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.
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http://dx.doi.org/10.1093/glycob/cwac011 | DOI Listing |
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.
Viruses
January 2025
Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM 87131, USA.
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 PDFPlants (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 PDFNutrients
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.
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.
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