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Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike.

<div class='caption-title'>Design of the x3 disulfide bond to stabilise the SARS-CoV-2 spike in the “locked” state.</div>
<div class='caption-title'>Biochemical properties of purified x3 spikes comparing to x2 spikes.</div>
<div class='caption-title'>Structural features of spike proteins in different conformations as determined by cryo-EM.</div>
Qu K, Chen Q, Ciazynska KA, Liu B, Zhang X, Wang J, He Y, Guan J, He J, Liu T, Zhang X, Carter AP, Xiong X, Briggs JAG
OpenAccess logo PLoS Pathog 18 e1010583 (2022)
Related entries: 7xtz, 7xu0, 7xu1, 7xu2, 7xu3, 7xu4, 7xu6

Cited: 7 times
EuropePMC logo PMID: 35905112

Abstract

The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct "S-R/x3" to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked-1 and locked-2 conformations. For the D614G spike, based on which all variants of concern were evolved, only the locked-2 conformation was observed. Analysis of the structures suggests that rigidified domain D in the locked conformations interacts with the hinge to domain C and thereby restrains RBD movement. Structural change in domain D correlates with spike conformational change. We propose that the locked-1 and locked-2 conformations of S are present in the acidic high-lipid cellular compartments during virus assembly and egress. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed or open conformations. The dynamics of this transition can be altered by mutations that modulate domain D structure, as is the case for the D614G mutation, leading to changes in viral fitness. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.

Reviews citing this publication (1)

  1. Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike. Wrobel AG. Curr Opin Struct Biol 81 102619 (2023)

Articles citing this publication (6)

  1. A Tailored Strategy to Crosslink the Aspartate Transcarbamoylase Domain of the Multienzymatic Protein CAD. Del Caño-Ochoa F, Rubio-Del-Campo A, Ramón-Maiques S. Molecules 28 660 (2023)
  2. Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy. Toelzer C, Gupta K, Berger I, Schaffitzel C. Acta Crystallogr D Struct Biol 79 111-121 (2023)
  3. Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes. Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X. Life Sci Alliance 6 e202201796 (2023)
  4. Heme binding to the SARS-CoV-2 spike glycoprotein. Freeman SL, Oliveira ASF, Gallio AE, Rosa A, Simitakou MK, Arthur CJ, Mulholland AJ, Cherepanov P, Raven EL. J Biol Chem 299 105014 (2023)
  5. SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope. He P, Liu B, Gao X, Yan Q, Pei R, Sun J, Chen Q, Hou R, Li Z, Zhang Y, Zhao J, Sun H, Feng B, Wang Q, Yi H, Hu P, Li P, Zhang Y, Chen Z, Niu X, Zhong X, Jin L, Liu X, Qu K, Ciazynska KA, Carter AP, Briggs JAG, Chen J, Liu J, Chen X, He J, Chen L, Xiong X. Nat Microbiol 7 1635-1649 (2022)
  6. Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy. D'Arco A, Di Fabrizio M, Mancini T, Mosetti R, Macis S, Tranfo G, Della Ventura G, Marcelli A, Petrarca M, Lupi S. Int J Mol Sci 24 9550 (2023)


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