title: Computer modelling approach to study the modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein.
abstract: The modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein (ABP) have been studied by energy minimization using the low resolution (2.4 A) X-ray data of the protein. These studies suggest that these sugars preferentially bind in the alpha-form to ABP, unlike L-arabinose where both alpha- and beta-anomers bind almost equally. The best modes of binding of alpha- and beta-anomers of D-galactose and D-fucose differ slightly in the nature of the possible hydrogen bonds with the protein. The residues Arg 151 and Asn 232 of ABP from bidentate hydrogen bonds with both L-arabinose and D-galactose, but not with D-fucose or D-glucose. However in the case of L-arabinose, Arg 151 forms hydrogen bonds with the hydroxyl group at the C-4 atom and the ring oxygen, whereas in case of D-galactose it forms bonds with the hydroxyl groups at the C-4 and C-6 atoms of the pyranose ring. The calculated conformational energies also predict that D-galactose is a better inhibitor than D-fucose and D-glucose, in agreement with kinetic studies. The weak inhibitor D-glucose binds preferentially to one domain of ABP leading to the formation of a weaker complex. Thus these studies provide information about the most probable binding modes of these sugars and also provide a theoretical explanation for the observed differences in their binding affinities.
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
authors.forename: C
authors.initials: C
authors.lastname: Mukhopadhyay
authors.forename: V S
authors.initials: VS
authors.lastname: Rao
mesh_terms: D001089:Arabinose / Q000378:metabolism*; D002352:Carrier Proteins / Q000378:metabolism*; D003198:Computer Simulation; D029968:Escherichia coli Proteins; D005643:Fucose / Q000378:metabolism*; D005690:Galactose / Q000378:metabolism*; D005947:Glucose / Q000378:metabolism*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation
chemical_list: C016242:AraF protein, E coli; D002352:Carrier Proteins; D029968:Escherichia coli Proteins; D005643:Fucose; D001089:Arabinose; D005947:Glucose; D005690:Galactose