Andrew Almond — Page 2

PubMed2002

Predicting the molecular shape of polysaccharides from dynamic interactions with water.

How simple monosaccharides, once polymerized, become the basis for structural materials remains a mystery. A framework is developed to investigate the role of water in the emergence of dynamic structure in polysaccharides, using the important beta(1-->4) linkage as an example. This linkage is studied within decasaccharide fragments of cellulose, chitin, mannan, xylan, and hyaluronan, using molecular simulations in the presence of explicit water solvent. Although cellulose, mannan, chitin, and xylan are chemically similar, their intramolecular hydrogen-bond dynamics and interaction with water are predicted to differ. Cellulose, mannan, and chitin favor relatively static intramolecular hydrogen bonds, xylan prefers dynamic water bridges, and multiple water configurations are predicted at the beta(1-->4) linkages of hyaluronan. With such a variety of predicted dynamics, the hypothesis that the beta(1-->4) linkage is stabilized by intramolecular hydrogen bonds was rejected. Instead, it is proposed that favored molecular configurations are consistent with maximum rotamer and water degrees of freedom, explaining observations made previously by X-ray diffraction. Furthermore, polysaccharides predicted to be conformationally restricted in simulations (cellulose, chitin, and mannan) prefer the solid state in reality, even as oligosaccharides. Those predicted to be more flexible (xylan and hyaluronan) are known to be soluble, even as high polymers. Therefore an intriguing correlation between chemical composition, water organization, polymer properties, and biological function is proposed.

Carbohydrate Conformation↗

PubMed2002

Physical interpretation of residual dipolar couplings in neutral aligned media.

A novel method is described for rapidly calculating alignment tensors from hydrodynamic shape, required for the prediction of residual dipolar couplings in neutral aligned media. Simulations of alignment were used to show that for steric restriction at a planar surface, the alignment process is dependent on linear hydrodynamic length. However, as discussed, previous methods are not in agreement with this observation. Therefore, the method presented here is the first to provide simple, accurate predictions of the alignment tensor for neutral and dilute media, while being consistent with simulations of alignment. It provides predictions in a fraction of the time of a simulation approach, while aiding physical intuition by providing a direct link between shape and alignment. Not only is this physically gratifying, but it also permits residual dipolar couplings to be applied in demanding situations where simulations of alignment are not desirable, such as in studies of molecular dynamics.

Dimyristoylphosphatidylcholine↗