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- Epitopes that have been described in the literature and included in this database tend to cluster in conserved regions and be absent or rarely found in highly variable regions in Nef, Env, and p17.
- While the uneven distribution of epitopes may be in part due to a limited cross-recognition of specific responses because of differences between peptides used to probe the immune response and autologous strains, regions with a paucity of defined epitopes also had higher frequencies of amino acids that tend to not be found in C-terminal positions of epitopes, and had lower cleavage prediction scores for epitope processing. This suggests that in the regions of the virus where variation is best tolerated, traces of immune escape have left an imprint on the viral population. Epitopes also were concentrated in alpha-helix and turn regions in the proteins.
- In the more conserved p24, and Pol proteins RT and Protease, epitopes are more evenly distributed.
- What was learned from proteins where many epitopes have been defined (Gag, Pol, Env and Nef) was used to develop an algorithm to predict where epitopes would be localized in Rev, Tat, Vif, and Vpr. Predictions were made blinded, and then compared to the first 15 epitopes defined in these proteins; the epitopes were concentrated in the predicted regions.
Karina Yusim, Can Kesmir, Brian Gaschen, Marylyn M. Addo, Marcus Altfeld, S\oren Brunak, Alexandre Chigaev, Vincent Detours, and Bette T. Korber. Clustering Patterns of Cytotoxic T-Lymphocyte Epitopes in Human Immunodeficiency Virus Type 1 (HIV-1) Proteins Reveal Imprints of Immune Evasion on HIV-1 Global Variation. J. Virol., 76(17):8757-8768, Sep 2002. PubMed ID: 12163596.
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