Figure 3.

Identification of multiple potential bacterial mimics of HLA-DR3 restricted 7 SmD core T-epitopes by bioinformatics analysis. (A) Two peptide libraries were constructed. One was a Bacterial Peptides Library, which is generated first by dividing all the bacterial protein sequences from NCBI protein database (Taxonomy ID: 2) into 15mers overlapping with 14 aa. This 15mer library is very large and is reduced by a custom-designed software. In examining the seven 15mer core epitopes (figure 2B), the core epitopes within each 15mers have 11mers with at least four sequential aa that are critical for the reactive hybridoma to bind either DR3 or the reactive TCR. Thus the software were designed to identify in the bacterial library with four aa identical to the seven core T-epitopes. The bacterial 15mer library with the desired aa sequences were then collected and designated as our bacterial peptides library (right panel). The second library is constructed as the collection of the 15mer SmD T-epitopes with conservative substitutions at certain positions and free substitutions at the other positions (left panel). Our software then compared the two libraries to identify peptides with identical sequences. These are the candidate 15mers that contain the bacterial mimics of SmD T-epitopes. All candidate peptides were then analysed for their binding affinity to HLA-DR3 by the IEDB database. Those binding affinities <5000 μM were considered as good mimics for SmD T-epitopes. (B) Summary of numbers of potential bacterial mimics of SmD core T-epitopes and their binding affinities to HLA-DR3 are listed.