Fig. 4: Redesigned V4 hypervariable (HV) loop of the subtype B Env consensus sequence. | Nature Communications

Fig. 4: Redesigned V4 hypervariable (HV) loop of the subtype B Env consensus sequence.

From: Contemporary HIV-1 consensus Env with AI-assisted redesigned hypervariable loops promote antibody binding

Fig. 4: Redesigned V4 hypervariable (HV) loop of the subtype B Env consensus sequence.

A The Shannon entropy of non-HV surrounding surface sites is shown for V1HV (n = 20), V2HV (n = 15), V4HV (n = 14) and V5HV (n = 17) of each subtype/CRF, with median values reported. The box plots depict the median and 25th/75th percentiles of the distribution, with the minima and maxima shown as whiskers. (B) Sequence logo of 2495 subtype B viruses around the V4HV loop, with the N-/C-anchor and spacer labeled. The height of each amino acid letter represents its frequency at the position. The letter ‘O’ represents potential N-linked glycosylation sites. The consensus B Env with unmodified V4HV (C) and redesigned V4HV loop (D) modeled by AlphaFold2 are shown with the N-anchor, C-anchor, and spacer sites colored blue, orange, and light green, respectively. Non-HV residues that interact with anchor sites are shown as spheres (hydrophobic interactions) or sticks (charge-charge interactions). Source data for panels (A) and (B) are provided in the Source Data files.

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