Structures and dynamics of the novel S1/S2 protease cleavage site loop of the SARS-CoV-2 spike glycoprotein

Lemmin, Thomas; Kalbermatter, David; Harder, Daniel; Plattet, Philippe; Fotiadis, Dimitrios

doi:10.1016/j.yjsbx.2020.100038

Cited by 42 publications

(59 citation statements)

References 36 publications

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“…3b – d ). Our analysis of the published structures [ 3 , 4 , 87 , 88 ] indicates that a full alanine mutation of this site may simply collapse the exposed S1/S2 loop. Our finding that exogenous trypsin treatment of cells expressing the S2’ or cathepsin site mutants does not restore cleavage at the S1/S2 border ( Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Our finding that exogenous trypsin treatment of cells expressing the S2’ or cathepsin site mutants does not restore cleavage at the S1/S2 border ( Fig. 5a and 5b ) suggests that these mutations result in proteins with altered furin loop structure [ 87 ], rendering it inaccessible. However, these mutants are still synthesized and trafficked to the surface despite not being cleaved ( Fig.…”

Section: Discussionmentioning

confidence: 99%

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Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function

Barrett

Neal

Edmonds

et al. 2021

Preprint

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The SARS-CoV-2 spike protein (S) is the sole viral protein responsible for both viral binding to a host cell and the membrane fusion event needed for cell entry. In addition to facilitating fusion needed for viral entry, S can also drive cell-cell fusion, a pathogenic effect observed in the lungs of SARS-CoV-2 infected patients. While several studies have investigated S requirements involved in viral particle entry, examination of S stability and factors involved in S cell-cell fusion remain limited. We demonstrate that S must be processed at the S1/S2 border in order to mediate cell-cell fusion, and that mutations at potential cleavage sites within the S2 subunit alter S processing at the S1/S2 border, thus preventing cell-cell fusion. We also identify residues within the internal fusion peptide and the cytoplasmic tail that modulate S cell-cell fusion. Additionally, we examine S stability and protein cleavage kinetics in a variety of mammalian cell lines, including a bat cell line related to the likely reservoir species for SARS-CoV-2, and provide evidence that proteolytic processing alters the stability of the S trimer. This work therefore offers insight into S stability, proteolytic processing, and factors that mediate S cell-cell fusion, all of which help give a more comprehensive understanding of this highly sought-after therapeutic target.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function

Barrett

Neal

Edmonds

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Second, local conformational changes near the S1/S2 region may differ between cleaved and intact structures, as observed in influenza viruses 54 . Third, multiple conformations, if not a disordered state, may exist near that region, as indicated by microseconds molecular dynamics simulations and ab initio modeling 55 . Therefore, it has been difficult to resolve that region, and the majority of cryo-EM studies of SARS-CoV-2 S protein complexed with Abs have resorted to mutant S proteins where the 682 RRAR 685 segment has been replaced by GSAS or SGAG 22–28,40 ( Table 1 ).…”

Section: Discussionmentioning

confidence: 99%

“…These ‘mutant spikes’ may have precluded the discovery of binding of Abs to the S1/S2 site. Molecular modeling and simulations provided insights into the interactions at this region, including those with proteases and other receptors 8,55,56 . We undertook such modeling studies ( Figs 2, 3, 4c-e and 6 ), and performed live-virus experiments ( Fig.…”

Section: Discussionmentioning

confidence: 99%

A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro

Cheng

Porritt

Rivas

et al. 2020

Preprint

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We recently discovered a superantigen-like motif, similar to Staphylococcal enterotoxin B (SEB), near the S1/S2 cleavage site of SARS-CoV-2 Spike protein, which might explain the multisystem-inflammatory syndrome (MIS-C) observed in children and cytokine storm in severe COVID-19 patients. We show here that an anti-SEB monoclonal antibody (mAb), 6D3, can bind this viral motif, and in particular its PRRA insert, to inhibit infection by blocking the access of host cell proteases, TMPRSS2 or furin, to the cleavage site. The high affinity of 6D3 for the furin-cleavage site originates from a poly-acidic segment at its heavy chain CDR2, a feature shared with SARS-CoV-2-neutralizing mAb 4A8. The affinity of 6D3 and 4A8 for this site points to their potential utility as therapeutics for treating COVID-19, MIS-C, or common cold caused by human coronaviruses (HCoVs) that possess a furin-like cleavage site.

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“…Instead of O‐linked glycosylation site, the role of N‐glycans neighboring (N61 and N603) to furin cleavage site, specifically in regulation of furin cleavage site accessibility has been strongly proposed. The S1/S2 protease cleavage site loop apex makes strong and stable interaction with N‐glycans at N61 and N603 making furin cleavage site more accessible [57]. Apart from the extensively studied furin cleavage site, GTNGTKR motif is also present in S1‐NTD domain which is thought to bind other receptors like protein or sugar receptor.…”

Section: Virus Proteinsmentioning

confidence: 99%

SARS‐CoV‐2, the pandemic coronavirus: Molecular and structural insights

et al. 2021

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The outbreak of a novel coronavirus associated with acute respiratory disease, called COVID‐19, marked the introduction of the third spillover of an animal coronavirus (CoV) to humans in the last two decades. The genome analysis with various bioinformatics tools revealed that the causative pathogen (SARS‐CoV‐2) belongs to the subgenus Sarbecovirus of the genus Betacoronavirus, with highly similar genome as bat coronavirus and receptor‐binding domain (RBD) of spike glycoprotein as Malayan pangolin coronavirus. Based on its genetic proximity, SARS‐CoV‐2 is likely to have originated from bat‐derived CoV and transmitted to humans via an unknown intermediate mammalian host, probably Malayan pangolin. Further, spike protein S1/S2 cleavage site of SARS‐CoV‐2 has acquired polybasic furin cleavage site which is absent in bat and pangolin suggesting natural selection either in an animal host before zoonotic transfer or in humans following zoonotic transfer. In the current review, we recapitulate a preliminary opinion about the disease, origin and life cycle of SARS‐CoV‐2, roles of virus proteins in pathogenesis, commonalities, and differences between different corona viruses. Moreover, the crystal structures of SARS‐CoV‐2 proteins with unique characteristics differentiating it from other CoVs are discussed. Our review also provides comprehensive information on the molecular aspects of SARS‐CoV‐2 including secondary structures in the genome and protein–protein interactions which can be useful to understand the aggressive spread of the SARS‐CoV‐2. The mutations and the haplotypes reported in the SARS‐CoV‐2 genome are summarized to understand the virus evolution.

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Structures and dynamics of the novel S1/S2 protease cleavage site loop of the SARS-CoV-2 spike glycoprotein

Abstract: Graphical abstract

Cited by 42 publications

References 36 publications

Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function

Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function

A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro

SARS‐CoV‐2, the pandemic coronavirus: Molecular and structural insights

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