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Solvent accessibility studies on polysaccharides.

P Kaliannan1, M M Gromiha, M Elanthiraiyan

  • 1Department of Physics, Bharathidasan University, Tiruchirapalli-620024, India. kal@bdu.ernet.in

International Journal of Biological Macromolecules
|February 13, 2001
PubMed
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This study computed the solvent accessible surface area (ASA) for five polysaccharides. Results show D-configuration residues have higher ASA than L-configuration residues, offering insights into polysaccharide-solvent interactions.

Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Structural Biology

Background:

  • Polysaccharides play crucial roles in biological systems.
  • Understanding their solvent interactions is key to elucidating function.
  • Limited data exists on the solvent accessible surface area (ASA) of various polysaccharides.

Purpose of the Study:

  • To compute and analyze the solvent accessible surface area (ASA) of five distinct polysaccharides.
  • To investigate how molecular structure and configuration affect solvent accessibility.

Main Methods:

  • Employed the solvent accessibility technique developed by Lee and Richards.
  • Calculated ASA for carrageenan (1CAR), agarose (1AGA), guaran (GUR), capsular polysaccharide (1CAP), and hyaluronan (1HUA).
  • Performed residue-wise analysis to identify patterns in ASA variation.

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Main Results:

  • Average ASA variations per atom ranged from 1-30 Ų.
  • Charged groups in carrageenan (1CAR) showed consistent solvent interaction regardless of sulfation position.
  • Interchain interactions in agarose (1AGA) and carrageenan (1CAR) were minimal.
  • Residue-wise ASA exhibited an alternating high-low-high pattern, akin to protein beta-strands.
  • D-configuration residues demonstrated higher ASA compared to L-configuration residues.

Conclusions:

  • The study provides quantitative insights into the solvent accessibility of key polysaccharides.
  • Findings suggest structural similarities between polysaccharide residue behavior and protein secondary structures.
  • D-configuration residues are more exposed to solvents than L-configuration residues in these polysaccharides.