Conformational analysis of saccharides

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

K. Rasmussen and J. Fabricius, Optimized Potential Energy Fxmctions in Conformational Analysis of Saccharides. ACS Symposium Series No 430. Am. Chem. Soc. (1990) 177. 

NMR and UV-vis spectroscopic studies as well as molecular mechanics calculations have been performed for the trans and cis isomers of a series of chlorine substituted stilbenes. In a continuing study on the use of hydroxy protons in conformational analysis of saccharides in aqueous solution by NMR, a number of disaccharides with 1,3-, 1,4- and 1,6-hnkages were investigated. ... 

Several interesting papers have been devoted to determination of the structure of carbohydrates. This includes a review by Duus et alP devoted to modem NMR methods and their limitations and a short review written by Ferrier on the use of Vhc and Vcc couplings and other NMR parameters in conformational analysis of saccharides. 

A Monte Carlo Method for Conformational Analysis of Saccharides. 

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. 

In 1937 Isbell published an important paper on the conformational analysis of aldopyranoses, in which several of the forms were depicted (see Fig. 2). They comprise a 4C, chair (I), afl03 boat (II), two half-chairs (III and IV), and a coplanar pyranose (V). He correctly favored the chair form (I) and predicted that, in the case of saccharides, the chair would tend to assume a somewhat flatter conformation than that of carbocycles such as cyclohexane because of the smaller bond angles of oxygen as compared to those of carbon (105° instead of 109.5°). We now know that such coplanarity is strongly avoided because of the strain that would be produced and because of the repulsive forces between the substituents. 

Several applications of these couplings to the conformational analysis of various mono- and oligosaccharides have also been described.138 140 143 149 150 These applications incorporate both theoretical and experimental approaches toward determination of the conformation of saccharides in solution, a question still controversial because of the time-averaged character of the NMR data obtained (NOE and couplings) and the occurrence of conformational equilibria.3 Variations of Vc H values for maltose according to the solvent used have been observed,46 and... 

Nyholm P-G, Pascher I. Orientation of the saccharide chains of glycolipids at the membrane surface Conformational analysis of... 

Paulsen, H, Synthesis, conformation, and x-ray analysis of saccharide chains of glycoprotein core regions, Angew. Chem., 102, 851-867, 1990. 

Spin-lattice relaxation and transient nuclear Overhauser enhancement (tnOe) experiments with C- and H-labelled substrates have been used for the conformational analysis of several mono- and di-saccharides. An investigation of the molecular dynamics of polyciystalline mono- and di-saccharides involved measurements of the temperature dependencies of proton spin-lattice relaxation times and second moments of n.m.r. lines. ... 

Reviews have been published on progress over the last 20 years in computional methods for studying oligo- and poly-saccharide conformations in the solid state and in solution, and on the newer techniques of H-n.m.r. spectroscopy which have proved useful in the elucidation of oligosaccharide structures. A review and a symposium report have appeared on the conformational analysis of oligosaccharides in solution by n.m.r. methods combined with... 

Nyholm, P.-G. and Pascher, I., Orientation of the saccharide chains of glycolipids at the membrane surface Conformational analysis of the glucose-ceramide and the glucose-glyceride linkages using molecular mechanics (MM3), Biochemistry, 1993, 32 1225-1234. 

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... 

C-NMR relaxation parameters may also be employed to access the rates of overall and internal motions for saccharide molecules.230 Longitudinal and transversal heteronuclear relaxation times as well as hetero-nuclear NOEs depend on the molecular motion of the molecule, including overall and internal motions. Thus, careful analysis of these parameters can be employed to demonstrate the presence of conformational heter-eogeneity and/or dynamics, as well as the restriction to motion and the timescale of the existing fluctuations. Different examples of application of this methodology to trisaccharides,231 232 tetrasaccharides,233 pentasaccharides,234 and polysaccharides235,236 have been described. 

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