Team:KULeuven/Modelling/Vanillin Receptor

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==Vanillin diffusion==
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{{Team:KULeuven/Common/BeginHeader}}
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{{Team:KULeuven/Common/SubMenu_Project}}
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{{Team:KULeuven/Common/EndHeader}}
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=== intro ===
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=Vanillin Sensor=
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Because the VirA protein sensor domain is located in the cytoplasmic region, it senses intercellular
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vanillin concentration.
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Because the objective of this project is to regulate the extracellular vanillin concentration we investigate the
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relation between the intercellular and extracellular vanillin concentration.
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It will be shown that on the time-scale we are interested in, intracellular and extracellular concentration are equal.
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We can approximate the relationship with following continuity equation (equilibrium in cytoplasm and extracellular):
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== Overview ==
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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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[[image:Biologie_vanillin_receptor.png|center]]
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[[image:Biologie_antikey.png|center]]
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<math>d[V_inter]/dt = V_production-k_diffusion(V_inter-V_extra)</math>
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==Models==
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[[image:Vanillin_receptor.png|600px|center]]
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V_inter: intercellular concentration
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==Vanillin diffusion==
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V_extra: extracellular concentration
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V_production: production of vannilin
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k_diffusion: speed of diffusion in and out cell
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rewriting the above equation gives
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<math>V_extra = V_intra+1/k_diffusion*(d[V_inter]/dt - V_production)</math>
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If the k_diffusion is big, on the time-scale we are interested in, we are not interested in phenomena which occur
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within 1 minute, V_extra and V_intra can be regarded as equal.
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=== simulation ===
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The following more exact treatise will try to determine the time scale on which the vanillin concentration reaches equilibrium conditions (V_extra = V_inter).
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The process is described by following (more general) continuity equation:
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<math> d[V]/dt = V_production+k_degradation*V+d[D_V*d[V]/dx]/dx</math>
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V: Vanillin concentration
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V_production: Vanillin production
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k_degradation: speed of degradation but will here be considered 0
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D_V: diffusion coefficient of vanillin
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[[image:Cell_wall.png|600px|center]]
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[[image:virA_virG.JPG|600px|center]]
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Inner Membrane thickness: 8 nm
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Outer Membrane thickness: 12 nm
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Periplasm thickness: 10 nm
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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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We neglect the outer membrane because the porins make the membrane permeable.
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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]]

Latest revision as of 14:22, 20 August 2009

Contents

Vanillin Sensor

Overview

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.

Biologie vanillin receptor.png
Biologie antikey.png

Models

Vanillin receptor.png

Vanillin diffusion

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. vanillin_sensing

VirA is a transmembrane sensory protein kinase that phosphorylates VirG. It's triggered by phenols, monosaccharides and acid
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