Comparison of aqueous molecular dynamics with NMR relaxation and residual dipolar couplings favors internal motion in a mannose oligosaccharide

An investigation has been performed to assess how aqueous dynamical simulat ions of flexible molecules can be compared against NMR data. The methodolog y compares state-of-the-art NMR data (residual dipolar coupling, NOESY, and C-13 relaxation) to molecular dynamics simulations in water over several n anoseconds. In contrast to many previous applications of residual dipolar c oupling in structure investigations of biomolecules, the approach described here uses molecular dynamics simulations to provide a dynamic representati on of the molecule. A mannose pentasaccharide, alpha -D-Manp-(1 -->3)-alpha -D-Manp-(1 -->3)-alpha -D-Manp(1 -->3)-alpha -D-Manp-(1 -->2)-D-Manp, was chosen as the model compound for this study. The presence of a-linked manna n is common to many glycopeptides, and therefore an understanding of the st ructure and the dynamics of this molecule is of both chemical and biologica l importance. This paper sets out to address the following questions. (1) A re the single structures which have been used to interpret residual dipolar couplings a useful representation of this molecule? (2) If dynamic flexibi lity is included in a representation of the molecule, can relaxation and re sidual dipolar coupling data then be simultaneously satisfied? (3) Do aqueo us molecular dynamics simulations provide a reasonable representation of th e dynamics present in the molecule and its interaction with water? In summa ry, two aqueous molecular dynamics simulations, each of 20 ns, were compute d. They were started from two distant conformations and both converged to o ne flexible ensemble. The measured residual dipolar couplings were in agree ment with predictions made by averaging the whole ensemble and from a speci fic single structure selected from the ensemble. However, the inclusion of internal motion was necessary to rationalize the relaxation data. Therefore , it is proposed that although residual dipolar couplings can be interprete d as a single-structure, this may not be a correct interpretation of molecu lar conformation in light of other experimental data. Second, the methodolo gy described here shows that the ensembles from aqueous molecular dynamics can be effectively tested against experimental data sets. In the simulation , significant conformational motion was observed at each of the linkages, a nd no evidence for intramolecular hydrogen bonds at either alpha (1 -->) or alpha (1 -->3) linkages was found. This is in contrast to simulations of o ther linkages, such as beta (1 -->4), which are often predicted to maintain intramolecular hydrogen bonds and are coincidentally predicted to have les s conformational freedom in solution.