Solvent accessibility studies on glycosaminoglycans.
Theoretical calculations on the solvent accessible surface area of the commonly occurring glycosaminoglycans (GAGs) have been carried out by employing the solvent accessibility technique of Lee and Richards. The results indicate that the average variation of solvent accessible surface area (ASA) for the different atoms is in the range of 2-28 A2. The average ASA for carbon (9.02 A2) and oxygen (19.3 A2) are relatively very high compared to that for nitrogen and sulfur. The total contribution of ASA by the buried atoms in all the molecules has been found to be small. Heparin complexed with the protein is less accessible to the solvent than the uncomplexed. The iduronic acid is also found to have a varied ASA due to its conformational flexibility. The sulfate groups in heparin have 50% of the total ASA of the molecule. Residue analysis indicates that in general D-configuration residues have higher ASA than L-configuration residues.
Kaliannan
P
P
Department of Physics, Bharathidasan University, India. phys@bdu.ernet.in
Gromiha
M M
MM
Ramamurthi
K
K
Elanthiraiyan
M
M
D002240:Carbohydrate Sequence; D002241:Carbohydrates / Q000737:chemistry; D006025:Glycosaminoglycans / Q000737:chemistry*; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D010100:Oxygen / Q000737:chemistry; D012997:Solvents; D013431:Sulfates / Q000737:chemistry; D013499:Surface Properties
D002241:Carbohydrates; D006025:Glycosaminoglycans; D012997:Solvents; D013431:Sulfates; D010100:Oxygen