Interaction of Ca2+ and Na+ ions with polygalacturonate chains: a molecular dynamics study

Partially esterified polygalacturonic acid is the main component of pectin in higher plants. The carboxylic groups and their methyl esters markedly affect the ability of the pectin molecules to bind oppositely charged ions and to form gels. In order to make a contribution to the understanding of the mechanisms which regulate the ionic transfer at the soil-root interface and in the apoplast, we report the results of a set of molecular dynamics experiments in which the interactions of four fully deprotonated fragments of polygalacturonic acid, each counting 12 units, 300 water molecules and 48 or 24 Na+ and Ca2+ ions were studied. We observed the formation of Ca2+ bridges between the polygalacturonate chains. The forces driving the aggregation processes are characterized by the formation of strong coulombic interactions between the metal ions and the carboxylate groups. The results are consistent with experiment evidence of the formation of Ca-polygalacturonate organized gels. The Ca-polygalacturonate complex exhibits a lower energy compared to that of Na-polygalacturonate. The ratio of the Na+ and Ca2+ diffusion coefficients agree well with experimental reports.