Hyaluronan random coils in electrolyte solutions—a molecular dynamics study

A computational method of modeling random coils of hyaluronan was developed based on the molecular-dynamics simulations. An oligosaccharide of 48 monosaccharide units was equilibrated within a 70–100 ns simulation and randomly chosen pieces of this molecule from different simulation frames were combined to constitute a long polysaccharide chain, both for hyaluronan and its non-ionic analog containing glucose instead of glucuronic acid. The dihedral angles of the glycoside connections of the pieces obeyed the statistics deduced from the simulation. The simulations were performed at various concentrations of NaCl and MgCl2. The calculated radii of gyration show a striking agreement with experimental data from the literature and indicate a key importance of the polymer-ion interactions for the random-coil conformation, but a low influence of the excluded volume of the chain and the carboxylate-groups repulsion. The method has thus the potential to become a versatile tool of modeling macromolecules of various semirigid polymers. © 2017 Elsevier LtdNational Grid Infrastructure MetaCentrum, provided under the program "Projects of Large Research, Development, and Innovations Infrastructures" [CESNET LM2015042