How Accurate Is the Egg-Box Model in Describing the Binding of Calcium to Polygalacturonate? A Molecular Dynamics Simulation Study

We performed molecular dynamics (MD) simulations of octameric galacturonate, GalA 8, chains in the presence of Ca 2+ in a ratio of R = [Ca 2+ ]/[GalA] = 0.25 in order to determine to which extent the popular “egg-box model” (EBM) is able to describe the association between Ca 2+ cations and polygalacturonate (polyGalA) chains. To this aim, we slightly revised the empirical parameters for the interaction between Ca 2+ and the carboxylate oxygen atoms of GalA units so as to reproduce the experimental Ca 2+ –GalA association constant. We also defined an ad hoc order parameter, referred to as the egg-box score (EBS), that quantifies any deviation of the local coordination geometry of calcium cations with respect to an “ideal” EBM coordination geometry. The results reveal that the local coordination geometry of Ca 2+ cations bound to polyGalA chains differs from that of the EBM. Moreover, polyGalA chains exhibit significant conformational disorder, and the cross-link angles formed between polyGalA chain axes are broadly distributed. Overall, the present study suggests that the EBM fails to describe accurately the association modes between calcium and polyGalA chains at a molar ratio R of 0.25.