Free energy surfaces for the interaction of D-glucose with planar aromatic groups in aqueous solution.
Multidimensional potentials of mean force for the interactions in aqueous solution of both anomers of D-glucopyranose with two planar aromatic molecules, indole and para-methyl-phenol, have been calculated using molecular dynamics simulations with umbrella sampling and were subsequently used to estimate binding free energies. Indole and para-methyl-phenol serve as models for the side chains of the amino acids tryptophan and tyrosine, respectively. In all cases, a weak affinity between the glucose molecules and the flat aromatic surfaces was found. The global minimum for these interactions was found to be for the case when the pseudoplanar face of β-D-glucopyranose is stacked against the planar surfaces of the aromatic residues. The calculated binding free energies are in good agreement with both experiment and previous simulations. The multidimensional free energy maps suggest a mechanism that could lend kinetic stability to the complexes formed by sugars bound to sugar-binding proteins.
Wohlert
Jakob
J
Department of Food Science Stocking Hall, Cornell University, Ithaca, New York 14850, USA.
Schnupf
Udo
U
Brady
John W
JW
D001665:Binding Sites; D005947:Glucose / Q000031:analogs & derivatives* / Q000737:chemistry; D007211:Indoles / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D019800:Phenol / Q000737:chemistry*; D012996:Solutions / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D007211:Indoles; D012996:Solutions; D014867:Water; D019800:Phenol; C030374:indole; D005947:Glucose