Conformational Properties of Single-Chain Polyuronates: A Comparative Molecular Simulation Study of Polyglucuronates, Polygalacturonates, and Alginates

Polyuronates are polyelectrolytes widely distributed in nature with a broad range of practical applications. Linear polysaccharide molecules, such as polyglucuronates, polygalacturonates, and alginates, despite having similar chemical character, exhibit distinct conformational properties due to several details in their molecular structure. This study focuses on the detailed conformational analysis of individual polyuronate chains, including alginates of heterogeneous composition. The research employed molecular dynamics atomistic simulations and Monte Carlo simulations based on a coarse-grained model, enabling the consideration of chains with lengths of up to hundreds of monomers. The results obtained for all polyuronates allowed us to rank the local rigidity of their chains and interpret these data in the context of the available conformational space for rotations around glycosidic linkages. The descriptors of local chain stiffness (persistence length and characteristic ratio) are strongly correlated with the average number of consecutive linkages in a polyuronate chain that remain in the dominant <i>syn-exo</i> conformation. Surprisingly, the block composition of the alginate chain does not significantly affect the global conformation of the longer chains. The only significant factor is the content of mannuronate (M) and guluronate (G) monomers. This observation was used to establish relationships among the fractions of MM, GG, and MG blocks in the alginate chain and its conformational properties. The differences in the persistence length of alginates under standard ionic strength conditions are not drastically large, reaching at most 6 nm when comparing the most (MM) and least (MG) flexible blocks. However, applying the Odijk-Skolnick-Fixman model and simulation data revealed a significant increase in both the persistence length values (for all polyuronates studied) and the differences between the corresponding values for alginates with varying compositions (they can reach hundreds of nanometers). This suggests the theoretical possibility of estimating the composition of an alginate chain through conformational measurements under conditions of extremely low ionic strength.