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

Authors: 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, submitted on 21 October 2019)

How to cite this entry

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), 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

No Explore or Discover sections associated with this archive entry.

Files

File name Size Description
README.txt
MD5MD5: 96738ca4b360f79ae7de2e2517f39a57
1.9 KiB README.txt file with description of files.
hevein.zip
MD5MD5: f5ea99b6229c0cc67734fe0f2203d2b7
220.1 MiB Trajectory files

License

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

External references

Journal reference (After first round of review in Sci. Rep. )
C. O. Solanke, D. Trapl, Z. Sucur, V. Mareska, I. Tvaroska, V. Spiwok, submitted.

Keywords

molecular dynamics simulation carbohydrate-protein interactions docking by dynamics

Version history

21 October 2019 [This version]

26 August 2019