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Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein

Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein
Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein
SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 receptor, and an open state that does so but displays more exposed antigenic surface. Spikes of variants of concern (VOCs) acquired amino acid changes linked to increased virulence and immune evasion. Here, using HDX-MS, we identified changes in spike dynamics that we associate with the transition from closed to open conformations, to ACE2 binding, and to specific mutations in VOCs. We show that the RBD-associated subdomain plays a role in spike opening, whereas the NTD acts as a hotspot of conformational divergence of VOC spikes driving immune evasion. Alpha, beta and delta spikes assume predominantly open conformations and ACE2 binding increases the dynamics of their core helices, priming spikes for fusion. Conversely, substitutions in omicron spike lead to predominantly closed conformations, presumably enabling it to escape antibodies. At the same time, its core helices show characteristics of being pre-primed for fusion even in the absence of ACE2. These data inform on SARS-CoV-2 evolution and omicron variant emergence.
2041-1723
Calvaresi, Valeria
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Wrobel, Antoni G.
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Toporowska, Joanna
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Hammerschmid, Dietmar
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Doores, Katie J.
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Bradshaw, Richard T.
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Parsons, Ricardo B.
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Benton, Donald J.
d1d6669c-b722-4152-be53-f1e5ea95214c
Roustan, Chloë
79188e09-cbb2-4d8e-83c0-97f52e2d5ab3
Reading, Eamonn
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Malim, Michael H.
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Gamblin, Steve J.
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Politis, Argyris
06febde7-4b5c-4435-9b3a-8915f50c47a3
Calvaresi, Valeria
3c061892-a4da-428d-98e3-d277d406aec3
Wrobel, Antoni G.
3db770c4-eff9-4b1b-9e09-7708f03e015a
Toporowska, Joanna
800f8507-408f-41c8-8b8a-0b2b11c5ffab
Hammerschmid, Dietmar
5934e033-df57-4533-8e58-645ed0315759
Doores, Katie J.
52d36150-7a62-4f9d-8348-c83a789d52e6
Bradshaw, Richard T.
5e37ccd1-f8a8-4eec-a205-d68b57a877f3
Parsons, Ricardo B.
a8921e55-7614-4769-962f-98000efb10f2
Benton, Donald J.
d1d6669c-b722-4152-be53-f1e5ea95214c
Roustan, Chloë
79188e09-cbb2-4d8e-83c0-97f52e2d5ab3
Reading, Eamonn
62fed933-f867-4c72-89e7-83aea573a836
Malim, Michael H.
db62896c-90fe-4cdb-971f-c9448790dc7f
Gamblin, Steve J.
3606ffcb-5221-4344-bc6c-9313d2abc3db
Politis, Argyris
06febde7-4b5c-4435-9b3a-8915f50c47a3

Calvaresi, Valeria, Wrobel, Antoni G., Toporowska, Joanna, Hammerschmid, Dietmar, Doores, Katie J., Bradshaw, Richard T., Parsons, Ricardo B., Benton, Donald J., Roustan, Chloë, Reading, Eamonn, Malim, Michael H., Gamblin, Steve J. and Politis, Argyris (2023) Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein. Nature Communications, 14 (1), [1421]. (doi:10.1038/s41467-023-36745-0).

Record type: Article

Abstract

SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 receptor, and an open state that does so but displays more exposed antigenic surface. Spikes of variants of concern (VOCs) acquired amino acid changes linked to increased virulence and immune evasion. Here, using HDX-MS, we identified changes in spike dynamics that we associate with the transition from closed to open conformations, to ACE2 binding, and to specific mutations in VOCs. We show that the RBD-associated subdomain plays a role in spike opening, whereas the NTD acts as a hotspot of conformational divergence of VOC spikes driving immune evasion. Alpha, beta and delta spikes assume predominantly open conformations and ACE2 binding increases the dynamics of their core helices, priming spikes for fusion. Conversely, substitutions in omicron spike lead to predominantly closed conformations, presumably enabling it to escape antibodies. At the same time, its core helices show characteristics of being pre-primed for fusion even in the absence of ACE2. These data inform on SARS-CoV-2 evolution and omicron variant emergence.

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s41467-023-36745-0 - Version of Record
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Accepted/In Press date: 15 February 2023
Published date: 14 March 2023
Additional Information: © 2023. The Author(s).

Identifiers

Local EPrints ID: 478827
URI: http://eprints.soton.ac.uk/id/eprint/478827
ISSN: 2041-1723
PURE UUID: 91a22db2-392f-4ace-9c44-d788fa34ab8f
ORCID for Richard T. Bradshaw: ORCID iD orcid.org/0000-0002-8652-4301
ORCID for Eamonn Reading: ORCID iD orcid.org/0000-0001-8219-0052

Catalogue record

Date deposited: 11 Jul 2023 17:00
Last modified: 06 Jun 2024 02:17

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Contributors

Author: Valeria Calvaresi
Author: Antoni G. Wrobel
Author: Joanna Toporowska
Author: Dietmar Hammerschmid
Author: Katie J. Doores
Author: Richard T. Bradshaw ORCID iD
Author: Ricardo B. Parsons
Author: Donald J. Benton
Author: Chloë Roustan
Author: Eamonn Reading ORCID iD
Author: Michael H. Malim
Author: Steve J. Gamblin
Author: Argyris Politis

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