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. 2023 Oct 26;24(21):15610. doi: 10.3390/ijms242115610

Figure 4.

Figure 4

(A) Overlay of the frames (saved every 5 ns) of the trajectory poses obtained from the 50 ns MD simulations of CD44 (grey ribbons) in complex with DTYCF (green sticks). The complexes are here shown in increasing transparency over time. Snapshots showing the main short-range interactions between CD44 and DTYCF at 10 (B), 30 (C), and 45 (D) ns; H-bonds and salt-bridges are represented as yellow and pink dashed lines, respectively. Plotted representations of MD-derived data: (E) number of bonds (H-bonds and neighbor pairs within 0.35 nm) established between CD44 and DTYCF along the simulation, (F) RMSD values calculated on the protein atoms, and (G) Coulomb and Lennard–Jones short-range energies. All values were plotted as a function of time (ns).