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Published August 26, 2019 | Version v1
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Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain

  • 1. Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague
  • 2. Institute of Chemistry - Centre for Glycomics, Slovak Academy of Sciences, Bratislava

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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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References

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