The 8 Labels of Panel (A) Have the Following Meaning: Mdna Boundcat Refers to The

Figure S5. Convergence of the configurational entropy (TS) computed with the Schlitter method from the merged trajectories for different numbers of simulation snapshots (x-axis). Entropy calculations were performed using snapshots extracted from MD simulations that were either started from the canonical B-DNA conformation (generated using the 3DNA package [38, 43]) or from the crystal structures of the studied systems. Entropies were separately computed for DNA, protein, or for the full protein:DNA complexes. All simulations were performed for the methylated and non-methylated forms of DNA. The three panels show results for (A) DNA bound to the catalytic domain of R.DpnI, (B) DNA bound to the winged-helix domain of R.DpnI, and (C) DNA bound to MBD, respectively. In the simulations for the R.DpnI system, 2 long replicates (100 ns each) were merged with 10 shorter ones (30 ns each). In the simulations of the MBD system, 2 long replicates (100 ns each) were merged. For each simulated system, the merged trajectories were superimposed and the conformational entropy was calculated according to the Schlitter formula.

The 8 labels of panel (A) have the following meaning: mDNA boundcat refers to the configurational entropy of free methylated DNA started from the X-ray conformation when it is bound to the catalytic subunit; nDNA boundcat refers to free non-methylated DNA started from the X-ray conformation when it is bound to the catalytic subunit; mB-DNA refers to free methylated DNA started from the canonical B-DNA conformation; nB-DNA refers to free non-methylated DNA started from the canonical B-DNA conformation; mDNA:R.DpnIcat refers to methylated DNA bound to the catalytic subunit of R.DpnI; nDNA: R.DpnIcat refers to non- methylated DNA bound to the catalytic subunit of R.DpnI; bound R.DpnIme-DNA refers to the configurational entropy of the R.DpnI domain bound to methylated DNA; bound R.DpnInm-DNA refers to the conformational entropy of the R.DpnI domain bound to non-methylated DNA. The labels of panels (B) and (C) refer to the catalytic domain of R.DpnI and to MBD, respectively.

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