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
AbstractIn 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.
|Journal series||International Journal of Molecular Sciences, ISSN 1422-0067, (N/A 140 pkt)|
|Publication size in sheets||1.15|
|Keywords in English||procollagen C-proteinase enhancer-1, glycosaminoglycans, computational analysis of protein-glycosaminoglycan interactions, calcium ions, fragment-based docking|
|ASJC Classification||; ; ; ; ; ; ;|
|License||Repository; published final; ; with publication|
|Score||= 140.0, 28-02-2020, ArticleFromJournal|
|Publication indicators||: 2018 = 1.224; : 2018 = 4.183 (2) - 2018=4.331 (5)|
|Licencja||Utwór 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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