Fig. 3: Molecular dynamics reveals fragmentation mechanism.
From: Predicting glycan structure from tandem mass spectrometry via deep learning
a,b, Kernel density estimate distribution of the distance between the center of geometry of the carboxyl group of the sialic acid and the hydrogen of the hydroxyl group of C6 of the terminal HexNAc residues for the closed (a) and open (b) reducing GalNAc residue for both GlcNAcβ1-3(Neu5Acα2-6)GalNAc (blue) and GalNAcα1-3(Neu5Acα2-6)GalNAc (yellow green). The plots show how in GlcNAcβ1-3(Neu5Acα2-6)GalNAc, the carboxyl group is able to interact with the hydroxyl of the C6 of the HexNAc. However, this interaction is not observed in GalNAcα1-3(Neu5Acα2-6)GalNAc. c, A representative snapshot of the structure of GlcNAcβ1-3(Neu5Acα2-6)GalNAc is shown, with the interaction between the two moieties displayed by a dashed line (orange). KDE, kernel density estimation.
