The conformational sampling for a set of a- and �-(1?6)-linked oligosaccharides has been studied using explicit solvent molecular dynamics (MD) techniques and the CHARMM carbohydrate additive force field. Comparative performance of standard MD and Hamiltonian replica exchange (HREX) simulations towards adequate sampling of conformational space has been explored owing to the fact that these oligosaccharides are characterized by increased flexibility due to involvement of three dihedrals (F, ? and ?) in the (1?6)-linkage. Emphasis is placed on the conformational flexibility surrounding the glycosidic w torsion angle (gt:gg:tg), which is known to be important in the development of active inhibitors for N-acetylglucosylaminyl transferase V. From the simulations a number of transglycosidic J-coupling constants and proton-proton distances were calculated. The calculated values are in good agreement with NMR data, providing validation for the force field and simulation methodology employed in this study.

Conformational properties of (1→6)-linked oligosaccharides

244th National Meeting (2012)

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