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Figure 3.
Figure 3 The carbohydrate binding site of VP1. (A) Schematic
view of the interactions. Hydrogen bonds are represented by thin
broken lines, and hydrophobic contacts are shown as thick gray
broken lines. Asp85#, located at the tip of the BC2-loop of the
clockwise VP1 neighbor, approaches the N-acetyl group of
NeuNAc-1. The small circles labeled 'W' represent water
molecules. (B) Top view of the binding surface of VP1, showing
the groove that accommodates NeuNAc-1–(  2,3)–Gal
and the shallow pocket for NeuNAc-2. The yellow arrow indicates
the attachment site for additional sugars. The surface has been
calculated with MS (Connolly, 1983) using a probe radius of 1.4
Å. (C) View into the carbohydrate binding site, showing
the interactions with the NeuNAc-1–( 2,3)–Gal
moiety. (D) Interactions as in (C), with the viewpoint rotated
by 90°, so that we are looking along the oligosaccharide
chain from its sialic-acid end. (E) Interactions with NeuNAc-2.
In panels (C–E), residues that form hydrogen bonds with the
carbohydrate are colored orange and residues that form
hydrophobic contacts, magenta. Residues that do not directly
contact the carbohydrate are shown in gray. Water molecules are
represented with green spheres and hydrogen bonds are shown as
broken lines. Figure prepared with RIBBONS (Carson, 1987)
(panels A, C, D and E) and O (Jones et al., 1991) (panel B).
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