Inclusion of deuterated glycopeptides provides increased sequence coverage in hydrogen/deuterium exchange mass spectrometry analysis of SARS‐CoV‐2 spike glycoprotein

Rapid Communications in Mass Spectrometry, Год журнала: 2024, Номер 38(5)

Опубликована: Янв. 16, 2024

Rationale Hydrogen/deuterium exchange mass spectrometry (HDX‐MS) can provide precise analysis of a protein's conformational dynamics across varied states, such as heat‐denatured versus native protein structures, localizing regions that are specifically affected by conditional changes. Maximizing sequence coverage provides high confidence interest were located HDX‐MS, but one challenge for complete is N‐glycosylation sites. The deuteration peptides post‐translationally modified asparagine‐bound glycans (glycopeptides) has not always been identified in previous reports HDX‐MS analyses, causing significant gaps heavily glycosylated proteins and uncertainty structural many throughout glycoprotein. Methods We detected deuterated glycopeptides with Tribrid Orbitrap Eclipse spectrometer performing data‐dependent acquisition. An MS scan was used to identify precursor ions; if high‐energy collision‐induced dissociation MS/MS the indicated oxonium ions diagnostic complex glycans, then electron transfer low‐energy scans asparagine residue glycan's mass. As traditional analyzed at level samples labeled D 2 O. Results report SARS‐CoV‐2 spike ectodomain its trimeric prefusion form, which 22 predicted sites per monomer, without heat treatment. calculated their average isotopic shifts from deuteration. Inclusion increased 76% 84%, demonstrated had deuterated, improved results rearrangements. Conclusion improves glycoproteins viral surface antigens cellular receptors.

Язык: Английский

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Fc-independent SARS-CoV-2 infection-enhancing antibodies decouple N-terminal and receptor-binding domains by cross-linking neighboring spikes

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 21, 2024

Abstract Antibody dependent enhancement (ADE) is a serious concern in vaccine development. The canonical ADE pathways are on the fragment crystallizable (Fc) region of antibody. In SARS-CoV-2 several antibodies have been discovered that inflict vitro. These target N-terminal domain (NTD) spike protein. We previously proposed these NTD-targeting infection-enhancing (NIEAs) cross-link neighboring proteins via their NTDs, and this results decoupling between NTD receptor binding (RBD), facilitating “RBD down” to “up” transition. study we present combination molecular dynamics simulations cryogenic electron microscopy data that, together, demonstrate NIEAs indeed able proteins, cross-linking RBD domains. findings provide support for an Fc independent pathway not only relevant but also other viruses which undergo conformational change upon host cell entry.

Язык: Английский

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The first report of SARS-CoV-2 genome in the groundwater of Tehran, Iran: A call to action for public health

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Сен. 9, 2024

A pandemic of acute respiratory disease referred to as COVID-19 has been caused by the highly infectious and transmissible Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which threatened human health. Although SARS-CoV-2 RNA found in wastewater from numerous regions different countries due fecal shedding infected individuals, there is still little information available regarding how prevalent it other water matrices especially groundwater, where some areas rely on supply drinking water, irrigation farmlands, purposes. This study attempted assess presence this virus genome groundwater samples Tehran, Iran. These were collected seasonally 12 sites over years period (2021–2023). At first, a adsorption-elution (VIRADEL) concentration procedure was tested utilizing an avian coronavirus (infectious bronchitis virus, IBV) process control followed extraction. Subsequently, quantified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detect E S genes. As result, detected 1 out 96 with 2/53 × 103 3/16 copies/l for genes, respectively. Furthermore, positive sample subjected semi-nested PCR targeting partial gene, direct sequencing, phylogenetic mutation analysis. BA.1 Omicron only identified variant during study. findings show important water-based epidemiology monitor at community-level subsequent exposure, even when prevalence low.

Язык: Английский

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Application of HDX–MS for the Structural Characterization of Glycoproteins

Royal Society of Chemistry eBooks, Год журнала: 2024, Номер unknown, С. 300 - 314

Опубликована: Окт. 16, 2024

Glycosylation is one of the most common and complex post-translational modifications proteins, rendering many proteins evasive to structural analysis. The intrinsic heterogeneity flexibility pose major challenges for traditional elucidation tools. Hydrogen/deuterium exchange coupled mass spectrometry (HDX–MS) an increasingly widespread tool monitoring protein dynamics, including glycoproteins their interactions in fully glycosylated states. Recent advances have largely alleviated historical applying HDX–MS enable in-depth characterization even pinpoint local effects glycosylation.

Язык: Английский

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Inclusion of glycopeptides in hydrogen/deuterium exchange mass spectrometry analysis of SARS-CoV-2 spike ectodomain provides in-creased sequence coverage

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Июнь 15, 2023

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) can provide precise analysis of a protein’s conformational dynamics across varied states, such as heat-denatured vs. native protein structures, localizing regions that are specifically affected by conditional changes. Maximizing sequence coverage provides high confidence interest were located HDX-MS, but one challenge for complete is N-glycosylation sites. The deuteration glycopeptides has not always been identified in previous reports HDX-MS analyses, causing significant gaps heavily glycosylated proteins and uncertainty structural many throughout glycoprotein. We report the SARS-CoV-2 spike ectodomain its trimeric pre-fusion form, which 22 predicted sites per monomer, with without heat treatment. calculated their isotopic shifts from deuteration. Inclusion deu-terated increased 76% to 84%, demonstrated had deuterated, improved results re-arrangements. deuterated improves glycoproteins viral surface antigens cellular receptors. Abstract Figure

Язык: Английский

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