Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions

Structure. 2021 Sep 2;29(9):1003-1013.e4. doi: 10.1016/j.str.2021.03.003. Epub 2021 Mar 24.

Abstract

Carbohydrate-binding proteins from pathogenic bacteria and fungi have been shown to be implicated in various pathological processes, where they interact with glycans present on the surface of the host cells. These interactions are part of the initial processes of infection of the host and are very important to study at the atomic level. Here, we report the room temperature neutron structures of PLL lectin from Photorhabdus laumondii in its apo form and in complex with deuterated L-fucose, which is, to our knowledge, the first neutron structure of a carbohydrate-binding protein in complex with a fully deuterated carbohydrate ligand. A detailed structural analysis of the lectin-carbohydrate interactions provides information on the hydrogen bond network, the role of water molecules, and the extent of the CH-π stacking interactions between fucose and the aromatic amino acids in the binding site.

Keywords: Photorhabdus; carbohydrate-binding; carbohydrates; fully deuterated L-fucose; lectin; ligand binding; neutron macromolecular crystallography (NMX); neutron structure; perdeuteration; stacking interaction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Fucose / chemistry*
  • Fucose / metabolism
  • Hydrogen / chemistry
  • Lectins / chemistry*
  • Lectins / metabolism
  • Photorhabdus / chemistry
  • Protein Binding

Substances

  • Bacterial Proteins
  • Lectins
  • Fucose
  • Hydrogen

Supplementary concepts

  • Photorhabdus laumondii