Extended Data Fig. 7: Molecular dynamics simulations of the free disialoside.
From: Sialoglycan binding triggers spike opening in a human coronavirus
10 µs MD-based conformational analysis of Neu5,9Ac2-α2,8-Neu5Ac-αOMe in explicit solvent. a, Example 3D structure with annotations of residue labels used (GLYCAM residue type labels are shown in brackets), atom numbering scheme and torsions (φ = C1-C2-O8-C8, ψ = C2-O8-C8-C7, γ = O8-C8-C7-C6, δ = C8-C7-C6-O6). b, Free energy φ/ψ map. (c, d) Trajectory plots and histograms of torsions φ, ψ, γ and δ. Conformational transitions between the population maxima (local energy minima) are fast for φ and γ. Only few transitions occurred for ψ and δ on a 10 µs timescale. Torsion δ has practically only one orientation (about −60°). Data were analysed using Conformational Analysis Tools.
