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Hierarchical and Programmable One-Pot Oligosaccharide Synthesis
Published on: September 6, 2019
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Shaping up for structural glycomics: a predictive protocol for oligosaccharide conformational analysis applied to
Benedict M Sattelle1, Andrew Almond1
1Faculty of Life Sciences, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK.
Carbohydrate Research
|November 21, 2013
Summary
Hardware-accelerated molecular dynamics simulations reveal microsecond motions in N-glycans, crucial for understanding inflammation and immunity. This approach predicts glycan conformational dynamics, aiding the design of novel carbohydrate-based drugs and biomaterials.
Area of Science:
- Carbohydrate Chemistry
- Structural Biology
- Computational Chemistry
Background:
- The human glycome contains vital 3D structural information for glycan recognition.
- Understanding glycan dynamics is key for designing targeted drugs and biomaterials.
Purpose of the Study:
- To predict oligosaccharide conformational populations and exchange rates at thermodynamic equilibrium.
- To model microsecond motions in N-glycans relevant to inflammation and immunity.
Main Methods:
- Hardware-accelerated aqueous molecular dynamics simulations.
- Simulations of N-glycans, including mannosyl cores and sialyl Lewis antennae.
- Analysis of 10μs and 25μs simulation data.
Main Results:
- Simulations agreed with experimental data for conformational equilibria.
- Sequence-dependent motions influence glycosidic linkage and ring flexibility.
- Microsecond timescales were required to predict rare conformational transitions.
- Sialyl Lewis structures showed rigidification, indicating potential binding signatures.
Conclusions:
- The simulation protocol provides conformational ensembles independent of initial structures.
- This method facilitates understanding of oligosaccharide recognition and structure-activity relationships.
- It offers a pathway for developing novel carbohydrate-based chemical entities.
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