Carbohydrate Structure Database oligosaccharide conformation tool.

Glycobiology

Laboratory of carbohydrate chemistry and biocides, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, Moscow 119991, Russia.

Published: May 2022

Population analysis in terms of glycosidic torsion angles is frequently used to reveal preferred conformers of glycans. However, due to high structural diversity and flexibility of carbohydrates, conformational characterization of complex glycans can be a challenging task. Herein, we present a conformation module of oligosaccharide fragments occurring in natural glycan structures developed on the platform of the Carbohydrate Structure Database. Currently, this module deposits free energy surface and conformer abundance maps plotted as a function of glycosidic torsions for 194 "inter"residue bonds. Data are automatically and continuously derived from explicit-solvent molecular dynamics (MD) simulations. The module was also supplemented with high-temperature MD data of saccharides (2,403 maps) provided by GlycoMapsDB (hosted by GLYCOSCIENCES.de project). Conformational data defined by up to 4 torsional degrees of freedom can be freely explored using a web interface of the module available at http://csdb.glycoscience.ru/database/core/search_conf.html.

Download full-text PDF

Source
http://dx.doi.org/10.1093/glycob/cwac011DOI Listing

Publication Analysis

Top Keywords

carbohydrate structure
8
structure database
8
database oligosaccharide
4
oligosaccharide conformation
4
conformation tool
4
tool population
4
population analysis
4
analysis terms
4
terms glycosidic
4
glycosidic torsion
4

Similar Publications

Hydroxyapatite Chitosan Gradient Pore Scaffold Activates Oxidative Phosphorylation Pathway to Induce Bone Formation.

Front Biosci (Landmark Ed)

January 2025

Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory of Stomatology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, 350005 Fuzhou, Fujian, China.

Background: In this study, we prepared a porous gradient scaffold with hydroxyapatite microtubules (HAMT) and chitosan (CHS) and investigated osteogenesis induced by these scaffolds.

Methods: The arrangement of wax balls in the mold can control the size and distribution of the pores of the scaffold, and form an interconnected gradient pore structure. The scaffolds were systematically evaluated and for biocompatibility, biological activity, and regulatory mechanisms.

View Article and Find Full Text PDF

Interactions between bacteriophages with mammalian immune cells are of great interest and most phages possess at least one molecular pattern (nucleic acid, sugar residue, or protein structure) that is recognizable to the immune system through pathogen associated molecular pattern (PAMP) receptors (i.e., TLRs).

View Article and Find Full Text PDF

Application of Biochar-Immobilized for Enhancing Phosphorus Uptake and Growth in Rice.

Plants (Basel)

January 2025

State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.

Phosphorus (P) is an essential nutrient for rice growth, and the presence of phosphate-solubilizing bacteria (PSB) is an effective means to increase soil P content. However, the direct application of PSB may have minimal significance due to their low survival in soil. Biochar serves as a carrier that enhances microbial survival, and its porous structure and surface characteristics ensure the adsorption of .

View Article and Find Full Text PDF

Profiles of 71 Human Milk Oligosaccharides and Novel Sub-Clusters of Type I Milk: Results from the Ulm SPATZ Health Study.

Nutrients

January 2025

Pediatric Epidemiology, Department of Pediatrics, Medical Faculty, Leipzig University, Liebigstr 20a, Haus 6, 04103 Leipzig, Germany.

Background/objectives: Although approximately 160 human milk oligosaccharides (HMOs) have been identified, current studies on HMO quantitation are limited to the 10-19 most abundant HMOs. We assessed the variations in the relative concentrations of 71 HMO structures over lactation in human milk samples by an advanced liquid chromatography-mass spectrometry approach.

Methods: Samples were collected from 64 mothers at 6 weeks, 6 months, and 12 months of lactation in the Ulm SPATZ Health Study, a German birth cohort.

View Article and Find Full Text PDF

Polysaccharide Modulates Characteristic Bacteria and Metabolites, Improving the Immune Function of Healthy Mice.

Nutrients

January 2025

State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China.

Objectives: Polysaccharides from are known to have several bioactive effects. Previous studies have found that low-molecular-weight polysaccharide (GP1) is degraded by and promotes the production of beneficial bacteria and metabolites, which improves immune disorder and intestinal injury, and then enhances the body's immune regulation ability. However, the immune regulation effect of GP1 on a healthy body has not been studied.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!