Conformational features of cepacian: the exopolysaccharide produced by clinical strains of Burkholderia cepacia.
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.
Nogueira
Carlos E Sampaio
CE
UNESP Sao Paulo State University, Department of Physics, IBILCE, Sao Jose do Rio Preto, Brazil.
Ruggiero
Jose R
JR
Sist
Paola
P
Cescutti
Paola
P
Urbani
Ranieri
R
Rizzo
Roberto
R
D019121:Burkholderia Infections / Q000382:microbiology; D016956:Burkholderia cepacia / Q000737:chemistry*; D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D003198:Computer Simulation; D004121:Dimethyl Sulfoxide; D020723:Glucuronic Acid / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D011135:Polysaccharides, Bacterial / Q000737:chemistry*; D014867:Water
D011135:Polysaccharides, Bacterial; C487212:cepacian; D014867:Water; D020723:Glucuronic Acid; D004121:Dimethyl Sulfoxide