On the dissection of binding epitopes on carbohydrate receptors for microbes using molecular modelling

The most common receptors for microbes on animal cells seem to be carbohydrates. One characteristic property of microbial protein-carbohydrate interaction is the recognition of sequences placed within an oligosaccharide chain. This leads to a series of isoreceptors defined as saccharides carrying the particular receptor sequence with different neighbouring groups. A microbial ligand may have different binding affinities for such isoreceptors depending upon steric hindrance from neighbouring groups upon access to the binding epitope. By a comparison of binding preferences to a series of isoreceptors with their calculated conformation, the binding epitope on a particular receptor sequence may be approximated by use of molecular modelling. This approach is illustrated for two bacteria recognising lactosylceramide. The potential importance of the procedure for further developments including drug design is briefly discussed.