RT Journal Article
SR Electronic
T1 A coarse-grained model of glycosaminoglycans for biomolecular simulations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.10.06.561318
DO 10.1101/2023.10.06.561318
A1 Shivgan, Aishwary T.
A1 Marzinek, Jan K.
A1 Krah, Alexander
A1 Matsudaira, Paul
A1 Verma, Chandra S.
A1 Bond, Peter J.
YR 2023
UL http://biorxiv.org/content/early/2023/10/10/2023.10.06.561318.abstract
AB Proteoglycans contain glycosaminoglycans (GAGs), negatively charged linear polymers made of repeating disaccharide units of uronic acid and hexosamine units. They play vital roles in numerous physiological and pathological processes, particularly governing cellular communication and attachment. Depending on their sulphonation state, acetylation, and glycosidic linkages, GAGs belong to different families. The high molecular weight, heterogeneity, and flexibility of GAGs hampers their characterization at atomic resolution, but this may be circumvented via coarse-grained (CG) approaches. In this work, we report a CG model for a library of common GAG types in their isolated or proteoglycan-linked states compatible with the widely popular CG Martini forcefields (versions 2.2 and 3.0). The model reproduces conformational and thermodynamic properties for a wide variety of GAGs, as well as matching structural and binding data for selected proteoglycan test systems. The parameters developed here may thus be employed to study a range of GAG-containing biomolecular systems, benefitting from the efficiency and broad applicability of the Martini framework.Competing Interest StatementThe authors have declared no competing interest.