Analysis of procollagen C-proteinase enhancer-1/glycosaminoglycan binding sites and of the potential role of calcium ions in the interaction

Jan Potthoff , Krzysztof Bojarski , Gergely Kohut , Agnieszka Lipska , Józef Adam Liwo , Efrat Kessler , Sylvie Ricard-Blum , Sergey Samsonov

Abstract

In this study, we characterize the interactions between the extracellular matrix protein, procollagen C-proteinase enhancer-1 (PCPE-1), and glycosaminoglycans (GAGs), which are linear anionic periodic polysaccharides. We applied molecular modeling approaches to build a structural model of full-length PCPE-1, which is not experimentally available, to predict GAG binding poses for various GAG lengths, types and sulfation patterns, and to determine the effect of calcium ions on the binding. The computational data are analyzed and discussed in the context of the experimental results previously obtained using surface plasmon resonance binding assays. We also provide experimental data on PCPE-1/GAG interactions obtained using inhibition assays with GAG oligosaccharides ranging from disaccharides to octadecasaccharides. Our results predict the localization of GAG-binding sites at the amino acid residue level onto PCPE-1 and is the first attempt to describe the effects of ions on protein-GAG binding using modeling approaches. In addition, this study allows us to get deeper insights into the in silico methodology challenges and limitations when applied to GAG-protein interactions.
Author Jan Potthoff (FCh)
Jan Potthoff,,
- Faculty of Chemistry
, Krzysztof Bojarski (FCh / DTCh / LMM)
Krzysztof Bojarski,,
- Laboratory of Molecular Modeling
, Gergely Kohut
Gergely Kohut,,
-
, Agnieszka Lipska (FCh / DTCh / LMM)
Agnieszka Lipska,,
- Laboratory of Molecular Modeling
, Józef Adam Liwo (FCh / DTCh / LMM)
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
, Efrat Kessler
Efrat Kessler,,
-
, Sylvie Ricard-Blum
Sylvie Ricard-Blum ,,
-
, Sergey Samsonov (FCh / DTCh / LMM)
Sergey Samsonov,,
- Laboratory of Molecular Modeling
Journal seriesInternational Journal of Molecular Sciences, ISSN 1422-0067, (N/A 140 pkt)
Issue year2019
Vol20
No20
Pages1-24
Publication size in sheets1.15
Article number5021
Keywords in Englishprocollagen C-proteinase enhancer-1, glycosaminoglycans, computational analysis of protein-glycosaminoglycan interactions, calcium ions, fragment-based docking
ASJC Classification2700 General Medicine; 1312 Molecular Biology; 1503 Catalysis; 1604 Inorganic Chemistry; 1605 Organic Chemistry; 1606 Physical and Theoretical Chemistry; 1607 Spectroscopy; 1706 Computer Science Applications
DOIDOI:10.3390/ijms20205021
Languageen angielski
LicenseRepository; published final; Uznanie Autorstwa (CC-BY); with publication
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Potthoff_Jan_Bojarski_Krzysztof_Lipska_Agnieszka_Liwo_Adam_Samsonov_Sergey_Analysis_of_Procollagen_2019.pdf 4.43 MB
Score (nominal)140
Score sourcejournalList
ScoreMinisterial score = 140.0, 28-02-2020, ArticleFromJournal
Publication indicators Scopus SNIP (Source Normalised Impact per Paper): 2018 = 1.224; WoS Impact Factor: 2018 = 4.183 (2) - 2018=4.331 (5)
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LicencjaUtwór jest udostępniany na licencji Creative Commons Uznanie autorstwa 4.0 Międzynarodowe (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/
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