Molecular Dynamics of Pectin Extension

A pectin 10mer under constant pulling speed and constant force was studied using the atomistic simulations. Molecular dynamics (MD) with the Amber99 and Amber‐Glycam04 forcefields were performed. The main result of the present Amber‐based MD simulations is that the two plateaux of the experimental force‐ extension dependence for pectin can be explained by transitions between three conformational states of pectin monomer ring (first from a chair (4C1) to boat conformation and second from boat to an inverted chair (1C4) conformation). A multi‐state dynamical model of single biopolymer extension under external force was elaborated and applied to extension of polymers with three‐state monomers relevant to pectin.