title: Exploration of CH···π mediated stacking interactions in saccharide: aromatic residue complexes through conformational sampling.
abstract: Saccharides interact with aromatic residues mostly through CH···π mediated stacking interactions. The energetics of such interactions depends upon the mutual position-orientations (POs) of the two moieties. The POs found in the crystal structures are only a subset of the various possible ways of interaction. Hence, potential energy surfaces of saccharide-aromatic residue complexes have been explored by mixed Monte Carlo multiple minimum/low mode sampling. The saccharides considered in this study are α/β-D-glucose, β-D-galactose, α-D-mannose, and α/β-L-fucose. p-Hydroxytoluene, toluene, and 3-methylindole were used as analogs of tyrosine, phenylalanine, and tryptophan, respectively. The saccharides interact from either above or below the π-cloud of an aromatic ring but not along the edges. The POs preferred by different saccharides, both in the preferred chair and skew-boat forms, for interacting with different aromatic amino acid residue analogs have been identified. Aromatic residues can interact with the same -CH group in many POs but not so with the -OH groups. Changes in the configurations of pyranose ring carbon atoms cause remarkable changes in stacking preferences. β-D-Galactose and β-L-fructose interact only through their b- and a-faces, respectively. Saccharides use a wide variety of apolar patches for stacking against aromatic residues and these have been analyzed in detail. As many as four -CH groups can simultaneously participate in CH···π interactions, especially with 3-methylindole owing to its larger surface area.
authors.affiliation: Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
authors.forename: Manju
authors.initials: M
authors.lastname: Kumari
authors.forename: Raghavan B
authors.initials: RB
authors.lastname: Sunoj
authors.forename: Petety V
authors.initials: PV
authors.lastname: Balaji
mesh_terms: D002236:Carbohydrate Conformation; D002241:Carbohydrates / Q000737:chemistry*; D008958:Models, Molecular; D012984:Software
chemical_list: D002241:Carbohydrates