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  • Mutational fitness landscap...
    Madan, Bharat; Zhang, Baoshan; Xu, Kai; Chao, Cara W; O'Dell, Sijy; Wolfe, Jacy R; Chuang, Gwo-Yu; Fahad, Ahmed S; Geng, Hui; Kong, Rui; Louder, Mark K; Nguyen, Thuy Duong; Rawi, Reda; Schön, Arne; Sheng, Zizhang; Nimrania, Rajani; Wang, Yiran; Zhou, Tongqing; Lin, Bob C; Doria-Rose, Nicole A; Shapiro, Lawrence; Kwong, Peter D; DeKosky, Brandon J

    Proceedings of the National Academy of Sciences - PNAS, 03/2021, Letnik: 118, Številka: 10
    Journal Article

    Vaccine-based elicitation of broadly neutralizing antibodies holds great promise for preventing HIV-1 transmission. However, the key biophysical markers of improved antibody recognition remain uncertain in the diverse landscape of potential antibody mutation pathways, and a more complete understanding of anti-HIV-1 fusion peptide (FP) antibody development will accelerate rational vaccine designs. Here we survey the mutational landscape of the vaccine-elicited anti-FP antibody, vFP16.02, to determine the genetic, structural, and functional features associated with antibody improvement or fitness. Using site-saturation mutagenesis and yeast display functional screening, we found that 1% of possible single mutations improved HIV-1 envelope trimer (Env) affinity, but generally comprised rare somatic hypermutations that may not arise frequently in vivo. We observed that many single mutations in the vFP16.02 Fab could enhance affinity >1,000-fold against soluble FP, although affinity improvements against the HIV-1 trimer were more measured and rare. The most potent variants enhanced affinity to both soluble FP and Env, had mutations concentrated in antibody framework regions, and achieved up to 37% neutralization breadth compared to 28% neutralization of the template antibody. Altered heavy- and light-chain interface angles and conformational dynamics, as well as reduced Fab thermal stability, were associated with improved HIV-1 neutralization breadth and potency. We also observed parallel sets of mutations that enhanced viral neutralization through similar structural mechanisms. These data provide a quantitative understanding of the mutational landscape for vaccine-elicited FP-directed broadly neutralizing antibody and demonstrate that numerous antigen-distal framework mutations can improve antibody function by enhancing affinity simultaneously toward HIV-1 Env and FP.