ese comparable dissociation constants, in combination with the comparable 
corresponding enthalpic and entropic contributions to the binding, suggest a low population and low contribution to the BAY-41-2272 biological activity binding affinity of this hydrogen bond with Ser23 in solution, which had been observed in the crystalline state at low temperatures for mannose. In general a significant reduction in binding affinity was observed, when equatorial substituents were introduced at the superimposing fucose-C1- or mannose-C5-position or their derivatives, e.g., compounds 2, 4, 5, and 6. In order to understand the steric and electrostatic reasons for this decrease of binding affinity when such an equatorial substituent is present, molecular dynamics simulations were performed. Thermodynamic PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19689277 integration, a highly accurate method to predict binding free energies, was used to calculate the relative affinities of 7 pairs of ligands. Such calculations are based on the idea of alchemistic modification of one structure into another one. For fast convergence, these alchemistic structural changes should be as small as possible and the pairs were chosen accordingly. Relative binding free energies were approximated by 14 / 22 Molecular Basis of Monosaccharide Selectivity of LecB summing over all single transitions leading from methyl a-L-fucoside to the specific ligand, that means 1 was chosen as arbitrary zero point of the energy scale. Generally, a very good agreement of theoretical values with experimental binding affinities was obtained. A good correlation coefficient was obtained with a good separation between the high- and low-affinity ligands. When looking at the independent steps of the TI simulation of the transition from 1-deoxy L-fucose to its equatorially substituted derivative 4, i.e., the simulation separating the two groups of ligands, it becomes evident that the loss in binding affinity is caused by an unfavorable steric fit and that this effect is reduced by stronger electrostatic interactions. Because the force-field parameters used gave good descriptions of the energetic features of binding, we performed extended simulations on specific complexes to analyze the structural basis for the differences in binding affinities. All complexes adopt very similar orientations of the ligands, which was further visualized by analyzing the time series of root mean square deviations of all ligand atoms compared to the X-ray structure of L-fucose. RMSDs are stable over the simulation time around 1 to 2 A. However, a significant difference can be seen in the pose of the low-affinity ligands compared to the high-affinity derivatives. Upon equatorial substitution of the carbon atom corresponding to C1 of fucose, the sugar moiety in the complexes of LecB with aD-mannose or PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19691363 hybrid 4 is pushed out from the binding site by approx. 0.7 A, due to unfavorable steric interactions of the equatorial hydroxymethyl substituent with Asp96. 15 / 22 Molecular Basis of Monosaccharide Selectivity of LecB In the crystal structure of the complex of L-fucose with LecB, the ligand is interacting with Asp96 by its atom HO2. Asp96 is highly restrained to its position due to formation of a large hydrogen-bond network with other residues. Addition of a b-substituent results in a steric clash with the protein, which is reduced in the simulations of the complex of both 4 and a-D-mannose by the outward shift of the ligand. In the simulation of a-D-mannose, 16 / 22 Molecular Basis of Monosaccharide Selectivi