Reconciling MA'AT and molecular dynamics models of linkage conformation in oligosaccharides

Context Effects on Human Milk Oligosaccharide Linkage Conformation and Dynamics Revealed by MA'AT Analysis

An emerging NMR method, MA'AT analysis, has been applied to investigate context effects on the conformational properties of several human milk oligosaccharides (HMOs). The MA'AT model of the β-(1→4) linkage in the disaccharide, methyl β-lactoside (MeL), was compared to those obtained for the same linkage in the HMO trisaccharides, methyl 2'-fucosyllactoside (Me2'FL) and methyl 3-fucosyllactoside (Me3FL), and in the tetrasaccharide, methyl 2',3-difucosyllactoside (Me2',3DFL). MA'AT analysis revealed significant context effects on the mean values and circular standard deviations (CSDs) of the psi (ψ) torsion angles in these linkages. α-Fucosylation at both O2'Gal and O3Glc of MeL to give Me2',3DFL significantly constrained librational motion about ψ (70% reduction in the CSD) and shifted its mean value by ∼18°. α-Fucosylation at the O3Glc of MeL to give Me3FL constrained ψ more than α-fucosylation at the O2Gal to give Me2'FL. These effects can be explained by the expected solution conformation of Me3FL, which closely resembles the Lewisx trisaccharide. Comparisons of MA'AT models of ψ to those obtained by 1 μs aqueous molecular dynamics simulation (GLYCAM06) revealed identical trends, that is, MA'AT analysis was able to recapitulate molecular behavior in solution that was heretofore only available from MD simulation. The results highlight the capabilities of MA'AT analysis to determine probability distributions of molecular torsion angles in solution as well as degrees of librational averaging of these angles.

NMR investigations of glycan conformation, dynamics, and interactions

Glycans are ubiquitous in nature, decorating our cells and serving as the initial points of contact with any visiting entities. These glycan interactions are fundamental to host-pathogen recognition and are related to various diseases, including inflammation and cancer. Therefore, understanding the conformations and dynamics of glycans, as well as the key features that regulate their interactions with proteins, is crucial for designing new therapeutics. Due to the intrinsic flexibility of glycans, NMR is an essential tool for unravelling these properties. In this review, we describe the key NMR parameters that can be extracted from the different experiments, and which allow us to deduce the necessary geometry and molecular motion information, with a special emphasis on assessing the internal motions of the glycosidic linkages. We specifically address the NMR peculiarities of various natural glycans, from histo-blood group antigens to glycosaminoglycans, and also consider the special characteristics of their synthetic analogues (glycomimetics). Finally, we discuss the application of NMR protocols to study glycan-related molecular recognition events, both from the carbohydrate and receptor perspectives, including the use of stable isotopes and paramagnetic NMR methods to overcome the inherent degeneracy of glycan chemical shifts.

NMR Coupling Constants, Karplus Equations, and Adjusted MD Statistics: Detecting Diagnostic Torsion Angles for the Solution Geometry of 6-[α-d-Mannopyranosyl]-d-Mannopyranose (Mannobiose)

The quantitative solution conformations of 2-(hydroxymethyl)-tetrahydropyran, α-methyl-d-mannopyranoside, and 6-[α-d-mannopyranosyl]-d-mannopyranose (mannobiose) are described. Parametrized Karplus equations for redundant spin pairs across the terminal ω-torsion and the glycosidic ω-torsion for mannobiose are developed, including ω/θ-hypersurfaces for the terminal hydroxymethylene group. Experimental NMR data, algorithmic spectral simulation (clustered Hamiltonian method), molecular dynamics (MD) simulations (GLYCAM06), energy minimizations by DFT, and adjusted torsion angle populations weighted over the Karplus-type equations are used. We demonstrate that spectral simulation is a powerful tool in the refinement of initial J values obtained from static GAIO DFT calculations. We also show that only as few as one of multiple redundant torsions can be diagnostic for conformational analysis of the disaccharide.

MA'AT analysis of the O-glycosidic linkages of oligosaccharides using nonconventional NMR J-couplings: MA'AT and MD models of phi

MA'AT analysis (Meredith et al., J. Chem. Inf. Model. 2022, 62, 3135-3141) is a new NMR-based method to treat ensembles of redundant NMR spin-coupling constants (J-couplings) to obtain experiment-based probability distributions of molecular torsion angles in solution. Work reported to date on modeling the conformations of O-glycosidic linkages of oligosaccharides using three conventional J-coupling constraints (2 J COC, 3 J COCH, 3 J COCC) has shown that the method gives mean torsion angles and circular standard deviations (CSDs) for psi in very good agreement with those obtained by MD simulation. On the other hand, CSDs for phi determined by MA'AT analysis have consistently been much larger than those determined by MD, calling into question either the reliability of MA'AT analysis or MD to accurately predict this behavior. Prior work has shown that this discrepancy does not stem from the limitations of DFT-based J-coupling equation parameterization where secondary conformational dependencies can introduce uncertainties. The present work re-visits this problem by incorporating a new nonconventional J-coupling constraint into MA'AT analyses of phi, namely, a geminal (two-bond) 2 J CCH J-value that exhibits a strong primary dependence on phi. The latter property pertains explicitly to linkages contributed by GlcNAc pyranosyl rings and pyranosyl rings devoid of substituents at C2 (i.e., deoxy residues) where known secondary contributions to 2 J CCH magnitude caused by C-O bond rotation involving the coupled carbon are negligible or absent. The results show that when 2 J CCH values are added to the analysis, phi CSDs reduce considerably, bringing them into better alignment with those obtained by MD simulation. The cause of the discrepancy when only three conventional J-couplings are used to treat phi appears to be associated with the two-bond 2 J COC, which has properties that make it less effective than the non-conventional 2 J CCH as a discriminator of different conformational models of phi.

