Saccharide conformation

FIGURE 9.27 The O-Unked saccharides of glycoproteins appear in many cases to adopt extended conformations that serve to extend the functional domains of these proteins above the membrane surface. (Adaptedfrom Jentofi, N., 1990, Trends in Biochemical Sciences 15 291-294.)... 

The reaction mixture is often complicated by condensation of mono-saccharidic molecules yielding unwanted homodisaccharides. This problem is also reduced by the minimum water approach (water activity of ca. 0.7-0.8). The organic solvent at low concentration probably deactivates the enzyme due to structural changes whereas high solvent concentrations with the necessary minimum water cause fixation of the enzyme structure in its active conformation. Unfortunately, glycosidases are rather instable in low-water media. This is a big drawback compared to highly solvent-resistant lipases.94... 

The conformational behaviour in solution of a dermatan-derived tetra-saccharide has been explored by means of NMR spectroscopy, especially by NOE-based conformational analysis. RDCs were also measured for the tetrasaccharide in a phage solution and interpreted in combination with restrained MD simulations. The RDC-derived data substantially confirmed the validity of the conformer distribution resulting from the NOE-derived simulations, but allowed an improved definition of the conformational behaviour of the oligosaccharides in solution, which show a moderate flexibility at the central glycosidic linkage. Differences in the shapes of the different species with the IdoA in skew and in chair conformations and in the distribution of the sulphate groups were also highlighted.28... 

Combining 2D-NOESY and 2D-ROESY NMR experiments with molecular modelling protocols, Kuhn and Kunz32 have been able to study the saccharide-induced peptide conformational behaviour of the recognition region of Ll-Cadherin. The detailed conformational analysis of this key biomolecule not only proves that the saccharide side chain exerts a marked influence on the conformation of the peptide chain, but also that the size and type of the saccharide indeed strongly affects the conformation of the main chain. 

Bernard , A., Raimondi, L., and Zanferrari, D., Conformational analysis of saccharides with Monte Carlo stochastic dynamics simulations, Theochem, 395, 361, 1997. 

Like the pentasaccharide, the octapeptide lies along the groove, roughly parallel to the Vh-Vl interface (Fig. 1A,B). One observes immediately that the peptide contacts some of the same areas of the binding site as the saccharide, but also extends into other areas of the site. The first four residues. Met Pl-Asp P2-Trp P3-Asn P4, adopt an extended conformation, and the last four residues. Met P5-His P6-Ala P7-Ala P8, form one turn of of-hefix. 

Optimized Potential Energy Functions in Conformational Anafysis of Saccharides... 

R. Stenutz, I. Carmichael, G. Widmalm, and A. S. Serianni, Hydroxymethyl group conformation in saccharides Structural dependencies of 2JHH, 3JHH, and 1JCH spin-spin coupling constants, J. Org. 

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