title: Differential proteasomal processing of hydrophobic and hydrophilic protein regions: contribution to cytotoxic T lymphocyte epitope clustering in HIV-1-Nef.
abstract: 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.
authors.affiliation: Department of Cellular Immunology, Max Planck Institute of Immunobiology, Stübeweg 51, D-79108 Freiburg, Germany.
authors.forename: Maria
authors.initials: M
authors.lastname: Lucchiari-Hartz
authors.forename: Viv
authors.initials: V
authors.lastname: Lindo
authors.forename: Niclas
authors.initials: N
authors.lastname: Hitziger
authors.forename: Simone
authors.initials: S
authors.lastname: Gaedicke
authors.forename: Loredana
authors.initials: L
authors.lastname: Saveanu
authors.forename: Peter M
authors.initials: PM
authors.lastname: van Endert
authors.forename: Fiona
authors.initials: F
authors.lastname: Greer
authors.forename: Klaus
authors.initials: K
authors.lastname: Eichmann
authors.forename: Gabriele
authors.initials: G
authors.lastname: Niedermann
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D002460:Cell Line; D003546:Cysteine Endopeptidases / Q000378:metabolism*; D000939:Epitopes; D015693:Gene Products, nef / Q000737:chemistry* / Q000378:metabolism; D015497:HIV-1 / Q000378:metabolism*; D006801:Humans; D019169:Jurkat Cells; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000378:metabolism*; D010455:Peptides / Q000737:chemistry; D046988:Proteasome Endopeptidase Complex; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D011994:Recombinant Proteins / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D013602:T-Lymphocytes, Cytotoxic / Q000378:metabolism; D054311:nef Gene Products, Human Immunodeficiency Virus
chemical_list: D000596:Amino Acids; D000939:Epitopes; D015693:Gene Products, nef; D009097:Multienzyme Complexes; D010455:Peptides; D011506:Proteins; D011994:Recombinant Proteins; D054311:nef Gene Products, Human Immunodeficiency Virus; D003546:Cysteine Endopeptidases; D046988:Proteasome Endopeptidase Complex