Vojtěch Spiwok^1*, Charles Oluremi Solanke^1*, Dalibor Trapl^1*, Zoran Šućur^1*, Václav Mareška^1*, Igor Tvaroška^2*

1 Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague

2 Institute of Chemistry - Centre for Glycomics, Slovak Academy of Sciences, Bratislava

* Corresponding authors emails: spiwokv@vscht.cz, solankecharlesoluremi@yahoo.com, traplda@vscht.cz, sucurz@vscht.cz, mareskav@vscht.cz, igor.tvaroska@savba.sk

DOI10.24435/materialscloud:2019.0042/v2 [version v2]

Publication date: Oct 21, 2019

How to cite this record

Vojtěch Spiwok, Charles Oluremi Solanke, Dalibor Trapl, Zoran Šućur, Václav Mareška, Igor Tvaroška, Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain, Materials Cloud Archive 2019.0042/v2 (2019), https://doi.org/10.24435/materialscloud:2019.0042/v2

Description

Unbiased molecular dynamics simulation was used to simulate systems containing hevein (HEV32) domain and mono-, di- or trisaccharide of GlcNAc. Carbohydrate molecules were placed outside the binding site. Three of six simulations led to formation of a carbohydrate-protein complex. Trajectories are available without water and are sampled every 100 ps. This study is one of the first application of docking by dynamics concept on carbohydrate-protein interactions.

Materials Cloud sections using this data

Files

File name	Size	Description
hevein.zip MD5md5:f5ea99b6229c0cc67734fe0f2203d2b7	220.1 MiB	Trajectory files
README.txt MD5md5:96738ca4b360f79ae7de2e2517f39a57	1.9 KiB	README.txt file with description of files.

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

External references

Keywords

molecular dynamics simulation carbohydrate-protein interactions docking by dynamics