The goal of this project is to determine the structure of bacterial capsular polysaccharides related to invasive disease in humans and to characterize the conformation of these bacterial polysaccharides through NMR studies and theoretical calculations. The binding to antibodies directed against the polysaccharides and the structure of the bound antigens are also to be determined within the confines of this project. The conformational preference of model disaccharides have been studied by NMR NOE methods and have been compared to NOE build-up curves predicted from molecular dynamics and Langevin dynamics simulations; a number of carbohydrate parameter sets (force fields) have been explored along with differing conditions - values for the dielectric constant and the explicit inclusion of water. Approximate methods to calculate NOEs when internal motions are on the same time scale as overall motions have been developed. Extensive NMR relaxation time studies (T1, T2, NOE at differing magnetic field strengths) of two, distinct size distributions of the Group B meningococcal capsular polysaccharide (an a-2->8 linked sialic acid polymer) have been carried out and fit to various motional dynamics models. Rigid helical models were not able to account for the data, whereas distributions of correlation time (rectangular or log-c2 distribution) could. The conformational dynamics of the Group B polymer (DP = 42) has been modelled by computer (Langevin dynamics) and show that the polymer does not maintain a helical conformation and are in general accord with the results of the NMR studies. A more detailed comparison of NMR and computer modelling is underway.
