Class I-Presented Influenza Peptides Predicted by an Algorithm that Selects Class II-Presented Peptides

Abstract

Class II MHC-restricted, CD4⁺ T cells recognize processed foreign peptides that form amphipathic helices. It also has been shown that class I MHC-restricted, CD8⁺ T cells recognize foreign peptide fragments rather than entire proteins. In light of this knowledge and the facts that 1) CD4⁺ and CD8⁺ T cells use the same gene families to generate their receptors, and 2) class I and class II MHC products hold many structural similarities, we hypothesized that peptides recognized by CD4⁺ and CD8⁺ T cells might have some structural homologies. To test this hypothesis, we screened a series of proteins, which contain CD8⁺ cytotoxic T lymphocyte (CTL)recognized epitopes, using a strip-of-helix algorithm that has been shown to predict well class II MHC-restricted peptides (1). This algorithm searched for amphipathic a helices by calculating the average hydrophobicity of amino acids at positions n, n+4, n+7, n+ll, n+14, and n+18 in a linear sequence, and could also be adapted to analyze 3₁₀ helices or β-pleated sheets.

This work was supported in part by NIH grant CA 37645. L.T. Chin was a Betty Lee Stone Fellow of the American Cancer Society, Massachusetts Division and was supported by training grant R25CA36762.