Figure 1.
Shannon's entropy of individual amino acids in the C2, V3 and C3 envelope regions in HIV-1 and HIV-2.
(A) HIV-1 alignment (PT dataset), sites were numbered according to codon env position of HIV-1 HXB2 reference strain; (B) HIV-2 alignment (PT dataset), sites were numbered according to codon env position of HIV-2 ALI reference strain.
Figure 2.
Frequency of N-glycosylation sites in the C2, V3 and C3 envelope regions in HIV-1 and HIV-2.
(A) HIV-1 alignment (PT dataset), sites were numbered according to codon env position of HIV-1 HXB2 reference strain; (B) HIV-2 alignment (PT dataset), sites were numbered according to codon env position of HIV-2 ALI reference strain.
Figure 3.
Positive selection in the C2, V3 and C3 envelope regions in HIV-1 and HIV-2.
dN-dS values were estimated by FEL and scaled by the total codon tree length. (A) HIV-1 alignment (PT dataset), sites were numbered according to codon env position of HIV-1 HXB2 reference strain; (B) HIV-2 alignment (PT dataset), sites were numbered according to codon env position of HIV-2 ALI reference strain.
Table 1.
Positively selected sites detected by SLAC, FEL, REL and/or IFEL in HIV-1 and HIV-2 env C2, V3 and C3 regions1.
Figure 4.
Conformational structure of C2, V3 and C3 envelope regions in HIV-1 and HIV-2.
The conformational structure of consensus amino acid sequences derived from the PT datasets was obtained by homology modeling as indicated in Material and Methods. In the schematics, C2 is shown in red, V3 in yellow and C3 in blue. (A) Balls represent the amino acids under positive selection. The red balls represent codons selected simultaneously by SLAC, FEL and REL methods, while green balls stand for codons selected by at least two of these methods; (B) Model structure showing the predicted interactions between V3, C2 and C3 in HIV-2 gp125. The non-covalent interaction involves residues Tyr296 and His301 in C2 binding, respectively, to Arg331 and Trp334 in V3, and Phe337 in C3 binding to Phe321 in V3.
Figure 5.
Solvent accessible surface area, positive selection and potential N-glycosylation sites in C2-V3-C3 region.
(A) HIV-1 alignment (PT dataset), sites were numbered according to codon env position of HIV-1 HXB2 reference strain; (B) HIV-2 alignment (PT dataset), sites were numbered according to codon env position of HIV-2 ALI reference strain. Coloured bars represent the amino acids under positive selection and have the same colours (red and green) as the corresponding positions (balls) highlighted in Figure 4A. The dark blue stars over the bars correspond to potential N-glycosylation sites conserved along the alignment (present in ≥50% of strains), whereas the light blue stars represent sites only present in less than 50% of sequences.