Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain
| العنوان: | Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain |
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| المؤلفون: | Igor Tvaroška, Dalibor Trapl, Václav Mareška, Vojtěch Spiwok, Charles Oluremi Solanke, Zoran Šućur |
| المصدر: | Scientific Reports, Vol 9, Iss 1, Pp 1-7 (2019) Scientific Reports |
| بيانات النشر: | Nature Publishing Group, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | 0301 basic medicine, Trisaccharide binding, Stereochemistry, Carbohydrates, Disaccharide, Oligosaccharides, lcsh:Medicine, Molecular dynamics, Molecular Dynamics Simulation, 01 natural sciences, Article, 03 medical and health sciences, chemistry.chemical_compound, Protein Domains, Trisaccharide, Binding site, lcsh:Science, chemistry.chemical_classification, Multidisciplinary, 010405 organic chemistry, Chemistry, lcsh:R, Ligand (biochemistry), Small molecule, 0104 chemical sciences, 030104 developmental biology, Models, Chemical, Docking (molecular), lcsh:Q, Molecular modelling, Plant Lectins, Antimicrobial Cationic Peptides, Protein Binding |
| الوصف: | Interactions between proteins and their small molecule ligands are of great importance for the process of drug design. Here we report an unbiased molecular dynamics simulation of systems containing hevein domain (HEV32) with N-acetylglucosamine mono-, di- or trisaccharide. Carbohydrate molecules were placed outside the binding site. Three of six simulations (6 × 2 μs) led to binding of a carbohydrate ligand into the binding mode in agreement with the experimentally determined structure. Unbinding was observed in one simulation (monosaccharide). There were no remarkable intermediates of binding for mono and disaccharide. Trisaccharide binding was initiated by formation of carbohydrate-aromatic CH/π interactions. Our results indicate that binding of ligands followed the model of conformational selection because the conformation of the protein ready for ligand binding was observed before the binding. This study extends the concept of docking by dynamics on carbohydrate-protein interactions. |
| اللغة: | English |
| تدمد: | 2045-2322 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::70d23d278cb58b5c27d868a18d8fce29 http://link.springer.com/article/10.1038/s41598-019-53815-w |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....70d23d278cb58b5c27d868a18d8fce29 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 20452322 |
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