Fig. 3: Effect of CG interaction parameters on safety-belt dynamics and DNA properties.
From: DNA actively regulates the “safety-belt” dynamics of condensin during loop extrusion
A Diffusion coefficient D for safety-belt diffusing along naked DNA as a function of the HEAT-DNA interaction strength εHD. The red dashed line marks an experimentally accessible mean diffusion coefficient reported for cohesin/condensin sliding54. Each data point was determined from a linear fit to the mean MSD curve. B Mean DNA bending angle versus εHD. The red dashed line indicates the reference bending angle from the cryo-EM structure (PDB: 7Q2Z)21. Box plots indicate the mean (white circle), median (black line), 25 and 75th percentile (box), and the range of data within 1.5 × interquartile range (whiskers), as well as outliers (single points) over n=10 independent MD simulations. C Normalized contact frequency between DNA and PAR residues 383-456, highlighting residue-level variation. Positively charged residues are marked with blue “+'', negatively charged with red “-''. D Probability density of the latch-buckle order parameter Q for different latch-buckle interaction strengths εLB (0.30-0.50). Q measures the fraction of latch-buckle native contacts present in the crystal structure. E Mean Q as a function of εLB, showing increased closure/stability with stronger latch-buckle interactions. Box plots indicate the mean (white circle), median (black line), 25 and 75th percentile (box), and the range of data within 1.5 × interquartile range (whiskers), as well as outliers (single points) over n=10 independent MD simulations.
