Oligosaccharides corresponding to biological repeating units of Shigella flexneri variant Y polysaccharide Part 5. Conformational analysis of a heptasaccharide hapten utilizing a combined molecular dynamics and NMR spectroscopic protocol

Abstract The conformational analysis of a heptasaccharide, α - L - Rhap -(1 → 2)- α - L - Rhap -(1 → 3)- α - L - Rhap -(1 → 3)- β - D - GlcpNAc -(1 → 2) - α - L - Rhap -(1 → 2)- α - L - Rhap -(1 → 3)- α - L - Rhap - OPr (ABCDA'B'C') corresponding to the O-antigen of Shigella flexneri variant Y is described. ROESY, T-ROESY and NOESY experiments have been used to derive proton-proton distances. These distances have been used as initial constraints to select a starting conformation for molecular dynamics (MD) calculations with the PIMM91 and CHARMm22 force fields in vacuum and in water, with and without the distance constraints. The time frames of the constrained and unconstrained dynamics simulations were employed to compute ROE build-up curves with crosrel , a program that performs a full-matrix relaxation treatment of cross relaxation. Experimental and calculated build-up curves agree favorably and are used to infer a model of conformation. Extension of this model to the polysaccharide leads to differences from the currently accepted model.