Carbohydrate derivatives, molecular modeling

Interest in the structure and reactivity of D-fiuctosamine and its derivatives is determined by their practical significance for the food industry and for control/ treatment of diabetes-related pathologies, but also by a notable structural flexibility of this carbohydrate derivative, which may provide for some models that are unique for the field of carbohydrate chemistry. As an important and a major class of intermediates in the Maillard reaction, the fiuctosamine structure serves as a precursor of a broad variety of both low- and high-molecular-weight Maillard reaction products, hundreds of which have so far been identified. Here we consider only the most immediate transformation steps of D-fiuctosamine, while some of the more important Maillard reaction products whose origin can be traced to the D-fructosamine intermediates will be considered in Section IV. 

C-Furanosyl compounds embody tetrasubstituted tetrahydrofurans which are analogs of naturally occurring furanosides, in which the anomeric oxygen has been replaced by a carbon atom, providing a non-labile ether functionality in place of the biochemically crucial acetal linkage. C-Furanosyl compounds occur widely in nature, and have been used as carbohydrate isosteres. We undertook preliminary molecular modelling studies on D-jylofuranosylethyne derivatives (Fig. 3), which we... 

The carbohydrates offer rich examples to analyze the hydrogen bonding in crystals, from which rules can be extracted to be further used in molecular modeling situations. Most of the basic rules have been established throughout the analysis of high accuracy X-ray analysis and most evidently from those crystalline structures that have been derived from neutron diffraction investigations. 

Since Tyr-, His- and Trp-residues are CIDNP-responsive and often involved in carbohydrate binding, alterations of the respective signal intensities of lectins can be detected after addition of a specific saccharide. It is possible to correlate such findings with the theoretical results derived by molecular modelling techniques. CIDNP... 

Many unidentified peaks are present in all chromatograms of the various methyl ether and methyl ester fractions. Certain peaks may be attributed to the presence of partially or fully methylated carbohydrates or their derivatives. Based upon predicted retention times, considerations of molecular weight, and polarity of such compounds, and preliminary investigations of model compounds, it seems highly improbable that all of the unidentified compounds are derived from carbohydrates. Hence, identification of other compounds in these chromatograms can be pertinent not only to a more precise description of products formed in the various reactions but also to basic information concerning lignin chemistry. 

The first structure of human renin was obtained from prorenin produced by expression of its cDNA in transfected mammalian cells. Prorenin was cleaved in the laboratory to renin using the protease trypsin. Because the carbohydrates in renin are not required for bioactivity, oligosaccharides were removed enzymatically. This process facilitates crystallization in some cases and also removes the contribution of the heterogeneous sugar chains to the diffraction pattern. The structure was determined without the use of heavy-atom derivatives, by application of molecular replacement techniques based on the atomic coordinates of porcine pepsinogen as the model. The molecular dynamic method of refinement was used extensively to arrive at a 2.5 A resolution structure. However, some of the loop regions were not well resolved in this structure (Sielecki et al, 1989 Sail et al, 1990). 

The special electronic structure of the anomeric center in pyranoid derivatives results in experimentally significant differences in molecular geometry (e.g., as reflected by bond lengths and valence angles) about the anomeric carbon atom between a- and 0-pyranoses and a- and /3-pyranosides. In the article by Jeffrey, a discussion of the structural properties of the anomeric center in pyranoses and pyranosides is given, and a comparison is made of crystallographic data of some carbohydrates with the results of theoretical calculations performed on model compounds. Paulsen and co-workers also present x-ray crystallographic data in their discussion of some aspects of the conformational analysis of pentopyranosyl acetates, benzoates, and halides, in comparison with extensive conformational data compiled by Durette and Horton for these compounds in solution. 

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