Computer simulations to predict the availability of peptides with known HLA class I motifs possibly generated by proteolysis of HIV-1 proteins in infected cells.
Cytotoxic T cells that recognize HIV-1 peptides generated from all viral proteins were reported. To predict the cleavage pattern of HIV-1 proteins by cytoplasmic proteasomes into peptides with motifs fitting known HLA class I molecules, the computer program Findpatterns was used. In this paper the combined amino acids patterns for proteolytic cleavages and the HLA class I haplotype-restricted peptides motifs are studied. It was noted that peptides with motifs of HLA class I A2 and A68 were abundant compared with HLA class 5B2, B8, B53, and B35.
Becker
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Department of Molecular Virology, Faculty of Medicine, Hebrew University of Jerusalem, Israel.
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000378:metabolism; D017951:Antigen Presentation; D003198:Computer Simulation; D003546:Cysteine Endopeptidases / Q000378:metabolism; D010450:Endopeptidases / Q000378:metabolism; D016333:HIV Protease / Q000378:metabolism; D015497:HIV-1 / Q000276:immunology*; D015395:Histocompatibility Antigens Class I / Q000276:immunology*; D006801:Humans; D008565:Membrane Proteins; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000378:metabolism; D010446:Peptide Fragments / Q000276:immunology / Q000378:metabolism; D046988:Proteasome Endopeptidase Complex; D012697:Serine Endopeptidases; D012984:Software; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology*; D017361:Viral Nonstructural Proteins / Q000276:immunology / Q000378:metabolism; D014764:Viral Proteins / Q000276:immunology* / Q000378:metabolism; D015678:Viral Structural Proteins / Q000276:immunology / Q000378:metabolism
D000596:Amino Acids; D015395:Histocompatibility Antigens Class I; D008565:Membrane Proteins; D009097:Multienzyme Complexes; D010446:Peptide Fragments; D017361:Viral Nonstructural Proteins; D014764:Viral Proteins; D015678:Viral Structural Proteins; D010450:Endopeptidases; D012697:Serine Endopeptidases; C026515:type I signal peptidase; D003546:Cysteine Endopeptidases; D016333:HIV Protease; D046988:Proteasome Endopeptidase Complex