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 by one- and two-dimensional homo- and heteronuclear NMR spectroscopy. Complete 1H and 13C NMR assignments have been generated, and the 13C spin-lattice relaxation times have been measured for the octasaccharide 2. A congener (6) of this octasaccharide containing one D-galactose residue with a specific 13C label at C-1 has been synthesized and used to measure interglycosidic 13C-1H coupling by the 2D J-resolved 1H NMR method. From the NMR data, three types of conformational restraints were developed: (a) 29 inter-residue, distance restraints; (b) 48 intra-residue, ring atom dihedral angle restraints, and (c) one heteronuclear, inter-residue dihedral angle restraint. The use of these restraints in a restrained molecular dynamics computation with simulated annealing yielded a conformation resembling a short, irregular spiral, with methyl substituents on the exterior.
Coxon
B
B
Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8311, USA. bruce.coxon@nist.gov
Sari
N
N
Batta
G
G
Pozsgay
V
V
D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019081:O Antigens / Q000737:chemistry*; D009844:Oligosaccharides / Q000138:chemical synthesis; D011135:Polysaccharides, Bacterial / Q000737:chemistry*; D012762:Shigella dysenteriae / Q000737:chemistry*
D019081:O Antigens; D009844:Oligosaccharides; D011135:Polysaccharides, Bacterial