ABSTRACT

Solvent accessibility and hydrophilicity of protein segments are among the properties thought to be correlated with the location of protein antigenic determinants. In this chapter, the author discusses these properties in the context of protein structure prediction, and presents some quantitative results on the prediction of a region in the folded protein from sequence properties such as hydrophilicity and charge. The most widely used methods are secondary structure prediction and hydrophobicity profile. They accompany practically every new published protein sequence. The authors describe two complementary methods which could, if they were sufficiently reliable, provide a crude picture of the geometry of a protein backbone. Hydrophobicity is an important factor in protein folding. Immunogenicity for B cells is the ability to stimulate antibodies; antigenic determinants are those segments of the protein which interact with antibodies. Prediction of the position of amino-acid residues in the protein globule from sequence information would provide a useful crude picture of the molecule.