Beyond Shielding: The Roles of Glycans in the SARS-CoV‑2 Spike Protein

The ongoing COVID-19
pandemic caused by severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000
infections and 900,000 deaths worldwide to date. Antibody development
efforts mainly revolve around the extensively glycosylated SARS-CoV-2
spike (S) protein, which mediates host cell entry by binding to the
angiotensin-converting enzyme 2 (ACE2). Similar to many other viral
fusion proteins, the SARS-CoV-2 spike utilizes a glycan shield to
thwart the host immune response. Here, we built a full-length model
of the glycosylated SARS-CoV-2 S protein, both in the open and closed
states, augmenting the available structural and biological data. Multiple
microsecond-long, all-atom molecular dynamics simulations were used
to provide an atomistic perspective on the roles of glycans and on
the protein structure and dynamics. We reveal an essential structural
role of N-glycans at sites N165 and N234 in modulating
the conformational dynamics of the spike’s receptor binding
domain (RBD), which is responsible for ACE2 recognition. This finding
is corroborated by biolayer interferometry experiments, which show
that deletion of these glycans through N165A and N234A mutations significantly
reduces binding to ACE2 as a result of the RBD conformational shift
toward the “down” state. Additionally, end-to-end accessibility
analyses outline a complete overview of the vulnerabilities of the
glycan shield of the SARS-CoV-2 S protein, which may be exploited
in the therapeutic efforts targeting this molecular machine. Overall,
this work presents hitherto unseen functional and structural insights
into the SARS-CoV-2 S protein and its glycan coat, providing a strategy
to control the conformational plasticity of the RBD that could be
harnessed for vaccine development.