Differential Proteasomal Processing of Hydrophobic and Hydrophilic Protein Regions: Contribution to Cytotoxic T Lymphocyte Epitope Clustering in HIV-1-Nef

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 100; no. 13; pp. 7755 - 7760
• Main Authors: Lucchiari-Hartz, Maria, Lindo, Viv, Hitziger, Niclas, Gaedicke, Simone, Saveanu, Loredana, van Endert, Peter M., Greer, Fiona, Eichmann, Klaus, Niedermann, Gabriele
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 24-06-2003; National Acad Sciences
• Subjects: Amino Acid Sequence; Amino acids; Amino Acids - chemistry; Antigens; Biological Sciences; Cell Line; Cysteine Endopeptidases - metabolism; Epitopes; Gene Products, nef - chemistry; Gene Products, nef - metabolism; HIV; HIV 1; HIV-1 - metabolism; HLA antigens; Human immunodeficiency virus; Humans; Immunology; Jurkat Cells; Ligands; Molecular Sequence Data; Multienzyme Complexes - metabolism; nef Gene Products, Human Immunodeficiency Virus; Peptides - chemistry; Proteasome Endopeptidase Complex; Protein Structure, Tertiary; Proteins; Proteins - chemistry; Recombinant Proteins - chemistry; Sequence Homology, Amino Acid; T lymphocytes; T-Lymphocytes, Cytotoxic - metabolism
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1232228100

HIV proteins contain a multitude of naturally processed cytotoxic T lymphocyte (CTL) epitopes that concentrate in clusters. The molecular basis of epitope clustering is of interest for understanding HIV immunogenicity and for vaccine design. We show that the CTL epitope clusters of HIV proteins predominantly coincide with hydrophobic regions, whereas the noncluster regions are predominantly hydrophilic. Analysis of the proteasomal degradation products of full-length HIV-Nef revealed a differential sensitivity of cluster and noncluster regions to proteasomal processing. Compared with the epitope-scarce noncluster regions, cluster regions are digested by proteasomes more intensively and with greater preference for hydrophobic P1 residues, resulting in substantially greater numbers of fragments with the sizes and COOH termini typical of epitopes and their precursors. Indeed, many of these fragments correspond to endogenously processed Nef epitopes and/or their potential precursors. The results suggest that differential proteasomal processing contributes importantly to the clustering of CTL epitopes in hydrophobic regions.