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Molecular Dynamics Simulation of Dextran Extension by Constant Force in Single Molecule AFM

Interdisciplinary Research Centre in Polymer Science and Technology and School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom

Correspondence: Address reprint requests to E. Paci, Tel.: 44-113-343-3806; E-mail: e.paci{at}leeds.ac.uk.

The extension of 1–6 polysaccharides has been studied in a series of recent single molecule AFM experiments. For dextran, a key finding was the existence of a plateau in the force-extension curve at forces between 700 and 1000 pN. We studied the extension of the dextran 10-mer under constant force using atomistic simulation with various force fields. All the force fields reproduce the experimental plateau on the force-extension curve. With AMBER94 and AMBER-GLYCAM04 force fields the plateau can be explained by a transition of the glucopyranose rings in the dextran monomers from the chair (⁴C₁) to the inverted chair (¹C₄) conformation while other processes occur at smaller (rotation around C5-C6 bond) or higher (chairs to boat transitions) forces. The CHARMM force field provides a different picture which associates the occurrence of the plateau to chair-boat transitions of the glucopyranose rings.