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

Francesco Strino ; Avi Nahmany ; Jimmy Rosen ; Graham J.L. Kemp (Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers)) ; Isabel Sá-correia ; Per-Georg Nyholm
Carbohydrate Research (0008-6215). Vol. 340 (2005), 5, p. 1019-1024.
[Artikel, refereegranskad vetenskaplig]

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.

Nyckelord: Burkholderia polysaccharide conformation genetic algorithm molecular mechanics



Denna post skapades 2010-02-28. Senast ändrad 2012-08-20.
CPL Pubid: 116533

 

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Institutioner (Chalmers)

Institutionen för medicinsk och fysiologisk kemi (1991-2005)
Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers)

Ämnesområden

Kemi

Chalmers infrastruktur