Figure 11.

Structure-based mutational profiling of the S-RBD complexes with class 1 RBD antibodies. The mutational screening evaluates binding energy changes induced by BA.2.86/JN.1/KP.2/KP.3 mutations in the RBD–antibody complexes. Mutational profiling of the S-RBD complex with S2K146, pdb id 7TAS (A), S-RBD Omicron complex with Omi-3, pdb id 7ZF3 (B), S-RBD Omicron complex with Omi-18, pdb id 7ZF8 (C) and S-RBD in complex with Omi-42, pdb id 8CBF (D). The binding free energy changes are shown as magenta-colored filled bars. The positive binding free energy values ΔΔG correspond to destabilizing changes and negative binding free energy changes are associated with stabilizing changes. The 3D structures of the RBD–antibody complexes are shown for RBD-S2K146 (E), RBD-Omi-3 (F), RBD-Omi-18 (G) and RBD- BD-515 complexes (H). The RBD is shown in cyan-colored surface representation. The RBD-binding epitope residues are shown in red and BA.2.86 mutational positions are shown in blue. The antibodies are shown as ribbons (heavy chain in magenta and light chain in green-colored ribbons).