Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV
Fig 6
Definition of interfacial BCR residues used to characterize AM simulations.
(A) VMD snapshots of (left) VRC01GL and (right) VRC01, in complex with HIV-based Ags. Ags are colored in silver and Abs in gray. Residues included in the in silico CD4bs interfacial residue definition are colored orange if overlapping between the two Abs and colored green otherwise, and interfacial residues excluded from the definition due to contact or alignment with HIV glycans (red) are colored cyan. (B) Interfacial amino acid compositions for VRC01GL and VRC01 are shown by hatched and solid pink bars, respectively, using the residues defined in orange/green in (A), which mimic the biological trends shown in Fig 3. For each amino acid type, the Abs’ target interfacial fraction in the CD4bs of HIV is indicated by a black bar (note that the Abs’ acidic interfacial compositions evolve to match the basic interfacial composition of the CD4bs, and vice versa).