Team:KULeuven/Modeling/Blue Light Receptor

From 2009.igem.org

(Difference between revisions)
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
|-
|-
-
| k<sub>transcription</sub>
+
| k<sub>transcription YcgF</sub>
 +
| 0.0154 s<sup>-1</sup>
 +
| Rate is faster than transcription rate of YcgE
 +
| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
 +
|-
 +
| k<sub>transcription YcgE</sub>
| 0.00848 s<sup>-1</sup>
| 0.00848 s<sup>-1</sup>
| estimate
| estimate
-
| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [6<html>]</html>]
+
| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
|-
|-
-
| k<sub>translation</sub>
+
! colspan="4" style="border-bottom: 1px solid #003E81;" | Dimerization Parameters
-
| 0.167 s<sup>-1</sup>
+
|-
-
| estimate
+
| k<sub>dimerization</sub>
-
| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [6<html>]</html>]
+
| 8.0E-11 (s molecule)<sup>-1</sup>
 +
| Rate of dimerization of YcgF [molecule = 1 W/m�^2]
 +
| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [2<html>]</html>]
 +
|-
 +
| k<sub>dissociation</sub>
 +
| 0.0058 s<sup>-1</sup>
 +
| Rate of dissociation of the YcgF complex
 +
| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [3<html>]</html>]
|-
|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Phosphorylation Parameters
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! colspan="4" style="border-bottom: 1px solid #003E81;" | YcgF/YcgE Interaction
|-
|-
-
| k<sub>autophosphorylation</sub>
+
| k<sub>bind</sub>
-
| 0.00237 (s molecule)<sup>-1</sup>
+
| 100 (s molecule)<sup>-1</sup>
-
| Rate of autophosphorylation of VirA protein
+
| Rate of binding of YcgF dimer to YcgE
| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [2<html>]</html>]
| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [2<html>]</html>]
|-
|-
-
| k<sub>phosphorylation</sub>
+
| k<sub>unbind</sub>
-
| 0.00416 s<sup>-1</sup>
+
| 1 s<sup>-1</sup>
-
| Rate of phosphorylation of VirG by phosphorylated VirA.
+
| Rate of dissociation of the YcgF/YcgE complex
| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [3<html>]</html>]
| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [3<html>]</html>]
|-
|-

Revision as of 08:29, 18 September 2009

Contents

Blue light Sensor

Biological Model

Biologie blue light.png

Mathematical Model

Bls.JPG
Parameter values (Vanillin Sensor)
Name Value Comments Reference
Degradation Rates
dmRNA 2.3105E-3 s-1 [4]
dProteins 1.9254E-5 s-1 [5]
Transcription Rates
ktranscription YcgF 0.0154 s-1 Rate is faster than transcription rate of YcgE [1]
ktranscription YcgE 0.00848 s-1 estimate [1]
Dimerization Parameters
kdimerization 8.0E-11 (s molecule)-1 Rate of dimerization of YcgF [molecule = 1 W/m�^2] [2]
kdissociation 0.0058 s-1 Rate of dissociation of the YcgF complex [3]
YcgF/YcgE Interaction
kbind 100 (s molecule)-1 Rate of binding of YcgF dimer to YcgE [2]
kunbind 1 s-1 Rate of dissociation of the YcgF/YcgE complex [3]

Simulation

The amount of produced RIBOKEY is positively correlated on the incident blue radiation. The build up of key in the begin period of is due to the relative slow build up of the active state of YcgF protein in compared to the build up of YcgE.

Blue light sensor.png

References

[1] Natalia Tschowri, Susan Busse and Regine Hengge, "The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli"

[2] Y. Nakasone et al., "Transient Dimerization and Conformational Change of a BLUF Protein: YcgF", Journal of the American Chemical Society, Apr. 2006

Retrieved from "http://2009.igem.org/Team:KULeuven/Modeling/Blue_Light_Receptor"