title: Definition of the Mamu A*01 peptide binding specificity: application to the identification of wild-type and optimized ligands from simian immunodeficiency virus regulatory proteins.
abstract: Single amino acid substitution analogs of the known Mamu A*01 binding peptide gag 181-190 and libraries of naturally occurring sequences of viral or bacterial origin were used to rigorously define the peptide binding motif associated with Mamu A*01 molecules. The presence of S or T in position 2, P in position 3, and hydrophobic or aromatic residues at the C terminus is associated with optimal binding capacity. At each of these positions, additional residues are also tolerated but associated with significant decreases in binding capacity. The presence of at least two preferred and one tolerated residues at the three anchor positions is necessary for good Mamu A*01 binding; optimal ligand size is 8-9 residues. This detailed motif has been used to map potential epitopes from SIVmac239 regulatory proteins and to engineer peptides with increased binding capacity. A total of 13 wild type and 17 analog candidate epitopes were identified. Furthermore, our analysis reveals a significantly lower than expected frequency of epitopes in early regulatory proteins, suggesting a possible evolutionary- and/or immunoselection directed against variants of viral products that contain CTL epitopes.
authors.affiliation: Epimmune, San Diego, CA 92121. New England Regional Primate Center, Southborough, MA 01772, USA.
authors.forename: J
authors.initials: J
authors.lastname: Sidney
authors.forename: J L
authors.initials: JL
authors.lastname: Dzuris
authors.forename: M J
authors.initials: MJ
authors.lastname: Newman
authors.forename: R P
authors.initials: RP
authors.lastname: Johnson
authors.forename: A
authors.initials: A
authors.lastname: Kaur
authors.forename: K
authors.initials: K
authors.lastname: Amitinder
authors.forename: C M
authors.initials: CM
authors.lastname: Walker
authors.forename: E
authors.initials: E
authors.lastname: Appella
authors.forename: B
authors.initials: B
authors.lastname: Mothe
authors.forename: D I
authors.initials: DI
authors.lastname: Watkins
authors.forename: A
authors.initials: A
authors.lastname: Sette
mesh_terms: D000465:Algorithms; D019943:Amino Acid Substitution; D000596:Amino Acids / Q000378:metabolism; D000818:Animals; D001665:Binding Sites / Q000276:immunology; D018984:Epitopes, T-Lymphocyte / Q000378:metabolism; D015395:Histocompatibility Antigens Class I / Q000378:metabolism*; D017874:Immediate-Early Proteins / Q000138:chemical synthesis / Q000378:metabolism; D008024:Ligands; D008253:Macaca mulatta; D009842:Oligopeptides / Q000138:chemical synthesis / Q000378:metabolism; D010446:Peptide Fragments / Q000138:chemical synthesis / Q000378:metabolism*; D010449:Peptide Mapping; D011485:Protein Binding / Q000276:immunology; D015202:Protein Engineering; D015302:Simian Immunodeficiency Virus / Q000276:immunology* / Q000378:metabolism; D054334:Viral Regulatory and Accessory Proteins / Q000138:chemical synthesis / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D018984:Epitopes, T-Lymphocyte; D015395:Histocompatibility Antigens Class I; D017874:Immediate-Early Proteins; D008024:Ligands; C110764:Mamu-A 01 antigen; D009842:Oligopeptides; D010446:Peptide Fragments; D054334:Viral Regulatory and Accessory Proteins