Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction.
calcium ions
computational analysis of protein-glycosaminoglycan interactions
fragment-based docking
glycosaminoglycans
procollagen C-proteinase enhancer-1
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
10 Oct 2019
10 Oct 2019
Historique:
received:
13
09
2019
revised:
07
10
2019
accepted:
09
10
2019
entrez:
30
10
2019
pubmed:
30
10
2019
medline:
1
4
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 31658765
pii: ijms20205021
doi: 10.3390/ijms20205021
pmc: PMC6829435
pii:
doi:
Substances chimiques
Extracellular Matrix Proteins
0
Glycosaminoglycans
0
Ions
0
PCOLCE protein, human
0
Calcium
SY7Q814VUP
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Narodowe Centrum Nauki
ID : UMO-2018/30/E/ST4/00037
Organisme : Narodowe Centrum Nauki
ID : UMO-2017/25/B/ST4/01026
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