ArticleThe journal of physical chemistry. B2011
Influence of solvent and intramolecular hydrogen bonding on the conformational properties of o-linked glycopeptides.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 60 citations in OpenAlex.
- Deciphering How Clustered O‑Glycosylation Shapes Substrate-Binding Preferences in an Intrinsically Disordered Protein Region.JACS Au · 2026Article
- Chemical synthesis uncovers the significant impact of natural glycosylation on islet amyloid polypeptide aggregation.Science advances · 2025Article
- Exploring the Conformational Changes and Dynamics of Mucins in Their Free State and in Complex with Mucin-Binding Proteins Using NMR.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Intramolecular interactions (O-H∙∙∙O, C-H∙∙∙N, N-H∙∙∙π) in isomers of neutral, cation, and anion dopamine molecules: A DFT study on the influence of solvents (water and ethanol).Journal of molecular modeling · 2023Article
- Article
- Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins.International journal of molecular sciences · 2021Article
- Synthesis ofTetrahedron letters · 2021Article
- Contrasting the conformational effects of α-O-GalNAc and α-O-Man glycan protein modifications and their impact on the mucin-like region of alpha-dystroglycan.Glycobiology · 2021Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- Drude Polarizable Force Field Parametrization of Carboxylate andJournal of chemical theory and computation · 2019Article
- Structural Aspects of the O-glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments.Chemphyschem : a European journal of chemical physics and physical chemistry · 2019Article
- Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP).Beilstein journal of organic chemistry · 2019Article
- Force Fields for Small Molecules.Methods in molecular biology (Clifton, N.J.) · 2019Article
- A Novel Integrated Way for Deciphering the Glycan Code for the FimH Lectin.Molecules (Basel, Switzerland) · 2018Article
- Mutation of Tyr137 of the universalIUCrJ · 2017Article
- Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.Physical chemistry chemical physics : PCCP · 2016Article
- Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae.Molecular & cellular proteomics : MCP · 2016Article
- An Unusual Carbohydrate Conformation is Evident in Moraxella catarrhalis Oligosaccharides.Molecules (Basel, Switzerland) · 2015Article
- Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.Journal of chemical theory and computation · 2015Article
- Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM).Journal of chemical theory and computation · 2015Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
A detailed investigation of the conformational properties of all the biologically relevant O-glycosidic linkages using the Hamiltonian replica exchange (HREX) simulation methodology and the recently developed CHARMM carbohydrate force field parameters is presented. Fourteen biologically relevant O-linkages between the five sugars N-acetylgalactosamine (GalNAc), N-acetylglucosamine (GlcNAc), D-glucose (Glc), D-mannose (Man), and L-fucose (Fuc) and the amino acids serine and threonine were studied. The force field was tested by comparing the simulation results of the model glycopeptides to various NMR (3)J coupling constants, NOE distances, and data from molecular dynamics with time-averaged restraints (tar-MD). The results show the force field to be in overall agreement with experimental and previous tar-MD simulations, although some small limitations are identified. An in-depth hydrogen bond and bridging water analysis revealed an interplay of hydrogen bonding and bridge water interactions influencing the geometry of the underlying peptide backbone, with the O-linkages favoring extended β-sheet and polyproline type II (PPII) conformations over the compact α(R)-helical conformation. The newly developed parameters were also able to identify hydrogen bonding and water mediated interactions between O-linked sugars and proteins. These results indicate that the newly developed parameters in tandem with HREX conformational sampling provide the means to study glycoproteins in the absence of targeted NMR restraint data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.