate of RFP 10-4 s-1 Estimated equal to GFP degradation rate
Delay due to CFP production and maturation 360 s Estimated equal to GFP delay (similar molecules)
Delay due to YFP production and maturation 360 s Estimated equal to GFP delay (similar molecules)
Delay due to ComK production and maturation 300 s Arbitrary
Delay due to ComS production and maturation 300 s Arbitrary
Delay for ComS repression by ComK 714 s [3]
Delay due tT7 RNA polymerase production and maturation 300 s [2]
Delay due GFP production and maturation 360 s BioNumbers
Delay due RFP production and maturation 360 s Estimated equal to GFP delay (similar molecules)
Delay due to mRNA production 30 s BioNumbers with an approximation: all our contructs are around 1-2kb

References

  1. Cytoplasmic expression of a reporter gene by co-delivery of T7 RNA polymerase and T7 promoter sequence with cationic liposomes, X Gao and L Huang, accessible here
  2. Molecular Biology for Masters by Dr. G. R. Kantharaj, accessible here
  3. An excitable gene regulatory circuit induces transient cellular differentiation, Süel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB, Nature. 2006 Mar 23;440(7083):545-50.
  4. Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits, Çağatay, Tolga and Turcotte, Marc and Elowitz, Michael B. and Garcia-Ojalvo, Jordi and Süel, Gürol M, Cell, 2009 139 (3). pp. (Supplementary Data)
  5. An Introduction to Systems Biology: Design Principles of Biological Circuits, Uri Alon

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