A conformational dynamics study of alpha-l-Rhap-(1-->2)[alpha-l-Rhap-(1-->3)]-alpha-l-Rhap-OMe in solution by NMR experiments and molecular simulations

Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields

D-Mannose is a structural component in N-linked glycoproteins from viruses and mammals as well as in polysaccharides from fungi and bacteria. Structural components often consist of D-Manp residues joined via α-(1→2)-, α-(1→3)-, α-(1→4)- or α-(1→6)-linkages. As models for these oligo- and polysaccharides, a series of mannose-containing disaccharides have been investigated with respect to conformation and dynamics. Translational diffusion NMR experiments were performed to deduce rotational correlation times for the molecules, 1D ¹H,¹H-NOESY and 1D ¹H,¹H-T-ROESY NMR experiments were carried out to obtain inter-residue proton-proton distances and one-dimensional long-range and 2D J-HMBC experiments were acquired to gain information about conformationally dependent heteronuclear coupling constants across glycosidic linkages. To attain further spectroscopic data, the doubly ¹³C-isotope labeled α-D-[1,2-¹³C₂]Manp-(1→4)-α-D-Manp-OMe was synthesized thereby facilitating conformational analysis based on ¹³C,¹³C coupling constants as interpreted by Karplus-type relationships. Molecular dynamics simulations were carried out for the disaccharides with explicit water as solvent using the additive CHARMM36 and Drude polarizable force fields for carbohydrates, where the latter showed broader population distributions. Both simulations sampled conformational space in such a way that inter-glycosidic proton-proton distances were very well described whereas in some cases deviations were observed between calculated conformationally dependent NMR scalar coupling constants and those determined from experiment, with closely similar root-mean-square differences for the two force fields. However, analyses of dipole moments and radial distribution functions with water of the hydroxyl groups indicate differences in the underlying physical forces dictating the wider conformational sampling with the Drude polarizable versus additive C36 force field and indicate the improved utility of the Drude polarizable model in investigating complex carbohydrates.

Bioactive polysaccharides and oligosaccharides from garlic (Allium sativum L.): Production, physicochemical and biological properties, and structure-function relationships

Garlic is a common food, and many of its biological functions are attributed to its components including functional carbohydrates. Garlic polysaccharides and oligosaccharides as main components are understudied but have future value due to the growing demand for bioactive polysaccharides/oligosaccharides from natural sources. Garlic polysaccharides have molecular weights of 1 × 10³ to 2 × 10⁶  Da, containing small amounts of pectins and fructooligosaccharides and large amounts of inulin-type fructans ((2→1)-linked β-d-Fruf backbones alone or with attached (2→6)-linked β-d-Fruf branched chains). This article provides a detailed review of research progress and identifies knowledge gaps in extraction, production, composition, molecular characteristics, structural features, physicochemical properties, bioactivities, and structure-function relationships of garlic polysaccharides/oligosaccharides. Whether the extraction processes, synthesis approaches, and modification methods established for other non-garlic polysaccharides are also effective for garlic polysaccharides/oligosaccharides (to preserve their desired molecular structures and bioactivities) requires verification. The metabolic processes of ingested garlic polysaccharides/oligosaccharides (as food ingredients/dietary supplements), their modes of action in healthy humans or populations with chronic conditions, and molecular/chain organization-bioactivity relationships remain unclear. Future research directions related to garlic polysaccharides/oligosaccharides are discussed.

Structural characterization of ulvan extracted from Ulva clathrata assisted by an ulvan lyase

Rhamnan-rich sulfated polysaccharides extracted from green algae (ulvan) constitute potentially useful natural materials for drug development. However, the characterization of their complex structures poses a challenge for their application. In this study, the structure of ulvan extracted from Ulva clathrata was analyzed with the assistance of an ulvan lyase belonging to the PL25 family. According to mass spectrometry and nuclear magnetic resonance analysis of the degraded oligosaccharides, the backbone of such a polysaccharide mainly consisted of →4)-β-d-GlcA-(1→4)-α-l-Rha3S-(1→ and →4)-β-d-Xyl-(1→4)-α-l-Rha3S-(1→ disaccharide repeating units, and the ratio is approximately 4:1. In addition, about 4% of the xylose moieties bear sulfate groups. Minor amounts of branches containing hexose and unsaturated glucuronic acid were found during the sequence analysis of hexa- to octasaccharides. These results indicated the presence of a long branch in the ulvan. The clarification of the detailed structure provides a foundation for ulvan modification and its structure-activity relationship studies.

Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and (13)C NMR spin relaxation: conformational preferences of α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe in water and dimethyl sulfoxide solutions

The monosaccharide L-rhamnose is common in bacterial polysaccharides and the disaccharide α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1'-(13)C]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR (3)JCH and (3)JCC coupling constants. Based on these spin-spin couplings the major state and the conformational distribution could be determined with respect to the ψ torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The (13)C NMR spin relaxation parameters T1, T2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d6 at two magnetic field strengths, with standard deviations ≤1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed (13)C relaxation parameters, with an average error of <2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of (13)C relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less.

Methyl 4-O-benzyl-α-l-rhamno-pyrano-side

In the title compound, C14H20O5, an inter-mediate in the synthesis of oligosaccharides, the glycosidic [H-C-O-C(H3)] torsion angle ϕH is 52.3° and the exo-cyclic [H-C-O-C(H2)] torsion angle θH is -11.7°. The hexa-pyran-ose ring has a chair conformation. In the crystal, mol-ecules are linked by O-H⋯O hydrogen bonds, forming chains propagating along [010]. Enclosed within the chains are R 3 (3)(12) ring motifs involving three mol-ecules. The chains are linked via C-H⋯π inter-actions, forming a three-dimensional network.

Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics

Lipopolysaccharide (LPS), a component of Gram-negative bacterial outer membranes, comprises three regions: lipid A, core oligosaccharide, and O-antigen polysaccharide. Using the CHARMM36 lipid and carbohydrate force fields, we have constructed a model of an Escherichia coli R1 (core) O6 (antigen) LPS molecule. Several all-atom bilayers are built and simulated with lipid A only (LIPA) and varying lengths of 0 (LPS0), 5 (LPS5), and 10 (LPS10) O6 antigen repeating units; a single unit of O6 antigen contains five sugar residues. From (1)H,(1)H-NOESY experiments, cross-relaxation rates are obtained from an O-antigen polysaccharide sample. Although some experimental deviations are due to spin-diffusion, the remaining effective proton-proton distances show generally very good agreement between NMR experiments and molecular dynamics simulations. The simulation results show that increasing the LPS molecular length has an impact on LPS structure and dynamics and also on LPS bilayer properties. Terminal residues in a LPS bilayer are more flexible and extended along the membrane normal. As the core and O-antigen are added, per-lipid area increases and lipid bilayer order decreases. In addition, results from mixed LPS0/5 and LPS0/10 bilayer simulations show that the LPS O-antigen conformations at a higher concentration of LPS5 and LPS10 are more orthogonal to the membrane and less flexible. The O-antigen concentration of mixed LPS bilayers does not have a significant effect on per-lipid area and hydrophobic thickness. Analysis of ion and water penetration shows that water molecules can penetrate inside the inner core region, and hydration is critical to maintain the integrity of the bilayer structure.

Long-range proton-carbon coupling constants: NMR methods and applications

A general review of novel NMR methods to measure heteronuclear long-range proton-carbon coupling constants ((n)JCH; n>1) in small molecules is made. NMR experiments are classified in terms of NMR pulse scheme and cross-peak nature. A discussion about simplicity, general applicability and accuracy for each particular NMR experiment is presented and exemplified. Important aspects such as the sign determination and measurement of very small coupling values involving protonated and non-protonated carbons as well as the complementarity between different experiments are also discussed. Finally, a compilation of applications in structural and conformational analysis of different types of molecules since 2000 is surveyed.

