[11] Prediction of α helices and T cell-presented sequences in proteins with algorithms based on strip-of-helix hydrophobicity index

This chapter presents the prediction of α helices and T cell-presented sequences in proteins with algorithms based on strip-of-helix hydrophobicity index (SOHHI). Recurrent aliphatic hydrophobic amino acids that occur in the sequence of a protein or a peptide at positions that form an axial, hydrophobic strip when the sequence is coiled as helix might stabilize coiling against hydrophobic surfaces. This effect can lead to helix formation against the hydrophobic cores of nascent proteins or excised T cell-presented peptides and to protease protection and scavenging for presentation by major histocompatibility complex (MHC) molecules. Such consensus sequences of recurrent hydrophobicity creating a scavenger “S” site might overlap to varying degrees the T cell-presented “T” epitope, which actually sits in the antigen-binding site of a MHC molecules, as long as a cleavage “C” site does not fall between them when they are relatively separated. Cooperatively among the residues in an axial, hydrophobic strip to stabilize helix formation is reflected in the SOHHI, which is the mean hydrophobicity of residues in such potential strips. Algorithms based on the SOHHI, with additional considerations related to length and caps, lead to the sensitive and efficient predictions of structural helices and of T cell-presented epitopes. In experimental tests of these ideas, the SOHHI was found to correlate to the helical coiling of amphiphilic peptides in the presence of lipid vesicles. These principles lead to hypotheses to alter the potency and range of MHC restriction of peptide vaccines or to decrease the immunogenicity of therapeutic proteins.