Efficient modeling of polysaccharide conformations based on Small-Angle X-ray Scattering experimental data

Small-Angle X-ray Scattering (SAXS) curves of pullulan oligomers and gellan gum were modeled with a new string of beads model. The model enables one to simulate polysaccharide single helices with different pitch values, number of monomers per pitch, and cross-sectional radius, as well as different random coils with excluded volume taken into account. The vast conformational space of possible polysaccharide structures is systematically scanned and, for each selected polysaccharide 3D structure, the SAXS curve is calculated and compared to the SAXS experimental data. All structures with RMSSD <= 1 are retained as the solutions. By allowing the distribution of equally good solutions to the given experimental SAXS curve, the new model enables one to get a phase space of possible polymer structures in the aqueous environment. Most importantly it avoids using pre-assumed secondary structure elements to fit the experimental data. (C) 2008 Elsevier Ltd. All rights reserved.