Fig. 2: The association pathway for the DH270.6 Fv identifies design targets.
From: Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies
A Association pathway for DH270.6 determined from an MSM prepared from the simulated set. Important regions of the gp120T (blue) include the V1 loop (purple), the V4 loop (light orange), the GDIK motif (gray), 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 each transition’s relative flux. Structures are positioned based on the probability that each state will move forward to the bound state. Transitions targeted for design are highlighted (pink). B Graphical representation of lineage-based design depicting a simplified phylogenetic tree leading from the inferred UCA and intermediates to the mature DH270.6 bnAb. Design targets D1-D4, each targeting low probability mutations (red), with the I3.6 targeting D2 identified as the primary focus for design. The I3.6 intermediate contains two key improbable mutations, the VH R98T and VL L48Y. C (left) Representative state from State 1 highlighting the position of the N408-glycan and the contacts between the design target D2 mutation sites VH T98 and VL Y48. (middle) Representative state from State 3 highlighting the position of the N442-glycan relative to the N301-glycan and its bound state interactive Y27 residue sidechain. (right) The bound state conformation. D (left) Association rates determined by SPR for the parent CH848 Env SOSIP ectodomain and each design (right) Association kinetics for a CH848 parent and design in which two glycans in the V1 loop have been eliminated via mutation (referred to as DT). Arrows and values indicate the fold change in ka between the parent and combined mutations. Three replicate measures are shown with the mean and error bars indicating the standard deviation. E (lower left) Simplified graphical representation of encounter transition in the DH270.6 interaction with gp120T. (upper right) Shapes placed in their relative positions on the gp120T (orange) map encounter states to the structure. Encounter state 1 maps to the cyan V4 block while Encounter state 2 and 3 map to the orange and yellow. Source data are provided as a Source Data file.
