MD simulations were performed to examine the co-complex (generated from a crystal structure of the ACE2-RBD co-complex, PDB: 6M0J; Lan et al., 2020) of glycosylated S with glycosylated ACE2 with the three different glycoforms models (Abundance, Oxford Class, and Processed; Table S1; Videos S5, S6, and S7). Information from these analyses is laid out along the primary structure (sequence) of the SARS-CoV-2 S protomer and ACE2 highlighting regions of glycan-protein interaction observed in the MD simulations (Table S14; Videos S5, S6, and S7). Interestingly, two glycans on ACE2 (at N090 and N322), which are highlighted in Figure 7 A and shown in a more close-up view in Figure 7B, are predicted to form interactions with the S protein (Table S15). The N322 glycan interaction with the S trimer is outside of the receptor-binding domain, and the interaction is observed across multiple simulations and throughout each simulation (Figures 7A and 7B; Video S5, S6, and S7). The ACE2 glycan at N090 is close enough to the S trimer surface to repeatedly form interactions; however, the glycan arms interact with multiple regions of the surface over the course of the simulations, reflecting the relatively high degree of glycan dynamics (Figures 7A and 7B; Video S3). Inter-molecule glycan-glycan interactions are also observed repeatedly between the glycan at N546 of ACE2 and those in the S protein at residues N0074 and N0165 (Figure 7D; Table S16). Finally, a full view of the ACE2-S complex with Oxford class glycoforms on ACE2 illustrates the extensive glycosylation at the interface of the complex (Figure 7C; Video S4).
Figure 7 Interactions of Glycosylated Soluble Human ACE2 and Glycosylated SARS-CoV-2 S Trimer Immunogen Revealed By 3D-Structural Modeling and MD Simulations
(A) MD simulation of glycosylated soluble human ACE2 and glycosylated SARS-CoV-2 S trimer immunogen interaction (see Videos S5, S6, and S7). ACE2 (top) is colored red with glycans in pink, whereas S is colored white with glycans in dark gray. Highlighted are ACE2 glycans that interact with S that are magnified to the right.
(B) Magnification of ACE2-S interface highlighting ACE2 glycan interactions by using 3D-SNFG icons (Thieker et al., 2016) with S protein (pink) as well as ACE2-S glycan-glycan interactions.
(C) Magnification of dynamics trajectory of glycans at the interface of soluble human ACE2 and S (see Videos S3 and S4).