FIGURE 6.

Dynamic simulation modeling of HBS in vaccinia viral protein sA27-aa. The backbone of HBS is shown as a blue solid ribbon in which the KKPE segment forms a turn-like conformation. To distinguish the positively charged residues, Lys²⁶, Lys²⁷, Lys³¹, and Arg³² are colored green. A, molecular dynamics simulation of the HBS in the absence of HS. The HBS molecule is shown using ball and stick representation (white, hydrogen atom; red, oxygen atom; blue, nitrogen atom; gray, carbon atom). For clarity, Lys²⁶, Lys²⁷, Glu²⁹, Ala³⁰, Lys³¹, and Arg³² residues are highlighted in yellow. B, docking of HS with the HBS without any solvent molecules. A tetrasaccharide, unsaturated 2-O-sulfate uronic acid (ΔUA2S), 2-N-sulfo-,6-O-sulfate glucosamine (GlcNS6S), 2-O-sulfate iduronic acid (IdoA2S), and 2-N-sulfo-, 6-O-sulfate glucosamine (GlcNS6S) (ΔUA2S-GlcNS6S-IdoA2S-GlcNS6S), was used as a GAG-binding substrate; its x-ray structure has been determined elsewhere (32). The HS molecule is shown in stick form wrapped around the HBS, revealing close multiple ionic interactions. C, molecular dynamics simulation of HBS in the presence of HS, including solvent molecules. The structures of both the HBS and HS show slight modification.