Computational study on the intramolecular self-organization of the macrorings of some ‘giant’ cyclodextrins (CDn, n = 40, 70, 85, 100)

Abstract

The conformations of some ‘giant’ cyclodextrins (CDn, n = 40, 70, 85, 100) were examined by molecular dynamic simulations using the Glycam06 force field. CD14 and CD26, the largest cyclodextrins, for which crystallographic data are available, were also studied as reference structures. Principal component analysis was used for the analyses of the simulation trajectories. In cases where band-flips were not present in the starting geometry (e.g. CD40), flips appeared later during the conformational search. The results for CDn (n = 14, 26, 40) confirmed an interesting observation for the distribution of band-flips along the perimeters of the macrorings, namely, band-flips separate portions of lengths of about six or twelve glucoses. This allows the formation of energetically favorable small loops of six–seven glucoses or the creation of short two-turns single helices that further enhance the stability of the structures. It was found that flip dihedrals define distributions of fragment lengths 12–6, 12–12, and 12–12–6 residues in the larger CDs (CD70, CD85, CD100). Contributions from 77% (CD40) to 88% (CD26) are from the first three highest-eigenvalue principal components, i.e., a limited number of modes determine the overall deformations of the macrorings. The flexibility of the macrorings increases, going from CD40 to the CDs, with higher degrees of polymerization. CD14 and CD26 present interesting cases – CD26 manifests domination of one deformation mode (ca. 72%), whereas CD14 demonstrates significantly higher flexibility. These results confirm our earlier conclusion, namely, LR-CDs may have more than one cavity. Thus they have the potential to accommodate more than one substrate molecule, as well as larger species by an ‘induced fit’ mechanism.