Solvent accessibility studies on polysaccharides.

Abstract

The solvent accessible surface area (ASA) of the polysaccharides, namely (i) carrageenan (1CAR); (ii) agarose (1AGA); (iii) guaran (GUR); (iv) capsular polysaccharide (1CAP); and (v) hyaluronan (1HUA), have been computed using the solvent accessibility technique of Lee and Richards. The results show that the average variation of ASA for the various atoms in the molecules lie in the range 1-30 A(2). Irrespective of position of sulfation, either at two or four in the sugar residues in 1CAR, the charged groups interact almost equally with the solvent. The ASA values for the chains A and B in 1AGA and 1CAR indicate that there are not much interchain interactions and the chains in both the molecules interact equally with the solvent. Residue-wise analysis indicates that the ASAs of residues vary alternately, high-low-high value pattern that is similar to that of the hydrophobic behaviour of beta-strands in proteins. The results also suggest that in these polysaccharides D-configuration residues have higher ASA than L-configuration residues.