NMR spectroscopy, molecular dynamics, and conformation of a synthetic octasaccharide fragment of the O-specific polysaccharide of Shigella dysenteriae type 1

A synthetic octasaccharide fragment (2) of the O-specific polysaccharide (1 ) of Shigella dysenteriae type 1 has been studied as its methyl glycoside b y one- and two-dimensional homo- and heteronuclear NMR spectroscopy. Comple te H-1 and C-13 NMR assignments have been generated, and the C-13 spin-latt ice relaxation times have been measured for the octasaccharide 2. A congene r (6) of this octasaccharide containing one D-galactose residue with a spec ific C-13 label at C-1 has been synthesized and used to measure interglycos idic C-13-H-1 coupling by the 2D J-resolved H-1 NMR method. From the NMR da ta, three types of conformational restraints were developed: (a) 29 inter-r esidue, distance restraints; (b) 48 intra-residue, ring atom dihedral angle restraints, and (c) one heteronuclear, inter-residue dihedral angle restra int. The use of these restraints in a restrained molecular dynamics computa tion with simulated annealing yielded a conformation resembling a short, ir regular spiral, with methyl substituents on the exterior. Published by Else vier Science Ltd.