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

Authors: Vojtech 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/v1 (version v1, submitted on 26 August 2019)

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How to cite this entry

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), doi: 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.

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Files

File name Size Description
README.txt
MD5MD5: 43ca1643971d220f92ec6a9efe44a8db
2.8 KiB README.txt file with description of files.
hevein.zip
MD5MD5: 75dbff0062dc24ce8940a141b6e51f2f
207.8 MiB Trajectory files and files for essential dynamics analysis of protein motions.

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.

External references

Journal reference
C. O. Solanke, D. Trapl, Z. Sucur, V. Mareska, I. Tvaroska, V. Spiwok, to be submitted.

Keywords

molecular dynamics simulation carbohydrate-protein interactions docking by dynamics

Version history

21 October 2019

26 August 2019 [This version]