Figure 2

Prevalence of Gag amino acid variants reported in patients failing PI-based therapies and their mapping to HIV-1 protein structures. (A) Prevalence of amino acid variations at 55 Gag positions in 8 HIV-1 subtypes (A1, B, C, D, F1, G, 01_AE and 02_AG) given the Los Alamos full-length Gag sequence dataset (Table 2). Only Gag positions where amino acid substitutions have been observed during PI-based treatment are shown. For each position, the HXB2 index is shown at the top, followed by the most prevalent amino acids (bold) and amino acid variations in our sequence datasets. Amino acids with blue superscripts have prevalence above 10% and other amino acids have orange superscripts. (B) Structural representation of Gag polyprotein and mapping of the 13 PI-associated Gag substitutions identified in Table 3. The annotation of Gag polyproteins is shown at the top. Individual Gag protein structures are shown at the bottom. Gag substitutions are annotated and colored accordingly. Red surfaces indicate PI-associated Gag substitutions at the Gag C-terminal domain; other substitutions are shown in green. PDB data of Gag protein structures: matrix, 1HIW; capsid, 3NTE; p2, 1U57; nucleocapsid, 2M3Z; p6, 2C55. Visualization software: PyMOL V1.5 (http://www.pymol.org/).