Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity
Fig 5
Sialic acid recognizing lectin binding sites are much deeper and more concave than the fairly flat and shallow binding sites of lectins that bind high mannose.
Representative lectin interactions with a terminal NeuAc glycan (panel A, PDB ID: 1SID), NeuAc monosaccharide (panel B, PDB ID: 1HGH), and high mannose (panel C, PDB ID: 1CVN) demonstrate the differences in the 3D interaction site space between NeuAc-binding lectins and high-mannose-binding lectins. Panel D shows the D2 distributions summarizing pocket geometry for each of these representative interactions. The lectin binding sites containing sialic acid glycans are wider and more concave while the high-mannose-accepting binding sites are more shallow and compact, being nearly entirely defined by the lowest threshold used for pocket generation as seen in the inset subpanels in A-C and in the D2 distributions in panel D. In panels A-C, residues are colored by their binned distance from the glycan (red: bin 1, orange: bin 2, sand: bin 3, pale yellow: bin 4), the glycan is colored by atom-type with carbons in white, and the rest of the lectin structure is in grey. PLIP interactions are colored blue for hydrogen bonds, pale blue for water bridges, yellow for electrostatic interactions, and grey for hydrophobic interactions. In the insets, 0.5 Å3 spheres were placed at each voxel center in the pocket and colored by the distance threshold used (magenta/red/orange/yellow: 4/6/8/10 Å). In panel D, vertical lines were placed at the median D2 measure from each threshold with the same coloring as used from the insets in panels A-C. All structures were rendered in PyMol and glycan symbols follow the SNFG symbols.