A One-Bead-Per-Saccharide (1BPS) Model for Glycosaminoglycans

J Chem Theory Comput. 2023 Aug 22;19(16):5491-5502. doi: 10.1021/acs.jctc.3c00238. Epub 2023 Jul 17.

Abstract

Glycosaminoglycans (GAGs) are polysaccharide compounds that play key roles in various biological processes. GAGs are important structural components of cartilage and the extracellular matrix of the brain. Due to the large size of these polysaccharides, coarse-grained approaches are indispensable for modeling these biopolymers. We develop a one-bead-per-saccharide model of chondroitin sulfates and hyaluronic acid based on an existing three-bead-per-saccharide coarse-grained model. Our coarse graining is carried out by using iterative Boltzmann inversion (IBI), including an additional coupling potential to incorporate the correlation between dihedral angles. The predictions of the model are verified against those of the existing three-bead-per-saccharin model and the experimental radius of gyration for hyaluronic acid.

MeSH terms

  • Chondroitin Sulfates / chemistry
  • Glycosaminoglycans* / chemistry
  • Hyaluronic Acid* / chemistry
  • Polysaccharides

Substances

  • Glycosaminoglycans
  • Hyaluronic Acid
  • Chondroitin Sulfates
  • Polysaccharides