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

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.

SUBMITTER: Shakibi S

PROVIDER: S-EPMC10448712 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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

Shakibi Saber S Onck Patrick R PR Van der Giessen Erik E

Journal of chemical theory and computation 20230717 16

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 grai ...[more]

PMID: 37459601

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