Validation Tools for Predicted Linear B-Epitopes: Beta Turns

Abstract

It is claimed that amino acid replacements in surface loops usually do not perturb the three-dimensional structure of the protein, since surface loops are relatively flexible (Saunders and Baker 2002). Thus, the conservation variability of epitopes might be biased by the abundance of loops in epitopes. These results imply that epitopes do not tend to overlap functional regions, but rather cover separate regions. Pellequera, et. al., (1993), developed new turn scales based on the occurrence of amino acids at each of the four positions of a turn using a structural database comprised of 87 proteins. It is found that the scales correctly predicted a fraction of the turn regions in proteins with approximately 80% confidence. They used the turn scales for predicting the location of antigenic sites in proteins. The method was developed with the specific aim of predicting only a few peaks for each protein. They found that it leads to a high level of accurate prediction around 70% of correct prediction of known epitopes. In this article we update turn scales using large numbers of proteins and epitopes. Improved method will be more helpful in selecting protein regions to be synthesized in order to produce anti-peptide antibodies cross-reacting with the parent protein.