Structural and conformational dynamics of human milk oligosaccharides, lacto-N-fucopentaose I and II, through molecular dynamics simulation

Carbohydrates, also known as glycans or sugars are the nature’s most abundant biomolecules. Human breast milk contains soluble oligosaccharides that are involved in the biological recognition process. Oligosaccharides occur in numerous conformational states due to their flexible nature at glycosidic linkages. Molecular dynamics simulation is used to investigate the structural flexibility of glycosidic linkage and intramolecular interactions between molecules. The work focused on human milk oligosaccharide (HMOs), lacto-N-fucopentaose (LNFP) I and II, investigated through MD simulation for 250 ns, and its replicate. Possible conformational models for LNFP I and II were determined and deposited in the open-access database 3DSDSCAR. The structural analysis was carried out for the two HMOs with the CPPTRAJ module.