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Published in:
2006 | OriginalPaper | Chapter
New Molecular Mechanism of Dextran Extension in Single Molecule AFM
Authors : Igor Neelov, David Adolf, Tom McLeish
Published in: Computational Science and Its Applications - ICCSA 2006
Publisher: Springer Berlin Heidelberg
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A dextran monomer and a 10mer under constant pulling speed or constant force were studied using the atomistic simulations. Molecular dynamics (MD) with the Amber94 and Amber-Glycam04 forcefields were performed. The main result of the present Amber-based MD simulations is that the experimental plateau of the force-extension dependence for dextran can be explained by a transition of the glucopyranose rings in the dextran monomers from a chair (
4
C
1
) to a inverted chair (
1
C
4
) conformation whereas chair to boat transitions occur at higher forces. MD simulation of coarse-grained model of dextran consisting of two- or three-state monomers were performed to clarify the molecular mechanism of dextran extension.