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

Vojtěch Spiwok1*, Charles Oluremi Solanke1*, Dalibor Trapl1*, Zoran Šućur1*, Václav Mareška1*, Igor Tvaroška2*

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), doi: 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

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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

Journal reference
C. O. Solanke, D. Trapl, Z. Šućur, V. Mareška, I. Tvaroška, V. Spiwok, Sci. Rep. 9, 18918 (2019) doi:10.1038/s41598-019-53815-w

Keywords

molecular dynamics simulation carbohydrate-protein interactions docking by dynamics