A perspective on the primary and three-dimensional structures of carbohydrates

Abstract

Carbohydrates, in more biologically oriented areas referred to as glycans, constitute one of the four groups of biomolecules. The glycans, often present as glycoproteins or glycolipids, form highly complex structures. In mammals ten monosaccharides are utilized in building glycoconjugates in the form of oligo-(up to about a dozen monomers) and polysaccharides. Subsequent modifications and additions create a large number of different compounds. In bacteria, more than a hundred monosaccharides have been reported to be constituents of lipopolysaccharides, capsular polysaccharides, and exopolysaccharides. Thus, the number of polysaccharide structures possible to create is huge. NMR spectroscopy plays an essential part in elucidating the primary structure, i.e., monosaccharide identity and ring size, anomeric configuration, linkage position, and sequence, of the sugar residues. The structural studies may also employ computational approaches for NMR chemical shift predictions (CASPER program).Once the components and sequence of sugar residues have been unraveled, the threedimensional arrangement of the sugar residues relative to each other (conformation), their flexibility (transitions between and populations of conformational states), together with the dynamics (timescales) should be addressed. To shed light on these aspects we have utilized a combination of experimental liquid state NMR techniques together with molecular dynamics simulations. For the latter a molecular mechanics force field such as our CHARMM-based PARM22/SU01 has been used. linkage two torsion angles φ and ψ are defined and for 6-substituted residues also the ω torsion angle is required. Major conformers can be identified for which highly populated states are present. Thus, in 2 many cases a well-defined albeit not rigid structure can be identified. However, on longer timescales, oligosaccharides must be considered as highly flexible molecules since also anti-conformations have been shown to exist with H-C-O-C torsion angles of ~180°, compared to syn-conformations in which the protons at the carbon atoms forming the glycosidic linkage are in close proximity.The accessible conformational space governs possible interactions with proteins and both minor changes and significant alterations occur for the oligosaccharides in these interaction processes.Transferred NOE NMR experiments give information on the conformation of the glycan ligand when bound to the proteins whereas saturation transfer difference NMR experiments report on the carbohydrate part in contact with the protein. It is anticipated that the subtle differences in conformational preferences for glycan structures facilitate a means to regulate biochemical processes in different environments. Further developments in analysis of glycan structure and in particular its role in interactions with other molecules, will lead to clarifications of the importance of structure in biochemical regulation processes essential to health and disease.

Pneumococcal Capsules and Their Types: Past, Present, and Future

“…However, discussion of the technical aspects of structural determination of PS is outside the scope of this article. The reader is referred to a number of reviews (31,38,39) for more details.…”

Development of a Karplus equation for 3JCOCH in ester-functionalized glucopyranoses and methylglucuronate.

“…α:ß 42:58. 1 NMR methods. Samples were prepared with concentrations between 0.1-0.5 M in the appropriate solvent as specified above.…”

“…26,27 The molecular dynamics treatment of the model compound was employed due to its known capability to characterize the internal molecular motion and flexible nature of carbohydrates. 1,28 The MD simulations were analyzed with respect to the population maxima of  (C4-C5-C6-O6),  (C5-C6-O6-C1') and ' (C6-O6-C1'-C2') and 9 major conformational regions could be distinguished for both α-1 and ß-1 (sampling window ± 37°). The results are summarized in Table 1 and Table 2 and Figure 3 and 4).…”

“…NMR spectroscopy, taken in conjunction with computational techniques and fitting procedures, can provide a near-complete picture of a molecule's solution geometry. [1][2][3][4][5] A particularly useful tool to determine a molecule's geometry is the Karplus relation between a coupling constant and dihedral angle of the coupled atoms, based originally on the Fermi Contact contribution in the early theories of NMR coupling phenomena. [6][7][8] The Karplus equation can describe quantitatively the correlation of experimental coupling constant to the dihedral angle between the coupled nuclei and has been used very successfully to derive molecular structures.…”

Recent Advances in NMR Studies of Carbohydrates

“…Widmalm [39] summarizes the achievements and presents the perspectives in 3D structure determination as a combination of experimental liquid state NMR techniques together with molecular dynamic simulations. Schmeider et al [40] determined the phosphorylation site of starch and glycogen.…”