Fig. 4: ssDNA enhances the PprI-DdrO interactions.
From: The Deinococcus protease PprI senses DNA damage by directly interacting with single-stranded DNA
a FRET showing the interactions between PprI and DdrO. The transfer efficiency is represented by the RFU ratio of 530/480 nm. Data represent the means of the three replicates and the bars represent their standard deviations. One-way ANOVA method followed by Tukey’s post-hoc test was performed to compare the significant differences. b A Snapshot of all-atom molecular dynamics (MD) simulations of the PprI-DdrO-ssDNA model. The DG-PprI, DdrO, and ssDNA are labeled and shown as surface, cartoon and sticks, respectively. The cleavage center of DG-PprI and the CSR loop of DdrO (Arg118) are highlighted in red and green, respectively. c Close view of cleavage center of PprI and CSR of DdrO during MD simulations. R118 of DdrO interacts with the phosphate group of ssDNA through hydrogen bonds. d RMSD of CSR loop in the ternary complex model during 500 ns simulations. e The relative binding free energy change (ΔΔG) of R118A mutation in the presence of ssDNA was estimated through free energy perturbation (FEP) calculations. Data are presented as mean values +/− SEM from 3 independent experiments. f Cleavage (lanes 1–10) and ssDNA activation (lanes 11-20) assays of the DdrO mutants (E116A, L117A, R118A, and G119A). The reaction conditions is the same as in Fig. 3d. Source data are provided as a Source Data file.
