Stacking interactions between carbohydrate and protein quantified by combination of theoretical and experimental methods.
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.
CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic. michaw@chemi.muni.cz
Michaela
M
Wimmerová
Stanislav
S
Kozmon
Ivona
I
Nečasová
Sushil Kumar
SK
Mishra
Jan
J
Komárek
Jaroslav
J
Koča
D024322:Amino Acids, Aromatic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D002236:Carbohydrate Conformation; D002241:Carbohydrates / Q000737:chemistry*; D018360:Crystallography, X-Ray; D005643:Fucose / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D037102:Lectins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D043368:Ralstonia solanacearum / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics
D024322:Amino Acids, Aromatic; D001426:Bacterial Proteins; D002241:Carbohydrates; D037102:Lectins; D011506:Proteins; D005643:Fucose