Conformational investigation of a cyclic enterobacterial common antigen employing NMR spectroscopy and molecular dynamics simulations

The three-dimensional structure of a cyclic enterobacterial common antigen (ECA) having four trisaccharide repeating units has been investigated by NM R spectroscopy and molecular dynamics simulations. Three different NMR para meters were determined: (a) H-1,H-1 cross-relaxation rates from NOE experim ents were used for determination of proton-proton distances; (b) trans-glyc osidic (3)J(C,H) scalar coupling constants analyzed via a Karplus-type rela tionship provided information on torsion angles; and (c) H-1,C-13 one-bond dipolar couplings obtained in a dilute liquid-crystalline medium were inter preted in terms of the orientational order and molecular conformations. The molecular dynamics simulations of the dodecasaccharide were performed with explicit water and counterions, which are important factors that strongly influence molecular conformation. Subsequently, the results from computer s imulation were used to generate a three-dimensional structure of the cyclic ECA which is consistent with the experimental NMR parameters.