Figure 2. Explicit ion modeling reproduces the energetics of nucleosomal DNA unwrapping.

(A) Illustration of the umbrella simulation setup using the end-to-end distance between two DNA termini as the collective variable. The same color scheme as in Figure 1 is adopted. Only ions close to the nucleosomes are shown for clarity. (B) Comparison between simulated (black) and experimental (red) free energy profile as a function of the unwrapped DNA base pairs. Error bars were computed as the standard deviation of three independent estimates. (C) The average number of Na⁺ ions within 10 Å of the nucleosomal DNA (top) and Cl⁻ions within 10 Å of histone proteins (bottom) are shown as a function of the unwrapped DNA base pairs. Error bars were computed as the standard deviation of three independent estimates.

Figure 2—figure supplement 1. The explicit ion model predicts the binding affinities of protein-DNA complexes well, related to Figure 1 of the main text.

Experimental and simulated binding free energies are compared for nine protein-DNA complexes (Privalov et al., 2011), with a Pearson correlation coefficient of 0.6. The PDB ID for each complex is indicated in red, and the diagonal line is drawn in blue. The significant correlation between simulated and experimental values supports the accuracy of the model. To further enhance the agreement between the two, it will be necessary to implement specific non-bonded interactions that can resolve differences among amino acids and nucleotides beyond simple electrostatics. Such modifications will be interesting avenues for future research. See text section ‘Binding free energy of protein-DNA complexes’ for simulation details.