Conformation of the exopolysaccharide of Burkholderia cepacia predicted with molecular mechanics (MM3) using genetic algorithm search.
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.
Strino
Francesco
F
Department of Medical Biochemistry/Centre for Structural Biology, Göteborg University, Medicinaregatan 7B, 405 30 Göteborg, Sweden.
Nahmany
Abraham
A
Rosen
Jimmy
J
Kemp
Graham J L
GJ
Sá-correia
Isabel
I
Nyholm
Per-Georg
PG
D000465:Algorithms; D016956:Burkholderia cepacia / Q000737:chemistry*; D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D008969:Molecular Sequence Data; D011135:Polysaccharides, Bacterial / Q000737:chemistry*; D012984:Software
D011135:Polysaccharides, Bacterial