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. Author manuscript; available in PMC: 2023 Aug 30.
Published in final edited form as: J Mol Biol. 2022 Jun 17;434(16):167685. doi: 10.1016/j.jmb.2022.167685

Figure 3. Simulation of TRF2-dependent DNA condensation.

Figure 3.

A. Schematic of setup for coarse-grained Monte Carlo simulations. A single DNA molecule of 80 beads was simulated with 4000 single-bead TRF2 molecules. The DNA end-to-end distance was constrained via a harmonic potential applied to the ends of the DNA (beads) with a variable force constant, mimicking force experiments. Under no force, TRF2 molecules lead to DNA condensation, forming a spherical globule. Under low force, parts of the DNA are extended with a single spherical globule of DNA and TRF2 in the center. Under high force, the DNA molecule is fully extended with no TRF2 bound. B. Simulation results depend on the presence or absence of weak homotypic TRF2 interactions. If TRF2:TRF2 interactions are set to zero (i.e., implying TRF2 is infinitely soluble) we observed a continuous increase in chain dimensions as a function of force constant, both under weak (purple squares) and strong (green circles) protein-DNA interactions (top). If weak TRF2:TRF2 interactions are included (leading to a solubility limit of ~0.5 mM for TRF2), we observe apparent two-state behavior (bottom). Here the DNA is either compact or expanded, as characterized by the sharp transition as a function of force and the co-existing populations giving rise to a bimodal distribution. The force constant at which expansion occurs depends on the strength of the protein:DNA interaction. Arrows reference simulation traces in panels 3C and 3D. C. Individual simulation traces for simulations performed absent TRF2:TRF2 interactions. Red lines are true data, black line is a smoothed trace. Occasional troughs are transitions into short-lived metastable compact globular states. D. Individual simulation traces for simulations performed with weak TRF2:TRF2 interactions, revealing two-state behavior. During a single simulation, the system oscillates between two fixed points (compact and expanded). This oscillation is analogous to an infinitely cooperative transition, as seen when sitting at a phase boundary. Red lines are true data, black line is a smoothed trace.