Polysaccharide helical model

Five articles on polysaccharide helices solved prior to 1979 have appeared in the volumes published between 1967 and 1982.2-6 The first was a review on X-ray fiber diffraction and its application to cellulose, chitin, amylose, and related structures, and the rest were bibliographic accounts. Since then, X-ray structures of several new polysaccharides composed of simple to complex repeating units have been successfully determined, thanks to technological advances in fiber-diffraction techniques, the availability of fast and powerful computers, and the development of sophisticated software. Also, some old models have been either re-... 

The earliest attempts at model analysis of polysaccharides -typified by the x-ray crystal structure analysis of amylose triacetate - were usually conducted in three steps ( L). In the first step, a model of the chain was established which was in agreement with the fiber repeat and the lattice geometry, as obtained from diffraction data. In the second step, the invariant chain model was packed into the unit cell, subject to constraints imposed by nonbonded contacts. This was followed, in the third step, by efforts to reconcile calculated and observed structure factor amplitudes. It was quickly realized that helical models of polysaccharide chains could be easily generated and varied using the virtual bond method. Figure 1 illustrates the generation of a two-fold helical model of a (l- U)-linked polysaccharide chain. 

Figure 1. Construction of a two-fold helical model of a polysaccharide with the virtual bond method. Increasing the length VB of the virtual bond is shown by...

It has been known for almost 200 years that starch gives a deep blue color when a solution of potassium iodide and iodine is added [47]. More than a century later it was suggested that the complex consisted of a helical polysaccharide, with triiodide in the center of the helix [48]. Using flow dichroism, it was demonstrated that the triiodide was stacked in a linear structure, as required for the helical model [49]. Another study of the optical properties of crystals of the amylose-triiodide complex showed it to be consistent with a helical structure [50] and X-ray diffraction showed the triiodide complex gave the dimensions of a unit-cell of a helix with six glucose residues per turn [51]. This confirmed a helical structure for the amyiose complex with triiodide that predated the helical models proposed by Pauling for polypeptides [52] and the double helical model for DNA by Watson and Crick [53] by 10 years. 

Current methods take root in the early 1960s, when the conformational analysis of macromolecules became of general interest [29-30]. Anderson et al. [31] used model building and X-ray diffraction studies to determine the double helical structures of polysaccharides using crystalline structure data as an initial set of coordinates followed by computational sampling of new structures by rotation around selected covalent bonds. The details of these so-called hard-sphere calculations are described in Rees and Skerrett [32] and Rees and Smith [33]. This approach was also applied to carbohydrate conformations in the analysis of bacteria and polysaccharidic structures and linkages [34-35]. 

At 6 A resolution, the macromolecule usually appears as a blob of electron density and the chain backbone is generally unrecognizable. At 3.0 A resolution, it is possible to trace the path of the macromolecular chain backbone. The double helices of nucleic acids are traced readily. At 2.0 A resolution, almost all protein side chains, nucleic acid nucleotides and polysaccharide glycoses are visible. A model of the protein, nucleic acid or glycan can be constructed if the amino acid, nucleotide or monosaccharide sequence is known. At higher resolution, individual atoms begin to be seen. It is possible to identify amino acid side chains, nucleotides and glycose units directly from the electron density map. 

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