S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study

Abstract

SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans results in stabilized interactions on the direct RBD-ACE2. Calculation of the distances between RBD and two major H1, H2 helices of ACE2 and the interacting pairs of amino acids in the interface showed that the elongated O-glycan maintains these interactions by forming several polar contacts with the neighbouring residues while it would not interfere in the direct binding interface. Relative binding free energy of RBD-ACE2 is also more favorable in the O-glycosylated models with longer glycans. The increase of RBD binding affinity to ACE2 depends on the size of attached O-glycan. By increasing the size of O-glycan, the RBD-ACE2 binding affinity will increase. Hence, this crucial factor must be taken into account for any further inhibitory approaches towards RBD-ACE2 interaction.

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: the case of the spike A222V mutation

“…before, the closed-to-open transition of the RBD was analysed by performing PCA on the RBD (residues 330-530) and continuous density distributions for PC1 RBD were finally plotted (red and blue dashed lines in Figure5d). In line with other published data(Casalino et al 2020;Pang et al 2021;Rahnama et al 2021), glycosylation seems to affect the extent of the RBD opening. Even more shifted density distributions were in fact registered for both the S:D614G and [S:A222V + S:D614G] mutants…”

“…Other map-to-model quality figures, like FSC-Q (Ramírez-Aportela et al 2021), agreed in this respect (data not shown).Molecular dynamics simulations were also carried out to provide complementary and perhaps less discrete structural details about the subject under study. Considering the importance of glycosylation for the spike dynamics(Casalino et al 2020;Pang et al 2021, Rahnama et al 2021, MD trajectories were collected starting from our cryo-EM structures as well as from previously reported structural models with and without glycosylation.Results from PCA relative to the RBD closed-to-open transition pointed out the preference for a more open RBD for the [S:A222V + S:D614G] mutant, with glycosylation additionally enhancing the openness of the open RBD, inagreement with a recent study(Pang et al 2021). Furthermore, dynamic network analysis allowed us to go deeper into the allosteric nature of the possible changes induced by the S:A222V mutation.…”

The glycosylation in SARS-CoV-2 and its receptor ACE2

“…Attachment of the O-glycans to S494 can increase the binding affinity of virus to ACE2. 354 The predicted O-linked glycosylation residues at S673, T678 and S686 are near the RRAR position, 36 , 337 implying their potential functions in virus penetration. 332 , 337 , 359…”

“…Among them, the levels of O-glycosylation at T323 and S325 are relative higher, while the glycosylation of other O-glycosites are in low occupancy. 40 , 63 , 70 , 329 , 332 , 336 – 338 The O-glycans identified on O-glycosites of S protein and RBD from human cells as well as deduced O-glycan structures were summarized 70 , 80 , 328 , 332 , 336 , 338 , 340 – 342 , 354 – 357 (Table 2 , Table 3 ). O-linked glycans such as Core-1, 336 disialylated Core-1, 332 Core-2, 328 mucin-type, 339 and sialylated mucin type are reported on the recombinant S protein.…”

Implications of the Immune Polymorphisms of the Host and the Genetic Variability of SARS-CoV-2 in the Development of COVID-19

“…Additionally, the size of O-glycan in the glycosylated S protein appears as a factor that modulates the affinity of virus-receptor interaction. An increase in the size of O-glycan in the S protein enhances its interaction with the ACE2 receptor [80]. In addition, it has been suggested that to enter human cells, SARS-CoV2 requires furin protease [81].…”