Figure 3. Explicit ion modeling predicts salt-dependent conformations of a 12-mer nucleosome array.

(A) Top: Comparison of simulated and experimental (Correll et al., 2012) sedimentation coefficients of chromatin at different salt concentrations. Bottom: Number of DNA charges neutralized by bound cations (yellow, left y-axis label) and the fraction of ions bound to DNA (red, right y-axis label) at different salt concentrations. The error bars were estimated from the standard deviation of simulated probability distributions (Figure 3—figure supplement 1). (B) Representative chromatin structures with sedimentation coefficients around the mean values at different salt concentrations.

Figure 3—figure supplement 1. Probability distributions used to compute means and standard deviations of the quantities presented in Figure 3 of the main text.

(A) Probability distribution of sedimentation coefficients calculated from the simulation with Na⁺ ions. (B) Probability distribution of sedimentation coefficients calculated from the simulation with Mg²⁺ ions. (C) Probability distribution of neutralized charges calculated from the simulation with Na⁺ ions. (D) Probability distribution of neutralized charges calculated from the simulation with Mg²⁺ ions. (E) Probability distribution of the fraction of bound ions calculated from the simulation with Na⁺ ions. (F) Probability distribution of the fraction of bound ions calculated from the simulation with Mg²⁺ ions.