Comparison of Aqueous Molecular Dynamics with NMR Relaxation and Residual Dipolar Couplings Favors Internal Motion in a Mannose Oligosaccharide

Abstract

An investigation has been performed to assess how aqueous dynamical simulations of flexible molecules can be compared against NMR data. The methodology compares state-of-the-art NMR data (residual dipolar coupling, NOESY, and (13)C relaxation) to molecular dynamics simulations in water over several nanoseconds. In contrast to many previous applications of residual dipolar coupling in structure investigations of biomolecules, the approach described here uses molecular dynamics simulations to provide a dynamic representation 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 alpha-linked mannan is common to many glycopeptides, and therefore an understanding of the structure and the dynamics of this molecule is of both chemical and biological importance. This paper sets out to address the following questions. (1) Are the single structures which have been used to interpret residual dipolar couplings a useful representation of this molecule? (2) If dynamic flexibility is included in a representation of the molecule, can relaxation and residual dipolar coupling data then be simultaneously satisfied? (3) Do aqueous molecular dynamics simulations provide a reasonable representation of the dynamics present in the molecule and its interaction with water? In summary, two aqueous molecular dynamics simulations, each of 20 ns, were computed. They were started from two distant conformations and both converged to one flexible ensemble. The measured residual dipolar couplings were in agreement with predictions made by averaging the whole ensemble and from a specific 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 interpreted as a single-structure, this may not be a correct interpretation of molecular conformation in light of other experimental data. Second, the methodology 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, and no evidence for intramolecular hydrogen bonds at either alpha(1-->2) or alpha(1-->3) linkages was found. This is in contrast to simulations of other linkages, such as beta(1-->4), which are often predicted to maintain intramolecular hydrogen bonds and are coincidentally predicted to have less conformational freedom in solution.

Dynamic properties of biologically active synthetic heparin-like hexasaccharides

“…There are several examples of carbohydrates whose relaxation properties have been satisfactorily interpreted by isotropic models although their shapes would allow presuming a non-isotropic molecular motion. This was the case for some pentasaccharides reported in the literature (Mäler et al, 1996b;Rundlöf et al, 1999;Almond et al, 2001). In case of the Lacto-Nfucopentaose (LNF)-1 pentasaccharide, the computed anisotropy ratio from 13 C-NMR relaxation data (τ ⊥ /τ || ∼1.4) differed from that obtained from hydrodynamics (τ ⊥ /τ || ∼1.8) (Rundlöf et al, 1999).…”

Conformational studies of blood group A and blood group B oligosaccharides using NMR residual dipolar couplings

“…In this way, dipolar couplings can be predicted through Eq. predict the principal axes of the orientation tensor has been reported also by Almond et al 36 Further analysis and graphs were done with ORIGIN 6.0 (Microcal Software, Inc., Northampton, MA). Glycosidic dihedral angles were defined according to the IUPAC heavy-atom convention in which f is defined by O 5 -C 1 -O 1 -C x and c by C x-1 -C x -O 1 -C 1 .…”

“…14 -20 This method is particularly well suited for the study of molecules with internal motions of the first kind having motions on a pico-second time scale within a local minimum with limited excursions of the glycosidic dihedral angles ( 9 15°), 21 although extensions for the analysis of flexible models of oligosaccharides have been recently proposed. 22,23 The aim of this work is to determine whether the solution conformations of blood group A and B oligosaccharides are adequately described by a relatively rigid model with internal motion of the first kind or whether a more flexible model with exchange between conformers is required. One-bond C H residual dipolar couplings in partially oriented liquid crystal solutions were analyzed by energy calculations and dipolar coupling simulations.…”

Towards understanding the interaction between oligosaccharides and water molecules

“…Simulations of oligosaccharides 1, 2, and 4 have been published previously; [13][14][15] the others have not. Also, simulations of oligosaccharides 1, 2, 4, 5, and 6 have been subjected to extensive experimental testing against NMR (NOESY crosspeaks, scalar, and residual dipolar couplings), X-ray fiber diffraction, and hydrodynamic data.…”