Molecular dynamics simulation of dextran extension by constant force in single molecule AFM.
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 ((4)C(1)) to the inverted chair ((1)C(4)) 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.
Neelov
Igor M
IM
Interdisciplinary Research Centre in Polymer Science and Technology and School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom.
Adolf
David B
DB
McLeish
Tom C B
TC
Paci
Emanuele
E
D003198:Computer Simulation; D003911:Dextrans / Q000737:chemistry* / Q000648:ultrastructure*; D004548:Elasticity; D018625:Microscopy, Atomic Force / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D011487:Protein Conformation; D013314:Stress, Mechanical
D003911:Dextrans