Figure 3.

Epistatic effect of the double Q498R N501Y mutant. (A) A closeup of the complex between ACE2 (in cyan) and RBD (in pink) showing chemical interactions involving RBD residues 501 and 498. Hydrophobic contacts are in grey, π-π interactions are in purple, hydrogen bonds are shown as black dashed lines, unsatisfied polar groups are in cyan, and all distances are measured in Å. (B) Cooperativity of the Q498R N501Y double mutant probed by FEP and SPR computed as a difference between a hypothetical ΔΔG (if the double mutant had an additive effect of two single point mutations) and the actual ΔΔG of the double mutant. Yeast display assay values are from Zahradnik et al.⁶⁴ (C) Absence of cooperativity probed by FEP and SPR for the L452R T478K double mutant. Experimental result for the Delta RBD variant is from Liu et al.⁹² (see Methods for details), ΔΔG of single mutants are from the current study (Table 2). The FEP+ results are from 100 ns trajectories.