A perspective on the primary and three-dimensional structures of carbohydrates

Carbohydrates, in more biologically oriented areas referred to as glycans, constitute one of the four groups of biomolecules. The glycans, often present as glycoproteins or glycolipids, form highly complex structures. In mammals ten monosaccharides are utilized in building glycoconjugates in the form of oligo- (up to about a dozen monomers) and polysaccharides. Subsequent modifications and additions create a large number of different compounds. In bacteria, more than a hundred monosaccharides have been reported to be constituents of lipopolysaccharides, capsular polysaccharides, and exopolysaccharides. Thus, the number of polysaccharide structures possible to create is huge. NMR spectroscopy plays an essential part in elucidating the primary structure, that is, monosaccharide identity and ring size, anomeric configuration, linkage position, and sequence, of the sugar residues. The structural studies may also employ computational approaches for NMR chemical shift predictions (CASPER program). Once the components and sequence of sugar residues have been unraveled, the three-dimensional arrangement of the sugar residues relative to each other (conformation), their flexibility (transitions between and populations of conformational states), together with the dynamics (timescales) should be addressed. To shed light on these aspects we have utilized a combination of experimental liquid state NMR techniques together with molecular dynamics simulations. For the latter a molecular mechanics force field such as our CHARMM-based PARM22/SU01 has been used. The experimental NMR parameters acquired are typically (1)H,(1)H cross-relaxation rates (related to NOEs), (3)JCH and (3)JCCtrans-glycosidic coupling constants and (1)H,(13)C- and (1)H,(1)H-residual dipolar couplings. At a glycosidic linkage two torsion angles ϕ and ψ are defined and for 6-substituted residues also the ω torsion angle is required. Major conformers can be identified for which highly populated states are present. Thus, in many cases a well-defined albeit not rigid structure can be identified. However, on longer timescales, oligosaccharides must be considered as highly flexible molecules since also anti-conformations have been shown to exist with H-C-O-C torsion angles of ∼180°, compared to syn-conformations in which the protons at the carbon atoms forming the glycosidic linkage are in close proximity. The accessible conformational space governs possible interactions with proteins and both minor changes and significant alterations occur for the oligosaccharides in these interaction processes. Transferred NOE NMR experiments give information on the conformation of the glycan ligand when bound to the proteins whereas saturation transfer difference NMR experiments report on the carbohydrate part in contact with the protein. It is anticipated that the subtle differences in conformational preferences for glycan structures facilitate a means to regulate biochemical processes in different environments. Further developments in the analysis of glycan structure and in particular its role in interactions with other molecules, will lead to clarifications of the importance of structure in biochemical regulation processes essential to health and disease.

Methyl α-l-rhamnosyl-(1→2)[α-l-rhamnosyl-(1→3)]-α-l-rhamnoside penta-hydrate: synchrotron study

The title hydrate, C₁₉H₃₄O₁₃·5H₂O, contains a vicinally disubstituted tris­accharide in which the two terminal rhamnosyl sugar groups are positioned adjacent to each other. The conformation of the tris­accharide is described by the glycosidic torsion angles ϕ2 = 48 (1)°, ψ2 = −29 (1)°, ϕ3 = 44 (1)° and ψ3 = 4 (1)°, whereas the ψ2 torsion angle represents a conformation from the major state in solution, the ψ3 torsion angle conformation may have been caught near a potential energy saddle-point when compared to its solution structure, in which at least two but probably three conformational states are populated. Extensive inter­molecular O—H⋯O hydrogen bonding is present in the crystal and a water-containing channel is formed along the b-axis direction.

Measurement and applications of long-range heteronuclear scalar couplings: recent experimental and theoretical developments

The use of long-range heteronuclear couplings, in association with (1)H-(1)H scalar couplings and NOE restraints, has acquired growing importance for the determination of the relative stereochemistry, and structural and conformational information of organic and biological molecules. However, the routine use of such couplings is hindered by the inherent difficulties in their measurement. Prior to the advancement in experimental techniques, both long-range homo- and heteronuclear scalar couplings were not easily accessible, especially for very large molecules. The development of a large number of multidimensional NMR experimental methodologies has alleviated the complications associated with the measurement of couplings of smaller strengths. Subsequent application of these methods and the utilization of determined J-couplings for structure calculations have revolutionized this area of research. Problems in organic, inorganic and biophysical chemistry have also been solved by utilizing the short- and long-range heteronuclear couplings. In this minireview, we discuss the advantages and limitations of a number of experimental techniques reported in recent times for the measurement of long-range heteronuclear couplings and a few selected applications of such couplings. This includes the study of medium- to larger-sized molecules in a variety of applications, especially in the study of hydrogen bonding in biological systems. The utilization of these couplings in conjunction with theoretical calculations to arrive at conclusions on the hyperconjugation, configurational analysis and the effect of the electronegativity of the substituents is also discussed.

Sucrose in aqueous solution revisited, Part 2: adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation

We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic Φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R₁) and transverse (R₂) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S²) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80-90% of the conformations having ϕ-ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures.

Searching and optimizing structure ensembles for complex flexible sugars

NMR restrictions are suitable to specify the geometry of a molecule when a single well-defined global free energy minimum exists that is significantly lower than other local minima. Carbohydrates are quite flexible, and therefore, NMR observables do not always correlate with a single conformer but instead with an ensemble of low free energy conformers that can be accessed by thermal fluctuations. In this communication, we describe a novel procedure to identify and weight the contribution to the ensemble of local minima conformers based on comparison to residual dipolar couplings (RDCs) or other NMR observables, such as scalar couplings. A genetic algorithm is implemented to globally minimize the R factor comparing calculated RDCs to experiment. This is done by optimizing the weights of different conformers derived from the exhaustive local minima conformational search program, fast sugar structure prediction software (FSPS). We apply this framework to six human milk sugars, LND-1, LNF-1, LNF-2, LNF-3, LNnT, and LNT, and are able to determine corresponding population weights for the ensemble of conformers. Interestingly, our results indicate that in all cases the RDCs can be well represented by only a few most important conformers. This confirms that several, but not all of the glycosidic linkages in histo-blood group "epitopes" are quite rigid.

