Fig. 4: Interactions in condensin safety-belt at the distinct states when DNA is outside and inside the safety-belt loop based on CG MD simulations.
From: DNA actively regulates the “safety-belt” dynamics of condensin during loop extrusion
A Schematic representations of states Snl ("non-looped'') and Sl ("looped''). DNA is modeled as an infinitely large closed loop (red), while the Brn1 loop combined with the dashed segment forms the second closed loop used for calculating the linking number. B Fraction of native latch-buckle contacts, Q, in the Sf (DNA-free state), Snl, and Sl as a function of the latch-buckle interaction strength εLB. The error bars represent the mean ± SEM (n = 10 blocks). For each condition, all qualifying data points from the simulation replicas were pooled together. This collection was then divided into 10 non-overlapping blocks of approximately equal size. The mean of each block is plotted as an individual black dot. C DNA-Brn1 contact frequency maps in the Snl and Sl at εLB = 0.30, 0.35, 0.37, 0.40, 0.45. Contact counts are normalized to the maximum within each panel to highlight residue-level differences; bar plots at right summarize the average contact number per state at each εLB. Error bars represent the mean ± SEM over n=50 independent MD simulations.
