#GotGlycans: Role of N343 Glycosylation on the SARS-CoV-2 S RBD Structure and Co-Receptor Binding Across Variants of Concern DOI Creative Commons
Callum M. Ives, Linh Nguyen, Carl A. Fogarty

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 5, 2023

Abstract Glycosylation of the SARS-CoV-2 spike (S) protein represents a key target for viral evolution because it affects both evasion and fitness. Successful variations in glycan shield are difficult to achieve though, as glycosylation is also critical folding structural stability. Within this framework, identification sites that structurally dispensable can provide insight into evolutionary mechanisms inform immune surveillance. In work we show through over 45 μs cumulative sampling from conventional enhanced molecular dynamics (MD) simulations, how structure immunodominant S receptor binding domain (RBD) regulated by N -glycosylation at N343 glycan’s role changes WHu-1, alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2) omicron (BA.1 BA.2.86) variants. More specifically, find amphipathic nature -glycan instrumental preserve integrity RBD hydrophobic core loss triggers specific consistent conformational change. We change allosterically regulates conformation motif (RBM) RBDs, but not variants, due mutations reinforce architecture. support these findings, monosialylated ganglioside co-receptors highly dependent on RBD, affinity significantly across VoCs. Ultimately, functional reinforces our understanding function allows us identify constraints within which site become hotspot shield.

Language: Английский

SARS-CoV-2 spike glycosylation affects function and neutralization sensitivity DOI Creative Commons

Fengwen Zhang,

Fabian Schmidt,

Frauke Muecksch

et al.

mBio, Journal Year: 2024, Volume and Issue: 15(2)

Published: Jan. 9, 2024

The glycosylation of viral envelope proteins can play important roles in virus biology and immune evasion. spike (S) glycoprotein severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) includes 22 N-linked sequons 17 O-linked glycosites. We investigated the effect individual sites on SARS-CoV-2 S function pseudotyped infection assays sensitivity to monoclonal polyclonal neutralizing antibodies. In most cases, removal decreased infectiousness virus. For mutants N-terminal domain receptor-binding (RBD), reduction pseudotype infectivity was predicted by a commensurate level virion-incorporated protein reduced trafficking cell surface. Notably, presence glycan at position N343 within RBD had diverse effects neutralization RBD-specific antibodies cloned from convalescent individuals. overall plasma COVID-19 individuals, suggesting role for However, vaccination individuals produced activity that resilient inhibitory glycan.IMPORTANCEThe attachment glycans viruses during their synthesis movement through secretory pathway affect properties. This study shows attached enable its surface incorporation into particles. Certain glycans, including one is asparagine 343 protein, also increase or decrease antibodies, likely direct antibody epitopes modulation conformation. context mixture serum reduce sensitivity. Overall, this highlights complex

Language: Английский

Citations

13
Conserved role of spike S2 domain N-glycosylation across betacoronaviruses DOI Creative Commons
Qi Yang, Anju Kelkar, Balaji Manicassamy

et al.

npj Viruses, Journal Year: 2025, Volume and Issue: 3(1)

Published: Jan. 25, 2025

Abstract Besides acting as an immunological shield, the N-glycans of SARS-CoV-2 are also critical for viral life cycle. As S2 subunit spike is highly conserved across betacoronaviruses, we determined functional significance five ‘stem N-glycans’ located in between N1098-N1194. Studies were performed with 31 Asn-to-Gln mutants, betacoronavirus virus-like particles and single-cycle replicons. Deletions stem enhanced S1 shedding from trimeric spike, reduced ACE2 binding abolished syncytia formation. When three or more deleted, expression on cell surface incorporation into virions was both reduced. Viral entry function progressively lost upon deleting N1098 glycan combination additional glycosite modifications. In addition to SARS-CoV-2, SARS-CoV MERS-CoV prevented target cells. These data suggest multiple roles N-glycans, evolutionarily properties these complex carbohydrates human betacoronaviruses.

