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Modeling of the structure in aqueous solution of the exopolysaccharide produced by Lactobacillus helveticus 766
Author(s) -
Faber Elisabeth J.,
van Kuik J. Albert,
Kamerling Johannis P.,
Vliegenthart Johannes F. G.
Publication year - 2002
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.1063
Subject(s) - glycosidic bond , chemistry , lactobacillus helveticus , molecular dynamics , dihedral angle , disaccharide , conformational isomerism , oligosaccharide , random coil , carbohydrate conformation , macromolecule , crystallography , molecular mechanics , aqueous solution , polysaccharide , computational chemistry , stereochemistry , molecule , lactobacillus , organic chemistry , biochemistry , hydrogen bond , circular dichroism , fermentation , enzyme
A method is described for constructing a conformational model in water of a heteropolysaccharide built up from repeating units, and is applied to the exopolysaccharide produced by Lactobacillus helveticus 766. The molecular modeling method is based on energy minima, obtained from molecular mechanics calculations of each of the constituting disaccharide fragments of the repeating unit in vacuo, as starting points. Subsequently, adaptive umbrella sampling of the potential of mean force is applied to extract rotamer populations of glycosidic dihedral angles of oligosaccharide fragments in solution. From these analyses, the most probable conformations are constructed for the hexasaccharide‐repeating unit of the polysaccharide. After exploring the conformational space of each of the individual structures by molecular dynamics simulations, the different repeating unit conformations are used as building blocks for the generation of oligo‐ and polysaccharide models, by using a polysaccharide building program. The created models of the exopolysaccharide produced by L. helveticus 766 exhibit a flexible twisted secondary structure and tend to adopt a random coil conformation as tertiary structure. © 2002 John Wiley & Sons, Inc. Biopolymers 63: 66–76, 2002