title: Coarse-grained model of glycosaminoglycans.
abstract: Glycosaminoglycans (GAGs) represent a class of anionic periodic linear polysaccharides, which mediate cell communication processes by interactions with their protein targets in the extracellular matrix. Due to their high flexibility, charged nature, periodicity, and polymeric nature, GAGs are challenging systems for computational approaches. To deal with the length challenge, coarse-grained (CG) modeling could be a promising approach. In this work, we develop AMBER-compatible CG parameters for GAGs using all-atomic (AA) molecular dynamics (MD) simulations in explicit solvent and the Boltzmann conversion approach. We compare both global and local properties of GAGs obtained in the simulations with AA and CG approaches, and we conclude that our CG model is appropriate for the MD approach of long GAG molecules at long time scales.
authors.affiliation: Structural Bioinformatics, BIOTEC TU Dresden , Tatzberg 47-51, D-01307 Dresden, Germany.
authors.forename: Sergey A
authors.initials: SA
authors.lastname: Samsonov
authors.forename: Leon
authors.initials: L
authors.lastname: Bichmann
authors.forename: M Teresa
authors.initials: MT
authors.lastname: Pisabarro
mesh_terms: D019295:Computational Biology / Q000379:methods; D006025:Glycosaminoglycans / Q000737:chemistry* / Q000378:metabolism; D006493:Heparin / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012997:Solvents
chemical_list: D006025:Glycosaminoglycans; D011506:Proteins; D012997:Solvents; D006493:Heparin