Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F19%3A43918062" target="_blank" >RIV/60461373:22330/19:43918062 - isvavai.cz</a>
Result on the web
<a href="https://www.nature.com/articles/s41598-019-53815-w" target="_blank" >https://www.nature.com/articles/s41598-019-53815-w</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1038/s41598-019-53815-w" target="_blank" >10.1038/s41598-019-53815-w</a>

Result language
angličtina
Original language name
Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain
Original language description
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 x 2 mu s) 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/pi 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.
Czech name
—
Czech description
—

Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10608 - Biochemistry and molecular biology

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Similar results(10)