Structural Studies of Oligosaccharides Using NMR Methods and Molecular Dynamics Simulations

A series of disaccharides containing beta-(1->4) O-glycosidic linkages were synthesized with 13C-enrichment at the two carbons involved in the linkage. Karplus equations for these six trans-glycoside J-couplings were derived from DFT calculations. Molecular dynamics (MD) simulations using both the CHARMM and AMBER force fields for five representative disaccharides containing Ìøå¢beta-(1->4) O-glycosidic linkage have been carried out to study the structural and dynamic properties of the linkage. Comparisons between experimental trans-glycoside J-couplings and calculated ensemble-averaged J-couplings were made for these five disaccharides. This comparison shows that the AMBER force field may be more reliable than the CHARMM force field. Similar conformational studies on three disaccharides containing ÌøåÁalpha/beta (1->2) O-glycosidic linkages were also performed. Amide cis-trans isomerization (CTI) in methyl 2-deoxy-2-acylamido-D-glucopyranosides was investigated by 1H and 13C NMR spectroscopy. Singly 13C-labeled methyl 2-deoxy-2-formamido-D-glucopyranoside (GlcNFm) anomers provided standard 1H and 13C chemical shifts, and 1H-1H and 13C-13C spin-coupling constants, for cis and trans amides that are detected readily in aqueous solution. Equipped with this information, doubly 13C-labeled methyl 2-deoxy-2-acetamido-D-glucopyranoside (GlcNAc) anomers were investigated, leading to the detection and quantification of cis and trans amides in this biologically important aminosugar. Eight new Karplus relationships have been determined for use in conformational studies of saccharide N-acetyl side-chains in solution by NMR spectroscopy. Six J-couplings sensitive to the C2-N2 torsion angle were parametrized: 3JH2,NH, 3JH2,CO, 3JC1,NH, 3JC3,NH, 3JC1,CO and 3JC3,CO. Two J-couplings sensitive to amide bond configuration (cis and trans amide) were also investigated, namely, 3JNH,CH3 and 3JC2,CH3. In relevant cases, comparisons were made to analogous coupling pathways found in proteins to evaluate the effects of peptide vs saccharide pathway structure on coupling magnitude. These new parametrizations will enable multiple, redundant J-couplings within the N-acetyl fragment of saccharides, and related structures, to be used for more confident assignments of side-chain conformation in biologically important saccharides, especially those where this structural element may play a role in molecular recognition or other biological processes. Lastly, an X-ray crystal structure of methyl beta-D-galactopyranosyl-(1->4)-alpha-D-mannopyranoside is presented with a full structural analysis, including discussion of ring-puckering behavior and comparison with other structurally related sugars.