BIOPHYSICAL THEORY AND MODELING |
Molecular dynamics simulation of dextran extension by constant force in single molecule AFM
Igor Neelov 1, David B Adolf 1, Emanuele Paci 1* and Tom CB McLeish 1
1 University of Leeds
* To whom correspondence should be addressed. E-mail: e.paci{at}leeds.ac.uk.
Submitted on December 6, 2005
Revised on January 13, 2006
Accepted on 7 August 2006
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Abstract |
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The extension of 1-6 polysaccharides has been studied in a serThe extension of 1-6 polysaccharides has been studied in a series of recent single molecule AFM experiments. For dextran, a key funding was the existence of a plateau in the force-extension curve at forces between 700 and 1000pN. We studied the extension of the dextran 10mer under constant force of different magnitude using atomistic simulation with various forcefields. All the forcefields reproduce the experimental plateau on the force-extension curve. With AMBER94 and AMBER-GLYCAM04 forcefields 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 forcefield provides a different picture which associates the occurrence of the plateau to chair-boat transitions of the glucopyranose rings.
Key Words:
1-6 polysaccharides, alpha-D-glucopyranose, atomic force spectroscopy, dextran, force fields, molecular dynamics
