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Team:ETH Zurich/Modeling/Parameters
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* ''assumption'' have been assumed from intuition | * ''assumption'' have been assumed from intuition | ||
* ''estimate'' have been calculated from gels, approximate experimental numbers or other related biological numbers | * ''estimate'' have been calculated from gels, approximate experimental numbers or other related biological numbers | ||
| - | * ''optimized'' have been adjusted such that the constructs | + | * ''optimized'' have been adjusted such that the constructs work optimally. These are target constraints that biologists should care for when selecting promoters. |
{{:Team:ETH_Zurich/Templates/Footer}} | {{:Team:ETH_Zurich/Templates/Footer}} | ||
Revision as of 01:00, 27 September 2012
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 | assumption | 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 | 
| n/a | n/a | n/a | [Drepper2007] [Christie1999] |
| ycgf | 0.24 | 1.13e3 | 
| n/a | n/a | n/a | [Tyagi2009] |
| ccas | 0.15 | 2.7e3 | 
| 0.12 | 3.0e3 | 
| [Hirose2008] [Hirose2010] |
| cph1 | 0.15 | 8.5e3 | 
| 0.12 | 8.5e3 | 
| [VanThor2001] [Lamparter2002] |
From Photon effectiveness
| Receptor | Activation photon effectiveness | Deactivation photon effectiveness | References |
|---|---|---|---|
| UVR8 | 
| n/a |
UVR8
| Parameter | Description | Value | Reference |
|---|---|---|---|
| k_UVR8_hv | Light dependent dissociation rate UVR8 dimer | s-1 | from photoinduction model |
| k_UVR8_decay | Dimerization rate UVR8 monomer | 8.4·10-10 nM-1 s-1 | estimate |
| KM_TetR | TetR repression coefficient | 100 nM | assumption |
| n_TetR | TetR cooperativity coefficient | 1 | [GarciaOjalvo2004] |
| k_Ptet | Tet promoter expression strength | 50 nM s-1 | assumption |
| A | Basal expression fraction | 0.15 | assumption |
| n | Hill-like pABA cooperativity coefficient | 1 | assumption |
| k_deg | Protein degradation rate | 0.03 s-1 | assumption |
| KM_PabAB | PabAB Michaelis constant | 9.60·105 nM | [Roux1992] |
| k_cat | PabAB catalysis rate | 0.65 s-1 | [Roux1992] |
| Chor0 | Intracellular chorismate concentration | 1.4·105 nM | assumption |
| k_out | pABA outflux rate | 0.01 s-1 | assumption |
UVR8-TetRDBD-LovTAP
| Parameter | Description | Value | Reference |
|---|---|---|---|
| k_UVR8_hv | Light dependent dissociation rate UVR8 dimer | s-1 | from photoinduction model |
| k_LOV_hv | Light dependent activation rate | s-1 | from photoinduction model |
| KM_LOV | LOV repression coefficient | 142 nM | [Strickland2007] |
| KM_LacI | LacI repression coefficient | 800 nM | [Basu2005] |
| KM_cI | cI repression coefficient | 8 nM | [Basu2005] |
| KM_TetR | TetR repression coefficient | 100 nM | assumption |
| n_LacI | LacI cooperativity coefficient | 2 | [Basu2005] |
| n_cI | cI cooperativity coefficient | 2 | [Basu2005] |
| n_TetR | TetR cooperativity coefficient | 1 | [GarciaOjalvo2004] |
| n_LOV | LOV cooperativity coefficient | 1 | assumption |
| k_UVR8_decay | Dimerization rate UVR8 monomer | 8.4·10-10 nM-1 s-1 | estimate |
| k_LOV_decay | Dark decay rate of active LOV | 5.8·10-3 s-1 | [Drepper2007] |
| k_Ptrp | Trp promoter expression strength | 2.34 nM s-1 | optimized |
| k_P_R | Lambda P_R expression strength | 4.21·10-2 nM s-1 | optimized |
| k_P_L | Lambda P_L expression strength | 2.1579·10-2 nM s-1 | optimized |
| A | Basal expression fraction | 0.15 | assumption |
| k_deg | Protein degradation rate | 1.9·10-3 s-1 | assumption |
LovTAP-Cph8
| Parameter | Description | Value | Reference |
|---|---|---|---|
| k_Cph8_hv | Light dependent activation rate | s-1 | from photoinduction model |
| KM_LOV | LOV repression coefficient | 142 nM | [Strickland2007] |
| KM_Cph8 | Cph8 activation coefficient | 1000 nM | estimate |
| KM_LacI | LacI repression coefficient | 800 nM | [Basu2005] |
| KM_cI | cI repression coefficient | 8 nM | [Basu2005] |
| KM_TetR | TetR repression coefficient | 100 nM | assumption |
| n_LacI | LacI cooperativity coefficient | 2 | [Basu2005] |
| n_cI | cI cooperativity coefficient | 2 | [Basu2005] |
| n_TetR | TetR cooperativity coefficient | 1 | [GarciaOjalvo2004] |
| n_Cph8 | Cph8 cooperativity coefficient | 1 | assumption |
| n_LOV | LOV cooperativity coefficient | 1 | assumption |
| k_LOV_decay | Dark decay rate of active LOV | 5.8·10-3 s-1 | [Drepper2007] |
| k_Cph8_decay | Dark decay rate of active Cph8 | 5.8·10-3 s-1 | estimate |
| k_Ptrp | Trp promoter expression strength | 2.23 nM s-1 | optimized |
| k_PompC | OmpC promoter expression strength | 3.454·10-1 nM s-1 | optimized |
| k_P_R | Lambda P_R expression strength | 4.21·10-2 nM s-1 | optimized |
| k_P_L | Lambda P_L expression strength | 3.0·10-2 nM s-1 | optimized |
| A | Basal expression fraction | 0.15 | assumption |
| k_deg | Protein degradation rate | 1.9·10-3 s-1 | assumption |
Parameters denoted with
- assumption 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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- Christie, J. M., Arvai, A. S., Baxter, K. J., Heilmann, M., Pratt, A. J., O’Hara, A., Kelly, S. M., et al. (2012). Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science (New York, N.Y.), 335(6075), 1492–6.
- Cloix, C., & Jenkins, G. I. (2008). Interaction of the Arabidopsis UV-B-specific signaling component UVR8 with chromatin. Molecular plant, 1(1), 118–28.
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