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Fig. 1 | Journal of Biomedical Science

Fig. 1

From: Dissecting the conformation of glycans and their interactions with proteins

Fig. 1

Biacore analysis, molecular docking and molecular dynamics. a For analysis of protein-glycan interactions using Biacore, recombinant protein is immobilized on the sensor chip. Generally, the carboxyl groups on CM5 chips, which are made of carboxymethyl-dextran matrix, are activated by EDC (1-ethyl-3-[3-dimethylaminopropyl]-carbodiimide hydrochloride) and NHS (N-hydroxysuccinimide). Subsequently, the primary amines on the protein form amide linkages with these activated carboxyl groups, followed by deactivation using ethanolamine. Therefore, the Biacore system can detect the association and dissociation of glycan molecules that interact with the proteins on the sensor chip. b Molecular docking programs can randomly generate conformers of glycans and proteins, and this is followed by assembly and scoring of their complex structures. Binding analysis for the top rank complexes, which are predicted by good scores, is useful for prediction of glycan-binding sites with various types of molecular interactions. c The conformational energies of glycan (solid line) vary with the glycosidic angles. The conformers of glycans (histograms) found within database of protein-glycan complexes are mainly distributed at the low energy states. d Molecular dynamics software can generate low energy conformers of a glycan molecule by simulation of its molecular motion in solution. e The low energy glycan conformer is then used to simulate the formation of the protein-glycan complex. The molecular interactions and stabilities of these complexes can thus be evaluated by methods such as calculation of RMSD and H-bonds

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