Team:KULeuven/Modeling/Blue Light Receptor

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=Blue light Sensor=
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__NOTOC__
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==Overview==
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=Blue Light Receptor: Modeling=
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The purpose of the sensor is to enter the wanted vanillin concentration. Under the influence of the intensity of a blue light, the RIBOKEY is transcribed. The light used to perform the test has a wavelength of 470nm.
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==Biological Model==
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The biology works as follows:
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YcgF protein is believed to dimerize upon photo-excitation. The YcgE protein functions as a repressor for the transcription of the mRNA_RIBOKEY. However, the dimer form of YcgF is capable of interacting with the operator-bound YcgE, thereby releasing it from the DNA and starting transcription.
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<center>
<center>
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==Models==
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==Mathematical Model==
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The entire network of interactions is visualized in the diagram below
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[[Image:Bls.JPG|center|thumb|600px|Regulation of the production of mRNA key by incident blue light]]
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==Reactions==
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[[image:Bls.JPG|650px|center]]
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===Dimerization of YcgF===
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<center>
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{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"
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|+ ''Parameter values (Vanillin Sensor)''
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! width=15% | Name
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! width=15% | Value
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! width=40% | Comments
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! width=10% | Reference
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates
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|-
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| d<sub>mRNA</sub>
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| 2.3105E-3 s<sup>-1</sup>
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|
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [3<html>]</html>]
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|-
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| d<sub>Proteins</sub>
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| 1.9254E-5 s<sup>-1</sup>
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|
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [4<html>]</html>]
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
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|-
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| k<sub>YcgF</sub>
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| 0.0154 s<sup>-1</sup>
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| Rate is faster than transcription rate of YcgE
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
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|-
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| k<sub>YcgE</sub>
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| 0.00848 s<sup>-1</sup>
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| estimate
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates
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|-
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| k<sub>YcgF</sub>
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| 0.167s<sup>-1</sup>
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| Rate is faster than transcription rate of YcgE
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [5<html>]</html>]
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|-
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| k<sub>YcgE</sub>
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| 0.167 s<sup>-1</sup>
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| estimate
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [5<html>]</html>]
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Dimerization Parameters
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|-
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| k<sub>dimerization</sub>
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| 8.0E-11 (s W/m^2)<sup>-1</sup>
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| Rate of dimerization of YcgF
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
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|-
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| k<sub>dissociation</sub>
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| 0.0058 s<sup>-1</sup>
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| Rate of dissociation of the YcgF complex
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [2<html>]</html>]
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | YcgF/YcgE Interaction
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|-
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| k<sub>bind</sub>
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| 100 (s molecule)<sup>-1</sup>
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| Rate of binding of YcgF dimer to YcgE
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
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|-
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| k<sub>unbind</sub>
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| 1 s<sup>-1</sup>
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| Rate of dissociation of the YcgF/YcgE complex
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
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|-
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|}
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</center>
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"Transient Dimerization and Conformational Change of a BLUF Protein:  YcgF", [http://pubs.acs.org/doi/full/10.1021/ja065682q]
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==Simulation==
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[[Image:YcgFdimerization.gif|center|thumb|450px|Sensor interface]]
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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.
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"Light Induced Structural Changes of a Full-length Protein and Its BLUF Domain in
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[[image:Blue_light_sensor.png|700px|center]]
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YcgF(Blrp), a Blue-Light Sensing Protein That Uses FAD (BLUF)"
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[http://pubs.acs.org/doi/abs/10.1021/bi051820x]
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"Influence of a Joining Helix on the BLUF Domain of the
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==References==
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YcgF Photoreceptor from Escherichia coli"
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[http://www3.interscience.wiley.com/cgi-bin/fulltext/121407023/PDFSTART]
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===YcgF - YcgE interaction===
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[1] Natalia Tschowri, Susan Busse and Regine Hengge, "The BLUF-EAL protein YcgF acts as
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a direct anti-repressor in a blue-light response of Escherichia coli"
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"The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli"
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[2] Y. Nakasone et al., "Transient Dimerization and Conformational Change of a BLUF Protein:  YcgF", Journal of the American Chemical Society, Apr. 2006
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[http://genesdev.cshlp.org/content/23/4/522.full.pdf+html]
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===Transcription of the RIBOKEY===
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[3] J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702
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https://2008.igem.org/Team:KULeuven/Model/Filter
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[4] K. Nath et al., “Protein degradation in Escherichia Coli,” The Journal of Biological Chemistry, vol. 246, Nov. 1971, pp. 6956-6967
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===Degradation of the RIBOKEY===
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[5] S.L. Gotta et al., “rRNA Transcription Rate in Escherichia Coli,” Journal of Bacteriology, vol. 173, Oct. 1991, pp. 6647-6649
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https://2008.igem.org/Team:KULeuven/Model/Filter
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{{Team:KULeuven/Common2/PageFooter}}
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==References==
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[1] Natalia Tschowri, Susan Busse and Regine Hengge, "The BLUF-EAL protein YcgF acts as
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a direct anti-repressor in a blue-light response of Escherichia coli"
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Latest revision as of 12:49, 18 October 2009


Blue Light Receptor: Modeling

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 [3]
dProteins 1.9254E-5 s-1 [4]
Transcription Rates
kYcgF 0.0154 s-1 Rate is faster than transcription rate of YcgE [1]
kYcgE 0.00848 s-1 estimate [1]
Translation Rates
kYcgF 0.167s-1 Rate is faster than transcription rate of YcgE [5]
kYcgE 0.167 s-1 estimate [5]
Dimerization Parameters
kdimerization 8.0E-11 (s W/m^2)-1 Rate of dimerization of YcgF [1]
kdissociation 0.0058 s-1 Rate of dissociation of the YcgF complex [2]
YcgF/YcgE Interaction
kbind 100 (s molecule)-1 Rate of binding of YcgF dimer to YcgE [1]
kunbind 1 s-1 Rate of dissociation of the YcgF/YcgE complex [1]

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

[3] J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702

[4] K. Nath et al., “Protein degradation in Escherichia Coli,” The Journal of Biological Chemistry, vol. 246, Nov. 1971, pp. 6956-6967

[5] S.L. Gotta et al., “rRNA Transcription Rate in Escherichia Coli,” Journal of Bacteriology, vol. 173, Oct. 1991, pp. 6647-6649

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