ReviewBiophysical reviews2012
Conformational flexibility of N-glycans in solution studied by REMD simulations.
Review in Biophysical reviews, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 43 citations in OpenAlex.
- Towards a molecular picture of the archaeal cell surface.Nature communications · 2024Article
- Biomolecular Recognition of the Glycan Neoantigen CA19-9 by Distinct Antibodies.Journal of molecular biology · 2021Article
- Identification of Isomeric N-Glycans by Conformer Distribution Fingerprinting using Ion Mobility Mass Spectrometry.Chemistry (Weinheim an der Bergstrasse, Germany) · 2021Article
- Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase.Biophysical journal · 2020Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- Investigating Conformational Dynamics of Lewis Y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics.ACS omega · 2020Article
- Structural and Functional Insights into GluK3-kainate Receptor Desensitization and Recovery.Scientific reports · 2019Article
- Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa.Scientific reports · 2017Article
- 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
- Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.Physical chemistry chemical physics : PCCP · 2016Article
- 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
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-glycan recognition regulates a wide range of biological and pathogenic processes. Conformational diversity of glycans in solution is apparently incompatible with specific binding to their receptor proteins. One possibility is that among the different conformational states of a glycan, only one conformer is utilized for specific binding to a protein. However, the labile nature of glycans makes characterizing their conformational states a challenging issue. All-atom molecular dynamics (MD) simulations provide the atomic details of glycan structures in solution, but fairly extensive sampling is required for simulating the transitions between rotameric states. This difficulty limits application of conventional MD simulations to small fragments like di- and tri-saccharides. Replica-exchange molecular dynamics (REMD) simulation, with extensive sampling of structures in solution, provides a valuable way to identify a family of glycan conformers. This article reviews recent REMD simulations of glycans carried out by us or other research groups and provides new insights into the conformational equilibria of N-glycans and their alteration by chemical modification. We also emphasize the importance of statistical averaging over the multiple conformers of glycans for comparing simulation results with experimental observables. The results support the concept of "conformer selection" in protein-glycan recognition.
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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.