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

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.

Deciphering the conformational preferences of furanosides. A molecular dynamics study.

Furanoses are an important group of natural saccharides as well as the components of crucial biomolecules such as nucleic acids. Contrary to pyranoses, they exhibit much larger inherent flexibility which amplifies the difficulty in determining their conformational preferences. We carried out a series of molecular dynamics simulations oriented at systematic analysis of conformational properties of unfunctionalized furanose monosaccharides (all members of d-aldopento- and d-aldotetrofuranoses).

A GROMOS Force Field for Furanose-Based Carbohydrates.

The article describes a GROMOS force field parameter set for molecular dynamics simulations of furanose carbohydrates. The proposed united-atom force field is designed and validated with respect to the conformational properties of furanose mono-, di-, oligo-, and polymers in aqueous solvent. The set accounts for the possibility of arbitrary glycosidic linkage connectivity between units, O-alkylation, as well as of different anomery.