Language: Английский

Citations

1
Evolving spike-proteinN-glycosylation in SARS-CoV-2 variants DOI Creative Commons
Sabyasachi Baboo, Jolene K. Diedrich, Jonathan L. Torres

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 9, 2023

Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution with immunity provides an excellent opportunity study interaction between viral pathogens and their hosts. heavily

Language: Английский

Citations

11
Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern DOI Creative Commons
Callum M. Ives, Linh Nguyen, Carl A. Fogarty

et al.

eLife, Journal Year: 2024, Volume and Issue: 13

Published: March 27, 2024

Glycosylation of the SARS-CoV-2 spike (S) protein represents a key target for viral evolution because it affects both evasion and fitness. Successful variations in glycan shield are difficult to achieve though, as glycosylation is also critical folding structural stability. Within this framework, identification sites that structurally dispensable can provide insight into evolutionary mechanisms inform immune surveillance. In work, we show through over 45 μs cumulative sampling from conventional enhanced molecular dynamics (MD) simulations, how structure immunodominant S receptor binding domain (RBD) regulated by N -glycosylation at N343 glycan’s role changes WHu-1, alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2), omicron (BA.1 BA.2.86) variants. More specifically, find amphipathic nature -glycan instrumental preserve integrity RBD hydrophobic core loss triggers specific consistent conformational change. We change allosterically regulates conformation motif (RBM) alpha, RBDs, but not variants, due mutations reinforce architecture. support these findings, monosialylated ganglioside co-receptors highly dependent on RBD, affinity significantly across VoCs. Ultimately, functional work reinforces our understanding function allows us identify constraints within which site become hotspot shield.

Language: Английский

Citations

4
SARS-related coronavirus S-protein structures reveal synergistic RBM interactions underpinning high-affinity human ACE2 binding DOI Creative Commons
Jingjing Wang,

Yong Ma,

Zimu Li

et al.

Science Advances, Journal Year: 2025, Volume and Issue: 11(11)

Published: March 14, 2025

High-affinity and specific binding toward the human angiotensin-converting enzyme 2 (hACE2) receptor by severe acute respiratory syndrome coronavirus (SARS)–related coronaviruses (SARSr-CoVs) remains incompletely understood. We report cryo–electron microscopy structures of eight different S-proteins from SARSr-CoVs found across Asia, Europe, Africa. These all adopt tightly packed, locked, prefusion conformations. enable classification SARSr-CoV into three types, based on their receptor-binding motif (RBM) ACE2 characteristics. Type-2 often preferentially bind bat (bACE2) over hACE2. a structure type-2 BtKY72-RBD in complex with bACE2 to understand specificity. Structure-guided mutagenesis reveals that multiple synergistic mutations four regions RBM are required achieve high-affinity hACE2 binding. Similar changes can also confer another BM48-31 S-protein, which is primarily non-ACE2 results provide an understanding how may be acquired S-proteins.

Language: Английский

Citations

0
Epistasis between N-terminal and receptor-binding domains drives cell entry in a bat coronavirus spike DOI
Alexandra L. Tse, Cory M. Acreman, Inna Ricardo-Lax

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 27, 2024

Understanding the zoonotic risks posed by bat coronaviruses (CoVs) is critical for pandemic preparedness. Herein, we generated recombinant vesicular stomatitis viruses (rVSVs) bearing spikes from divergent CoVs to investigate their cell entry mechanisms. Unexpectedly, successful recovery of rVSVs spike SHC014, a SARS-like CoV, was associated with acquisition novel substitution in S2 fusion peptide-proximal region (FPPR). This enhanced viral both VSV and coronavirus contexts increasing availability receptor-binding domain recognize its cellular receptor, ACE2. A second N-terminal domain, uncovered through forward-genetic selection, interacted epistatically FPPR synergistically enhance spike:ACE2 interaction entry. Our findings identify genetic pathways adaptation during spillover host-to-host transmission, fitness trade-offs inherent these pathways, potential Achilles' heels that could be targeted countermeasures.

Language: Английский

Citations

3
Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation DOI
Hung Van Nguyen, Hoang Linh Nguyen, Pham Dang Lan

et al.

