FIGURE 4.

Evolution of the structure and hydrogen bonds formed by the DNA apta2 (67-nt) interacting with the S-protein trimer in the closed conformation. Lower panel. Time plot of the major H-bonds formed by nucleotides (numbers 1–67) and S-protein residues (numbers >300). Thin lines indicate the H-bonds between the aptamer and the RBD of monomer 1, the thick red line indicates the extra H-bond with the RBD of monomer 2 (setting in at times t > 100 ns The cyan shaded band indicates the typical interval of H-bond length (2.4–3.6 $\stackrel{°}{A}$). Upper panel. Snapshots of the aptamer-S-protein contact, at times t = 0,50, 100, 150 ns DNA is depicted in yellow; protein surface in light grey, with the RBD of monomer one in dark grey; glycans in purple. The red arrow at t = 150 indicates the site of the extra H-bond with the RBD of monomer 2. All figures with the central axis perpendicular to the plane.