NMR analysis of conformationally dependent (n)J(C, H) and (n)J(C, C) in the trisaccharide α-L-Rhap-(1 → 2)[α-L-Rhap-(1 → 3)]-α-L-Rhap-OMe and a site-specifically labeled isotopologue thereof

An array of NMR spectroscopy experiments have been carried out to obtain conformationally dependent (1)H,(13)C- and (13)C,(13)C-spin-spin coupling constants in the trisaccharide α-L-Rhap-(1 → 2)[α-L-Rhap-(1 → 3)]-α-L-Rhap-OMe. The trisaccharide was synthesized with (13)C site-specific labeling at C2' and C2″, i.e. in the rhamnosyl groups in order to alleviate (1)H spectral overlap. This facilitated the measurement of a key trans-glycosidic proton-proton cross-relaxation rate using 1D (1)H,(1)H-T-ROESY experiments as well as a (3)J(C, H) coupling employing 1D (1)H,(13)C-long-range experiments, devoid of potential interference from additional J coupling. By means of both the natural abundance compound and the (13)C-labeled sample 2D (1)H,(13)C-J-HMBC and (1)H,(13)C-HSQC-HECADE NMR experiments, total line-shape analysis of (1)H NMR spectra and 1D (13)C NMR experiments were employed to extract (3)J(C, H) , (2)J(C, H), (3)J(C, C), and (1)J(C, C) coupling constants. The (13)C site-specific labeling facilitates straightforward determination of (n)J(C, C) as the splitting of the (13)C natural abundance resonances. This study resulted in eight conformationally dependent coupling constants for the trisaccharide and illustrates the use of (13)C site-specific labeling as a valuable approach that extends the 1D and 2D NMR methods in current use to attain both hetero- and homonuclear spin-spin coupling constants that subsequently can be utilized for conformational analysis.

Brucella melitensis 16M produces a mannan and other extracellular matrix components typical of a biofilm

Mutations in the Brucella melitensis quorum-sensing (QS) system are involved in the formation of clumps containing an exopolysaccharide. Here, we show that the overexpression of a gene called aiiD in B. melitensis gives rise to a similar clumping phenotype. The AiiD enzyme degrades AHL molecules and leads therefore to a QS-deficient strain. We demonstrated the presence of exopolysaccharide and DNA, two classical components of extracellular matrices, in clumps produced by this strain. We also observed that the production of outer membrane vesicles is strongly increased in the aiiD-overexpressing strain. Moreover, this strain allowed us to purify the exopolysaccharide and to obtain its composition and the first structural information on the complex exopolysaccharide produced by B. melitensis 16M, which was found to have a molecular weight of about 16 kDa and to be composed of glucosamine, glucose and mostly mannose. In addition, we found the presence of 2- and/or 6-substituted mannosyl residues, which provide the first insights into the linkages involved in this polymer. We used a classical biofilm attachment assay and an HeLa cell infection model to demonstrate that the clumping strain is more adherent to polystyrene plates and to HeLa cell surfaces than the wild-type one. Taken together, these data reinforce the evidence that B. melitensis could form biofilms in its lifecycle.

Analysis and validation of carbohydrate three-dimensional structures

Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein-carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein-carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures.

Structural glycobiology: a game of snakes and ladders

Oligo- and polysaccharides are infamous for being extremely flexible molecules, populating a series of well-defined rotational isomeric states under physiological conditions. Characterization of this heterogeneous conformational ensemble has been a major obstacle impeding high-resolution structure determination of carbohydrates and acting as a bottleneck in the effort to understand the relationship between the carbohydrate structure and function. This challenge has compelled the field to develop and apply theoretical and experimental methods that can explore conformational ensembles by both capturing and deconvoluting the structural and dynamic properties of carbohydrates. This review focuses on computational approaches that have been successfully used in combination with experiment to detail the three-dimensional structure of carbohydrates in a solution and in a complex with proteins. In addition, emerging experimental techniques for three-dimensional structural characterization of carbohydrate-protein complexes and future challenges in the field of structural glycobiology are discussed. The review is divided into five sections: (1) The complexity and plasticity of carbohydrates, (2) Predicting carbohydrate-protein interactions, (3) Calculating relative and absolute binding free energies for carbohydrate-protein complexes, (4) Emerging and evolving techniques for experimental characterization of carbohydrate-protein structures, and (5) Current challenges in structural glycoscience.