Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein
Fig 3
The relationship between loop lengths and number of glycosylation sites in the gp120 variable regions V1-V5.
These plots are based on the Los Alamos Database (www.hiv.lanl.gov) alignment, which contains 4,633 curated HIV-1 Env sequences. This alignment contains intact, full length Env sequences, and includes only one sequence per sampled individual. Sequences of poor quality (frameshifts, ambiguity codes or inappropriate stop codons) were excluded from the alignment. The relative width of the box plots is proportional to the square root of the number of sequences in this set that have a given number of potential N-linked glycosylation sites, having the sequence pattern (NX[ST]), were N is an Asparagine, followed by X, any amino acid except Proline, followed by either a Serine or Threonine. Also shown is the epitope region, spanning HXB2 positions 152–184, from the V1V2 peptide construct. In the case of hyper-variable loops, V1, V2, V4, and V5, a p-value < 2.2e-16 was estimated for the correlation between length and number of N-linked glycosylation sites using Kendall's tau statistic (estimated using the R statistical package; it is non-exact due to ties and large sample sizes). The Variable Length Characteristics tool was used to evaluate these regions, and the full loop regions were included in the analysis (V1, HXB2 positions 131–157; V2 158–196; V3 296–331; V4 385–418; and V5 360–469).