Use of hydrophilicity plotting procedures to identify protein antigenic segments and other interaction sites

Hydrophilicity analysis of the surface properties of proteins continues to be an important means for understanding the interactions that occur between proteins and other macromolecules. We have shown that the procedure of Hopp and Woods is useful in developing synthetic peptide immunogens and for understanding the relationship of protein sequence and folding to the interactions between macromolecules. Using a standardized procedure and the optimized hydrophilicity scale of amino acid values, it is possible to display the surface-exposed and buried portions of a polypeptide chain, as well as such features as membrane-spanning segments. Finally, an example was provided to show that hydrophilicity analysis has a place in protein engineering, allowing the creation of new surface segments with predictable properties.