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Analysis of SARS-CoV-2 S and human ACE2 protein by LC-MS

ABSTRACT: Analysis of intact N-linked glycopeptides for SARS-Cov-2 S and huamn ACE2 protein by LC-MS

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Severe Acute Respiratory Syndrome Coronavirus 2

TISSUE(S): Epithelial Cell

SUBMITTER: Peng Zhao

LAB HEAD: Lance Wells

PROVIDER: PXD019937 | Pride | 2020-09-09

REPOSITORIES: Pride

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Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor.

Zhao Peng P Praissman Jeremy L JL Grant Oliver C OC Cai Yongfei Y Xiao Tianshu T Rosenbalm Katelyn E KE Aoki Kazuhiro K Kellman Benjamin P BP Bridger Robert R Barouch Dan H DH Brindley Melinda A MA Lewis Nathan E NE Tiemeyer Michael M Chen Bing B Woods Robert J RJ Wells Lance L

Cell host & microbe 20200824 4

The SARS-CoV-2 betacoronavirus uses its highly glycosylated trimeric Spike protein to bind to the cell surface receptor angiotensin converting enzyme 2 (ACE2) glycoprotein and facilitate host cell entry. We utilized glycomics-informed glycoproteomics to characterize site-specific microheterogeneity of glycosylation for a recombinant trimer Spike mimetic immunogen and for a soluble version of human ACE2. We combined this information with bioinformatics analyses of natural variants and with existi ...[more]

PMID: 32841605

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Analysis of SARS-CoV-2 S and human ACE2 protein by LC-MS

Project description:Analysis of deglycosylated N-linked glycopeptides for SARS-Cov-2 S and human ACE2 protein by LC-MS

2020-09-09 | PXD019938 | Pride

Re-analysis of glycoproteomics data with Glyco-Decipher

Project description:Reanalysis of submissions PXD005411, PXD005413, PXD005412, PXD005553, PXD005555, PXD005565 and PXD019937 using Glyco-Decipher. Identification results of peptide-spectrum matches supporting Glyco-Decipher manuscript (Glyco-Decipher: glycan database-independent peptide matching enables discovery of new glycans and in-depth characterization of site-specific N-glycosylation). Recently, several elegant bioinformatics tools have been developed to identify glycopeptides from tandem mass spectra for site-specific glycoproteomics studies. These glycan database-dependent tools have substantially improved glycoproteomics analysis but fail to identify glycopeptides with unexpected glycans. We present a platform called Glyco-Decipher to interpret the glycoproteomics data of N-linked glycopeptides. It adopts a glycan database-independent peptide matching scheme that allows the unbiased profiling of glycans and the discovery of new glycans linked with modifications. Reanalysis of several large-scale datasets showed that Glyco-Decipher outperformed the open search method in glycan blind searching and the popular glycan database-dependent software tools in glycopeptide identification. Our glycan database-independent search also revealed that modified glycans are responsible for a large fraction of unassigned glycopeptide spectra in shotgun glycoproteomics.

2022-03-04 | PXD031032 | Pride

Analysis of SARS-CoV-2 S and human ACE2 protein by LC-MS

Project description:Analysis of intact O-linked glycopeptides for SARS-Cov-2 S and human ACE2 protein by LC-MS

2020-09-09 | PXD019940 | Pride

RNAseq analyses in HEK293T-ACE2 cells infected with SARS-CoV-2 (VOC Delta, 24hours) vs untreated cells

Project description:In this study a gene expression (i.e., RNAseq) analysis was performed in HEK293T-ACE2 cellular model upon infection with viral particle belonging to VOC Delta (MOI: 0.026) for 24 hours in order to have a global picture of the transcriptome landscape in response to early phase of infection of SARS-CoV-2 ( VOC Delta infection and to evaluate the role of Ca2+ in HEK293-ACE2 cellular model and transfer to homeostasis in SARS-COV-2 patients (by Pasqualino de Antonellis1-2* and Veronica Ferrucci 1-2* (first authors) et al. and Massimo Zollo1-2# (corresponding author). Manuscript in preparation 2022 July 15th 2022. Short title "ATP2B1 (PMCA1), regulated by FOXO3, influences susceptibility to severe COVID19".

2022-12-01 | E-MTAB-11973 | biostudies-arrayexpress

Analysis of SARS-CoV-2 S protein by LC-MS

Project description:Analysis of disulfide bonds for SARS-Cov-2 S protein by LC-MS

2020-09-09 | PXD019939 | Pride

Analysis of SARS-CoV-2 S protein by LC-MS

Project description:Analysis of disulfide bonds for SARS-Cov-2 S protein by LC-MS

2021-06-08 | PXD026560 | Pride

Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein: HDX-MS analysis of the spike of alpha, beta, delta and omicron variants - in apo state and in complex with the ACE2 receptor

Project description:The spike glycoprotein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates binding to the ACE2 receptor 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 different opening probabilities, increased SARS-CoV-2 virulence and immune evasion. Here, using hydrogen-deuterium exchange mass spectrometry (HDX-MS), we analyzed the spike of the original Wuhan isolate, G614 mutant, spike of alpha, beta, delta and omicron VOCs and the isolated ancestral receptor binding domain (RBD) - in apo state and in complex with the ACE2 receptor. We identified changes in spike dynamics that we associated with the transition from closed to open conformation, 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 a strong ACE2 binding increases the dynamics of their core helices, priming spikes for fusion. Conversely, substitutions in omicron spike lead to predominantly binding-incompetent 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.

2023-03-15 | PXD039762 | Pride

MDM2 influences ACE2 stability and SARS-Cov2 uptake

Project description:The Angiotensin-converting enzyme 2 (ACE2) receptor is the central entry point for SARS-Cov2. Several SAR-Cov2 substrains have developed mutations in their spike protein to maximize their use of ACE2, e.g. to strengthen ACE2 binding for increased uptake or adapt to specific amino acid properties of ACE2 to cross the species barrier. But little is known about the effect of host regulators on ACE2 and subsequently their impact on SARS-Cov2 infection. Here we identify the E3 ligase MDM2 as a ACE2 modulator. The knockout of MDM2 induced a strong pro-viral effect specific for SARS-Cov2 and we could see the increase of ACE2 levels. This effect is likely dependent on the ubiquitination site Lysine 788, which MDM2 uses to induce proteasomal degradation of ACE2. Substituting this amino acid led to increased ACE2 levels and increased SARS-CoV2 infection facilitated by enhanced SARS-Cov2 uptake.

2023-09-08 | PXD040891 | Pride

Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein: HDX-MS analysis of the spike of the original Wuhan isolate, G614 spike mutant, and the isolated ancestral RBD - in apo state and in complex with the ACE2 receptor

2023-03-15 | PXD039760 | Pride

SARS-CoV-2 S protein ACE2 interaction reveals novel allosteric targets

Project description:SARS-CoV-2 spike protein binding to receptor ACE2 allosterically enhances furin proteolysisat distal S1/S2 cleavage sites

2021-08-09 | PXD023138 | Pride