ArticleGlycobiology2016
Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins.
Article in Glycobiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 39 citations in OpenAlex.
- Directional information flow as a tool for analyzing protein allostery.bioRxiv : the preprint server for biology · 2026Article
- Effect of glycosylation on protein folding: From biological roles to chemical protein synthesis.iScience · 2025Review
- Gas Phase Conformation of Trisaccharides and Core Pentasaccharide: A Three-Step Tree-Based Sampling and Quantum Mechanical Computational Approach.Molecules (Basel, Switzerland) · 2023Article
- Lectins as potential tools for cancer biomarker discovery from extracellular vesicles.Biomarker research · 2023Review
- Discovery of indole-modified aptamers for highly specific recognition of protein glycoforms.Nature communications · 2021Article
- Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition.Scientific reports · 2020Article
- Dissecting the conformation of glycans and their interactions with proteins.Journal of biomedical science · 2020Review
- Structural base for the transfer of GPI-anchored glycoproteins into fungal cell walls.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Analysis of the SARS-CoV-2 spike protein glycan shield: implications for immune recognition.bioRxiv : the preprint server for biology · 2020Article
- Article
- CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates.Glycobiology · 2019Article
- Predicting the Structures of Glycans, Glycoproteins, and Their Complexes.Chemical reviews · 2018Review
- Article
- Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank.Bioinformatics (Oxford, England) · 2017Article
- Conformational Heterogeneity of the HIV Envelope Glycan Shield.Scientific reports · 2017Article
- Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.PLoS computational biology · 2017Article
- Replica exchange molecular dynamics simulations reveal the structural and molecular properties of levan-type fructo-oligosaccharides of various chain lengths.BMC bioinformatics · 2016Article
- Roles of glycans in interactions between gp120 and HIV broadly neutralizing antibodies.Glycobiology · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
N-linked glycans are on protein surfaces and have direct and water/ion-mediated interactions with surrounding amino acids. Such contacts could restrict their conformational freedom compared to the same glycans free in solution. In this work, we have examined the conformational freedom of the N-glycan core pentasaccharide moiety in solution using standard molecular dynamics (MD) simulations as well as temperature replica-exchange MD simulations. Both simulations yield the comparable conformational variability of the pentasaccharide in solution, indicating the convergence of both simulations. The glycoprotein crystal structures are analyzed to compare the conformational freedom of the N-glycan on the protein surface with the simulation result. Surprisingly, the pentasaccharide free in solution shows more restricted conformational variability than the N-glycan on the protein surface. The interactions between the carbohydrate and the protein side chain appear to be responsible for the increased conformational diversity of the N-glycan on the protein surface. Finally, the transfer entropy analysis of the simulation trajectory also reveals an unexpected causality relationship between intramolecular hydrogen bonds and the conformational states in that the hydrogen bonds play a role in maintaining the conformational states rather than driving the change in glycosidic torsional states.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.