Molecular Dynamics of Pectin Extension

Summary: 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.