Figure 4. Close contacts give rise to strong inter-nucleosomal interactions.

(A) Illustration of the simulation protocol employed to mimic the nucleosome unbinding pathway dictated by the DNA-origami device (Funke et al., 2016). The three configurations, A1, A2, and A3, corresponding to the three cyan dots in part B at distances 62.7, 80.2, and 96.3 Å. For comparison, a tightly bound configuration uncovered in simulations without any restraints of nucleosome movement is shown as A1’. The number of contacts formed by histone tails and DNA (Htail-DNA) and by histone core and DNA (Hcore-DNA) from different nucleosomes is shown for A1 and A1’. (B) Free energy profile as a function of the distance between the geometric centers of the two nucleosomes, computed from unrestrained (black) and DNA-origami-restrained simulations (red). Error bars were computed as the standard deviation of three independent estimates. (C) Average inter-nucleosomal contacts between DNA and histone tail (orange) and core (blue) residues, computed from unrestrained and DNA-origami-restrained simulations. Error bars were computed as the standard deviation of three independent estimates.

Figure 4—figure supplement 1. Illustration of the restrained two nucleosome simulations setup, related to Figure 4 of the main text.

(A) Schematics of the DNA-origami-based force spectrometer, reproduced from Figure 1 of Funke et al., 2016. (B) Schematics for the spatial restraints imposed on nucleosomes in our simulations to mimic the DNA-origami setup. The vertex angle between two arms of the DNA-origami system is denoted by ${\displaystyle \mathrm{\Phi }}$. The two cartoons on the side illustrate the angle between two nucleosome dyad axes and the angle between two nucleosome planes. To define the coordinate system and other notations, please refer to section ‘Simulations at high salt concentrations’ and the accompanying text.

Figure 4—figure supplement 2. Explicit ion modeling reproduces the experimental free energy profiles of nucleosome binding.

(A) Comparison between the simulated (black) and experimental (red) free energy profile as a function of the inter-nucleosome distance. Error bars were computed as the standard deviation of three independent estimates. The barrier observed between 60 Å and 80 Å arises from the unwinding of nucleosomal DNA when the two nucleosomes are in close proximity, as highlighted in the orange circle. (B) Comparison between the simulated (black) and experimental (red) free energy profile as a function of the vertex angle. Error bars were computed as the standard deviation of three independent estimates. (C) Illustration of the vertex angle ${\displaystyle \mathrm{\Phi }}$ used in panel (B).

Figure 4—figure supplement 3. Compared with DNA-origami-restrained simulations, the unrestrained simulations produce more histone-DNA contacts across nucleosomes, related to Figure 4 of the main text.

The average number of inter-nucleosome contacts between DNA and histone tails (A) or histone cores (B) is plotted as a function of the distance ${\displaystyle r}$. The error bars were estimated as the standard deviation of three equal partitions of the simulations.

Figure 4—figure supplement 4. The unrestricted simulations favor a smaller angle ${\displaystyle \theta }$ between two nucleosomal planes compared to the DNA-origami-restrained simulations, related to Figure 4 of the main text.

(A) Illustration of the collective variables used in the umbrella-sampling simulation. ${\displaystyle \theta }$ is the angle between two nucleosomal planes, and ${\displaystyle r}$ is the distance between the geometric centers of two nucleosomes. ${\displaystyle \overrightarrow{w_1}}$ and ${\displaystyle \overrightarrow{w_2}}$ represent the vectors perpendicular to the nucleosome planes. See text section ‘Simulations at high salt concentrations’ for further definitions of the collective variables. (B) 2D free energy landscape for nucleosome interactions under 35 mM NaCl and 11 mM MgCl₂ salt, plotted as a function of ${\displaystyle r}$ and ${\displaystyle \theta }$. (C) The average value of ${\displaystyle \theta }$ as a function of the distance ${\displaystyle r}$ for the unrestricted (red) and the DNA-origami-restrained (black) simulations. The error bars were estimated as the standard deviation of three equal partitions of the simulations.