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
-
|assumption
+
|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
-
|
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|<span class='eth_reference'>[Brown2009]</span>
|}
|}
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!Reference
!Reference
|-
|-
-
| k_UVR8_decay||Dimerization rate UVR8 monomer||8.4·10<sup>-10</sup>||estimate
+
| k_UVR8_hv||Light dependent dissociation rate UVR8 dimer|| 2.08·10<sup>-3</sup> s<sup>-1</sup>||from gels
|-
|-
-
| k_UVR8_hv||Light dependent dissociation rate UVR8 dimer|| ||from photoinduction model
+
| 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||asmp
+
| 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||50||asmp
+
| k_Ptet||Tet promoter expression strength||1.1 nM s<sup>-1</sup>||optimised
|-
|-
-
| A||Basal expression fraction||0.15||asmp
+
| A||Basal expression fraction||0.05||assumed
|-
|-
-
| n||Hill-like pABA cooperativity coefficient||1||asmp
+
| n||Hill-like pABA cooperativity coefficient||10<sup>-5</sup>||assumed
|-
|-
-
| k_deg||Protein degradation rate||0.03||asmp
+
| k_deg||Protein degradation rate||3.85·10<sup>-5</sup> s<sup>-1</sup>||assumed
|-
|-
-
| KM_PabAB||PabAB Michaelis constant||9.60·10<sup>5</sup>||<span class='eth_reference'>[Roux1992]</span>
+
| KM_PabAB||PabAB Michaelis constant||960·10<sup>3</sup> nM||<span class='eth_reference'>[Roux1992]</span>
|-
|-
-
| k_cat||PabAB catalysis rate||0.65||<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||1.4·10<sup>5</sup>||asmp
+
| Chor0||Intracellular chorismate concentration||100 mM||assumed
|-
|-
-
| k_out||pABA outflux rate||0.01||asmp
+
| k_out||pABA outflux rate||3.85·10<sup>-4</sup> s<sup>-1</sup>||assumed
|}
|}
-
=== UVR8-TetRDBD-LovTAP ===
+
=== LovTAP-Cph8  ===
{|
{|
Line 144: Line 144:
!Value
!Value
!Reference
!Reference
 +
|-| k_LOV_hv||Light dependent activation rate|| s<sup>-1</sup>||from photoinduction model
|-
|-
-
| k_UVR8_hv||Light dependent dissociation rate UVR8 dimer|| ||from photoinduction model
+
| k_Cph8_hv||Light dependent activation rate|| s<sup>-1</sup>||from photoinduction model
|-
|-
-
| k_LOV_hv||Light dependent activation rate|| ||from photoinduction model
+
| KM_LOV||LOV repression coefficient||142 nM||<span class='eth_reference'>[Strickland2007]</span>
|-
|-
-
| KM_LOV||LOV repression coefficient||142||<span class='eth_reference'>[Strickland2007]</span>
+
| KM_Cph8||Cph8 activation coefficient||1000 nM||estimate
|-
|-
-
| KM_LacI||LacI repression coefficient||800||<span class='eth_reference'>[Basu2005]</span>
+
| KM_LacI||LacI repression coefficient||800 nM||<span class='eth_reference'>[Basu2005]</span>
|-
|-
-
| KM_cI||cI repression coefficient||8||<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||asmp
+
| 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>
Line 163: Line 164:
| 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_LOV||LOV cooperativity coefficient||1||asmp
+
| n_Cph8||Cph8 cooperativity coefficient||1||assumed
|-
|-
-
| k_UVR8_decay||Dimerization rate UVR8 monomer||8.4·10<sup>-10</sup>||estimate
+
| n_LOV||LOV cooperativity coefficient||1||assumed
|-
|-
-
| k_LOV_decay||Dark decay rate of active LOV||5.8·10<sup>-3</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||2.34||optimized
+
| k_Cph8_decay||Dark decay rate of active Cph8||5.8·10<sup>-3</sup> s<sup>-1</sup>||estimate
|-
|-
-
| k_P_R||Lambda P_R expression strength||4.21·10<sup>-2</sup>||optimized
+
| k_Ptrp||Trp promoter expression strength||2.23 nM s<sup>-1</sup>||optimized
|-
|-
-
| k_P_L||Lambda P_L expression strength||2.1579·10<sup>-2</sup>||optimized
+
| k_PompC||OmpC promoter expression strength||3.454·10<sup>-1</sup> nM s<sup>-1</sup>||optimized
|-
|-
-
| A||Basal expression fraction||0.15||asmp
+
| k_P_R||Lambda P_R expression strength||4.21·10<sup>-2</sup> nM s<sup>-1</sup>||optimized
|-
|-
-
| k_deg||Protein degradation rate||1.9·10<sup>-3</sup>||asmp
+
| k_P_L||Lambda P_L expression strength||3.0·10<sup>-2</sup> nM s<sup>-1</sup>||optimized
 +
|-
 +
| A||Basal expression fraction||0.05||assumed
 +
|-
 +
| 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.
-
=== LovTAP-Cph8  ===
+
=== Sun Protection Factor ===
-
{|
+
{| {{table}}
-
!Parameter
+
! Parameter||Description||Value||Reference
-
!Description
+
-
!Value
+
-
!Reference
+
-
|-| k_LOV_hv||Light dependent activation rate|| ||from photoinduction model
+
|-
|-
-
| k_Cph8_hv||Light dependent activation rate|| ||from photoinduction model
+
| ecoli_v||Volume of E.coli||2.0e-18 m3||[http://bionumbers.hms.harvard.edu/Includes/KeyNumbersLinks.pdf Bionumbers]
|-
|-
-
| KM_LOV||LOV repression coefficient||142||<span class='eth_reference'>[Strickland2007]</span>
+
| ecoli_extcoeff||Extinction coefficient of E.coli at 600nm||6.022e10 m2 mol-1||Computed via OD600
|-
|-
-
| KM_Cph8||Cph8 activation coefficient||1000||estimate
+
| ecoli_absorption||Absorption spectrum E.coli||[[File:ETH_modeling_abs_ecoli.png|frameless|150px]]||<span class='eth_reference'>[Kiefer2010]</span>
|-
|-
-
| KM_LacI||LacI repression coefficient||800||<span class='eth_reference'>[Basu2005]</span>
+
| pABA_extcoeff||Extinction coefficient of pABA at 290nm||1.9e3 m2 mol-1||<span class='eth_reference'>[Quinlivan2003]</span>
|-
|-
-
| KM_cI||cI repression coefficient||8||<span class='eth_reference'>[Basu2005]</span>
+
| pABA_absorption||Absorption spectrum pABA||[[File:ETH_modeling_abs_paba.png|frameless|150px]]||<span class='eth_reference'>[EC2006]</span>
|-
|-
-
| KM_TetR||TetR repression coefficient||100||asmp
+
| pABA_molarweight||Molar weight of pABA||137.14 g mol-1||[http://www.sigmaaldrich.com/catalog/product/sigma/a9878?lang=de®ion=DE Datasheet]
|-
|-
-
| n_LacI||LacI cooperativity coefficient||2||<span class='eth_reference'>[Basu2005]</span>
+
| layer_height||Height of sunscreen layer||2e-5 m||<span class='eth_reference'>[Vainio2001]</span>
|-
|-
-
| n_cI||cI cooperativity coefficient||2||<span class='eth_reference'>[Basu2005]</span>
 
