The Immunodominant Epitope of HIV-1 Protein gp120
Forms a Double -Turn in Solution

A. M. Andrianov

Institute of Bioorganic Chemistry, Belarus National Academy of Sciences, Minsk, 220141 Belarus

Received February 2, 1998; in final form, July 2, 1998

Abstract—A joint analysis of the Brookhaven PDB data and the results of studying the HIV-1 principal neu-
tralizing determinant was performed to prove that the previously proposed model of the three-dimensional
structure of hexapeptide Gly-Pro-Gly-Arg-Ala-Phe, which forms the putative immunodominant epitope of the
virus, adequately describes the basic conformational peculiarities of the corresponding region of protein gp120.
This assumption was verified as follows. First, a computer-aided search was made for protein fragments whose
primary structures are homologous to the hexapeptide structure. For this purpose, the amino acid sequences of
62 proteins with known spatial structures were analyzed. Second, the Gly-Pro-Gly-Arg-Ala-Phe hexapeptide
conformation occurring in fragments of the HIV-1 principal neutralizing determinant (peptides rp70, rp142, and
rp342) was collated with the conformations of homologous fragments 39–44 of the Bence Jones protein REI,
41–46 of immunoglobulin , and 50–55 of the -chain of horse hemoglobin. A comparative conformational
study showed that the double -turn structure in the Gly-Pro-Gly-Arg-Ala-Phe site of rp70, rp142, and rp342
is not substantially deformed when involved in more intricate networks of contacts between residues. The data
obtained suggest that the double -turn conformation is also very likely to be retained in the polypeptide chain
of the HIV-1 gp120.

Key words: spatial structure, conformation, HIV-1, gp120, immunodominant epitope

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