Team:ETH Zurich/Modeling/Parameters
From 2012.igem.org
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|room | |room | ||
|sun*0.3, (UV<350nm)*0.05, (UV>=350nm)*0,90 | |sun*0.3, (UV<350nm)*0.05, (UV>=350nm)*0,90 | ||
- | | | + | |assumed |
|210 W m<sup>-2</sup> | |210 W m<sup>-2</sup> | ||
|n/a | |n/a | ||
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|[[File:ETH_modeling_act_uvr8_a.png|frameless|150px]] | |[[File:ETH_modeling_act_uvr8_a.png|frameless|150px]] | ||
|n/a | |n/a | ||
- | | | + | |<span class='eth_reference'>[Brown2009]</span> |
|} | |} | ||
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!Reference | !Reference | ||
|- | |- | ||
- | | k_UVR8_hv||Light dependent dissociation rate UVR8 dimer|| s<sup>-1</sup>||from | + | | k_UVR8_hv||Light dependent dissociation rate UVR8 dimer|| 2.08·10<sup>-3</sup> s<sup>-1</sup>||from gels |
|- | |- | ||
| k_UVR8_decay||Dimerization rate UVR8 monomer||8.4·10<sup>-10</sup> nM<sup>-1</sup> s<sup>-1</sup>||estimate | | k_UVR8_decay||Dimerization rate UVR8 monomer||8.4·10<sup>-10</sup> nM<sup>-1</sup> s<sup>-1</sup>||estimate | ||
|- | |- | ||
- | | KM_TetR||TetR repression coefficient ||100 nM|| | + | | KM_TetR||TetR repression coefficient ||100 nM||assumed |
|- | |- | ||
| n_TetR||TetR cooperativity coefficient||1||<span class='eth_reference'>[GarciaOjalvo2004]</span> | | n_TetR||TetR cooperativity coefficient||1||<span class='eth_reference'>[GarciaOjalvo2004]</span> | ||
|- | |- | ||
- | | k_Ptet||Tet promoter expression strength|| | + | | k_Ptet||Tet promoter expression strength||1.1 nM s<sup>-1</sup>||optimised |
|- | |- | ||
- | | A||Basal expression fraction||0. | + | | A||Basal expression fraction||0.05||assumed |
|- | |- | ||
- | | n||Hill-like pABA cooperativity coefficient|| | + | | n||Hill-like pABA cooperativity coefficient||10<sup>-5</sup>||assumed |
|- | |- | ||
- | | k_deg||Protein degradation rate|| | + | | k_deg||Protein degradation rate||3.85·10<sup>-5</sup> s<sup>-1</sup>||assumed |
|- | |- | ||
- | | KM_PabAB||PabAB Michaelis constant|| | + | | KM_PabAB||PabAB Michaelis constant||960·10<sup>3</sup> nM||<span class='eth_reference'>[Roux1992]</span> |
|- | |- | ||
| k_cat||PabAB catalysis rate||0.65 s<sup>-1</sup>||<span class='eth_reference'>[Roux1992]</span> | | k_cat||PabAB catalysis rate||0.65 s<sup>-1</sup>||<span class='eth_reference'>[Roux1992]</span> | ||
|- | |- | ||
- | | Chor0||Intracellular chorismate concentration|| | + | | Chor0||Intracellular chorismate concentration||100 mM||assumed |
|- | |- | ||
- | | k_out||pABA outflux rate|| | + | | k_out||pABA outflux rate||3.85·10<sup>-4</sup> s<sup>-1</sup>||assumed |
|} | |} | ||
- | === | + | === LovTAP-Cph8 === |
{| | {| | ||
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!Value | !Value | ||
!Reference | !Reference | ||
+ | |-| k_LOV_hv||Light dependent activation rate|| s<sup>-1</sup>||from photoinduction model | ||
|- | |- | ||
- | | | + | | k_Cph8_hv||Light dependent activation rate|| s<sup>-1</sup>||from photoinduction model |
- | + | ||
- | + | ||
|- | |- | ||
| KM_LOV||LOV repression coefficient||142 nM||<span class='eth_reference'>[Strickland2007]</span> | | KM_LOV||LOV repression coefficient||142 nM||<span class='eth_reference'>[Strickland2007]</span> | ||
+ | |- | ||
+ | | KM_Cph8||Cph8 activation coefficient||1000 nM||estimate | ||
|- | |- | ||
| KM_LacI||LacI repression coefficient||800 nM||<span class='eth_reference'>[Basu2005]</span> | | KM_LacI||LacI repression coefficient||800 nM||<span class='eth_reference'>[Basu2005]</span> | ||
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| KM_cI||cI repression coefficient||8 nM||<span class='eth_reference'>[Basu2005]</span> | | KM_cI||cI repression coefficient||8 nM||<span class='eth_reference'>[Basu2005]</span> | ||
|- | |- | ||
- | | KM_TetR||TetR repression coefficient||100 nM|| | + | | KM_TetR||TetR repression coefficient||100 nM||assumed |
|- | |- | ||
| n_LacI||LacI cooperativity coefficient||2||<span class='eth_reference'>[Basu2005]</span> | | n_LacI||LacI cooperativity coefficient||2||<span class='eth_reference'>[Basu2005]</span> | ||
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| n_TetR||TetR cooperativity coefficient||1||<span class='eth_reference'>[GarciaOjalvo2004]</span> | | n_TetR||TetR cooperativity coefficient||1||<span class='eth_reference'>[GarciaOjalvo2004]</span> | ||
|- | |- | ||
- | | | + | | n_Cph8||Cph8 cooperativity coefficient||1||assumed |
|- | |- | ||
- | | | + | | n_LOV||LOV cooperativity coefficient||1||assumed |
