Conformation of the exopolysaccharide of Burkholderia cepacia predicted with molecular mechanics (MM3) using genetic algorithm search.
Journal article, 2005

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.

Burkholderia polysaccharide conformation genetic algorithm molecular mechanics


F. Strino

University of Gothenburg

Avi Nahmany

University of Gothenburg

Jimmy Rosen

University of Gothenburg

Graham Kemp

Chalmers, Computer Science and Engineering (Chalmers), Computing Science (Chalmers)

Isabel Sá-correia

Instituto Superior Tecnico

Per-Georg Nyholm

University of Gothenburg

Carbohydrate Research

0008-6215 (ISSN)

Vol. 340 5 1019-1024

Subject Categories

Other Basic Medicine



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