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Frequencies of Subtype-Specific Amino Acid Combinations in HIV-B- and HIV-C-Infected Individuals and an Outline of the Overlapping 25-mer Peptides Used as Proteasomal Substrates. For example, CF1 fragment, subtype B, Subtype-Specific Motif 27V, 41T, AWVKVVEEKAFSPEVIPMF, was used for the study.
Antigen processing is one crucial step in the pathway responsible for HLA presentation of HIV epitopes to CTL. It is a multistep process, where viral proteins synthesized in infected cells are first degraded by cytosolic proteasomes. A multilevel linear model was used to examine the influence of the presenting HLA allelic frequencies, HIV region (NF1, CF1, MF2&CF2), and ethnic group (Africans, whites) on epitope yield.
A strong relationship between epitope yield and HLA allelic frequency was found for NF1, CF1 and MF2&CF2, but, whereas similar variation in HLA frequency had similar effects on epitope yields in NF1 and MF2&CF2 regardless of ethnic group, a significant difference between ethnic groups was found with respect to CF1 (p < 0.0001).
Vulnerable regions within other HIV proteins may also demonstrate variable adaptation to the same HLA selective pressure, in line with the different HIV B and HIV C CF1 epitope yields.
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