Local Dynamics of Carbohydrates. 1. Dynamics of Simple Glycans with Different Chain Linkages

Abstract

The present work gives the preliminary results of a systematic theoretical investigation of the relationship of structure and dynamics for a series of naturally occurring carbohydrate polymers as a function of the topological features, i.e., sugar composition and linkage type. Specifically, homopolymeric (1f3)-and (1f4)-linked Rand β-D-glucans and homopolymeric (1f4)-linked Rand β-D-galactans are considered. These polysaccharide chains cover a broad spectrum of macromolecular stiffness and extension. The theoretical calculations are developed within a diffusive approach that takes accurately into account the polymer connectivity and the corresponding conformational energy surface. This theoretical approach to the polymer dynamics, designated as the optimized Rouse Zimm local dynamics (ORZLD) theory, has been improved and implemented for applications to random coil polysaccharides in solution. The results show that correlation times, such as those obtainable from appropriate NMR, fluorescence, radiation scattering, and rheological relaxation experiments, are very sensitive to the details of the molecular structure and reveal patterns that are useful for characterizing the different chain topologies. Correlations are also illustrated among the dynamic chain pattern (i.e., the position and chain length dependence of the correlation times), equilibrium chain stiffness parameters, and the primary structure of the chain.

Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM

“…Under these conditions the end-toend distance is simply the algebraic sum of the lengths of all of the virtual bond vectors O i O j s . This approximation holds for flexible polysaccharides like dextran, but may be less accurate for polysaccharides like amylose, which have a preferred pseudohelical trajectory (26). These constraints could be corrected by taking into account the angle between the force vector and the virtual bond vector O i O j s for a given chain structure.…”

Biophysical functionality in polysaccharides: from Lego-blocks to nano-particles

“…Within the multiplicity of structural and conformational features (for a seminal review see Brant 1999), rules of thumb for chain topologies were assigned early to schematically ordered (Rees 1977) or statistically averaged (Burton and Brant 1983) chains and more recently extended to dynamic properties (Perico et al 1999) of simple homo and copolyglycans. Exploitation of the latter properties has been made possible by progress in FT-NMR techniques which are among the most valuable tools for studying conformations and dynamics of molecules in solution, by determining chemical shifts, coupling constants, NOEs and relaxation times (Dais 1995;Duus et al 2000).…”

“…This approach, designated optimized Rouse Zimm local dynamics (ORZLD) theory, has been improved and implemented for application to random coil polysaccharides in solution. By using ORZLD, the second-order orientational correlation time, s i , has been calculated for each bond in the chain model for the different chain linkages and for several chain lengths (Perico et al 1999). As an example, the insets of Fig.…”

Challenges for the modern analytical ultracentrifuge analysis of polysaccharides

“…In this way data from the ultracentrifuge can provide the basis for some powerful modelling of the overall conformation and flexibility of polysaccharides in solution, complementing approaches such as those of David Brant and co-workers who have been at the forefront of investigating the local spatial distribution and dynamic properties of polysaccharides using NMR, X-ray scattering and atomic force microscopy as the basis of such modelling. [6][7][8][9][10][11] This article highlights some of the key advances and challenges in the following areas: (1) Polysaccharide polydispersity and simple shape analysis by sedimentation velocity, and in particular using new approaches such as SEDFIT analysis which take advantage of the automatic data capture and analyses facilities of the new generation XL-I analytical ultracentrifuge; (2) polysaccharide molecular-weight analysis by sedimentation equilibrium focussing on model-independent procedures such as MSTAR, and how these procedures complement analysis of size exclusion chromatography coupled to multi-angle laser light scattering; (3) polysaccharide conformation analysis using traditional procedures such as the Wales-van Holde ratio, power law or ÔscalingÕ relations, more specialised treatments for rigid cylindrical structures, semi-flexible chains and worm-like coils and complications through draining effects; (4) analysis of polysaccharide interactions and in particular complex formation phenomena, involving interesting applications in the areas of mucoadhesion and sedimentation fingerprinting and (5) finally we look at the possibilities for macromolecular charge and charge screening measurement.…”