Glucose orientation and dynamics in alpha-, beta-, and gamma-cyclodextrins

We investigate, using molecular dynamics (MD) computer simulations, the conformational behavior of alpha-, beta-, and gamma-cyclodextrins (CDs). Our analysis of a 30 ns trajectory of CD solution dynamics reveals the underlying conformational behaviours of the CDs that explain their relative flexibility. The distributions of the torsion angles related to the glycosidic linkages, P(phi,psi) were calculated for the three CDs. Most noticeable is the limited range in phi torsion rotations compared with psi rotations for all the CDs. This difference between the three CDs is amplified in the motion and dynamics of their glucose monomers when we monitor their orientational and librational positions relative to the macrocyclic mean plane. The relaxation times of the monomers to their equilibrium orientations follow the pattern gamma-CD > alpha-CD > beta-CD. The root-mean-square deviations of the motion of the monomer centers of mass from the mean macrocyclic planes exhibit the same trend.