Studies on the solution conformation and dynamics of the trisaccharide repeating unit of the KPS from Sinorhizobium fredii SVQ293

The conformational behaviour of the major trisaccharide repeating unit (alp ha-D-Galp-(1 -->2)beta-D-Ribf-(1-->9)-alpha-5-O-Me-Kdnp-) of the polysaccha ride from Sinorhizobium fredii SVQ293, a mutant derivative has been analyse d by NMR spectroscopy and extensive molecular dynamics simulations. The res ults obtained indicate that the five-membered ring adopts an almost unique conformation as do the pyranose rings. The Ribf-(1-->9)-alpha-5-O-Me-Kdnp l inkage may adopt a variety of conformations while the alpha-D-Galp-(1-->2)- beta-D-Ribf- also populates an extended surface of the Phi/Psi map. Two 10 ns MD simulations using the GB/SA continuum solvent model for water and the MM3* force field provides a population distribution of conformers which sa tisfactorily agrees with the experimental NMR data for both the glycosidic linkages and the hydroxymethyl groups.