Modeling conformational changes in alginic acid oligomers induced by external forces

Abstract

In this study, the mechanism and nature of mechanical force-induced conformational transitions of alginate oligomers with different ratios of β-D-mannuronic acid (M unit) and α-L-guluronic acid (G unit) units were investigated. The influence of the type of glycosidic linkage in either homo- or heterooligomers on the nature of conformational transitions was also considered. For this purpose, two different theoretical methods were used: quantum mechanics (QM) at the DFT level with the EGO (Enforced Geometry Optimization) approach previously tested also for other saccharide systems, and molecular dynamics (MD) simulations within hybrid interaction potentials, which take into account both the ab initio (QM) level of theory and classical molecular mechanics (MM) force fields. This allowed to characterize in detail the structural and energetic properties of the conformational transition occurring upon the influence of external, mechanical forces (e.g. ring conformations at the path of ring-inversion process as well as the energies corresponding to initial, final and intermediate states). The results indicate qualitatively various responses against the applied force, depending on the G:M ratio, which have their source in differing topologies of glycosidic linkage in either G or M units. This is of potential relevance for determining the content of naturally heterogeneous alginate chains by the AFM experimental studies. The effects of explicit solvent and non-zero temperature are not of primarily importance in the context of determined stretching properties.