Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL

PLoS One. 2017 Dec 12;12(12):e0189375. doi: 10.1371/journal.pone.0189375. eCollection 2017.

Abstract

Protein-carbohydrate interactions are very often mediated by the stacking CH-π interactions involving the side chains of aromatic amino acids such as tryptophan (Trp), tyrosine (Tyr) or phenylalanine (Phe). Especially suitable for stacking is the Trp residue. Analysis of the PDB database shows Trp stacking for 265 carbohydrate or carbohydrate like ligands in 5 208 Trp containing motives. An appropriate model system to study such an interaction is the AAL lectin family where the stacking interactions play a crucial role and are thought to be a driving force for carbohydrate binding. In this study we present data showing a novel finding in the stacking interaction of the AAL Trp side chain with the carbohydrate. High resolution X-ray structure of the AAL lectin from Aleuria aurantia with α-methyl-l-fucoside ligand shows two possible Trp side chain conformations with the same occupation in electron density. The in silico data shows that the conformation of the Trp side chain does not influence the interaction energy despite the fact that each conformation creates interactions with different carbohydrate CH groups. Moreover, the PDB data search shows that the conformations are almost equally distributed across all Trp-carbohydrate complexes, which would suggest no substantial preference for one conformation over another.

MeSH terms

  • Carbohydrate Metabolism*
  • Crystallography, X-Ray
  • Databases, Protein
  • Lectins / chemistry
  • Lectins / metabolism*
  • Protein Conformation
  • Tryptophan / chemistry
  • Tryptophan / metabolism*

Substances

  • Lectins
  • lectin, Aleuria aurantia
  • Tryptophan

Grant support

This work has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) and Czech Science Foundation (13-25401S). Additional computational resources were provided by the CESNET LM2015042 and the CERIT Scientific Cloud LM2015085, provided under the programme "Projects of Large Research, Development, and Innovations Infrastructures". The research has been financed by the program SASPRO (ArIDARuM, 0005/01/02 - SK) and was co-funded by the People Programme (Marie Curie Actions 7FP, grant agreement REA no. 609427 - SK) and co-financed by the Slovak Academy of Sciences. SKM is an international fellow of the Japan Society for Proportion of Science.