Team:KULeuven/Modeling/Vanillin Receptor

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__NOTOC__
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=Vanillin Sensor=
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=Vanillin Receptor: Modeling=
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== Overview ==
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== Biological Model ==
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The vanillin receptor senses the vanillin concentration outside the cell. This information is needed to create the feedback loop to control vanillin synthesis. Under influence of vanillin, Vir A gets autophosphorylated and phosphorylates on its turn Vir G. Vir G then triggers the transcription of Anti-key.
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<center>
[[image:Biologie_vanillin_receptor.png|center]]
[[image:Biologie_vanillin_receptor.png|center]]
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{{kulpart|BBa_K238003}}
[[image:Biologie_antikey.png|center]]
[[image:Biologie_antikey.png|center]]
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{{kulpart|BBa_K238001}}
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</center>
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==Models==
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==Mathematical Model==
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[[image:Vanillin_receptor.png|600px|center]]
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[[image:Vanillin_receptor.png|650px|center]]
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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 [4<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 [5<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>transcription</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 [6<html>]</html>]
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|-
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| k<sub>translation</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 [6<html>]</html>]
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Phosphorylation Parameters
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|-
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| k<sub>autophosphorylation</sub>
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| 0.00237 (s molecule)<sup>-1</sup>
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| Rate of autophosphorylation of VirA protein
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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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| k<sub>phosphorylation</sub>
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| 0.00416 s<sup>-1</sup>
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| Rate of phosphorylation of VirG by phosphorylated VirA.
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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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|}
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</center>
==Simulation==
==Simulation==
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A scan of the influence of vanillin on the production of Anti Key is shown is the figure below.
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The steady state level of Anti Key is quite linearly dependent on the amount vanillin, a half rise time
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of 3 hours is estimated by this simulation.
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[[image:Vanillin_sensor.png|750px|center|thumb|The concentration of vanillin [µM] regulates the production mRNA AntiKey]]
==Vanillin diffusion==
==Vanillin diffusion==
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Because VirA senses the vanillin concentration in the cytoplasm, we showed that the extracellular concentration equals the intracellular concentration of vanillin for all our purposes. [https://2009.igem.org/Image:Vanillin_sensing.pdf vanillin_sensing]
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Because VirA senses the vanillin concentration in the cytoplasm, it's important to estimate the diffusion of vanillin over the cell membrane. Also because vanillin is not actively removed from the extracellular medium, the rate of evaporation of vanillin is an important figure if we want to regulate the concentration of vanillin in the extracellular medium. A detailed analysis can be found in following document. [https://2009.igem.org/Image:Vanillin_sensing.pdf vanillin_sensing]
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The most important figures are that the time to reach steady state between the concentration of the inter and extracellular concentration of vanillin in the order of 10 ms, the half-life through evaporation of vanillin in water
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is 20 hours. 
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An equivalent model (single cell) of vanillin in the aqueous medium and evaporation was conducted.
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[[Image:Diffusion_matlabmodel.jpg|center|thum|500px|Equivalent model of vanillin]]
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Following simulation shows the time-scale of evaporation of vanillin out of the lb(aqueous) medium, the slow
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evaporation rate of vanillin is not surprising considering its use in the perfume industries as an aroma in the ground note.
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[[Image:Evaporation.png|center|thumb|500px|Evaporation rate of vanillin out of lb medium]]
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If this evaporation rate would show to slow, several active techniques exists to speed the process of removing the vanillin from the extracellular medium.
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==Reference==
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[1] A. Vian et al., "Structure of the b-Galactosidase Gene from Thermus sp. Strain T2: Expression in Escherichia coli and Purification in a Single Step of an Active Fusion Protein," Department of Microbiology, University of Washington, Applied and Environmental Microbiology, Jun. 1998, p. 2187–2191
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[2] W.T. Peng et al., "The Phenolic Recognition Profiles of the Agrobacterium tumefaciens VirA Protein Are Broadened by a High Level of the Sugar Binding Protein ChvE," Department of Microbiology, University of Washington, JOURNAL OF BACTERIOLOGY, Nov. 1998, p. 5632–5638
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[3] S. Jin et al., "Phosphorylation of the VirG Protein of Agrobacterium tumefaciens by the Autophosphorylated VirA Protein: Essential Role in Biological Activity of VirG," Departments of Microbiology and Pharmacology University of Washington, Journal of Bacteriology, Sept. 1990, p. 4945-4950
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[4] 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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[5] 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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[[Image:Viravirg.JPG|center|thumb|425px|VirA is a transmembrane sensory protein kinase that phosphorylates VirG. It's triggered by phenols, monosaccharides and acid]]
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[6] 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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{{Team:KULeuven/Common2/PageFooter}}

Latest revision as of 07:35, 12 October 2009


Vanillin Receptor: Modeling

Biological Model

Biologie vanillin receptor.png
Biologie antikey.png

Mathematical Model

Vanillin receptor.png
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 0.00848 s-1 estimate [6]
ktranslation 0.167 s-1 estimate [6]
Phosphorylation Parameters
kautophosphorylation 0.00237 (s molecule)-1 Rate of autophosphorylation of VirA protein [2]
kphosphorylation 0.00416 s-1 Rate of phosphorylation of VirG by phosphorylated VirA. [3]

Simulation

A scan of the influence of vanillin on the production of Anti Key is shown is the figure below. The steady state level of Anti Key is quite linearly dependent on the amount vanillin, a half rise time of 3 hours is estimated by this simulation.

The concentration of vanillin [µM] regulates the production mRNA AntiKey

Vanillin diffusion

Because VirA senses the vanillin concentration in the cytoplasm, it's important to estimate the diffusion of vanillin over the cell membrane. Also because vanillin is not actively removed from the extracellular medium, the rate of evaporation of vanillin is an important figure if we want to regulate the concentration of vanillin in the extracellular medium. A detailed analysis can be found in following document. vanillin_sensing

The most important figures are that the time to reach steady state between the concentration of the inter and extracellular concentration of vanillin in the order of 10 ms, the half-life through evaporation of vanillin in water is 20 hours.

An equivalent model (single cell) of vanillin in the aqueous medium and evaporation was conducted.

Equivalent model of vanillin

Following simulation shows the time-scale of evaporation of vanillin out of the lb(aqueous) medium, the slow evaporation rate of vanillin is not surprising considering its use in the perfume industries as an aroma in the ground note.

Evaporation rate of vanillin out of lb medium

If this evaporation rate would show to slow, several active techniques exists to speed the process of removing the vanillin from the extracellular medium.

Reference

[1] A. Vian et al., "Structure of the b-Galactosidase Gene from Thermus sp. Strain T2: Expression in Escherichia coli and Purification in a Single Step of an Active Fusion Protein," Department of Microbiology, University of Washington, Applied and Environmental Microbiology, Jun. 1998, p. 2187–2191

[2] W.T. Peng et al., "The Phenolic Recognition Profiles of the Agrobacterium tumefaciens VirA Protein Are Broadened by a High Level of the Sugar Binding Protein ChvE," Department of Microbiology, University of Washington, JOURNAL OF BACTERIOLOGY, Nov. 1998, p. 5632–5638

[3] S. Jin et al., "Phosphorylation of the VirG Protein of Agrobacterium tumefaciens by the Autophosphorylated VirA Protein: Essential Role in Biological Activity of VirG," Departments of Microbiology and Pharmacology University of Washington, Journal of Bacteriology, Sept. 1990, p. 4945-4950

[4] 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

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

[6] 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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