The conformational space available to the flexible molecule α-D-Manp-(1-->2)-α-D-Manp-OMe, a model for the α-(1-->2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determined using experimental data and molecular simulation combined with a maximum entropy approach that leads to a converged population distribution utilizing different input information. A database survey of the Protein Data Bank where structures having the constituent disaccharide were retrieved resulted in an ensemble with >200 structures. Subsequent filtering removed erroneous structures and gave the database (DB) ensemble having three classes of mannose-containing compounds, viz., N- and O-linked structures, and ligands to proteins. A molecular dynamics (MD) simulation of the disaccharide revealed a two-state equilibrium with a major and a minor conformational state, i.e., the MD ensemble. These two different conformation ensembles of the disaccharide were compared to measured experimental spectroscopic data for the molecule in water solution. However, neither of the two populations were compatible with experimental data from optical rotation, NMR (1)H,(1)H cross-relaxation rates as well as homo- and heteronuclear (3)J couplings. The conformational distributions were subsequently used as background information to generate priors that were used in a maximum entropy analysis. The resulting posteriors, i.e., the population distributions after the application of the maximum entropy analysis, still showed notable deviations that were not anticipated based on the prior information. Therefore, reparameterization of homo- and heteronuclear Karplus relationships for the glycosidic torsion angles Φ and Ψ were carried out in which the importance of electronegative substituents on the coupling pathway was deemed essential resulting in four derived equations, two (3)J(COCC) and two (3)J(COCH) being different for the Φ and Ψ torsions, respectively. These Karplus relationships are denoted JCX/SU09. Reapplication of the maximum entropy analysis gave excellent agreement between the MD- and DB-posteriors. The information entropies show that the current reparametrization of the Karplus relationships constitutes a significant improvement. The Φ(H) torsion angle of the disaccharide is governed by the exo-anomeric effect and for the dominating conformation Φ(H) = -40 degrees and Ψ(H) = 33 degrees. The minor conformational state has a negative Ψ(H) torsion angle; the relative populations of the major and the minor states are approximately 3 : 1. It is anticipated that application of the methodology will be useful to flexible molecules ranging from small organic molecules to large biomolecules.

The conformation of saccharides in solution is challenging to characterize in the context of a single well-defined three-dimensional structure. Instead, they are better represented by an ensemble of conformations associated with their structural diversity and flexibility. In this study, we delineate the conformational heterogeneity of five trisaccharides via a combination of experimental and computational techniques. Experimental NMR measurements target conformationally sensitive parameters, including J couplings and effective distances around the glycosidic linkages, while the computational simulations apply the well-calibrated additive CHARMM carbohydrate force field in combination with efficient enhanced sampling molecular dynamics simulation methods. Analysis of conformational heterogeneity is performed based on sampling of discreet states as defined by dihedral angles, on root-mean-square differences of Cartesian coordinates and on the extent of volume sampled. Conformational clustering, based on the glycosidic linkage dihedral angles, shows that accounting for the full range of sampled conformations is required to reproduce the experimental data, emphasizing the utility of the molecular simulations in obtaining an atomic detailed description of the conformational properties of the saccharides. Results show the presence of differential conformational preferences as a function of primary sequence and glycosidic linkage types. Significant differences in conformational ensembles associated with the anomeric configuration of a single glycosidic linkage reinforce the impact of such changes on the conformational properties of carbohydrates. The present structural insights of the studied trisaccharides represent a foundation for understanding the range of conformations adopted in larger oligosaccharides and how these molecules encode their conformational heterogeneity into the monosaccharide sequence.

An investigation of the conformational properties of methyl β-maltoside, methyl α-cellobioside and methyl β-cellobioside disaccharides, using NMR spectroscopy and molecular dynamics (MD) techniques, is presented. Emphasis is placed on validation of a recently presented force field for hexopyranose disaccharides followed by elucidation of the conformational properties of two different types of glycosidic linkages, α-(1→4) and β-(1→4). Both gas-phase and aqueous-phase simulations are performed to gain insight into the effect of solvent on the conformational properties. A number of transglycosidic J-coupling constants and proton-proton distances are calculated from the simulations and are used to identify the percent sampling of the three glycosidic conformations, syn, anti-φ and anti-ψ, and, in turn, describe the flexibility around the glycosidic linkage. The results show the force field to be in overall good agreement with experiment, though some very small limitations are evident. Subsequently, a thorough hydrogen bonding analysis is performed to obtain insights into the conformational properties of the disaccharides. In methyl β-maltoside competition between HO2′-O3 intramolecular hydrogen bonding and intermolecular hydrogen bonding of those groups with solvent lead to increased sampling of syn φ,ψ conformations and better agreement with NMR J-coupling constants. In methyl α and β-cellobioside, O5′-HO6 and HO2′-O3 hydrogen bonding interactions are in competition with intermolecular hydrogen bonding involving the solvent molecules. This competition leads to retention of the O5′-HO3 hydrogen bond and increased sampling of the syn region of the φ/ψ map. Moreover, glycosidic torsions are correlated to the intramolecular hydrogen bonding occurring in the molecules. The present results verify that in the β-(1→4)-linkage intramolecular hydrogen bonding in the aqueous phase is due to the decreased ability of water to successfully compete for the O5′ and HO3 hydrogen bonding moieties in contrast to that occurring between the O5′ and HO6 atoms in this α-(1→4)-linkage.

