Mutational fitness landscapes reveal genetic and structural improvement pathways for an HIV-1 broadly neutralizing antibody

Vaccine-based elicitation of broadly neutralizing antibodies holds great promisefor preventing HIV-1 transmission. However, the key biophysical markers ofimproved antibody recognition remain uncertain among the diverse landscape ofpotential antibody mutation pathways, and a more complete understanding ofanti-HIV-1 fusion peptide (FP) antibody development will accelerate rationalvaccine designs. Here we surveyed the mutational landscape of a vaccineelicitedanti-FP antibody, vFP16.02 to determine the genetic, structural, andfunctional features that are associated with antibody improvement or fitness.Using site-saturation mutagenesis and yeast display functional screening, wefound that 1.0% of possible single mutations improved HIV-1 envelope (Env)trimer affinity, but these generally comprised rare somatic hypermutations thatmay not arise frequently in vivo. We observed that many single mutations couldenhance soluble FP affinity >1,000-fold, although affinity improvements againstthe HIV-1 trimer were more measured and rare. The most potent variantsenhanced affinity to both soluble FP and Env, were concentrated in antibodyframework regions, and achieved up to 37% neutralization breadth. Alteredheavy and light chain interface angles and conformational dynamics, as well asreduced Fab thermal stability, were associated with improved HIV-1neutralization breadth and potency. We also observed parallel sets of mutationsthat enhanced viral neutralization through similar structural mechanisms. Thesedata provide a quantitative understanding of the mutational landscape for an FPdirectedbroadly neutralizing antibody, and demonstrate that numerous antigendistalframework mutations can improve antibody function by enhancing affinitysimultaneously towards HIV-1 Env and FP.