Complex Carbohydrate Structure Data

NMR techniques used in combination with databases is helpful for carbohydrate analysis. For example, SUGABASE is a carbohydrate-NMR database that combines CarbBank complex carbohydrate structure data (CCSD) with proton and carbon chemical shift values (151). 

Table 6 Structural data for [Bu2Sn(IV)] and [Et2Sn(IV)] carbohydrates and related compounds complexes, obtained by X-ray diffraction and... 

One special feature in the interpretation of the quantitative results seems not to have been exploited in practical analysis, and it certainly deserves attention. The result of the methylation analysis is sometimes complex, and can reveal the occurrence of 10 to 20 different methylated sugars. In this situation, it is not easy to decide, by simple inspection of the analytical data, whether the result could be caused by one complex, carbohydrate chain, or by a structure containing several saccharide chains bound to a common aglycon. In addition, it is not always easy to decide whether the result could fit any natural structure, or mixture of structures, or whether the complex result is attributable to undermethylation. 

Fig. 7. (A) A detailed model of the amino-terminal al(IV) and a2(IV) chains containing the 7 S domain and an adjacent segment of the main triple helix. The terminal sequence of both chains is nonhelical and contains lysines (K), hydroxylysines (K), and cysteines (C) that participate in intra- and intermolecular cross-linking. A helical cross-linking site is located about 30 nm from the amino terminus (N) of the molecule and contains cysteines and a hydroxylysine in the al(IV) chain involved in cross-linking plus a complex carbohydrate attachment site (CHO). The cap site within the main triple helix identifies a series of four triplets containing proline (P) and hydroxyproline (P), a composition that would be expected to form a very stable helical structure, [Data from Glanville et al. (1985) Siebold et al. (1987)]. (B) The antiparallel arrangement of type IV molecules with alignment of cross-linking sites.

For the carbohydrates especially, the amount of available crystal structural data decreases sharply with molecular complexity [479]. With the exception of the cyclodextrins, discussed in Part III, Chapter 18, there are less than 40 crystal structure analyses of oligosaccharides, of which less than 10 are trisaccharides, one is a tetrasaccharide, and one a hexasaccharide (Part III, Chap. 18). The majority of the basic monosaccharides that are the subunits of the polysaccharides that occur naturally have been studied for example, the pyranose forms of /7-arabinose, a-xylose, a- and -glucose, / fructose, a-sorbose, a-mannose, a- and -galactose, a-fucose, a-rhamnose, N-acetyl glucosamine, and mannosamine (Box 13.2). How-... 

In our opinion, this development was facilitated mainly by two key factors the technical progress of all analytical methods, particularly in the fields of NMR spectroscopy and X-ray diffractometry, and the plenty of structural data meanwhile available for metal complexes of model compounds of carbohydrates. The basic research on the structural chemistry of the latter complexes followed by a transfer of the thereby gained knowledge in stability and regioselectivity of metal coordination into reducing carbohydrates has proved to be very successful. By this way, the improvement of existing and the development of new applications of metal complexes of carbohydrates, which provide a cheap and renewable feedstock, is merely a matter of time. 

A monograph on carbohydrate chemistry has appeared in Topics in Current Chemistry, the history of the subject from its origins has been surveyed in a Chinese language publication and a data bank of the structures of all complex carbohydrates larger than disaccharides has been set up. Reports of papers given at an American Chemical Society Symposium on computer modelling of carbohydrate comp>ounds have appeared in a collected volume. ... 

In solution, complex carbohydrates do not exhibit distinct secondary structural motifs, and any force field must be able to describe the structure of 9 cariwhydrate in terms of an ensemble of conformations. Unfortunately, without extensive experimental data it is often difficult to assess the validity of such a conformational ensemble and force field validation remains a challenge. 

In summary, the CIDNP method is a potent addition to the arsenal of biophysical methods which are successfully used in the field of structural glycosciences. The combination of X-ray data, molecular modelling, trNOE-methods and laser-photo CIDNP provides valuable structural information about protein-carbohydrate complexes. This is of particular importance, when multidimensional NMR-data can not be recorded due to the size of the molecule. Furthermore, the analysis of similar carbohydrate-binding proteins sharing a sufficient sequence homology is possible when complete structural data are available only for a few of them and CIDNP-and molecular modelling data are present for all of them. The successful role, which CIDNP-experiments can play for the solution of important structural glyco-... 

Infrared and Raman spectroscopy are in current use fo r elucidating the molecular structures of nucleic acids. The application of infrared spectroscopy to studies of the structure of nucleic acids has been reviewed,135 as well as of Raman spectroscopy.136 It was noted that the assignments are generally based on isotopic substitution, or on comparison of the spectrum of simple molecules that are considered to form a part of the polynucleotide chain to that of the nucleic acid. The vibrational spectra are generally believed to be a good complementary technique in the study of chemical reactions, as in the study76 of carbohydrate complexation with boric acid. In this study, the i.r. data demonstrated that only ribose forms a solid complex with undissociated H3B03, and that the complexes are polymeric. 

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