Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition

Abstract

Here we have generated 3D structures of glycoforms of the spike (S) glycoprotein from SARS-CoV-2, based on reported 3D structures and glycomics data for the protein produced in HEK293 cells. We also analyze structures for glycoforms representing those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi), as well as those that are commonly observed on antigens present in other viruses. These models were subjected to molecular dynamics (MD) simulation to determine the extent to which glycan microheterogeneity impacts the antigenicity of the S glycoprotein. Lastly, we have identified peptides in the S glycoprotein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the innate and adaptive immune response to the SARS-CoV-2 virus or to a related vaccine. The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain, and also that the degree of shielding is largely insensitive to the specific glycoform. Despite the relatively modest contribution of the glycans to the total molecular weight of the S trimer (17% for the HEK293 glycoform) they shield approximately 40% of the protein surface.

The Nucleocapsid protein triggers the main humoral immune response in COVID-19 patients

“…Interestingly, also the N protein of the related SARS-CoV was shown to be highly immunogenic [ 14 ]. In contrast, even though the overall IgG response to the SARS-CoV-2 S protein was lower, possibly due to the glycosylation status of this protein [ 15 ], the majority of the COVID-19 patients did trigger a response to a region in the S1 subunit of the protein, containing the RBD.…”

Influence of N-glycosylation on Expression and Function of Pseudorabies Virus Glycoprotein gB

“…Glycan processing involves trimming of glucose and mannose residues and subsequent addition of various terminal sugars resulting in different classes of glycans, including high mannose, hybrid and complex N-glycans [ 28 , 32 ]. Functional and structural studies on N-linked glycans from several viral fusion proteins, including influenza hemagglutinin [ 33 , 34 ], coronavirus spike protein [ 35 , 36 , 37 , 38 ], Ebola virus glycoprotein GP [ 39 ], envelope glycoprotein (Env) of human immunodeficiency virus-1 (HIV-1) [ 40 , 41 ], or envelope (E) protein of the flaviviruses Zika [ 42 ] and Dengue virus [ 43 ] have shown that these structures can play diverse functional and structural roles, e.g., in immune evasion by shielding from neutralizing antibodies, enhancement of infection, or stability and maturation of the respective fusion protein.…”

Conformational diversity of CDR region during affinity maturation determines the affinity and stability of Sars-Cov-1 VHH-72 nanobody

“…The other caveat in our studies is that we did not consider glycosylation of RBD in our simulation. However studies indicate that of the residues of RBD known to interact with neutralizing antibody 94% were predicted to be antibody accessible (Grant et al, 2020) . Rigidity in protein will increase favorable enthalpy interactions with decrease in conformational entropy and it has been reported that weakening of HBN far from the mutation site provide enthalpy entropy compensation and counteracting changes in rigidity and flexibility will occur at remote sites to globally balance the rigidity and flexibility in protein structures (Li et al, 2014) .…”