Modeling of the structure in aqueous solution of the exopolysaccharide produced by Lactobacillus helveticus 766.
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.
Faber
Elisabeth J
EJ
Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, PO Box 80.075, NL-3508 TB Utrecht, The Netherlands.
van Kuik
J Albert
JA
Kamerling
Johannis P
JP
Vliegenthart
Johannes F G
JF
D001704:Biopolymers / Q000737:chemistry; D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D007778:Lactobacillus / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011135:Polysaccharides, Bacterial / Q000096:biosynthesis / Q000737:chemistry*; D012996:Solutions; D013816:Thermodynamics; D014867:Water
D001704:Biopolymers; D011135:Polysaccharides, Bacterial; D012996:Solutions; D014867:Water