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 A new method of determining the conformation of polysaccharides, developed using Alliance resources at the University of Kentucky, could prove significant in the pharmaceutical and medical industries.

It's tough to get a good look at a polysaccharide's shape. These chains of repeating sugar molecules make up a variety of organic compounds such as starch and cellulose, and they change wildly in no time. Their conformation, or the spatial arrangement of their component parts, are forever in flux. Torsion, or wrenching a body around an axis like a doorknob, twists the angles of the bonds that hold the molecules together. This complicates things as individual molecules can rotate around those bonds, changing their orientations.

"Carbons in an isolated sugar form a ring, and this cyclization leaves the molecule pretty rigid," says Guillermo Moyna, a chemistry professor at the University of the Sciences in Philadelphia. "The conformation of each sugar within a polysaccharide is very variable, however, because the sugars are only connected to one another by two highly flexible single bonds."

"There's a lot of flopping around," he adds. All this flexing and twisting has left researchers without any good experimental method of capturing a polysaccharide's conformation characteristics. X-ray crystallography and nuclear magnetic resonance spectroscopy (NMR), two common methods of studying biological macromolecules, are unsuitable because the polysaccharide conformations change too quickly. NMR, for example, gives an average of anything that happens within the sample over the course of about a millisecond to a second. Sounds fast, doesn't it? But torsion in a polysaccharide's bond can change in a nanosecond—one million times faster than a millisecond and one billion times faster than a second.

 Variation of the 13C chemical shift for the anomeric carbon (shown in red) with dihedral angles <> and <>of the model disaccharide -D-Glucocpyranose-(14)-D-Glucopyranose.
 Molecular model for the model disaccharide -D-Glucocpyranose-(14)-D-Glucopyranose.


Knowledge of a polysaccharide's conformation can have a huge payoff, despite the difficulties involved in capturing the information. These molecules are crucial to significant biological processes such as energy storage, molecular recognition, and the control of cell structure. Thus they are of great interest to the pharmaceutical, medical, and food industries.

With that in mind, Moyna and his collaborators are using two Alliance supercomputing systems at the University of Kentucky to develop a method by which researchers can determine the conformation of polysaccharides using data derived from NMR spectroscopy.


Access Online | Posted 2-13-2001

 

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