Conformational properties of inulin, levan and arabinan studied by molecular dynamics simulations

Abstract

Inulin, levan and arabinan are the polysaccharides that consist of exclusively furanose units. To date, their conformational features studied at the molecular scale have remained largely unexplained. To tackle this issue, we have performed a series of explicit-solvent molecular dynamics simulations, carried out within the furanose-dedicated force field. None of the polysaccharides exhibits a single, dominating structure type. Instead, they create a large number of separated conformational states originating from the intensive rotation around the φ and ω glycosidic angles. 21-helices are the preferential conformational forms for all compounds but they appear only locally, at the length of several consecutive residues. The flexibility of all three furanose-based polysaccharides is much greater in relation to the (1–4)-linked pyranose polysaccharides and is comparable to that of (1–6)-linked pyranoses. The dynamic geometries of both furanose rings and glycosidic linkages are nearly unchanged independently if considering them at the level of mono-, di- or polysaccharides.