Fig. 5. Theoretical polysaccharide chain lengths and ring pucker conformers as predicted by molecular dynamics simulations.

a Histograms show the end-to-end length relationship of decasaccharide models of mono-6OS-sulfated O-linked (red) chains or S-linked (yellow) hemi-A HS chains (see Supplementary Fig. 58 for other sulfation isomers) as a function of frequency (~500,000 data points/run). The cartoon depicts the wider range of predicted conformations exhibited by the S-linked HS analog showing both collapse (inset) and extension like a Slinky®. b The hypothetical pucker conformational states of the most interior GlcA ring and GlcNAc ring of the decasaccharide models for O- versus S-linked heparosan chains (unsulfated polymers here; sulfated versions in the SI) are shown as sinusoidal plots. The azimuthal angle θ discriminates boats from chairs (θ = 0° is a perfect ⁴C₁-chair and is at the south pole), while the meridional angle φ determines the pseudo-rotation of the boat conformations (in this definition φ = 0° represents the ^O,3B-boat). Both rings of natural O-link chains typically reside in the chair conformation ⁴C₁ state, but the rings of S-link chains are predicted to occupy alternative states more frequently (see Supplementary Fig. 61 for other details). One hypothetical disaccharide conformer in the hemi-A S-linked unit, ¹S₃−¹C₄, depicts a GlcA sugar with a distorted ring that is observed in some enzyme active sites and an axial glycosidic bond; the enzyme’s nucleophile could potentially attack this target scissile bond with optimal in-line geometry. However, the S-link is uncleavable thus results in competitive inhibition of the enzyme.