New Molecular Mechanism of Dextran Extension in Single Molecule AFM
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 (4C1) to a inverted chair (1C4) 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.
KeywordsContour Length Boat Conformation C5C6 Bond Carbohydrate Research Monomer Length
Unable to display preview. Download preview PDF.
- 3.Lee, G., Nowak, W., Jaroniec, J., Zhang, Q.M., Marszalek, P.E.: Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides (2004)Google Scholar
- 5.Neelov, I.M., Adolf, D.B., Paci, E., McLeish Biophys, T.C.B.: J. Molecular dynamics simulation of dextran extension by constant force in single molecule AFM (2006) (in press)Google Scholar
- 7.MacKerell, A.D., Bashford, D., Bellott, M., Dunbrack, R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., Karplus, M.: All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102, 3586–3616 (1998)CrossRefGoogle Scholar
- 17.Walther, K.A., Brujic, J., Li, H., Fernandes, J.F.: Sub Angstrom conformational changes of single molecule captured by AFM variance analysis. Biophysical J. (2006) (in press)Google Scholar