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[Preprint]. 2023 Nov 15:2023.05.16.541030. Originally published 2023 May 18. [Version 2] doi: 10.1101/2023.05.16.541030

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

Figure 2:

(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 Fig. 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.