Fig. 4: The association pathway for the CH235.12 Fv identifies design targets.
From: Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies
A Graphical representation of lineage-based design depicting a simplified phylogenetic tree leading from the inferred UCA and intermediates to the mature CH235.12 bnAb. Design targets D1-D4, each targeting low probability mutations (red), that are key for neutralization breadth. B Association pathway for CH235.12 determined from an MSM prepared from the simulated set. Important regions of the gp120T (blue) include the CD4bs loop (cyan), the V5 loop (red), the loop D (magenta), and the antibody HCDR3 (bright green). A single gp120 state is used throughout, with 50 representative samples of the antibody shown for each state (ensemble of line structures). Arrows show transition paths with sizes adjusted to indicate the relative flux through each transition. Structures are positioned based on the probability that each state will move forward to the bound state along the x-axis. Transitions targeted for design are highlighted (pink). C Representative state from encounter State 2 highlighting the position of the N276-glycan and contact of the HCDR3 with loop D. D Representative state from encounter State 3 highlighting the position of the N386-glycan and contact of the HCDR2 proximal sheet residues with the CD4bs loop. E Mature CH235.12 association rates for the CH505.M5.G458Y parent and the CH505.M5.G458Y CE0 and CE1 designs. Error bars are standard deviations from the mean of three replicate measures. F Aligned structures of the CH505.M5 trimer bound to the early intermediate CH235.I60 Fab or mature bnAb CH235.12 Fab bound to either CH505.M5 or CH505.M5.G458Y highlighting the difference in the V5 loop. The Y458 sidechain is shown for reference. G CH235 UCA, intermediate I60, and mature CH235.12 Fab affinities for the CH505.M5.G458Y parent and the CH505.M5.G458Y CE2 design. Error bars are standard deviations from the mean of three replicate measures. Log scaling is used for visual clarity. Source data are provided as a Source Data file.
