NMR spectroscopy in the structural elucidation of oligosaccharides and glycosides.

Anomeric-oxygen activation for glycoside synthesis: the trichloroacetimidate method.

The 3D structure of the bacterial peptidoglycan, the major constituent of the cell wall, is one of the most important, yet still unsolved, structural problems in biochemistry. The peptidoglycan comprises alternating N-acetylglucosamine (NAG) and N-acetylmuramic disaccharide (NAM) saccharides, the latter of which has a peptide stem. Adjacent peptide stems are cross-linked by the transpeptidase enzymes of cell wall biosynthesis to provide the cell wall polymer with the structural integrity required by the bacterium. The cell wall and its biosynthetic enzymes are targets of antibiotics. The 3D structure of the cell wall has been elusive because of its complexity and the lack of pure samples. Herein we report the 3D solution structure as determined by NMR of the 2-kDa NAG-NAM(pentapeptide)-NAG-NAM(pentapeptide) synthetic fragment of the cell wall. The glycan backbone of this peptidoglycan forms a right-handed helix with a periodicity of three for the NAG-NAM repeat (per turn of the helix). The first two amino acids of the pentapeptide adopt a limited number of conformations. Based on this structure a model for the bacterial cell wall is proposed.

https://www.pnas.org/content/pnas/103/12/4404.full.pdf

Three-dimensional structure of the bacterial cell wall peptidoglycan

Conformational studies of oligosaccharides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modelling.

A molecular mechanical force field is described for the conformational analysis of oligosaccharides. This force field has been derived by the addition of new parameters to the AMBER force field and is compatible with simulations of proteins. This new parametrization is assessed by comparison of the theoretically predicted conformations of Man alpha 1-3Man beta 1-4GlcNAc with the corresponding crystal structure. Molecular dynamics simulation data are presented for this structure both in vacuo and with the explicit inclusion of water molecules. While the former demonstrate significant torsional oscillations about glycosidic linkages at physiological temperature, in the latter these oscillations are highly damped due to the stabilizing influence of a "cage" of solvent-solvent and solvent-solute hydrogen bonds.

A molecular mechanical force field for the conformational analysis of oligosaccharides: comparison of theoretical and crystal structures of Man alpha 1-3Man beta 1-4GlcNAc.

Publisher Summary This chapter discusses the several possibilities regarding the specification of the energy associated with the anomeric effect, and the experimental data concerning the configurational and conformational equilibria of the anomeric center and the related variations of valence geometry. The free-energy aspect of the anomeric effect as displayed by the equilibria of isomers is the area wherein the very concept was incepted and developed, and which still dominates its investigation. A considerable amount of data has been accumulated during the past two decades on the anomeric effect in terms of structure, energy, reactivity, and other properties. The description and understanding of the nature of stereoelectronic effects is an appropriate field for the application of organic quantum chemistry. Although several molecular orbital (MO) methods successfully describe the stereochemical behavior of pyranose models, their application to the more complex carbohydrates and oligosaccharides is limited at present due to economical reasons. The various rationalizations of the anomeric effect have been offered over the past years; they may be roughly divided into two main groups—namely, the electrostatic and the delocalization rationalization of the anomeric effect. It may be expected that the intramolecular interactions involved in the anomeric effect also influence the other points on the generalized reaction hypersurface.

Igor Tvaroŝka

Papers

Anomeric and Exo-Anomeric Effects in Carbohydrate Chemistry