Molecular dynamics simulations of cyclohenicosakis-[(1-->2)-beta-D-gluco-henicosapyranosyl], a cyclic (1-->2)-beta-D-glucan (a 'cyclosophoraose') of DP 21.
We report molecular dynamics simulations of cyclohenicosakis-[(1-->2)-beta-D-gluco-henicosapyranosyl], termed 'cyclosophohenicosamer', a member of a class of cyclic (1-->2)-beta-D-glucans ('cyclosophoraoses'). Our goals were to provide insights into the conformational preferences of these cyclosophoraoses. Simulated annealing and constant-temperature molecular dynamics calculations were performed on the DP 21 cyclosophohenicosamer. The radius of gyration (R(G)) of the molecule and the conformation of glycosidic dihedral angles were used to analyze the result of computational studies. Most glycosidic linkages were concentrated in the lowest-energy region of the phi-psi energy map, and the values of radius of gyration from our simulations were consistent with the reported experimental value. The simulations produced various types of compact and asymmetric conformations within reasonable ranges of the glycosidic linkage conformation and radius of gyration. The results indicate the presence of a high degree of molecular flexibility of cyclosophohenicosamer and suggest the uniqueness of inclusion complexation with other molecules through this molecular flexibility.
Choi
Y H
YH
Department of Chemistry, Seoul National University, South Korea.
Yang
C H
CH
Kim
H W
HW
Jung
S
S
D002236:Carbohydrate Conformation / Q000187:drug effects; D003198:Computer Simulation; D003505:Cyclodextrins; D005936:Glucans / Q000737:chemistry*; D008958:Models, Molecular; D012231:Rhizobium / Q000737:chemistry; D012997:Solvents / Q000494:pharmacology; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors; D014618:Vacuum; D014867:Water / Q000494:pharmacology
D003505:Cyclodextrins; D005936:Glucans; D012997:Solvents; C416833:cyclohenicosakis((1-2)gluco-henicosapyranosyl); D014867:Water; C003328:sophorose