Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A)

The conformational preferences of cyclosophoroheptadecaose (Cys-A), which is a member of a class of cyclic (12)--D-glucan, were characterized by molecular dynamics simulations. Simulated annealing and constant temperature molecular dynamics simulations were performed on the Cys-A. The simulations produced various types of compact and asymmetrical conformations of Cys-A. Excellent agreement was found between experimental data and corresponding values predicted by molecular modeling. Most glycosidic linkages were concentrated in the lowest energy region of - energy map, and the values of radius of gyration (R_G) and the nuclear Overhauser effect (NOE) distance data derived from our simulations were finely consistent with the reported experimental values. This result will also give novel insights for the molecular complexation mechanism of Cys-A with various guest chemicals.