-
|-
 
-
| n_TetR||TetR cooperativity coefficient||1||<span class='eth_reference'>[GarciaOjalvo2004]</span>
 
-
|-
 
-
| n_Cph8||Cph8 cooperativity coefficient||1||asmp
 
-
|-
 
-
| n_LOV||LOV cooperativity coefficient||1||asmp
 
-
|-
 
-
| k_LOV_decay||Dark decay rate of active LOV||5.8·10<sup>-3</sup>||<span class='eth_reference'>[Drepper2007]</span>
 
-
|-
 
-
| k_Cph8_decay||Dark decay rate of active Cph8||5.8·10<sup>-3</sup>||estimate
 
-
|-
 
-
| k_Ptrp||Trp promoter expression strength||2.23||optimized
 
-
|-
 
-
| k_PompC||OmpC promoter expression strength||3.454·10<sup>-1</sup>||optimized
 
-
|-
 
-
| k_P_R||Lambda P_R expression strength||4.21·10<sup>-2</sup>||optimized
 
-
|-
 
-
| k_P_L||Lambda P_L expression strength||3.0·10<sup>-2</sup>||optimized
 
-
|-
 
-
| A||Basal expression fraction||0.15||asmp
 
-
|-
 
-
| k_deg||Protein degradation rate||1.9·10<sup>-3</sup>||asmp
 
|}
|}
 +
{{:Team:ETH_Zurich/Templates/Footer}}
{{:Team:ETH_Zurich/Templates/Footer}}

