Molecular dynamics insights into protein-glycosaminoglycan systems from microsecond-scale simulations

Krzysztof Bojarski , Adam Sieradzan , Sergey Samsonov


Heparin is a key player in cell signaling via its physical interactions with protein targets in the extracellular matrix. However, basic molecular level understanding of these highly biologically relevant intermolecular interactions is still incomplete. In this study, for the first time, microsecond- scale MD simulations are reported for a complex between fibroblast growth factor 1 and heparin. We rigorously analyze this molecular system in terms of the conformational space, structural, energetic, and dynamic characteristics. We reveal that the conformational selection mechanism of binding denotes a recognition specificity determinant. We conclude that the length of the simulation could be crucial for evaluation of some of the analyzed parameters. Our data provide novel significant insights into the interactions in the fibroblast growth factor 1 complex with heparin, in particular, and into the physical-chemical nature of protein-glycosaminoglycan systems in general, which have potential applicability for biomaterials development in the area of regenerative medicine.
Author Krzysztof Bojarski (FCh / DTCh / LMM)
Krzysztof Bojarski ,,
- Laboratory of Molecular Modeling
, Adam Sieradzan (FCh / DTCh / LMM)
Adam Sieradzan,,
- Laboratory of Molecular Modeling
, Sergey Samsonov (FCh / DTCh / LMM)
Sergey Samsonov,,
- Laboratory of Molecular Modeling
Journal seriesBiopolymers, ISSN 0006-3525, (A 25 pkt)
Issue year2019
Publication size in sheets0.7
Article numbere23252
Keywords in Englishfibroblast growth factor 1, heparin conformational analysis, molecular dynamics, proteinglycosaminoglycan interactions, ring puckering
ASJC Classification1605 Organic Chemistry; 2502 Biomaterials; 1303 Biochemistry; 2700 General Medicine; 1304 Biophysics
Languageen angielski
Score (nominal)25
ScoreMinisterial score = 25.0, 11-09-2019, 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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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.