|- | |- | ||
| k_LOV_decay||Dark decay rate of active LOV||5.8·10<sup>-3</sup> s<sup>-1</sup>||<span class='eth_reference'>[Drepper2007]</span> | | k_LOV_decay||Dark decay rate of active LOV||5.8·10<sup>-3</sup> s<sup>-1</sup>||<span class='eth_reference'>[Drepper2007]</span> | ||
|- | |- | ||
- | | k_Ptrp||Trp promoter expression strength||2. | + | | k_Cph8_decay||Dark decay rate of active Cph8||5.8·10<sup>-3</sup> s<sup>-1</sup>||estimate |
+ | |- | ||
+ | | k_Ptrp||Trp promoter expression strength||2.23 nM s<sup>-1</sup>||optimized | ||
+ | |- | ||
+ | | k_PompC||OmpC promoter expression strength||3.454·10<sup>-1</sup> nM s<sup>-1</sup>||optimized | ||
|- | |- | ||
| k_P_R||Lambda P_R expression strength||4.21·10<sup>-2</sup> nM s<sup>-1</sup>||optimized | | k_P_R||Lambda P_R expression strength||4.21·10<sup>-2</sup> nM s<sup>-1</sup>||optimized | ||
|- | |- | ||
- | | k_P_L||Lambda P_L expression strength|| | + | | k_P_L||Lambda P_L expression strength||3.0·10<sup>-2</sup> nM s<sup>-1</sup>||optimized |
|- | |- | ||
- | | A||Basal expression fraction||0. | + | | A||Basal expression fraction||0.05||assumed |
|- | |- | ||
- | | k_deg||Protein degradation rate||1.9·10<sup>-3</sup> s<sup>-1</sup>|| | + | | k_deg||Protein degradation rate||1.9·10<sup>-3</sup> s<sup>-1</sup>||assumed |
|} | |} | ||
+ | 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. | ||
- | === | + | === Sun Protection Factor === |
- | {| | + | {| {{table}} |
- | !Parameter | + | ! Parameter||Description||Value||Reference |
- | + | ||
- | + | ||
- | + | ||
- | | | + | |
|- | |- | ||
- | | | + | | ecoli_v||Volume of E.coli||2.0e-18 m3||[http://bionumbers.hms.harvard.edu/Includes/KeyNumbersLinks.pdf Bionumbers] |
|- | |- | ||
- | | | + | | ecoli_extcoeff||Extinction coefficient of E.coli at 600nm||6.022e10 m2 mol-1||Computed via OD600 |
|- | |- | ||
- | | | + | | ecoli_absorption||Absorption spectrum E.coli||[[File:ETH_modeling_abs_ecoli.png|frameless|150px]]||<span class='eth_reference'>[Kiefer2010]</span> |
|- | |- | ||
- | | | + | | pABA_extcoeff||Extinction coefficient of pABA at 290nm||1.9e3 m2 mol-1||<span class='eth_reference'>[Quinlivan2003]</span> |
|- | |- | ||
- | | | + | | pABA_absorption||Absorption spectrum pABA||[[File:ETH_modeling_abs_paba.png|frameless|150px]]||<span class='eth_reference'>[EC2006]</span> |
|- | |- | ||
- | | | + | | pABA_molarweight||Molar weight of pABA||137.14 g mol-1||[http://www.sigmaaldrich.com/catalog/product/sigma/a9878?lang=de®ion=DE Datasheet] |
|- | |- | ||
- | | | + | | layer_height||Height of sunscreen layer||2e-5 m||<span class='eth_reference'>[Vainio2001]</span> |
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{{:Team:ETH_Zurich/Templates/Footer}} | {{:Team:ETH_Zurich/Templates/Footer}} |
Latest revision as of 23:23, 26 October 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 | assumed | 210 W m-2 | n/a |
bulb200W | Incandescent light bulb | GE200Clear | 12 W m-2 | 1 m |
Photoconversion cross section
From Absorption spectrum
From Photon effectiveness
Receptor | Activation photon effectiveness | Deactivation photon effectiveness | References |
---|---|---|---|
UVR8 | n/a | [Brown2009] |
UVR8
Parameter | Description | Value | Reference |
---|---|---|---|
k_UVR8_hv | Light dependent dissociation rate UVR8 dimer | 2.08·10-3 s-1 | from gels |
k_UVR8_decay | Dimerization rate UVR8 monomer | 8.4·10-10 nM-1 s-1 | estimate |
KM_TetR | TetR repression coefficient | 100 nM | assumed |
n_TetR | TetR cooperativity coefficient | 1 | [GarciaOjalvo2004] |
k_Ptet | Tet promoter expression strength | 1.1 nM s-1 | optimised |
A | Basal expression fraction | 0.05 | assumed |
n | Hill-like pABA cooperativity coefficient | 10-5 | assumed |
k_deg | Protein degradation rate | 3.85·10-5 s-1 | assumed |
KM_PabAB | PabAB Michaelis constant | 960·103 nM | [Roux1992] |
k_cat | PabAB catalysis rate | 0.65 s-1 | [Roux1992] |
Chor0 | Intracellular chorismate concentration | 100 mM | assumed |
k_out | pABA outflux rate | 3.85·10-4 s-1 | assumed |
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 | assumed |
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 | assumed |
n_LOV | LOV cooperativity coefficient | 1 | assumed |
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 | 0.05 | assumed |
k_deg | Protein degradation rate | 1.9·10-3 s-1 | assumed |
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.
Sun Protection Factor
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.
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