ASYMMETRY IN THE STRUCTURE OF GLYCOPEPTIDE ANTIBIOTIC DIMERS - NMR-STUDIES OF THE RISTOCETIN-A COMPLEX WITH A BACTERIAL-CELL WALL ANALOG

The solution structure of a dimer complex of the glycopeptide antibiot ic ristocetin A has been determined from NOE constraints, energy minim ization, and molecular dynamics calculations. The structure is that of an asymmetric dimer in which the conformation of the two monomeric un its differs in the orientation of the tetrasaccharide attached to the aromatic ring of residue 4. Although hydrogen bonding interactions bet ween the peptide backbones of the two antibiotic monomers occur in a s ymmetrical head-to-tail orientation, the overall dimer assymmetry aris es as a consequence of a parallel, head-to-head alignment of the tetra saccharides. Thus, in the two monomeric antibiotic conformations that constitute the dimer, the orientations of the tetrasaccharides are rel ated by an approximate to 180 degrees rotation about the glucose-ring 4 glycosidic bond. The quite different orientation of the tetrasacchar ide in each half of the dimer results in significant differences in bi nding interactions with cell wall peptides occupying the two different sites on the dimer. In one site, the hydrophobic face of glucose inte racts with the methyl group of the C-terminal D-alanine of cell wall a nalogues, while the rhamnose sugar of the same tetrasachharide may act as a hydrophilic ''cap'' where three hydroxyl groups on the edge of t he sugar can mimic a group of water molecules through a network of hyd rogen bonds. An arabinose sugar of the other tetrasaccharide occupies a similar position to the rhamnose in the second ligand binding site; its single hydroxyl group may be less effective as a hydrophilic cap, and the hydrophobic interaction to a glucose face (see above) cannot n ow take place. These observations lead to the conclusion that there ma y be a marked difference in the ligand binding affinities for the two sites. This conclusion has been confirmed experimentally.