The conformational flexibility and dynamics of two (1-->6)-linked disaccharides that are related to the action of the glycosyl transferase GnT-V have been investigated. NMR NOE and T-ROE spectroscopy experiments, conformation-dependent coupling constants and molecular dynamics (MD) simulations were used in the analyses. To facilitate these studies, the compounds were synthesised as alpha-d-[6-(13)C]-Manp-OMe derivatives, which reduced the (1)H NMR spectral overlap and facilitated the determination of two- and three-bond (1)H,(1)H, (1)H,(13)C and (13)C,(13)C-coupling constants. The population distribution for the glycosidic omega torsion angle in alpha-d-Manp-(1-->6)-alpha-d-Manp-OMe for gt/gg/tg was equal to 45:50:5, whereas in alpha-d-Manp-OMe it was determined to be 56:36:8. The dynamic model that was generated for beta-d-GlcpNAc-(1-->6)-alpha-d-Manp-OMe by MD simulations employing the PARM22/SU01 CHARMM-based force field was in very good agreement with experimental observations. beta-d-GlcpNAc-(1-->6)-alpha-d-Manp-OMe is described by an equilibrium of populated states in which the phi torsion angle has the exo-anomeric conformation, the psi torsion angle an extended antiperiplanar conformation and the omega torsion angle a distribution of populations predominantly between the gauche-trans and the gauche-gauche conformational states (i.e., gt/gg/tg) is equal to 60:35:5, respectively. The use of site-specific (13)C labelling in these disaccharides leads to increased spectral dispersion, thereby making NMR spectroscopy based conformational analysis possible that otherwise might be difficult to attain.

(1)H and (13)C NMR chemical shift data are used by the computer program CASPER to predict chemical shifts of oligo- and polysaccharides. Three types of data are used, namely, those from monosaccharides, disaccharides, and trisaccharides. To improve the accuracy of these predictions we have assigned the (1)H and (13)C NMR chemical shifts of eleven monosaccharides, eleven disaccharides, twenty trisaccharides, and one tetrasaccharide; in total 43 compounds. Five of the oligosaccharides gave two distinct sets of NMR resonances due to the α- and β-anomeric forms resulting in 48 (1)H and (13)C NMR chemical shift data sets. In addition, the pyranose ring forms of Neu5Ac were assigned at two temperatures, due to chemical shift displacements as a function of temperature. The (1)H NMR chemical shifts were refined using total line-shape analysis with the PERCH NMR software. (1)H and (13)C NMR chemical shift predictions were subsequently carried out by the CASPER program (http://www.casper.organ.su.se/casper/) for three branched oligosaccharides having different functional groups at their reducing ends, namely, a mannose-containing pentasaccharide, and two fucose-containing heptasaccharides having N-acetyllactosamine residues in the backbone of their structures. Good to excellent agreement was observed between predicted and experimental (1)H and (13)C NMR chemical shifts showing the utility of the method for structural determination or confirmation of synthesized oligosaccharides.

The intrinsic flexibility of carbohydrates facilitates different three-dimensional structures in response to altered environments. At glycosidic (1→6)-linkages three torsion angles are variable and herein the conformation and dynamics of β-L-Fucp-(1→6)-α-D-Glcp-OMe are investigated using a combination of NMR spectroscopy and molecular dynamics (MD) simulations. The disaccharide shows evidence of conformational averaging for the ψ and ω torsion angles, best explained by a four-state conformational distribution. Notably, there is a significant population of conformations having ψ = 85° (clinal) in addition to those having ψ = 180° (antiperiplanar). Moderate differences in13 C R 1 relaxation rates are found to be best explained by axially symmetric tumbling in combination with minor differences in librational motion for the two residues, whereas the isomerization motions are occurring too slowly to be contributing significantly to the observed relaxation rates. The MD simulation was found to give a reasonably good agreement with experiment, especially with respect to diffusive properties among which the rotational anisotropy,, is found to be 2.35. The force field employed showed too narrow ω torsion angles in the gauche-trans and gauche-gauche states as well as overestimating the population of the gauchetrans conformer. This information can subsequently be used in directing parameter developments and emphasizes the need for refinement of force fields for (1→6)-linked carbohydrates.

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The dynamics of GATG glycodendrimers have been investigated by NMR translational diffusion and quantitative (13)C relaxation studies (Lipari-Szabo model-free), allowing the determination of the correlation times describing the dendrimer segmental orientational mobility.