Stacking interactions between carbohydrate and protein quantified by combination of theoretical and experimental methods

• Published in: PloS one Vol. 7; no. 10; p. e46032
• Main Authors: Wimmerová, Michaela, Kozmon, Stanislav, Nečasová, Ivona, Mishra, Sushil Kumar, Komárek, Jan, Koča, Jaroslav
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 08.10.2012; Public Library of Science (PLoS)
• Subjects: Acids; Adhesive bonding; Affinity; Alanine; Amino acids; Amino Acids, Aromatic - chemistry; Amino Acids, Aromatic - genetics; Amino Acids, Aromatic - metabolism; Analysis; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding; Binding Sites; Biology; Carbohydrate Conformation; Carbohydrates; Carbohydrates - chemistry; Cell adhesion; Cell adhesion & migration; Cell differentiation; Chemistry; Computation; Computer applications; Computer simulation; Crystallography, X-Ray; Dispersion; Experimental methods; Fucose - chemistry; Fucose - metabolism; Hydrogen; Hydrogen Bonding; Hydrogen bonds; Lectins; Lectins - chemistry; Lectins - genetics; Lectins - metabolism; Methods; Models, Molecular; Molecular dynamics; Mutants; Mutation; Phenylalanine; Protein Binding; Protein Conformation; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins; Proteins - chemistry; Proteins - genetics; Proteins - metabolism; Pseudomonas aeruginosa; Ralstonia solanacearum; Ralstonia solanacearum - genetics; Ralstonia solanacearum - metabolism; Research methodology; Residues; Science; Signaling; Thermodynamics; Czech Republic
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0046032

Carbohydrate-receptor interactions are an integral part of biological events. They play an important role in many cellular processes, such as cell-cell adhesion, cell differentiation and in-cell signaling. Carbohydrates can interact with a receptor by using several types of intermolecular interactions. One of the most important is the interaction of a carbohydrate's apolar part with aromatic amino acid residues, known as dispersion interaction or CH/π interaction. In the study presented here, we attempted for the first time to quantify how the CH/π interaction contributes to a more general carbohydrate-protein interaction. We used a combined experimental approach, creating single and double point mutants with high level computational methods, and applied both to Ralstonia solanacearum (RSL) lectin complexes with α-L-Me-fucoside. Experimentally measured binding affinities were compared with computed carbohydrate-aromatic amino acid residue interaction energies. Experimental binding affinities for the RSL wild type, phenylalanine and alanine mutants were -8.5, -7.1 and -4.1 kcal x mol(-1), respectively. These affinities agree with the computed dispersion interaction energy between carbohydrate and aromatic amino acid residues for RSL wild type and phenylalanine, with values -8.8, -7.9 kcal x mol(-1), excluding the alanine mutant where the interaction energy was -0.9 kcal x mol(-1). Molecular dynamics simulations show that discrepancy can be caused by creation of a new hydrogen bond between the α-L-Me-fucoside and RSL. Observed results suggest that in this and similar cases the carbohydrate-receptor interaction can be driven mainly by a dispersion interaction.