Chemical Society Reviews, Journal Year: 2023, Volume and Issue: 52(18), P. 6497 - 6553

Published: Jan. 1, 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of devastating global COVID-19 pandemic announced by WHO in March 2020.

Language: Английский

Citations

9
Effects of N-glycan modifications on spike expression, virus infectivity, and neutralization sensitivity in ancestral compared to Omicron SARS-CoV-2 variants DOI Creative Commons
Sabrina Lusvarghi, Charles B. Stauft, Russell Vassell

et al.

PLoS Pathogens, Journal Year: 2023, Volume and Issue: 19(11), P. e1011788 - e1011788

Published: Nov. 9, 2023

The SARS-CoV-2 spike glycoprotein has 22 potential N-linked glycosylation sites per monomer that are highly conserved among diverse variants, but how individual glycans affect virus entry and neutralization of Omicron variants not been extensively characterized. Here we compared the effects specific glycan deletions or modifications in BA.1 D614G spikes on expression, processing, incorporation into pseudoviruses, as well infectivity by therapeutic antibodies. We found loss at residues N717 N801 each conferred a pseudovirus for Delta variants. This decrease correlated with decreased processing pseudoviruses. Oligomannose-enriched pseudoviruses generated GnTI- cells presence kifunensine were non-infectious, whereas under similar conditions remained infectious. Similarly, growth live (authentic) resulted greater reduction titers BA.1.1 variant than relative to their respective, untreated controls. Finally, some N-glycans, including N343 N234, increased maximum percent class 3 S309 monoclonal antibody against while these altered potency 1 COV2-2196 Etesevimab antibodies without affecting neutralization. also varied composition, oligomannose-enriched conferring highest These results highlight differences interactions between can infectivity, susceptibility

Language: Английский

Citations

9
Enhanced Surface Accessibility of SARS-CoV-2 Omicron Spike Protein Due to an Altered Glycosylation Profile DOI Creative Commons
Dongxia Wang, Zijian Zhang,

Jakub Baudys

et al.

ACS Infectious Diseases, Journal Year: 2024, Volume and Issue: 10(6), P. 2032 - 2046

Published: May 10, 2024

SARS-CoV-2 spike (S) proteins undergo extensive glycosylation, aiding in proper folding, enhancing stability, and evading host immune surveillance. In this study, we used mass spectrometric analysis to elucidate the N-glycosylation characteristics disulfide bonding of recombinant derived from Omicron variant (B.1.1.529) comparison with D614G variant. Furthermore, conducted microsecond-long molecular dynamics simulations on resolve how different N-glycans impact conformational sampling two variants. Our findings reveal that protein maintains an overall resemblance terms site-specific glycan processing bond formation. Nonetheless, alterations glycans were observed at certain sites. These changes, synergy mutations within protein, result increased surface accessibility macromolecule, including ectodomain, receptor-binding domain, N-terminal domain. Additionally, mutagenesis pull-down assays role glycosylation a specific sequon (N149); furthermore, correlation MD simulation HDX-MS identified several high-dynamic areas proteins. insights contribute our understanding interplay between structure function, thereby advancing effective vaccination therapeutic strategies.

Language: Английский

Citations

2
Structural and Functional Insights into the Evolution of SARS-CoV-2 KP.3.1.1 Spike Protein DOI Creative Commons
Ziqi Feng, Jiachen Huang, Sabyasachi Baboo

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 10, 2024

Summary The JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigated how mutations a deletion in spike protein (S) affect ACE2 binding Mass spectrometry revealed new glycan site at residue N30 altered glycoforms neighboring N61. Cryo-EM structures showed that rearrangement of adjacent residues did not significantly change overall structure, up-down ratio receptor-binding domains (RBDs), or binding. Furthermore, S structure with hACE2 further confirmed an epistatic effect between F456L Q493E on Our analysis shows variants after late 2023 are now incorporating reversions to found other sarbecoviruses, including glycan, Q493E, others. Overall, these results inform structural functional consequences mutations, current evolutionary trajectory, immune evasion.

Language: Английский

Citations

2