Bioinformatic Analysis of Antigenic Proteins in Celiac Disease

Investigation of the chemistry of the gliadin proteins has played an important role in our comprehension of how celiac disease (CoD) develops and progresses as a response to challenge with this immune stimulus. Studies in this area have implicated gut enzymes, tissue transglutaminase-mediated deamidation, and peptide binding affinity for the HLA-DQ2 and DQ8 molecules in disease pathogenesis. As the number and availability of prolamin sequences increases, the complexity and cost of laboratory analysis will similarly increase. Freely available tools to bioinformatically analyze candidate protein sequences can be employed as a low-cost, high-return preliminary mechanism to focus one's laboratory analyses on the most rewarding sequences. This chapter describes the use of antigen prediction, deamidation prediction, and protease cleavage prediction as may be applied to CoD research.