Serial Deletion Mapping by Competition ELISA Assay: Characterization of a Linear Epitope in the V3 Loop of HIV-1

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Abstract
Precise epitope mapping and characterization is important for development of a subunit vaccine. To identify epitopes in the principal neutralizing determinant (PND) within the V3 loop of human immunodeficiency virus type 1 (HIV-1), sera were screened in a direct ELISA assay with a coating peptide consisting of IHIGPGRAF, a specific sequence commonly found in the loop, linked at the C terminus to GAGAAK, a nonspecific hexapeptide. Epitope mapping experiments revealed that a competition ELISA assay using IGPGRAFGAGAAK as coating peptide was superior to a direct ELISA assay for epitope definition and characterization. The competing peptides contained only specific sequences and were serially deleted of single amino acids first at the N terminus and then at the C terminus. Study of the most highly reactive serum identified in the initial screening identified the epitope (the shortest peptide with the most potent inhibitory activity) as IGPGRAF. Deletion of a single amino acid from the C terminus of the epitope resulted in complete loss of activity as competing peptide. In contrast, single amino acid deletions of three N-terminal amino acids resulted in a stepwise 2700-fold reduction in affinity. RAF was the shortest peptide with inhibitory activity. Additional studies are needed, especially with regard to choice of coating peptide, to establish the general utility of the described epitope mapping procedure. However, the above method, termed serial deletion mapping, may be useful for defining and characterizing linear epitopes and thus may be particularly informative in investigating the multiple overlapping epitopes of the PND.