Interactions between proteins and their small molecule ligands are of great importance for the process of drug design. Here we report an unbiased molecular dynamics simulation of systems containing hevein domain (HEV32) with N-acetylglucosamine mono-, di- or trisaccharide. Carbohydrate molecules were placed outside the binding site. Three of six simulations (6 × 2 μs) led to binding of a carbohydrate ligand into the binding mode in agreement with the experimentally determined structure. Unbinding was observed in one simulation (monosaccharide). There were no remarkable intermediates of binding for mono and disaccharide. Trisaccharide binding was initiated by formation of carbohydrate-aromatic CH/π interactions. Our results indicate that binding of ligands followed the model of conformational selection because the conformation of the protein ready for ligand binding was observed before the binding. This study extends the concept of docking by dynamics on carbohydrate-protein interactions.

• MeSH
• chemické modely * MeSH
• kationické antimikrobiální peptidy chemie   MeSH
• oligosacharidy chemie   MeSH
• proteinové domény MeSH
• rostlinné lektiny chemie   MeSH
• simulace molekulární dynamiky * MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• hevein MeSH Prohlížeč
• kationické antimikrobiální peptidy MeSH
• oligosacharidy MeSH
• rostlinné lektiny MeSH

Many carbohydrate-binding proteins contain aromatic amino acid residues in their binding sites. These residues interact with carbohydrates in a stacking geometry via CH/π interactions. These interactions can be found in carbohydrate-binding proteins, including lectins, enzymes and carbohydrate transporters. Besides this, many non-protein aromatic molecules (natural as well as artificial) can bind saccharides using these interactions. Recent computational and experimental studies have shown that carbohydrate-aromatic CH/π interactions are dispersion interactions, tuned by electrostatics and partially stabilized by a hydrophobic effect in solvated systems.

• Klíčová slova
• CH/π interactions, carbohydrate-protein interactions, interaction energy, lectins, non-canonical hydrogen bond,
• MeSH
• lektiny chemie   metabolismus   MeSH
• molekulární modely MeSH
• sacharidy chemie   MeSH
• vazba proteinů MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• lektiny MeSH
• sacharidy MeSH