Shiga toxins (STX) are produced by certain Escherichia coli strains that cause “hamburger disease”. The toxins contain three different sites that bind to a glycolipid, the cell surface receptor globotriaosylceramide (Gb3). Roles for Gb3 in normal cell functions are largely unknown. However, the human proteins CD19 and IFNAR1 have been found to contain STX-like amino acid sequences. We looked to expand the evidence for Gb3-related cell functions by searching for proteins with potential Gb3 binding sites. Using the BLAST protein software from NCBI, we searched for proteins with similar amino acid sequences to the Shiga toxin-like sequences of CD19 and IFNAR1. For proteins with associated protein data bank files, the program Cn3D was used to visualize the structure of the potential binding site in sequence similarity. The site on the model was assigned a grade (A to D) depending on how similar the binding site was to that of Shiga toxin. The results showed that, while many proteins have amino acid sequence similarities to STX B subunit sequences, relatively few structurally resemble STX in terms of forming likely Gb3-binding sites. However, we have recently expanded our searches by using short query sequences with substitutions of similar amino acids for BLAST.
