We use molecular dynamics (MD) simulations to probe the protein-sugar interactions by investigating LacY embedded in a fully hydrated lipid bilayer. MD simulations with β-D-galactopyranosyl-(1,1)-β-D-galactopyranoside (β-D-Galp-(1,1)-β-D-Galp), similar to the lactose homolog in the LacY crystal structure, result in a sugar binding structure that is in agreement with x-ray crystallography. Intermediates to β-D-Galp-(1,1)-β-D-Galp binding are proposed based on our simulations. For the other anomeric state of the disaccharide, α-D-Galp-(1,1)-α-D-Galp, an alternate protein binding structure to that of the x-ray crystal structure is found. The α-sugar interacts with similar LacY amino acids as the β-sugar (Glu126, Glu269, and Trp151), but with different sugar hydroxyl groups. Moreover, it also interacts with His322, which is not experimentally observed in the β-anomeric state.
MD simulations with D-Galp-(1,1)-D-Glcp are also run to determine the affect of a gluctopyranoside ring to binding. Common to all protein-sugar structures, water acts as a hydrogen bond bridge between the disaccharide and protein. Water mediated hydrogen bonds have been suggested previously, but the x-ray structure resolution prohibited the determination of water. In conclusion, the binding structure of LacY and disaccharide depend on the sugar anomeric state. Consequently, the experimentally observed increase affinity of LacY to α-disaccharides is the result of this different binding structure.