Fig. 5: Kinetics of DNA entry via the Ycg1-Brn1 “safety belt” from CG MD simulations.
From: DNA actively regulates the “safety-belt” dynamics of condensin during loop extrusion
A Schematic of four states: unbound (US), intermediate with DNA outside the Brn1 loop (ISout), intermediate with DNA inside the loop (ISin), and bound (BS). ISout is defined solely by the DNA path (outside the loop) and can occur with either an open- or closed-latch, so both configurations are shown. B Transition times between these states obtained from simulations tracking DNA movement into the binding pocket formed by the Brn1 loop and Ycg1 (i.e., the “safety belt''). The horizontal axis shows different latch-buckle interaction strengths (εLB), and the vertical axis presents transition times for US → ISout, ISout → ISin, ISin → BS, and US → BS. Error bars represent the mean ± SEM over n=50 independent MD simulations. C Diffusion coefficients of the safety belt sliding along naked DNA plotted against various εLB values (0.3, 0.35, 0.37, 0.4, 0.45), indicating how latch-buckle interaction strength affects mobility. Each data point was determined from a linear fit to the mean MSD curve. D Qualitative free-energy landscapes summarizing dominant pathways and barrier trends en route to the BS (typically US → ISout → ISin → BS) as a function of εLB. Right-side insets schematize the observed change in D with εLB.
