Three-dimensional structure determination oligosaccharide

A coirplete understanding of the role of carbohydrates in biological systems requires knowledge of the distribution at equilibrium of the various conformers in aqueous solution. The conformational behavior of carbohydrates in solution can be examined from different vantage points (1,), but the most relevant approach is, no doubt, study of dilute solutions themselves. At present, high resolution NMR spectroscopy is the primary tool for determination of three-dimensional structure of oligosaccharides in solution. Optical rotation is also very sensitive to conformation (2) and there is a new, semi-enqpirical theory of optical rotation of oligosaccharides ( ). 

Until now, the determination of three-dimensional structures of oligosaccharides in solution was based primarily on proton-proton distance information obtained from n.O.e. data. Here, we discuss the application of three-bond proton-carbon coupling constants. 

Over the last twenty years or so, several approaches have been made to determine the three-dimensional structure of oligosaccharides and theoretical calculations are becoming... 

The three-dimensional structure of the aminoglycosides plays an essential role in their interaction with both RNA and the enzymes involved in the antibiotic inactivation and thus determines their biological function. A proper understanding of the different factors that govern aminoglycoside-RNA/protein interactions requires a detailed knowledge of the three-dimensional structure, and conformational properties of these oligosaccharides in both the... 

The principle that sequences of monomeric subunits are rich in information emerges most fully in the discussion of nucleic acids (Chapter 8). However, proteins and some short polymers of sugars (oligosaccharides) are also information-rich molecules. The amino acid sequence is a form of information that directs the folding of the protein into its unique three-dimensional structure, and ultimately determines the function of the protein. Some oligosaccharides also have unique sequences and three-dimensional structures that are recognized by other macromolecules. 

Biological or chemical or physical properties of an oligosaccharide are largely determined by what is exposed to the outer surface. Most interactions with other molecules will occur at the surface of the molecules. Therefore, stereo plots of CPK models are used to illustrate the conformations of the three dimensional structures discussed. 

NMR spectroscopy has developed during the last few years into a very powerful method to establish both the conformation of an oligosaccharide in solution and in the crystalline state. The solution conformation of a saccharide can be determined generally by the combination of 13C-NMR and H-NMR techniques. 2-d methods became available in the last few years and are prerequisites for the elucidation of the three dimensional structure of an oligosaccharide [7]. Both NOE measurements [21] as well as traditional determination of coupling constants and chemical shifts are important tools for the determination of preferred conformations. 2-dimensional methods have greatly improved the accessibility of these parameters from complex molecules. 

In many instances, the linkage oligosaccharide is associated with a peptide moiety, and thus the amino acid sequence must be established and, in addition, the structural parameters of the CPL oligosaccharide determined. The latter comprise (i) primary structure, (i i) type and location of noncarbohydrate substituents, and (i i i) the linkage to the peptide backbone. For gaining insight into structure-function relations, it is important for the three-dimensional structure to be determined. 

The first crystal structure of an enzyme, that of lysozyme, was determined by David C. Phillips and coworkers " in 1965. The most striking feature in the three-dimensional structure of lysozyme is a prominent cleft that traverses one face of the molecule. The X-ray structure of lysozyme complexed with a three-residue oligosaccharide showed that this cleft was, indeed, the substrate-binding site. The crystal structure of this complex provided the first three-dimensional model for how enyzmes work. 

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