Protein surface analysis. Methods for identifying antigenic determinants and other interaction sites.

A variety of methods are currently employed in attempts to identify antigenic determinants and other features of proteins. Most of these involve calculations based on scales of values for the 20 amino acids that reflect their likelihood of occurrence at the surface of proteins or as part of secondary structures such as helices or beta-bends. The most successful of these procedures all use scales related to the water solubility of the individual amino acids. In particular, the highest success rates are obtained using hydrophilicity scales that emphasize the charged and polar amino acids, but are not overly selective for either positive or negative charges. Such a method can correctly pinpoint major antigenic sites on the proteins of most well characterized infectious organisms. The hydrophilicity profiles also contain information concerning other types of protein interaction sites and membrane spanning segments.