Molecular dynamics study of iduronate ring conformation

Abstract

AbstractMolecular dynamics (MD) simulations of the conformation of the iduronate ring in a methyl glycoside and as the central residue in a trisaccharide have been carried out. Separate simulations were carried out with initial 1C4, 2S0, and 4C1 iduronate ring conformations. Simulations were followed by observing the time development of the Cremer–Pople ring puckering parameters θ,ϕ2. Starting with chair geometries gave trajectories showing only ring oscillations close to the initial geometry. Simulations were performed with a 2S0 starting geometry using explicit water and in vacuum with dielectric constants (ε) of 1 and 80, as well as with distance‐dependent dielectric functions of 2r and 4r. In both the explicit water simulation and the vacuum (ε = 80) simulations, extensive pseudorotational motion was observed in which boat and twist‐boat ring conformers interconvert. The overall range of ϕ22 variation in the trisaccharide was about half of that observed in the methyl glycoside. The Haasnoot procedure for calculating H‐H coupling constants in saccharides was applied to structures obtained from MD trajectories. Using MD time averaged couplings along with experimental data allowed the relative fractions of chair and boat/twist‐boat forms to be derived. © 1993 John Wiley & Sons, Inc.