Vojtech 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/v1 [version v1]

Publication date: Aug 26, 2019

How to cite this record

Vojtech 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/v1 (2019), https://doi.org/10.24435/materialscloud:2019.0042/v1

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 MD5md5:75dbff0062dc24ce8940a141b6e51f2f	207.8 MiB	Trajectory files and files for essential dynamics analysis of protein motions.
README.txt MD5md5:43ca1643971d220f92ec6a9efe44a8db	2.8 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