Sugar Binding Pocket:
Crystallographic studes have shown that sugars generally bind to proteins weakly in
shallow grooves close to the surface of the protein, with
binding affinities in the range Kd ≅ 10-3―10-6M. In some
cases, however, the saccharide is buried inside a cleft in the center of the protein, essentially inaccessible
to bulk solvent, showing very high binding affinities in the range
Kd ≅ 10-6―10-10M. Sugar binding sites in lectins are not highly
descriminative but exhibit multiple specificities, though subtle variations in the size and nature of the
amino acides at the combining site can affect ligand affinity.
Hydrophobic Patches on Monosaccharides:
Though sugars are hydrophilic in nature, specific orientations of their non-polar CH groups can create a
hydrophobic patch, which interacts with a hydrophobic pocket at the receptor site
on the protein.
(Pictured are Gal, GlcNAc, and Fuc from left to right)
Metal Ion Binding:
In several lectins, divalent cations are required for binding to sugars. For example, one of the cations
(Ca2+) in legume lectins helps to position a major peptide element near the sugar binding
site by stabilizing a cis-peptide linkage.
Conformation of the Saccharide Ligands:
In all carbohydrate-protein complexes, pyranose saccharide rings generally exist in the most favored char
conformation, though some rare cases adopt high energy boat and deformed conformations which are otherwise
stabilized by strong intermolecular interactions. Conformational changes due to flexibility
in di- and oligo-saccharides allowing rotations about inter-unit glycosidic bonds is more common than
their monosaccharide components adapting high-engergy conformations.
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