Local and long range potentials for heparin-protein systems for coarse-grained simulations.
UNRES
heparin
physics-based unified coarse-grained model
potential of mean force
protein-glycosaminoglycan interactions
Journal
Biopolymers
ISSN: 1097-0282
Titre abrégé: Biopolymers
Pays: United States
ID NLM: 0372525
Informations de publication
Date de publication:
Aug 2019
Aug 2019
Historique:
received:
21
12
2018
revised:
21
02
2019
accepted:
22
02
2019
pubmed:
14
3
2019
medline:
9
1
2020
entrez:
14
3
2019
Statut:
ppublish
Résumé
Heparin belongs to glycosaminoglycans (GAGs), a class of periodic linear anionic polysaccharides, which are functionally important components of the extracellular matrix owing to their interactions with various protein targets. Heparin is known to be involved in many cell signaling processes, while the experimental data available for heparin are significantly more abundant than for other GAGs. At the same time, the length and conformational flexibility of the heparin represent major challenges for its theoretical analysis. Coarse-grained (CG) approaches, which enable us to extend the size- and time-scale by orders of magnitude owing to reduction of system representation, appear, therefore, to be useful in simulating these systems. In this work, by using umbrella-sampling molecular dynamics simulations, we derived and parameterized the CG backbone-local potentials of heparin chains and the orientational potentials for the interactions of heparin with amino acid side chains to be further included in the physics-based Unified Coarse-Grained Model of biological macromolecules. With these potentials, simulations of extracellular matrix processes where both heparin and multiple proteins participate will be possible.
Substances chimiques
Amino Acids
0
Monosaccharides
0
Proteins
0
Heparin
9005-49-6
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e23269Subventions
Organisme : Narodowe Centrum Nauki
ID : UMO-2016/21/P/ST4/03995
Organisme : Horizon 2020
Informations de copyright
© 2019 Wiley Periodicals, Inc.
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