Coarse-grained model of glycosaminoglycans

Publikation: Beitrag in FachzeitschriftForschungsartikelBeigetragenBegutachtung

Beitragende

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.

Details

OriginalspracheEnglisch
Seiten (von - bis)114-124
Seitenumfang11
FachzeitschriftACS: Journal of Chemical Information and Modeling
Jahrgang55
Ausgabenummer1
PublikationsstatusVeröffentlicht - 26 Jan. 2015
Peer-Review-StatusJa

Externe IDs

Scopus 84921746563

Schlagworte

Schlagwörter

  • Computational Biology/methods, Glycosaminoglycans/chemistry, Heparin/chemistry, Hydrogen Bonding, Models, Molecular, Molecular Dynamics Simulation, Proteins/chemistry, Solvents