Structural Plasticity and Immune Evasion of SARS-CoV-2 Spike Variants

Figure 1. (A) Schematic map of the full-length (1273 amino acids) Wuhan-Hu-1 or USA/WA1 SARS-CoV-2 Spike protein. S1 and S2 subunits are represented in different colors. S1 subunit comprises the N-terminal domain (NTD), receptor-binding domain (RBD), receptor–binding motif (RBM) within RBD, subunit domain 1 (SD1), and subunit domain 2 (SD2), followed by S1/S2 cleavage site. S2 subunit contains S2′, a protease cleavage site, followed by fusion peptide (FP), heptad repeat 1 (HR1), heptad repeat 2 (HR2), transmembrane domain (TM), and cytoplasmic tail (CT). (B–G) Representation of S structures in different conformational states, including but not limited to an uncleaved, closed ((B), PDB ID 6ZGE), a furin-cleaved, closed ((C), PDB ID 6ZGI), an intermediate ((D), PDB ID 6ZGE), the one-RBD-up state ((E), PDB ID 6ZGG), the two-RBDs-up (in complex with LCB3) ((F), PDB id: 7JZN), and the three-RBDs-up (in complex with three H014 Fabs) ((G), PDB ID 7CAK). The furin cleavage site (682-RRAR-685) at S1/S2 was disordered and thus not resolved in the structures (B–G), as shown in the zoomed-in windows. There is no detectable structural difference (Figure S1) between un-cleaved closed (B) and…

Figure 2. Schematics depicting the ligand-binding techniques used to characterize the binding of S to antibodies or hACE2. (A) Surface plasmon resonance (SPR) technique. SPR is an optical technique that can be used to analyze the binding of S protein with antibodies or hACE2. One of the interacting molecules is immobilized in the gold-layer sensor chip, and another interacting partner is flown through the microfluidic system. The interaction between the two molecules causes the change in the refractive index of the light, which is recorded as the response signal and measured in the response unit (RU). The plot generated by monitoring RU over time yields the binding kinetics for two interacting molecules. (B) Enzyme-linked immunosorbent assay (ELISA). ELISA, which is based on the antigen-antibody interaction, effectively profiles the binding of S or its fragment (such as RBD) to an antibody or hACE2. The quantification of binding is evaluated based on the HRP chemiluminescence (conjugated to secondary antibody) or the conjugated fluorescent protein. (C) Bio-layer interferometry (BLI) analysis. BLI is an optical technique for exploring the interaction between S and an antibody or hACE2. One…

Figure 3. Accumulated mutations in the S early VOCs. (A,B) Amino acid substitutions are shown in the S domain organization (A) and depicted in the one-RBD-up structure (B) of the S Alpha variant (PDB ID 7EDF). Amino acid substitutions are highlighted in two different RBD-oriented protomers (RBD-up and RBD-down). The dotted lines indicate the mutated amino acid residues which are not resolved in the structure. (C,D) Illustrations as in (A) and (B), respectively, for the S Beta variant (PDB ID 7VX1). (E,F) Illustrations as in (A/C) and (B/D), respectively, for the S Gamma variant (PDB ID 7SBS).

Figure 4. Accumulated mutations in the S Delta and Omicron variants. (A,B) Amino acid substitutions are shown in the S domains (A) and depicted in the one-RBD-up structure (B) of the S Delta variant (PDB ID 7SBL). Mutated amino acid residues are highlighted in the RBD-up and RBD-down protomers. The dotted lines indicate the mutated amino acid residues which are not resolved in the structure. (C,D) Illustrations as in (A,B), respectively, for the S Omicron variant (PDB ID 7TEI).