Transcription factor competition theoretical analysis

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.