Characteristics of HIV-1 Nef regions containing multiple CD8(+) T cell epitopes: Wealth of HLA-binding motifs and sensitivity to proteasome degradation

First and foremost among the many factors that influence epitope presentati on are the degradation of Ag, which results in peptide liberation, and the presence of HLA class I molecules able to present the peptides to T lymphoc ytes. To define the regions of HIV-1 Nef that can provide multiple T cell e pitopes, we analyzed the Nef sequence and determined that there are 73 pept ides containing 81 HLA-binding motifs. We tested the binding of these pepti des to six common HLA molecules (HLA-A2, -A3, -A24, -B7, -B8, and -B35), an d we showed that most of them were efficient binders (54% of motifs), espec ially peptides associating with HLA-A3, -B7/35, and -B8 molecules. Nef pept ides most frequently recognized by T cells of HIV-1-infected individuals we re 90-97, 135-143, 71-81, 77-85, 90-100, 73-82, and 128-137. The frequency of T cell recognition was not directly related to the strength of peptide-H LA binding. The generation of Nef epitopes is crucial; therefore, we invest igated the digestion by the 20S proteasome of a large peptide, Nef(66-100). This fragment was efficiently cleaved, and NH2-terminally extended precurs ors of epitope 71-81 were recognized by T cells of an HIV-1-infected indivi dual. These results suggest that a high frequency of T cell recognition may depend on proteasome cleavage.