Mechanical Stretching of Nature Inspired Linear and Branched Polysaccharide Motifs through Steered Molecular Dynamics

A variety of 10 polysaccharide motifs comprising naturally inspired sequences of monosaccharide building blocks are studied to understand the inter-relation between their structural and mechanical behaviors. Equilibrium and steered molecular dynamics (SMD) simulations are employed to investigate the stress-strain relationships and the associated conformational flips of the pyranose moieties along the polysaccharide chains. The presence of a variety of glycosidic linkages connecting the diverse monosaccharide units along with chain-branching in some cases induce wide diversity in the carbohydrate-Ramachandran plots of the glycosidic dihedrals. Similar variations are observed in the Cremer-Pople ring puckering patterns across the polysaccharide variants. The work further provides a comparison between the experimentally obtained atomic force microscopic data of mechanical stretching for some polysaccharides with the stress-strain curves generated from our SMD simulations. Out of all the systems studied, pectin having an axial-axial orientation of the glycosidic linkage showed maximum stretching potential, while acetan-M, with an equatorial-equatorial disposition of the glycosidic bond, stretched the least. The experimental Young's modulus of the corresponding natural polysaccharides could be reasonably compared to the values obtained from our simulation models. Force distribution analysis is done to understand the propagation of punctual stress in the polysaccharides under SMD conditions. Changes in local electrophilicity or nucleophilicity of atomic centers in puckered pyranose rings are estimated through the condensed Fukui functions. All of this information can help understand the physical behavior and chemical reactivity of complex polysaccharides in a complicated milieu of electronic and steric effects experienced by them.