Premium
Conformational analysis of the exopolysaccharide from Burkholderia caribensis strain MWAP71: Impact on the interaction with soils
Author(s) -
Vanhaverbeke Cécile,
Heyraud Alain,
Mazeau Karim
Publication year - 2003
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10432
Subject(s) - chemistry , glycosidic bond , polysaccharide , force field (fiction) , molecular dynamics , dihedral angle , crystallography , polymer , stereochemistry , computational chemistry , molecule , hydrogen bond , organic chemistry , artificial intelligence , computer science , enzyme
The strain MWAP71 of Burkholderia caribensis produces a branched charged exopolysaccharide (EPS) that is responsible for soil aggregation. Understanding the conformational properties of the isolated polysaccharide is a prerequisite for proper investigation of the interactions between the polysaccharide and the soil at the atomic level. The aim of this study is first to have an overall view of the flexibility of the backbone and then to ascertain the role played by side groups in the conformational properties of the main chain. Conformational analysis of each oligomeric segment of the polysaccharide has been performed by means of adiabatic mapping of the backbone glycosidic torsion angles using the MM3(92) force field. Substitution by an acetyl group or by a Kdo unit has only a slight effect on the potential energy surfaces of the fragment model compounds. Calculated partition functions, however, indicate that the overall flexibility is slightly larger for the substituted oligomers than for the unsubstituted ones. Prediction of selected average interproton distances from the AB and BC potential energy surfaces allows comparison between modeling results and NMR measurements performed on the ABC fragment. Agreement between the experimental and the predicted data suggests that the established surfaces correctly reflect the observed conformational behavior of such fragments and validate the modeling protocol. The above results have been extended to regular and disordered long polymer chains, differing in Kdo content. It is found that Kdo affects the helical conformations of the polysaccharide. The number of stable helices is considerably larger with Kdo than without Kdo. On the contrary, Kdo has only a moderate effect on unperturbed disordered conformations of the polysaccharide. Predicted persistence length of 70 Å suggests that the polymer is semirigid with moderate extension. A further validation of the modeling results is obtained by the good concordance between this predicted value and the experimental one of 95 Å, measured from light scattering and viscosity experiments. The results lead to an understanding of the interactions of this polysaccharide with soils. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 480–497, 2003