Fig 3. Characterization of epitopes of the FabA clones 43 and 177 on the 6-Helix bundle conformation of HIV-1 envelope gp41.

Each set of antibody specific mimotopes obtained by biopanning for both isotype FabA clones 43 (A) and 177 (B) were docked on the crystal structure of gp41 under its 6-Helix bundle conformation. Each gp41 monomer in the trimer is highlighted by a different hue of blue. Epitopes are visualized in a color scale according to the scores returned by the PEPsurf algorithm at each position of the sequence (mean of the 3 chains, over 15 conformations extracted each 10 ns from the molecular dynamic simulations) for each set of mimotope. A common color scale varying from never (yellow) to the most frequent on all clades and structures (red) is used, allowing to directly compare epitopes on the three gp41 clades. For each score, a set of random sequences at each position of the sequence had been subtracted to remove background noise.