SARS‐CoV heptad repeat 2 is a trimer of parallel helices

Celigoy, Jessica; Ramirez, Benjamin E.; Caffrey, Michael

doi:10.1002/pro.736

Cited by 5 publications

(6 citation statements)

References 29 publications

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“…The HR regions of Class 1 viral fusion glycoproteins, including SARS-CoV S protein, are known to oligomerize into helix trimers through Leu/Ile zippers (Hakansson-McReynolds et al, 2006;Xu et al, 2004). Accordingly, peptide GG38, encompassing the entire S protein HR2 sequence (aa 1149-1186), both oligomerized into α helix trimers and heteromerized with the HR1 peptide into the 6-HB (Bosch et al, 2004;Celigoy et al, 2011) (S3 Fig.). The discrepancy between the known oligomerization potential of the HR sequences and their underrepresentation among self-binding peptides identified in this study may be due to that our peptide array of 20-aa length, which while well suited to identify shortsequence-mediated self-interactions (e.g.…”

Section: Resultsmentioning

confidence: 99%

“…2b). A possible explanation for this phenomenon is that the peptides C6, E11, K2A and K4A contained oligomerization sequences, as does the positive control HR2 peptide GG38, which contains a trimerizing sequence (Celigoy et al, 2011;Hakansson-McReynolds et al, 2006). The potential oligomerization sequences within C6, E11, K2A and K4A could enable the non-biotinylated peptides to bind to S1188HA during pre-treatment, and further serve as oligomerization sites for their biotinylated analogues during pull down experiments.…”

Section: Tablementioning

confidence: 99%

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Identification and application of self-binding zipper-like sequences in SARS-CoV spike protein

Zhang

Liao

Neo

et al. 2018

The International Journal of Biochemistry & Cell Biology

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Self-binding peptides containing zipper-like sequences, such as the Leu/Ile zipper sequence within the coiled coil regions of proteins and the cross-β spine steric zippers within the amyloid-like fibrils, could bind to the protein-of-origin through homophilic sequence-specific zipper motifs. These self-binding sequences represent opportunities for the development of biochemical tools and/or therapeutics. Here, we report on the identification of a putative self-binding β-zipper-forming peptide within the severe acute respiratory syndrome-associated coronavirus spike (S) protein and its application in viral detection. Peptide array scanning of overlapping peptides covering the entire length of S protein identified 34 putative self-binding peptides of six clusters, five of which contained octapeptide core consensus sequences. The Cluster I consensus octapeptide sequence GINITNFR was predicted by the Eisenberg's 3D profile method to have high amyloid-like fibrillation potential through steric β-zipper formation. Peptide C6 containing the Cluster I consensus sequence was shown to oligomerize and form amyloid-like fibrils. Taking advantage of this, C6 was further applied to detect the S protein expression in vitro by fluorescence staining. Meanwhile, the coiled-coil-forming Leu/Ile heptad repeat sequences within the S protein were under-represented during peptide array scanning, in agreement with that long peptide lengths were required to attain high helix-mediated interaction avidity. The data suggest that short β-zipper-like self-binding peptides within the S protein could be identified through combining the peptide scanning and predictive methods, and could be exploited as biochemical detection reagents for viral infection.

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Section: Resultsmentioning

confidence: 99%

Section: Tablementioning

confidence: 99%

Identification and application of self-binding zipper-like sequences in SARS-CoV spike protein

Zhang

Liao

Neo

et al. 2018

The International Journal of Biochemistry & Cell Biology

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“…To investigate the structure-function relationship of MPER-containing peptides in inhibiting the entry of pseudo-HIV-1, the secondary structures of the peptides were determined by circular dichroism (Fig 2C). The HR2 region of another class I viral fusion glycoprotein, the spike (S) protein of the severe acute respiratory syndrome associated coronavirus (SARS-CoV), has previously been shown to be largely α-helical and a synthetic peptide (HR2-S) derived from this region served as a control peptide in the following CD study [56]. The peptides were prepared in 10% TFE that mimics the lipidic environment at the juxtamembrane junction.…”

