Team:ETH Zurich/Modeling/Parameters

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Contents

Parameters for modeling

Photoinduction

Light sources

Name Description Reference approx. flux at probe Distance source - probe
sun natural sun light ISO 9845-1, ASTMG173 640 W m-2 n/a
room sun*0.3, (UV<350nm)*0.05, (UV>=350nm)*0,90 assumed 210 W m-2 n/a
bulb200W Incandescent light bulb GE200Clear 12 W m-2 1 m

Photoconversion cross section

From Absorption spectrum
Receptor Activation Deactivation References
Quantum yield Ext. coeff. Absorption spectrum Quantum yield Ext. coeff. Absorption spectrum
lov 0.26 1.0655e3 ETH modeling abs lov a.png n/a n/a n/a [Drepper2007]
[Christie1999]
ycgf 0.24 1.13e3 ETH modeling abs ycgf a.png n/a n/a n/a [Tyagi2009]
ccas 0.15 2.7e3 ETH modeling abs ccas a.png 0.12 3.0e3 ETH modeling abs ccas d.png [Hirose2008]
[Hirose2010]
cph1 0.15 8.5e3 ETH modeling abs cph1 a.png 0.12 8.5e3 ETH modeling abs cph1 d.png [VanThor2001]
[Lamparter2002]
From Photon effectiveness
Receptor Activation photon effectiveness Deactivation photon effectiveness References
UVR8 ETH modeling act uvr8 a.png n/a [Brown2009]

UVR8

Parameter Description Value Reference
k_UVR8_hvLight dependent dissociation rate UVR8 dimer s-1from photoinduction model
k_UVR8_decayDimerization rate UVR8 monomer8.4·10-10 nM-1 s-1estimate
KM_TetRTetR repression coefficient 100 nMassumed
n_TetRTetR cooperativity coefficient1[GarciaOjalvo2004]
k_PtetTet promoter expression strength50 nM s-1assumed
ABasal expression fraction0.15assumed
nHill-like pABA cooperativity coefficient1assumed
k_degProtein degradation rate0.03 s-1assumed
KM_PabABPabAB Michaelis constant9.60·105 nM[Roux1992]
k_catPabAB catalysis rate0.65 s-1[Roux1992]
Chor0Intracellular chorismate concentration1.4·105 nMassumed
k_outpABA outflux rate0.01 s-1assumed

UVR8-TetRDBD-LovTAP

Parameter Description Value Reference
k_UVR8_hvLight dependent dissociation rate UVR8 dimer s-1from photoinduction model
k_LOV_hvLight dependent activation rate s-1from photoinduction model
KM_LOVLOV repression coefficient142 nM[Strickland2007]
KM_LacILacI repression coefficient800 nM[Basu2005]
KM_cIcI repression coefficient8 nM[Basu2005]
KM_TetRTetR repression coefficient100 nMassumed
n_LacILacI cooperativity coefficient2[Basu2005]
n_cIcI cooperativity coefficient2[Basu2005]
n_TetRTetR cooperativity coefficient1[GarciaOjalvo2004]
n_LOVLOV cooperativity coefficient1assumed
k_UVR8_decayDimerization rate UVR8 monomer8.4·10-10 nM-1 s-1estimate
k_LOV_decayDark decay rate of active LOV5.8·10-3 s-1[Drepper2007]
k_PtrpTrp promoter expression strength2.34 nM s-1optimized
k_P_RLambda P_R expression strength4.21·10-2 nM s-1optimized
k_P_LLambda P_L expression strength2.1579·10-2 nM s-1optimized
ABasal expression fraction0.15assumed
k_degProtein degradation rate1.9·10-3 s-1assumed


LovTAP-Cph8

Parameter Description Value Reference
k_Cph8_hvLight dependent activation rate s-1from photoinduction model
KM_LOVLOV repression coefficient142 nM[Strickland2007]
KM_Cph8Cph8 activation coefficient1000 nMestimate
KM_LacILacI repression coefficient800 nM[Basu2005]
KM_cIcI repression coefficient8 nM[Basu2005]
KM_TetRTetR repression coefficient100 nMassumed
n_LacILacI cooperativity coefficient2[Basu2005]
n_cIcI cooperativity coefficient2[Basu2005]
n_TetRTetR cooperativity coefficient1[GarciaOjalvo2004]
n_Cph8Cph8 cooperativity coefficient1assumed
n_LOVLOV cooperativity coefficient1assumed
k_LOV_decayDark decay rate of active LOV5.8·10-3 s-1[Drepper2007]
k_Cph8_decayDark decay rate of active Cph85.8·10-3 s-1estimate
k_PtrpTrp promoter expression strength2.23 nM s-1optimized
k_PompCOmpC promoter expression strength3.454·10-1 nM s-1optimized
k_P_RLambda P_R expression strength4.21·10-2 nM s-1optimized
k_P_LLambda P_L expression strength3.0·10-2 nM s-1optimized
ABasal expression fraction0.15assumed
k_degProtein degradation rate1.9·10-3 s-1assumed

Parameters denoted with

  • assumed have been assumed from intuition
  • estimate have been calculated from gels, approximate experimental numbers or other related biological numbers
  • optimized have been adjusted such that the constructs work optimally. These are target constraints that biologists should care for when selecting promoters.


References

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