Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services

López, Rodrigo; Cowley, Andrew Peter; Li, Weizhong; McWilliam, Hamish

doi:10.1002/cpbi.74

Cited by 40 publications

(25 citation statements)

References 47 publications

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“…Occupancy of each O-linked glycosylation site was calculated using spectral counts assigned to any glycosylated peptides and their unmodified counterparts from searches without MS/MS filtering.Sequence Analysis of SARS-CoV-2 S and Human ACE2 ProteinsThe genomes of SARS-CoV as well as bat and pangolin coronavirus sequences reported to be closely related to SARS-CoV-2 were downloaded from NCBI. The S protein sequences from all of those genomes were aligned using EMBOSS needle v6.6.0 (61) via the EMBL-EBI provided web service(69). Manual analysis was performed in the regions containing canonical Nglycosylation sequons (N-X-S/T).…”

mentioning

confidence: 99%

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

Zhao

Praissman

Grant

et al. 2020

Preprint

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SUMMARYThe current COVID-19 pandemic is caused by the SARS-CoV-2 betacoronavirus, which utilizes its highly glycosylated trimeric Spike protein to bind to the cell surface receptor 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 bioinformatic analyses of natural variants and with existing 3D-structures of both glycoproteins to generate molecular dynamic simulations of each glycoprotein alone and interacting with one another. Our results highlight roles for glycans in sterically masking polypeptide epitopes and directly modulating Spike-ACE2 interactions. Furthermore, our results illustrate the impact of viral evolution and divergence on Spike glycosylation, as well as the influence of natural variants on ACE2 receptor glycosylation that, taken together, can facilitate immunogen design to achieve antibody neutralization and inform therapeutic strategies to inhibit viral infection.

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mentioning

confidence: 99%

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

Zhao

Praissman

Grant

et al. 2020

Preprint

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“…Open source Python modules with in-house scripts were used to test for associations (statsmodel v0.11), to filter differentially enrichment peptides and to perform different statistical tests (sklearn v0.23, scipy v1.14.1). Multiple sequence alignments were done using the MAFFT [73,74] via EMBL-EBI's web services and Java Alignment Viewer (Jalview) for visualization [75]. Residue-wise linear B cell epitopes were predicted using BepiPred-2.0 [76].…”

Section: Softwarementioning

confidence: 99%

Distinct antibody repertoires against endemic human coronaviruses in children and adults

Khan

Rahman

Ali

et al. 2020

Preprint

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19Four endemic human coronaviruses (HCoVs) are commonly associated with acute respiratory 20 infection in humans but immune responses to these "common cold" viruses remain 21 incompletely understood. Moreover, there is evidence emerging from independent studies 22 which suggests that endemic HCoVs can induce broadly cross-reactive T cell responses and 23 may thereby affect clinical outcomes of acute infections with the phylogenetically related 24 epidemic viruses, namely MERS-CoV and SARS-CoV-2. Here we report a comprehensive 25 retrospective analysis of CoV-specific antibody specificities in a large number of samples from 26 children and adults using Phage-Immunoprecipitation Sequencing (PhIP-Seq). We estimate 27 the seroprevalence for endemic HCoVs to range from ~4% to ~27% depending on species and 28 cohort. Most importantly, we identified a large number of novel linear B cell epitopes of HCoV 29 proteins and demonstrate that antibody repertoires against endemic HCoVs are qualitatively 30 different in children in comparison to the general adult population and healthy adult blood 31 bank donors. We show that anti-HCoV IgG specificities more frequently found among children 32 target functionally important and structurally conserved regions of the HCoV spike and 33 nucleocapsid proteins and some antibody specificities are broadly cross-reactive with 34 peptides of epidemic human and non-human coronavirus isolates. Our findings shed light on 35 the humoral immune responses to natural infection with endemic HCoVs and may have 36 important implications for understanding of the highly variable clinical outcomes of human 37 coronavirus infections, for the development of prophylactic or therapeutic monoclonal 38 antibodies and vaccine design. 39 parainfluenza viruses (HPIVs), albeit with differences in seasonality and prevalence of the 48 viruses depending on the species [5-7]. In addition to the four endemic HCoV, three epidemic 49 coronaviruses (CoVs) have emerged in humans over the last two decades, including Severe 50 Acute Respiratory Syndrome-associated CoV (SARS-CoV) [8], Middle East Respiratory 51

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“…To provide an integrative annotation of known phosphoproteins and p-sites, we provided a variety of cross-references to public data sources. For example, gene and protein names were taken mainly from UniProt 24 , whereas corresponding accession numbers were integrated from UniProt 24 , Ensembl 33 , EMBL 34 , KEGG 35 and NCBI GenBank 36 . Moreover, functional descriptions, protein/ nucleotide sequences, and keywords were derived from UniProt 24 to provide the basic information for each phosphoprotein entry, while the primary references with PMIDs were provided for each p-site.…”

Section: Distribution Of Phosphoproteins and P-sites For Different Rementioning

confidence: 99%

dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes

et al. 2020

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In prokaryotes, protein phosphorylation plays a critical role in regulating a broad spectrum of biological processes and occurs mainly on various amino acids, including serine (S), threonine (T), tyrosine (Y), arginine (R), aspartic acid (D), histidine (H) and cysteine (C) residues of protein substrates. Through literature curation and public database integration, here we reported an updated database of phosphorylation sites (p-sites) in prokaryotes (dbPSP 2.0) that contains 19,296 experimentally identified p-sites in 8,586 proteins from 200 prokaryotic organisms, which belong to 12 phyla of two kingdoms, bacteria and archaea. To carefully annotate these phosphoproteins and p-sites, we integrated the knowledge from 88 publicly available resources that covers 9 aspects, namely, taxonomy annotation, genome annotation, function annotation, transcriptional regulation, sequence and structure information, family and domain annotation, interaction, orthologous information and biological pathway. In contrast to version 1.0 (~30 MB), dbPSP 2.0 contains ~9 GB of data, with a 300fold increased volume. We anticipate that dbPSP 2.0 can serve as a useful data resource for further investigating phosphorylation events in prokaryotes. dbPSP 2.0 is free for all users to access at: http:// dbpsp.biocuckoo.cn.

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Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services

Cited by 40 publications

References 47 publications

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

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

Distinct antibody repertoires against endemic human coronaviruses in children and adults

dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes

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