Variability analysis of HIV-1 gp120 V3 region: IV. Distribution functions for intra- and inter-subtype amino acid hamming distances.

Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions are discussed to confirm the applicability of different hierarchical cluster procedures for HIV-1 V3 classification. Two-mode distribution for the subtype E could sertificate that this subtype includes two thinner taxons.

Variability analysis of HIV-1 gp120 V3 region: III. Distinctions between various sets of peptide fragments derived from the sequences belonging to different HIV-1 taxons.

Distinction criterion for various sets of fixed length peptide fragments and integral distinction measure for various sets of peptide fragments with different length and start position ranges have been introduced on the base of an enumeration procedure and a point estimators for the amino acid distribution characteristics introduced previously (M. Yu. Shchelkanov, A. N. Yudin, A. V. Antonov, N. S. Starikov, A. A. Vedenov, E. V. Karamov, J. Biomol. Struct. Dyn. 15, 231-241 (1997)). Differences between 6-10-mer peptides derived from the majority of HIV-1 taxon pairs are demonstrated to be located generally in the vicinity of the V3-loop top. This validates the suitability of V3 top mimicking synthetic peptides for HIV-1 serotyping. A significant difference between E subtype V3 C-terminus peptides and the corresponding peptides derived from the other subtypes has been demonstrated. Taking into account the Langerhans' cells tropism of E subtype virus variants we have hypothesized the influence of mutations in the V3 C-terminus on HIV-1 cell tropism.