Team:NYMU-Taipei/Project/Removal/Modeling

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Contents

Oscillator Modelling 1

NYMU oscillator modelling.png

  • TetR concentration
  • CII concentration.
  • 1/3min intervals.

Variables Used

Protein Name Half-life (min) Promoter Promoter Strength (relative)
Inducer CII 8 [1] pRE 0.025 (est)
Repressor TetR 40 (est due to LVA tag) pTet 1
Reporter GFP 2160 [2]

Time segment used for the calculation: 1/3mins Maximum amount of Repressors that can stop promoter activity: 10 (an arbitrary number)

Formulas used

Calculating the strength of the pTet promoter when there are repressors around: 

pTetcurrent = pTetmax*1-1/Tetmax*[TetR]     ----- (1)

Calculate the amount of each protein produced: 

CII = pTetcurrent     ----- (2)

TetR = [CII] * pREmax     ----- (3)

GFP = [CII] pTetcurrent     ----- (4)


The calculation of amount of substrates remaining w.r.t the half lives: 

[CII] = [CII] x 0.5(Δt / CII-t1/2)     ----- (5)

[TetR] = [TetR] x 0.5(Δt / TetR-t1/2)     ----- (6)

[GFP] = [GFP] x 0.5(Δt / GFP-t1/2)     ----- (7)

Conclusion

The only variables are:

  • The relative strength of pRE relative to pTet (since it has not been measured yet)
    • the weaker pRE is relative to pTet, the slower the oscillator dampens.
  • Maximum amount of repressor such that adding more repressors will not affect the strength of pTet anymore.
    • Amplitude of TetR oscillation is directly proportional.

References

[1] Shotland, et al: [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=94496 Proteolysis of Bacteriophage λ CII by Escherichia coli FtsH (HflB)]. J Bacteriol. 2000, 182(11): 3111–3116

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