Transcription factor competition theoretical analysis
Version 1

The zip file contains two executable Matlab functions.

File named 'fnct_gen_tfcompmod.m' generates a Simbiology model based on the following interactions: R + X RX -> R + X + Px R + Y RY -> R + Y + Py R + Z RZ -> R + Z + Pz Y + Pz -> Pz Px -> Py -> Pz ->

We assume much higher reaction speeds of sigma factor RNApol binding/unbinding compared to protein expression. Protein expression can therefore be represented by Michaelis-Menten like kinetic laws with three competing inhibitors (X,Y,Z). The analysis is based on four 'experiments': measurement of sigma factor specific reporter proteins (Px,Py,Pz) in the wild type (+x+y+z) and in three mutants where in each one sigma factor is knocked out (1. -x+y+z / 2. +x-y+z / 3. +x+y-z). Four plots are automatically generated showing the wildtype dynamics of the three reporter proteins, and three plots for the dynamics of each protein in all genetic backgrounds.

The file named 'fnct_gen_tfcomplineburk.m' analyses the model outlined above using a Lineweaver-Burg representation. The x-axis shows the reciprocal of the concentration of one sigma factor while the y-axis represents reporter protein signals. Different slopes, i.e. expression intensities, occur for different concentrations of competitive sigma factors. This graphical representation allows deduction of total level of RNApol and the relative competitive strength of the sigma factors.


1 item is associated with this Model:
  • (Zip file - 3.86 KB)

Organism: Bacillus subtilis

Model type: Ordinary differential equations (ODE)

Model format: Matlab package

Execution or visualisation environment: Matlab

Model image: No image specified

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Views: 2369   Downloads: 2

Created: 15th Apr 2010 at 14:56

Last updated: 28th May 2014 at 09:36

Last used: 25th Jun 2022 at 09:19

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Version 1 Created 15th Apr 2010 at 14:56 by Ulf Liebal

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