Aspects of conformational mobility in charged oligosaccharides

Abstract Three aspects of conformational mobility in charged oligosaccharides are discussed in this paper. Statistical thermodynamics is used to provide a simple definition of conformational mobility, or flexibility. The use of the Boltzmann distribution law, including the partition function, and the thermodynamic equilibrium condition is discussed in some detail, pointing out the importance of including both the enthalpic and entropic terms when calculating relative probabilities. A simple measure of the entropy or number of micro-canonical states based on the conformationally accessible space within 1 2 kT of a potential energy minimum is suggested. The differences between and combined use of grid-search maps of the potential energy (enthalpy) surface and equilibrium MD simulations for the free energy term are described, taking a tetrasaccharide glycopeptide as an example. Ring conformational mobility in a galactopyranose ring carrying both positively and negatively charged substituents is described for a bacterial lipoteichoic acid. The effects of branching on glycosidic linkage conformational mobility is discussed with reference to a branched tetrasaccharide containing two neuraminic acid substituents.