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J Chem Inf Model. 2015 Jan 26;55(1):114-24. doi: 10.1021/ci500669w. Epub 2014 Dec 19.

Coarse-grained model of glycosaminoglycans.

Author information

1
Structural Bioinformatics, BIOTEC TU Dresden , Tatzberg 47-51, D-01307 Dresden, Germany.

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.

PMID:
25490039
DOI:
10.1021/ci500669w
[Indexed for MEDLINE]

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