Dihedral angles, polysaccharides

The nonbonded energy (van der Waals) is computed for isolated helical amylose chains as a function of the dihedral angles (, relative orientations of the glucose residues in the polysaccharide chain. In conformity with x-ray data, different helical conformations ere proposed for different crystalline modifications of amylose. 

The conformation of the backbone of the Klebsiella polysaccharide K23[-(l-3)-a-L-Rha-(l-3)-p-D-Glc-]n has been calculated using a force field which includes terms for non bonded interactions, the exo anomeric effect, and hydrogen bonds [203]. The calculated data were checked using NMR spectroscopy. The P-D-Glc-(l-3)-ot-L-Rha bond shows dihedral angles

[Pg.194]

Figure 4.22 Definition of dihedral angles about the glycosidic bond in methyl P-lactoside. This is drawn in the preferred conformation in water, deduced from the following three-bond coupling constants via the appropriate Karplus equations (the prime referring to the glucose moiety) — 3,8 Hz, 7c2,c4 3,1 Hz, defining cp, and /ci h4 4,9 Hz, Vci, c3 = 0Hz, Jci,c5 = 1-6Hz, defining ij/. The disaccharide unit in cellulose and other 1 4 diequatorially linked polysaccharides adopts a very similar conformation.

Figure 12.2.1. Example of the chemical structure of a polysaccharidic chain as a sequence of 5-(l-4)- linked D-glucose units having a side chain of P-glucose linked (1-6) to the backbone. The glycosidic dihedral angles are also indicated.

If one compares the conformational energy surface of proteins and polysaccharides in terms of the usual dihedral angles which determine local conformations and flexibility, the results show that 15% of the conformations for the peptide bonds of the alanyl peptide are within 5 kcal/mole of the energy minimum. On the other hand, rotation around the 8(1 4) glycosidic linkage for... 

Fig. 2 Dihedral angle < >, ij/) of the glycoside (upper structure) and peptide (lower structure) bonds that determine the higher-order structure of polysaccharides and proteins.

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