Prediction of three-dimensional structures of enzyme-substrate and enzyme-inhibitor complexes of lysozyme.
Conformational energy calculations were used to predict the three-dimensional structures of enzyme-substrate and enzyme-inhibitor complexes of lysozyme. A global search method, involving the use of a disaccharide fragment molecule, was used initially to determine all favorable binding regions at the active site. It is shown that the binding of a series of (nonfragmented) oligomers of N-acetylglucosamine is highly specific. The results show further that (a) the enzyme recognizes only one backbone conformation of the oligomer, corresponding to a left-handed helix, and (b) for saccharides containing two or more N-acetylglucosamine residues, two residues bind preferentially to the C and D sites. The calculations also suggest that the chair form of N-acetylglucosamine can bind to the D region. The saccharide residues of tetra-N-acetylglucosamine bind to the A-B-C-D sites, with the residues at the A-B-C sites having essentially the same conformation and orientation as those in the x-ray structure of tetra-N-acetylglucosamine-delta-lactone bound to lysozyme.
D000117:Acetylglucosamine / Q000378:metabolism; D001665:Binding Sites; D008024:Ligands; D008958:Models, Molecular; D009113:Muramidase / Q000037:antagonists & inhibitors / Q000378:metabolism; D009844:Oligosaccharides / Q000378:metabolism; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D008024:Ligands; D009844:Oligosaccharides; D009113:Muramidase; D000117:Acetylglucosamine