Latest revision as of 23:23, 26 October 2012

Eth ecolipseeth logo.png
Eth igem logo.png


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 2.08·10-3 s-1from gels
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 strength1.1 nM s-1optimised
ABasal expression fraction0.05assumed
nHill-like pABA cooperativity coefficient10-5assumed
k_degProtein degradation rate3.85·10-5 s-1assumed
KM_PabABPabAB Michaelis constant960·103 nM[Roux1992]
k_catPabAB catalysis rate0.65 s-1[Roux1992]
Chor0Intracellular chorismate concentration100 mMassumed
k_outpABA outflux rate3.85·10-4 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 fraction0.05assumed
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.

Sun Protection Factor

ParameterDescriptionValueReference
ecoli_vVolume of E.coli2.0e-18 m3[http://bionumbers.hms.harvard.edu/Includes/KeyNumbersLinks.pdf Bionumbers]
ecoli_extcoeffExtinction coefficient of E.coli at 600nm6.022e10 m2 mol-1Computed via OD600
ecoli_absorptionAbsorption spectrum E.coliETH modeling abs ecoli.png[Kiefer2010]
pABA_extcoeffExtinction coefficient of pABA at 290nm1.9e3 m2 mol-1[Quinlivan2003]
pABA_absorptionAbsorption spectrum pABAETH modeling abs paba.png[EC2006]
pABA_molarweightMolar weight of pABA137.14 g mol-1[http://www.sigmaaldrich.com/catalog/product/sigma/a9878?lang=de®ion=DE Datasheet]
layer_heightHeight of sunscreen layer2e-5 m[Vainio2001]



