title: Conformation of the exopolysaccharide of Burkholderia cepacia predicted with molecular mechanics (MM3) using genetic algorithm search.
abstract: We present a computational conformational analysis of the exopolysaccharide of Burkholderia cepacia, which is believed to play a role in colonization and persistence of B. cepacia in the lungs of cystic fibrosis patients. The repeating unit of the exopolysaccharide is a heptasaccharide with three branches, which cause significant steric restraints. Conformational searches using glygal, an in-house developed software using genetic algorithm search methods, were performed on fragments as well as on the complete repeating unit with wrap-over residues. The force field used for the calculations was MM3(96). The search showed four favored conformations for an isolated repeating unit. However, for a sequence of several repeating units, the calculations indicate a single, well-defined linear conformation.
authors.affiliation: Department of Medical Biochemistry/Centre for Structural Biology, Göteborg University, Medicinaregatan 7B, 405 30 Göteborg, Sweden.
authors.forename: Francesco
authors.initials: F
authors.lastname: Strino
authors.forename: Abraham
authors.initials: A
authors.lastname: Nahmany
authors.forename: Jimmy
authors.initials: J
authors.lastname: Rosen
authors.forename: Graham J L
authors.initials: GJ
authors.lastname: Kemp
authors.forename: Isabel
authors.initials: I
authors.lastname: Sá-correia
authors.forename: Per-Georg
authors.initials: PG
authors.lastname: Nyholm
mesh_terms: D000465:Algorithms; D016956:Burkholderia cepacia / Q000737:chemistry*; D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D008969:Molecular Sequence Data; D011135:Polysaccharides, Bacterial / Q000737:chemistry*; D012984:Software
chemical_list: D011135:Polysaccharides, Bacterial