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 Me2SO, 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 Me2SO. 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 Me2SO
solution, increasing the average dimension of the
polymer chains.