Molecular dynamics study of Ca-polygalacturonate clusters

A molecular dynamics (MD) experiment was carried on a system consisting of two fragments of polygalacturonic acid, each comprising six monomeric units and six calcium ions. The results are consistent with the experimental evidence of formation of Ca-polygalacturocate organized clusters. Moreover, the MD run provided evidence that the polymer chains organize in such a way that only the carboxylic groups are involved in the Ca2+ binding. The Ca2+ ions move inside channels formed by the polygalacturonic acid units with the carboxylic groups pointing towards the inner side of the channels.