Conformation, dynamics and ion-binding properties of single-chain polyuronates: a molecular dynamics study

Abstract

In the present study, we report and compare sixteen explicit-solvent molecular dynamics simulations (10 ns) of homopolyuronate single chains corresponding to poly-β(1 → 4)-d-glucuronate (pGlcU), poly-β(1 → 4)-d-mannuronate (pManU), poly-α(1 → 4)-d-galacturonate (pGalU) and poly-α(1 → 4)-l-guluronate (pGlcU). Eight main simulations are performed at 300 K in the presence of Ca2+ counter-ions (neutralising amount), and starting from alternative regular two- and three-fold helical structures. Eight simulation variants probe the effect of an elevated temperature or of a different counter-ion environment. The chains are made formally infinite by application of artificial periodicity along the chain axis (octameric or nonameric repeat unit). The main observations made in these simulations are: (i) the glycosidic linkages (and local helical parameters) show an important flexibility (in time) and variability (along the chains), and regular helical structures only account for a limited fraction of the conformational ensembles populated at 300 K; (ii) for all system considered, the binding of Ca2+ counter-ions is essentially non-specific, with the formation of a dense counter-ion atmosphere around the chains (condensation), but no specific (tight-binding) interactions at well-defined coordination sites; (iii) the 32-, 95-, 21- and 21-helices appear to be the preferential regular helical forms for single chain pGlcU, pManU, pGalU and pGulU, respectively, in aqueous solution, with the possibility of a 31-helix for pGalU (these forms should be viewed in the sense of helical propensities). Taken together, these observations suggest that if chain dimers are appropriately described by the egg-box model (or any other structural model with similar qualitative features) chain–chain association within junction zones in gels must be accompanied by a substantial chain stiffening and a dramatic change in the ion-binding mode.