Towards a multi-scale model of cartilage: coarse-graining glycosaminoglycans

A coarse-grained model for the computation of structural and thermodynamic properties of anionic glycosaminoglycans is presented. The model is based on an all-atom description of the biopolymer and incorporates solvent and salt screening effects on electrostatic interactions. The speed-up obtained relative to an all-atom model enables the simulation of the biologically relevant molecular weight range of glycosaminoglycans present in tissues such as cartilage. As an initial application and validation of the model we compute the persistence length for isolated hyaluronan, chondroitin, chondroitin-4-sulfate, and chondroitin-6-sulfate polymers at various salt concentrations. Persistence length is found to vary as the inverse square root of ionic strength in each case, in agreement with experimental findings of Ghosh et al. [1] for hyaluronan.