Local and long range potentials for heparin-protein systems for coarse-grained simulations

Sergey Samsonov , Emilia Lubecka , Krzysztof Bojarski , Robert Ganzynkowicz , Józef Adam Liwo

Abstract

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.
Author Sergey Samsonov (FCh / DTCh / LMM)
Sergey Samsonov,,
- Laboratory of Molecular Modeling
, Emilia Lubecka (FMPI / II)
Emilia Lubecka,,
- Institute of Informatics
, Krzysztof Bojarski (FCh / DTCh / LMM)
Krzysztof Bojarski,,
- Laboratory of Molecular Modeling
, Robert Ganzynkowicz (FCh / DTCh / LMM)
Robert Ganzynkowicz,,
- Laboratory of Molecular Modeling
, Józef Adam Liwo (FCh / DTCh / LMM)
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
Journal seriesBiopolymers, ISSN 0006-3525, (A 25 pkt)
Issue year2019
Vol110
No8
Pages1-12
Publication size in sheets0.55
Article numbere23269
Keywords in Englishheparin, physics-based unified coarse-grained model, potential of mean force, proteinglycosaminoglycan interactions, UNRES
ASJC Classification1605 Organic Chemistry; 2502 Biomaterials; 1303 Biochemistry; 2700 General Medicine; 1304 Biophysics
DOIDOI:10.1002/bip.23269
URL https://doi.org/10.1002/bip.23269
Languageen angielski
Score (nominal)25
ScoreMinisterial score = 25.0, 03-09-2019, ArticleFromJournal
Publication indicators Scopus SNIP (Source Normalised Impact per Paper): 2016 = 0.722; WoS Impact Factor: 2017 = 1.99 (2) - 2017=2.165 (5)
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