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

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


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.
Autor Sergey Samsonov (WCh / KChT / PMM)
Sergey Samsonov
- Pracownia Modelowania Molekularnego
, Emilia Lubecka (WMFiI / II)
Emilia Lubecka
- Instytut Informatyki
, Krzysztof Bojarski (WCh / KChT / PMM)
Krzysztof Bojarski
- Pracownia Modelowania Molekularnego
, Robert Ganzynkowicz (WCh / KChT / PMM)
Robert Ganzynkowicz
- Pracownia Modelowania Molekularnego
, Józef Adam Liwo (WCh / KChT / PMM)
Józef Adam Liwo
- Pracownia Modelowania Molekularnego
Tytuł czasopisma/seriiBiopolymers, ISSN 0006-3525, (A 25 pkt)
Rok wydania2019
Objętość publikacji w arkuszach wydawniczych0.55
Numer artykułue23269
Słowa kluczowe w języku angielskimheparin, physics-based unified coarse-grained model, potential of mean force, proteinglycosaminoglycan interactions, UNRES
Klasyfikacja ASJC1605 Organic Chemistry; 2502 Biomaterials; 1303 Biochemistry; 2700 General Medicine; 1304 Biophysics
URL https://doi.org/10.1002/bip.23269
Języken angielski
Punktacja (całkowita)25
PunktacjaPunktacja MNiSW = 25.0, 03-09-2019, ArticleFromJournal
Wskaźniki publikacji Scopus SNIP (Source Normalised Impact per Paper): 2016 = 0.722; Impact Factor WoS: 2017 = 1.99 (2) - 2017=2.165 (5)
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