Conformational features of cepacian: the exopolysaccharide produced by clinical strains of Burkholderia cepacia

• Published in: Carbohydrate research Vol. 340; no. 5; pp. 1025 - 1037
• Main Authors: Sampaio Nogueira, Carlos E., Ruggiero, Jose R., Sist, Paola, Cescutti, Paola, Urbani, Ranieri, Rizzo, Roberto
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Ltd 11.04.2005
• Subjects: Burkholderia cepacia; Burkholderia cepacia - chemistry; Burkholderia Infections - microbiology; Carbohydrate Conformation; Carbohydrate Sequence; Cepacian; Computer Simulation; Dimethyl Sulfoxide; Exopolysaccharide; Glucuronic Acid - chemistry; Humans; Hydrogen Bonding; Molecular dynamics; Molecular modelling; Molecular Sequence Data; Monte Carlo Method; Polymer chain statistics; Polysaccharides, Bacterial - chemistry; Water; MD, molecular dynamics; Molecular modelling; Me 2SO, dimethyl sulfoxide; Burkholderia cepacia; Polymer chain statistics; HB, hydrogen bond; Molecular dynamics; Exopolysaccharide; MC, Monte Carlo; Cepacian
• ISSN: 0008-6215; 1873-426X
• DOI: 10.1016/j.carres.2004.12.028

Molecular mechanics and molecular dynamics studies were carried out on Cepacian, the exopolysaccharide produced by the majority of clinical strains of the opportunistic pathogen B. cepacia involved in cystic fibrosis pulmonary infections. Conformational energy calculations and molecular dynamics investigations, both in water and in dimethyl sulfoxide, were carried out on the exopolysaccharide cepacian produced by the majority of the clinical strains of Burkholderia cepacia, an opportunistic pathogen causing serious lung infection in patients affected by cystic fibrosis, The investigation was aimed at defining the structural and conformational features, which might be relevant for clarification of the structure–function relationships of the polymer. The molecular dynamics calculations were carried out by Ramachandran-type energy plots of the disaccharides that constitute the polymer repeating unit. The dynamics of an oligomer composed of three repeating units were investigated in water and in Me 2SO, a non-aggregating solvent. Analysis of the time persistence of hydrogen bonds showed the presence of a large number of favourable interactions in water, which were less evident in Me 2SO. The calculations on the cepacian chain indicated that polymer conformational features in water were affected by the lateral chains, but were also largely dictated by the presence of solvent. Moreover, the large number of intra-chain hydrogen bonds in water disappeared in Me 2SO solution, increasing the average dimension of the polymer chains.