References

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  • Christie, J. M., Salomon, M., Nozue, K., Wada, M., & Briggs, W. R. (1999): LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): binding sites for the chromophore flavin mononucleotide. Proceedings of the National Academy of Sciences of the United States of America, 96(15), 8779–83.
  • 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.
  • Cox, R. S., Surette, M. G., & Elowitz, M. B. (2007). Programming gene expression with combinatorial promoters. Molecular systems biology, 3(145), 145. doi:10.1038/msb4100187
  • Drepper, T., Eggert, T., Circolone, F., Heck, A., Krauss, U., Guterl, J.-K., Wendorff, M., et al. (2007). Reporter proteins for in vivo fluorescence without oxygen. Nature biotechnology, 25(4), 443–5
  • Drepper, T., Krauss, U., & Berstenhorst, S. M. zu. (2011). Lights on and action! Controlling microbial gene expression by light. Applied microbiology, 23–40.
  • EuropeanCommission (2006). SCIENTIFIC COMMITTEE ON CONSUMER PRODUCTS SCCP Opinion on Biological effects of ultraviolet radiation relevant to health with particular reference to sunbeds for cosmetic purposes.
  • Elvidge, C. D., Keith, D. M., Tuttle, B. T., & Baugh, K. E. (2010). Spectral identification of lighting type and character. Sensors (Basel, Switzerland), 10(4), 3961–88.
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  • Hirose, Y., Narikawa, R., Katayama, M., & Ikeuchi, M. (2010). Cyanobacteriochrome CcaS regulates phycoerythrin accumulation in Nostoc punctiforme, a group II chromatic adapter. Proceedings of the National Academy of Sciences of the United States of America, 107(19), 8854–9.
  • Hirose, Y., Shimada, T., Narikawa, R., Katayama, M., & Ikeuchi, M. (2008). Cyanobacteriochrome CcaS is the green light receptor that induces the expression of phycobilisome linker protein. Proceedings of the National Academy of Sciences of the United States of America, 105(28), 9528–33.
  • Kast, Asif-Ullah & Hilvert (1996) Tetrahedron Lett. 37, 2691 - 2694., Kast, Asif-Ullah, Jiang & Hilvert (1996) Proc. Natl. Acad. Sci. USA 93, 5043 - 5048
  • Kiefer, J., Ebel, N., Schlücker, E., & Leipertz, A. (2010). Characterization of Escherichia coli suspensions using UV/Vis/NIR absorption spectroscopy. Analytical Methods, 9660. doi:10.1039/b9ay00185a
  • Kinkhabwala, A., & Guet, C. C. (2008). Uncovering cis regulatory codes using synthetic promoter shuffling. PloS one, 3(4), e2030.
  • Krebs in Deutschland 2005/2006. Häufigkeiten und Trends. 7. Auflage, 2010, Robert Koch-Institut (Hrsg) und die Gesellschaft der epidemiologischen Krebsregister in Deutschland e. V. (Hrsg). Berlin.
  • Lamparter, T., Michael, N., Mittmann, F., & Esteban, B. (2002). Phytochrome from Agrobacterium tumefaciens has unusual spectral properties and reveals an N-terminal chromophore attachment site. Proceedings of the National Academy of Sciences of the United States of America, 99(18), 11628–33.
  • Levskaya, A. et al (2005). Engineering Escherichia coli to see light. Nature, 438(7067), 442.
  • Mancinelli, A. (1986). Comparison of spectral properties of phytochromes from different preparations. Plant physiology, 82(4), 956–61.
  • Nakasone, Y., Ono, T., Ishii, A., Masuda, S., & Terazima, M. (2007). Transient dimerization and conformational change of a BLUF protein: YcgF. Journal of the American Chemical Society, 129(22), 7028–35.
  • Orth, P., & Schnappinger, D. (2000). Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nature structural biology, 215–219.
  • Parkin, D.M., et al., Global cancer statistics, 2002. CA: a cancer journal for clinicians, 2005. 55(2): p. 74-108.
  • Rajagopal, S., Key, J. M., Purcell, E. B., Boerema, D. J., & Moffat, K. (2004). Purification and initial characterization of a putative blue light-regulated phosphodiesterase from Escherichia coli. Photochemistry and photobiology, 80(3), 542–7.
  • Rizzini, L., Favory, J.-J., Cloix, C., Faggionato, D., O’Hara, A., Kaiserli, E., Baumeister, R., et al. (2011). Perception of UV-B by the Arabidopsis UVR8 protein. Science (New York, N.Y.), 332(6025), 103–6.
  • Roux, B., & Walsh, C. T. (1992). p-aminobenzoate synthesis in Escherichia coli: kinetic and mechanistic characterization of the amidotransferase PabA. Biochemistry, 31(30), 6904–10.
  • Strickland, D. (2008). Light-activated DNA binding in a designed allosteric protein. Proceedings of the National Academy of Sciences of the United States of America, 105(31), 10709–10714.
  • Sinha RP, Häder DP. UV-induced DNA damage and repair: a review. Photochem Photobiol Sci. (2002). 1(4):225-36
  • Sambandan DR, Ratner D. (2011). Sunscreens: an overview and update. J Am Acad Dermatol. 2011 Apr;64(4):748-58.
  • Tabor, J. J., Levskaya, A., & Voigt, C. A. (2011). Multichromatic Control of Gene Expression in Escherichia coli. Journal of Molecular Biology, 405(2), 315–324.
  • Thibodeaux, G., & Cowmeadow, R. (2009). A tetracycline repressor-based mammalian two-hybrid system to detect protein–protein interactions in vivo. Analytical biochemistry, 386(1), 129–131.
  • Tschowri, N., & Busse, S. (2009). The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes & development, 522–534.
  • Tschowri, N., Lindenberg, S., & Hengge, R. (2012). Molecular function and potential evolution of the biofilm-modulating blue light-signalling pathway of Escherichia coli. Molecular microbiology.
  • Tyagi, A. (2009). Photodynamics of a flavin based blue-light regulated phosphodiesterase protein and its photoreceptor BLUF domain.
  • Vainio, H. & Bianchini, F. (2001). IARC Handbooks of Cancer Prevention: Volume 5: Sunscreens. Oxford University Press, USA
  • Quinlivan, Eoin P & Roje, Sanja & Basset, Gilles & Shachar-Hill, Yair & Gregory, Jesse F & Hanson, Andrew D. (2003). The folate precursor p-aminobenzoate is reversibly converted to its glucose ester in the plant cytosol. The Journal of biological chemistry, 278.
  • van Thor, J. J., Borucki, B., Crielaard, W., Otto, H., Lamparter, T., Hughes, J., Hellingwerf, K. J., et al. (2001). Light-induced proton release and proton uptake reactions in the cyanobacterial phytochrome Cph1. Biochemistry, 40(38), 11460–71.
  • Wegkamp A, van Oorschot W, de Vos WM, Smid EJ. (2007 )Characterization of the role of para-aminobenzoic acid biosynthesis in folate production by Lactococcus lactis. Appl Environ Microbiol. Apr;73(8):2673-81.
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