Affinity maps of grid points and spacing were generated usin

Affinity maps of grid points and spacing were generated using the Autogrid program. AutoDock parameter set and distance-dependent dielectric functions were used in the calculation of the van der Waals and the electrostatic terms, respectively. Docking simulations were performed using the Lamarckian genetic algorithm and the Solis & Wets local search method. Initial position, orientation and torsions of the ligand molecules were set randomly. Each docking experiment was derived from 100 different runs that were set to terminate after a maximum of 2,500,000 PS-1145 energy evaluations. The population size was set to 150. During the search, a translational step of 0.2 A ��, and quaternion and torsion steps of 5 A �� were applied. The predicted distance are indicated in Angstro��ms. Glycans play important roles in diverse cellular functions of all eukaryotic cells. By attaching to backbones of numerous membrane and soluble proteins they induce structural changes, thereby regulating and modifying protein function. Functional consequences of alternative glycosylation of a particular protein can be drastic, as exemplified by the case of immunoglobulin G. Here, the attachment of a single additional monosaccharide can lead to BIBW-2992 various outcomes, including conversion of IgG from pro-inflammatory into an anti-inflammatory agent or activation of pathways implicated in various inflammatory diseases. Even though functional aspects of glycosylation of other proteins are less well understood, the importance of glycosylation in the regulation of biological activity of many other signaling and receptor proteins is certain. Amongst others, these are Notch, GLUT4 and NMDA receptor, whose glycosylation appears to play an important part in adaptive regulation of the cell surface in cell-cell adhesion and cellular communication. Biosynthesis of glycan and polypeptide parts of a glycoprotein is different. Contrary to polypeptide moieties, glycan moieties of glycoproteins are not synthesized from the direct genetic template. Instead, glycan structures result from the activity of a dynamic network of over 600 glyco-genes that code for various glycosyltransferases, glycosidases, enzymes for sugar nucleotide biosynthes