Structural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans

David Chmielewski; Eric A Wilson; Grigore Pintilie; Peng Zhao; Muyuan Chen; Michael F Schmid; Graham Simmons; Lance Wells; Jing Jin; Abhishek Singharoy; Wah Chiu

doi:10.1038/s41467-023-42836-9

Structural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans

Nat Commun. 2023 Nov 7;14(1):7175. doi: 10.1038/s41467-023-42836-9.

Authors

David Chmielewski^#¹, Eric A Wilson^#², Grigore Pintilie³, Peng Zhao⁴, Muyuan Chen⁵, Michael F Schmid⁵, Graham Simmons^{6

7}, Lance Wells⁴, Jing Jin^{8

9

10}, Abhishek Singharoy¹¹, Wah Chiu^{12

13

14}

Affiliations

¹ Biophysics Graduate Program, Stanford University, Stanford, CA, 94305, USA.
² School of Molecular Sciences, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
³ Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA.
⁴ Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
⁵ Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.
⁶ Vitalant Research Institute, San Francisco, CA, 94118, USA.
⁷ Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA.
⁸ Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA. jjin@vitalant.org.
⁹ Vitalant Research Institute, San Francisco, CA, 94118, USA. jjin@vitalant.org.
¹⁰ Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA. jjin@vitalant.org.
¹¹ School of Molecular Sciences, Biodesign Institute, Arizona State University, Tempe, AZ, USA. asinghar@asu.edu.
¹² Biophysics Graduate Program, Stanford University, Stanford, CA, 94305, USA. wahc@stanford.edu.
¹³ Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA. wahc@stanford.edu.
¹⁴ Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA. wahc@stanford.edu.

^# Contributed equally.

Abstract

Coronavirus spike glycoproteins presented on the virion surface mediate receptor binding, and membrane fusion during virus entry and constitute the primary target for vaccine and drug development. How the structure dynamics of the full-length spikes incorporated in viral lipid envelope correlates with the virus infectivity remains poorly understood. Here we present structures and distributions of native spike conformations on vitrified human coronavirus NL63 (HCoV-NL63) virions without chemical fixation by cryogenic electron tomography (cryoET) and subtomogram averaging, along with site-specific glycan composition and occupancy determined by mass spectrometry. The higher oligomannose glycan shield on HCoV-NL63 spikes than on SARS-CoV-2 spikes correlates with stronger immune evasion of HCoV-NL63. Incorporation of cryoET-derived native spike conformations into all-atom molecular dynamic simulations elucidate the conformational landscape of the glycosylated, full-length spike that reveals a role of hinge glycans in modulating spike bending. We show that glycosylation at N1242 at the upper portion of the stalk is responsible for the extensive orientational freedom of the spike crown. Subsequent infectivity assays implicated involvement of N1242-glyan in virus entry. Our results suggest a potential therapeutic target site for HCoV-NL63.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Glycosylation
Humans
Molecular Dynamics Simulation
Polysaccharides
SARS-CoV-2* / metabolism
Spike Glycoprotein, Coronavirus* / metabolism

Substances

Spike Glycoprotein, Coronavirus
Polysaccharides

Abstract

Publication types

MeSH terms

Substances

Grants and funding