Comparison between experimental and simulation results of PCNA ubiquitylation dynamics obtained on wild type yeast cells at 5 J/m2 UV dose. The figure shows the experimental measurements on WT yeast cells irradiated at 5 J/m2 UV dose and the comparison with the corresponding simulation results. (A) Representative image of a western blot showing a time-course measurement of mono-, di- and tri-ubiquitylated PCNA isoforms (top part, denoted by α-Ub) and of non modified PCNA (bottom part, denoted by α-His), sampled from 0 to 5 h after UV irradiation. The experiment was repeated 3 times. (B) Average dynamics of mono-ubiquitylated PCNA (blue line) and of poly-ubiquitylated PCNA (orange line), obtained from 100 independent stochastic simulations, executed starting from the same initial conditions (see Table 2 for molecular amounts and Table 3 for reaction constants) and with an estimated number of DNA lesions equal to 1001. (C) Comparison between the mean dynamics of mono-, di- and tri-ubiquitylated PCNA isoforms emerging from 100 independent stochastic simulations, and the mean value of experimental data , together with the respective standard deviation . Colored areas indicate the amplitude of stochastic fluctuations around the mean value . Data are plotted by using the units representation (see Additional file 5). (D) Comparison between the ratio of experimental (, left bars) and simulated (, right bars) ubiquitylated PCNA isoforms at every sampled time point where experimental measurements yield a detectable amount of modified PCNA. Mean and standard deviation bars of both experimental and simulated ratios are plotted by using the normalized representation (see Additional file 5).
Amara et al. BMC Systems Biology 2013 7:24 doi:10.1186/1752-0509-7-24