Section: Sequence Requirements Of the Mper-containing Peptides In Inhmentioning

confidence: 99%

Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins

et al. 2015

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The membrane proximal external region (MPER) is a highly conserved membrane-active region located at the juxtamembrane positions within class I viral fusion glycoproteins and essential for membrane fusion events during viral entry. The MPER in the human immunodeficiency virus type I (HIV-1) envelope protein (Env) interacts with the lipid bilayers through a cluster of tryptophan (Trp) residues and a C-terminal cholesterol-interacting motif. The inclusion of the MPER N-terminal sequence contributes to the membrane reactivity and anti-viral efficacy of the first two anti-HIV peptidyl fusion inhibitors T20 and T1249. As a type I transmembrane protein, Env also interacts with the cellular membranes during its biosynthesis and trafficking. Here we investigated the roles of MPER membrane-active sequences during both viral entry and assembly, specifically, their roles in the design of peptidyl fusion inhibitors and the biosynthesis of viral structural proteins. We found that elimination of the membrane-active elements in MPER peptides, namely, penta Trp→alanine (Ala) substitutions and the disruption of the C-terminal cholesterol-interacting motif through deletion inhibited the anti-viral effect against the pseudotyped HIV-1. Furthermore, as compared to C-terminal dimerization, N-terminal dimerization of MPER peptides and N-terminal extension with five helix-forming residues enhanced their anti-viral efficacy substantially. The secondary structure study revealed that the penta-Trp→Ala substitutions also increased the helical content in the MPER sequence, which prompted us to study the biological relevance of such mutations in pre-fusion Env. We observed that Ala mutations of Trp664, Trp668 and Trp670 in MPER moderately lowered the intracellular and intraviral contents of Env while significantly elevating the content of another viral structural protein, p55/Gag and its derivative p24/capsid. The data suggest a role of the gp41 MPER in the membrane-reactive events during both viral entry and budding, and provide insights into the future development of anti-viral therapeutics.

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“…In this model, the stalk is highly helical, has two coiled‐coil segments, and the flexibility is mediated by the three flexible hinges (Figure 1A). 7,10,11 Previous structural studies of isolated stalk domain and its segments from SARS‐CoV, which has an identical amino acid sequence of stalk domain as SARS‐CoV‐2, have identified different coiled‐coil assemblies, indicating a potential structural polymorphism 12,13 . Here, we use a combination of spectroscopy, small‐angle X‐ray scattering (SAXS), and protein crystallography to elucidate the stability and structural properties of the spike stalk domain.…”

Section: Introductionmentioning

confidence: 99%

Structural polymorphism of coiled‐coils from the stalk domain of SARS‐CoV‐2 spike protein

et al. 2022

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Spike trimer plays a key role in SARS-CoV-2 infection and vaccine development.It consists of a globular head and a flexible stalk domain that anchors the protein into the viral membrane. While the head domain has been extensively studied, the properties of the adjoining stalk are poorly understood. Here, we characterize the coiled-coil formation and thermodynamic stability of the stalk domain and its segments. We find that the N-terminal segment of the stalk does not form coiled-coils and remains disordered in solution. The C-terminal stalk segment forms a trimeric coiled-coil in solution, which becomes significantly stabilized in the context of the full-length stalk. Its crystal structure reveals a novel antiparallel tetramer coiled-coil with an unusual combination of a-d and e-a-d hydrophobic core packing. Structural analysis shows that a subset of hydrophobic residues stabilizes different coiled-coil structures: trimer, tetramer, and heterohexamer, underscoring a highly polymorphic nature of the SARS-CoV-2 stalk sequence.

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SARS‐CoV heptad repeat 2 is a trimer of parallel helices

Cited by 5 publications

References 29 publications

Identification and application of self-binding zipper-like sequences in SARS-CoV spike protein

Identification and application of self-binding zipper-like sequences in SARS-CoV spike protein

Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins

Structural polymorphism of coiled‐coils from the stalk domain of SARS‐CoV‐2 spike protein

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