Prediction of Glycosylation Sites in Proteins

Julenius, Karin; Johansen, M.; Brunak, Søren; Gupta, Ramneek

doi:10.1002/9780470029619.ch9

Cited by 7 publications

(2 citation statements)

References 96 publications

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“…When comparing antigen-specific plasmablast sequences, the SHM frequency full V-region was compared. N-glycan sites in the heavy and light chain variable regions were predicted by NetNGlyc 1.0 (76).…”

Section: Bioinformatic Analysis Of Ig Sequencesmentioning

confidence: 99%

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis

et al. 2023

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Periodontal disease is more common in individuals with rheumatoid arthritis (RA) who have detectable anti-citrullinated protein antibodies (ACPAs), implicating oral mucosal inflammation in RA pathogenesis. Here, we performed paired analysis of human and bacterial transcriptomics in longitudinal blood samples from RA patients. We found that patients with RA and periodontal disease experienced repeated oral bacteremias associated with transcriptional signatures of ISG15 + HLADR hi and CD48 high S100A2 pos monocytes, recently identified in inflamed RA synovia and blood of those with RA flares. The oral bacteria observed transiently in blood were broadly citrullinated in the mouth, and their in situ citrullinated epitopes were targeted by extensively somatically hypermutated ACPAs encoded by RA blood plasmablasts. Together, these results suggest that (i) periodontal disease results in repeated breaches of the oral mucosa that release citrullinated oral bacteria into circulation, which (ii) activate inflammatory monocyte subsets that are observed in inflamed RA synovia and blood of RA patients with flares and (iii) activate ACPA B cells, thereby promoting affinity maturation and epitope spreading to citrullinated human antigens.

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Section: Bioinformatic Analysis Of Ig Sequencesmentioning

confidence: 99%

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis

et al. 2023

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“…The S Protein was mutated using PyMOL59 to the D614G and A372T S protein variants. After mutation, energy minimization was performed using the OPLS3e force field.To identify glycosylation propensity and predicted glycosylated residues of the WT S Protein and the A372T mutant, the NetNGlyc 1.0 Server60 and Schrödinger-Maestro's BioLuminate (v. 2020-2) Reactive Residue package was used58,[61][62][63] . Schrödinger-Maestro's (v. 2020-2) Workspace Operations was used for glycosylation of the Asn370 with mannose, to identify various Asn370-glycan rotamers, to analyzes the surface residue properties of the WT S Protein and A372T mutant.…”

mentioning

confidence: 99%

A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation

Kang

Sharp

et al. 2021

Preprint

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While SARS-CoV-2 likely has animal origins, the viral genetic changes necessary to adapt this animal-derived ancestral virus to humans are largely unknown, mainly due to low levels of sequence polymorphism and the notorious difficulties in experimental manipulations of coronavirus genomes. We scanned more than 182,000 SARS-CoV-2 genomes for selective sweep signatures and found that a distinct footprint of positive selection is located around a non-synonymous change (A1114G; T372A) within the Receptor-Binding Domain of the Spike protein, which likely played a critical role in overcoming species barriers and accomplishing interspecies transmission from animals to humans. Structural analysis indicated that the substitution of threonine with alanine in SARS-CoV-2 concomitantly removes a predicted glycosylation site at N370, resulting in more favorable binding predictions to human ACE2, the cellular receptor. Using a novel bacteria-free cloning system for manipulating RNA virus genomes, we experimentally validated that this SARS-CoV-2-unique substitution significantly increases replication in human cells relative to its putative ancestral variant. Notably, this mutation's impact on virus replication in human cells was much more significant than that of the Spike D614G mutant, which has been widely reported to have been selected for during human-to-human transmission.

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