Theoretical study of hyaluronan oligosaccharides

Conformation, flexibility and hydration of hyaluronic acid by molecular dynamics simulations

Hyaluronic acid (HA) is a biopolymer of disaccharide with two alternate glycosidic bonds, β(1,3) and β(1,4). A molecular dynamics study presented here unveiled conformational variability in association with the flexibility of the glycosidic linkers, which depends on the number of disaccharide units. HA chain maintains a rigid rod-like conformation with short chain lengths. Crossover from a rod-like to a random-coil conformation is observed with increasing the chain length. The conformation with the β(1,4) linkage is more flexible than that with the β(1,3) linkage. Variation of the radius of gyration and conformational fluctuation showed that the β(1,4) linkers along with the HA chain length enhance the overall conformational flexibility and therefore elastic response of the polymer chain. Besides the inter-saccharide hydrogen bonding, Na⁺ binds preferably at the β(1,4) site. The hydration number of HA increases as an increase in the chain length. The hydration per disaccharide unit remains constant with the chain length.

Effect of solvent and ions on the structure and dynamics of a hyaluronan molecule

Hyaluronic acid (hyaluronan, HA) is a negatively charged polysaccharide forming highly swollen random coils in aqueous solutions. Their size decreases along with growing salt concentration, but the mechanism of this phenomenon remains unclear. We carry out molecular-dynamics simulations of a 48-monosaccharide HA oligomer in varying salt concentration and temperature. They identify the interaction points of Na⁺ ions with the HA chain and reveal their influence on the HA solvation-shell structure. The salt-dependent variation of the molecular size does not consist in the distribution of the dihedral angles of the glycosidic connections but is driven by the random flips of individual dihedral angles, which cause the formation of temporary hairpin-like structures effectively shortening the chain. They are induced by the frequency of cation-chain interactions that grow with the salt concentration, but is reduced by the simultaneous decrease of ions' activities. This leads to an anomalous random-coil shrinkage at 0.6 M salt concentration.

Multiscale modeling of glycosaminoglycan structure and dynamics: current methods and challenges

Glycosaminoglycans are long unbranched and complex polysaccharides that are an essential component of mammalian extracellular matrices. Characterization of their molecular structure, dynamics and interactions are essential to understand important biological phenomena in health and disease, and will lead to novel therapeutics and medical devices. However, this has proven to be a challenge experimentally and theoretical techniques are needed to develop new hypotheses, and interpret experiments. This review aims to examine the current theoretical (rather than experimental) methods used by researchers to investigate glycosaminoglycan structure, dynamics and interactions, from the monosaccharide to the macromolecular scale. It will consider techniques such as quantum mechanics, molecular mechanics, molecular dynamics, coarse graining and docking.