Glycosylation and Glycoproteins Research

The schizophrenia-associated variant in SLC39A8 alters N-glycosylation in the mouse brain

This study shows that the schizophrenia-associated SLC39A8 variant A391T alters N-glycosylation in the mouse brain, affecting glycoproteins involved in schizophrenia-related pathways.

Multi-attribute Glycan Identification and FDR Control for Glycoproteomics

The paper introduces a method to accurately identify glycan compositions in glycopeptide spectra and control false discovery rates, integrating it into a computational pipeline for glycoproteomics analysis.

Sialic acid and fucose residues on the SARS-CoV-2 receptor binding domain modulate IgG reactivity

The paper examines how carbohydrate modifications on the SARS-CoV-2 RBD affect IgG reactivity, finding that reduced sialylation and fucosylation enhance antibody binding.

The restricted nature of protein glycosylation in the mammalian brain

The paper analyzes glycosylation patterns in mouse brain regions and sexes, finding reduced complexity and minimal sex differences compared to plasma.

Intellectual disability-associated disruption of O-GlcNAcylation impairs neuronal development and cognitive function in Drosophila

This study shows that OGT mutations impair cognitive function in Drosophila by disrupting O-GlcNAcylation, and that blocking OGA can correct the deficit.

GlyNet: A Multi-Task Neural Network for Predicting Protein-Glycan Interactions

GlyNet predicts protein-glycan interactions with continuous relative binding strengths, outperforming classifiers and serving as a benchmark for quantitative glycobiology.

LectinOracle - A Generalizable Deep Learning Model for Lectin-Glycan Binding Prediction

LectinOracle predicts lectin-glycan interactions using deep learning, showing agreement with literature and generalizing to new glycans and lectins.

An insight into new glycotherapeutic in glial inflammation: Understanding the role of glycosylation from acute to chronic phase of inflammation

The paper investigates glycosylation changes in glial cells during spinal cord injury inflammation, identifying potential therapeutic targets for glycotherapeutics.

pGlycoQuant with a deep residual network for precise and minuscule-missing-value quantitative glycoproteomics enabling the functional exploration of site-specific glycosylation

pGlycoQuant is a tool for quantitative glycopeptide analysis that reduces missing values using a deep residual network, enabling site-specific glycosylation studies in hepatocellular carcinoma.

GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control

GproDIA improves glycoproteomics by enabling accurate glycopeptide identification and quantification using DIA data with comprehensive statistical control.

Attention please: modeling global and local context in glycan structure-function relationships

This paper introduces glyBERT, a deep learning model that captures local and global context in glycan structures to improve prediction and generation of glycan functional properties.

Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity

This study identifies global determinants of lectin specificity by analyzing 221 physicochemical and geometric features of lectin-glycan interactions and demonstrates predictive modeling of glycan recognition.

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design

This paper expands the Rosetta software suite with tools for glycan modeling, density fitting, and rational sequon design, achieving high accuracy in predicting and building glycan structures.

Shotgun scanning glycomutagenesis: a simple and efficient strategy for constructing and characterizing neoglycoproteins

This paper introduces a method to construct and analyze neoglycoproteins by systematically modifying glycosylation sites in proteins and assessing the effects of glycan addition.

The role of fucose-containing glycan motifs across taxonomic kingdoms

This study analyzes fucose-containing glycan motifs across taxonomic kingdoms, identifying differences in fucose usage and its role in molecular mimicry and biological processes.

Activity-dependent Golgi satellite formation in dendrites reshapes the neuronal surface glycoproteome

The paper shows that increased neuronal excitation leads to the formation of Golgi satellites in dendrites, which modify surface glycoproteins and impact neurotransmitter receptor function.

Phylogenetic evidence for asparagine to aspartic acid protein editing of N-glycosylated SARS-CoV-2 viral proteins by NGLY1 deglycosylation/deamidation suggests an unusual vaccination strategy

The paper suggests that viruses, including SARS-CoV-2, may use NGLY1/PNG-1 to edit N-glycosylated asparagines to aspartic acid, and proposes vaccinating with N to D edited viral peptides to enhance immunity.

Elevated colonic microbiota-associated paucimannosidic and truncated N-glycans in pediatric ulcerative colitis

This study identifies elevated paucimannosidic and truncated N-glycans in the microbiota of pediatric ulcerative colitis patients compared to controls, suggesting a potential role for glycan metabolism in disease pathogenesis.

GlycoSHIELD: a versatile pipeline to assess glycan impact on protein structures

GlycoSHIELD is a pipeline that grafts glycan conformers onto protein structures to model glycan impact on protein dynamics and interactions.

A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium.

This paper introduces a mass binning glycoproteomics approach to explore prokaryotic protein glycosylation, revealing unique surface layer modulation in an anammox bacterium.

A systems based framework to computationally predict putative transcription factors and signaling pathways regulating glycan biosynthesis

This paper predicts tissue-specific transcription factors and signaling pathways regulating glycan biosynthesis using multi-omics data across 29 cancer types.

Enhancing the interoperability of glycan data flow between ChEBI, PubChem, and GlyGen.

This paper describes a workflow to improve glycan data interoperability between ChEBI, PubChem, and GlyGen by integrating and prioritizing glycan annotations.

Glycowork: A Python package for glycan data science and machine learning

Glycowork is a Python package for glycan data science and machine learning, offering tools for annotation, visualization, and analysis of glycan data.

Differential expression of glycosyltransferases identified through comprehensive pan-cancer analysis

This study identifies differentially expressed glycosyltransferases across 16 cancers using a multifaceted genomics approach and integrates findings with experimental evidence.

Biomolecular recognition of the glycan neoantigen CA19-9 by distinct antibodies

The paper studies how two antibodies recognize the glycan antigen CA19-9 using crystallography and computational methods to improve antibody affinity.

A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal kingdom

The paper surveys fungal lectins through phylogenetic analysis and bioinformatics, identifying 33,485 putative lectin sequences across 1,223 fungal species.

Using Graph Convolutional Neural Networks to Learn a Representation for Glycans

This paper introduces SweetNet, a graph convolutional neural network for glycan sequence representation, showing it outperforms existing methods and predicts organismal traits and viral glycan-binding.

The medaka alg2 mutant is a model for hypo-N-glycosylation-associated retinitis pigmentosa

The paper models a hypo-N-glycosylation disorder in medaka fish, showing reduced N-glycan abundance and retinal degeneration, with mRNA rescue restoring viability.

Integration and comparison of multi-omics profiles of NGLY1 deficiency plasma and cellular models to identify clinically relevant molecular phenotypes

This study integrates metabolomics and proteomics data from NGLY1 deficiency patient samples and cellular models to identify molecular phenotypes linked to immune activation and metabolic disturbances.

Site-specific O-glycosylation analysis of SARS-CoV-2 spike protein produced in insect and human cells

The paper maps O-glycosylation sites on SARS-CoV-2 spike protein produced in insect and human cells, identifying 25 sites with distinct patterns between ectodomains and RBD.