Refining the toolkit for sugar analysis

Dance, Amber

doi:10.1038/d41586-021-03000-9

Cited by 4 publications

(5 citation statements)

References 7 publications

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“…One major obstacle in this direction is that, there is no established method to generate an antibody that recognizes a glycotope displayed on a specific protein scaffold. Technological breakthroughs and a platform enabling the development of such antibodies are highly anticipated (43).…”

Section: Discussionmentioning

confidence: 99%

Recent Progress in the Methodologies to Identify Physiological Ligands of Siglecs

et al. 2021

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Siglecs, a family of receptor-like lectins, recognize glycoproteins and/or glycolipids containing sialic acid in the extracellular space and transduce intracellular signaling. Recently, researchers uncovered significant contributions of Siglecs in cancer immunity, renewing interest in this family of proteins. Previous extensive studies have defined how Siglecs recognize glycan epitopes (glycotopes). Nevertheless, the biological role of these glycotopes has not been fully evaluated. Recent studies using live cells have begun unraveling the constituents of Siglec ligands. These studies demonstrated that glycoprotein scaffolds (counter-receptors) displaying glycotopes are sometimes just as important as the glycotope itself. These new insights may guide future efforts to develop therapeutic agents to target the Siglec – ligand axis.

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Section: Discussionmentioning

confidence: 99%

Recent Progress in the Methodologies to Identify Physiological Ligands of Siglecs

et al. 2021

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“…The negative effects of antibiotics are taken into serious consideration because of their inducement of long-term microbiota change, allergic symptoms, metabolic, immunological and inammatory dysfunctions. 4 As a vegetable, jute leaves are traditionally used to treat constipation, dysentery and dyspepsia. 22 Therefore, the potential biological protective effects of jute NCC on human gut bacteria were investigated.…”

Section: Protective Function Of Ncc On Human Gut Bacteria In Vitromentioning

confidence: 99%

“…There was another report that some plant functional components taken regularly might protect bacteroides species in human gut microbiota from erythromycin more effectively. 4 However, kanamycin treatment inhibited the growth of L. rhamnosus but did not kill the cell. A high concentration of jute cellulose (5 and 50 mg mL −1 ) signicantly inhibited the growth of L. rhamnosus under kanamycin treatment, while a high NCC concentration of 50 mg mL −1 had a slight potential protection effect on L. rhamnosus under kanamycin treatment at the time points of 8, 16, 24, and 32 h (P < 0.05) (Fig.…”

Section: Protective Function Of Ncc On Human Gut Bacteria In Vitromentioning

confidence: 99%

“…3 The collateral damage to intestinal microbiota caused by antibiotics has recently received increasing attention. 4 Some studies have highlighted the interaction between antibioticinduced long-term microbiota changes and various allergic, metabolic, immunological, and inammatory dysfunctions. [5][6][7] The gut microbial diversity is reduced aer ingesting antibiotics, and full restoration of the original bacterial community is rarely achieved.…”

Section: Introductionmentioning

confidence: 99%

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Dual roles of nanocrystalline cellulose extracted from jute (Corchorus olitorius L.) leaves in resisting antibiotics and protecting probiotics

Deng,

Pan,

Yang

et al. 2023

Nanoscale Adv.

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“…Yet remarkable advances are continuously made in the development of new high-precision tools and techniques [16][17][18][19][20][21][22][23][24][25][26] that allow us to shed light on different aspects of the glycome. Within this framework, the potentials of glycobioinformatics [27][28][29][30][31][32] databases and resources and of high-performance computing (HPC) molecular simulations 7,8 are extraordinary, especially within a context where information from multiple sources is required to decipher the GlycoCode 33 . Here we introduce GlycoShape (https://glycoshape.org) an open access (OA) web-based platform designed to supplement the missing 3D structural information on glycans and glycoproteins, leveraging on over 1 ms of molecular dynamics (MD) simulations ran in dilute solution at standard conditions of temperature, pressure and salt concentration.…”

Section: Introductionmentioning

confidence: 99%

Restoring Protein Glycosylation with GlycoShape

Ives,

Singh,

D’Andrea

et al. 2023

Preprint

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During the past few years, we have been witnessing a revolution in structural biology. Leveraging on technological and computational advances, scientists can now resolve biomolecular structures at the atomistic level of detail by cryogenic electron microscopy (cryo-EM) and predict 3D structures from sequence alone by machine learning (ML). One technique often supports the other to provide the view of atoms in molecules required to capture the function of molecular machines. An example of the extraordinary impact of these advances on scientific discovery and on public health is given by how structural information supported the rapid development of COVID-19 vaccines based on the SARS-CoV-2 spike (S) glycoprotein. Yet, none of these new technologies can capture the details of the dense coat of glycans covering S, which is responsible for its natural, biologically active structure and function and ultimately for viral evasion. Indeed, glycosylation, the most abundant post-translational modification of proteins, is largely invisible through experimental structural biology and in turn it cannot be reproduced by ML, because of the lack of data to learn from. Molecular simulations through high-performance computing (HPC) can fill this crucial information gap, yet the computational resources, the users’ skills and the long timescales involved limit applications of molecular modelling to single study cases. To broaden access to structural information on glycans, here we introduce GlycoShape (https://glycoshape.org) an open access (OA) glycan structure database and toolbox designed to restore glycoproteins to their native functional form by supplementing the structural information available on proteins in public repositories, such as the RCSB PDB (www.rcsb.org) and AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/), with the missing glycans derived from over 1 ms of cumulative sampling from molecular dynamics (MD) simulations. The GlycoShape Glycan Database (GDB) currently counts over 435 unique glycans principally covering the human glycome and with additional structures, fragments, and epitopes from other eukaryotic and prokaryotic organisms. The GDB feeds into Re-Glyco, a bespoke algorithm in GlycoShape designed to rapidly restore the natural glycosylation to protein 3D structures and to predictN-glycosylation occupancy, where unknown. Ultimately, integration of GlycoShape with other OA protein structure databases can provide a step-change in scientific discovery, from the structural and functional characterization of the active form of biomolecules, all the way down to pharmacological applications and drug discovery.

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Refining the toolkit for sugar analysis

Cited by 4 publications

References 7 publications

Recent Progress in the Methodologies to Identify Physiological Ligands of Siglecs

Recent Progress in the Methodologies to Identify Physiological Ligands of Siglecs

Dual roles of nanocrystalline cellulose extracted from jute (Corchorus olitorius L.) leaves in resisting antibiotics and protecting probiotics

Restoring Protein Glycosylation with GlycoShape

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