Methyl α-D-galactopyranosyl-(1→3)-β-D-galactopyranoside and methyl β-D-galactopyranosyl-(1→3)-β-D-galactopyranoside: Glycosidic linkage conformation determined from MA'AT analysis

MA'AT analysis has been applied to two biologically-important O-glycosidic linkages in two disaccharides, α-D-Galp-(1→3)-β-D-GalpOMe (3) and β-D-Galp-(1→3)-β-D-GalpOMe (4). Using density functional theory (DFT) to obtain parameterized equations relating a group of trans-O-glycosidic NMR spin-couplings to either phi (ϕ') or psi (ψ'), and experimental 3JCOCH, 2JCOC, and 3JCOCC spin-couplings measured in aqueous solution in 13C-labeled isotopomers, probability distributions of ϕ' and ψ' in each linkage were determined and compared to those determined by aqueous 1-μs molecular dynamics (MD) simulation. Good agreement was found between the MA'AT and single-state MD conformational models of these linkages for the most part, with modest (approximately <15°) differences in the mean values of ϕ' and ψ', although the envelope of allowed angles (encoded in circular standard deviations or CSDs) is consistently larger for ϕ' determined from MA'AT analysis than from MD for both linkages. The MA'AT model of the α-Galp-(1→3)-β-Galp linkage agrees well with those determined previously using conventional NMR methods (3JCOCH values and/or 1H-1H NOEs), but some discrepancy was observed for the β-Galp-(1→3)-β-Galp linkage, which may arise from errors in the conventions used to describe the linkage torsion angles. Statistical analyses of X-ray crystal structures show ranges of ϕ' and ψ' for both linkages that include the mean angles determined from MA'AT analyses, although both angles adopt a wide range of values in the crystalline state, with ϕ' in β-Galp-(1→3)-β-Galp linkages showing greater-than-expected conformational variability.

MA'AT Analysis: Probability Distributions of Molecular Torsion Angles in Solution from NMR Spectroscopy

ConspectusMonosaccharides adopt multiple conformations in solution, and this structural complexity increases significantly when they are assembled into oligosaccharides and polysaccharides. Characterization of the conformational properties of saccharides in solution by NMR spectroscopy has been hampered by several complicating factors, including difficulty interpreting spectra because of significant signal overlap, population averaging of NMR parameters, and unique properties of the spectra that make accurate measurements of NMR parameters prone to error (e.g., non-first-order effects on J-couplings). Current conformational assignments rely heavily on theoretical calculations, especially molecular dynamics (MD) simulations, to interpret the experimental NMR parameters. While these studies assert that the available experimental data fit the calculated models well, a lack of independent experimental validation of the force fields from which MD models are derived and an inability to test all possible models that might be compatible with the experimental data in an unbiased manner make the approach less than ideal.NMR spin couplings or J-couplings have been used as structure constraints in organic and other types of molecules for more than six decades. The dihedral angle dependence of vicinal (three-bond) 1H-1H spin couplings (3JHH) first described by Karplus led to an explosion of applications for a wide range of conformational problems. Other vicinal J-couplings (e.g., 3JCCOP, 3JHCOP, and 3JCOCH) have been found to exhibit similar dihedral angle dependencies. 3J values have been used to assign the preferred conformation in molecules that are conformationally homogeneous. However, many molecules, particularly those in biological systems, are conformationally flexible, which complicates structural interpretations of J values in solution. Three-state staggered models are often assumed in order to deconvolute the conformationally averaged J values into conformer populations. While widely applied, this approach assumes highly idealized models of molecular torsion angles that are likely to be poor representations of those found in solution. In addition, this treatment often gives negative populations and neglects the presence of librational averaging of molecular torsion angles.Recent work in this research group has focused on the development of a hybrid experimental-computational method, MA'AT analysis, that provides probability distributions of molecular torsion angles in solution that can be superimposed on those obtained by MD. Ensembles of redundant NMR spin couplings, including 3J (vicinal), 2J (geminal), and sometimes 1J (direct) values, are used in conjunction with circular statistics to provide single- and multistate models of these angles. MA'AT analysis provides accurate mean torsion angles and circular standard deviations (CSDs) of each mean angle that describe the librational motion about the angle. Both conformational equilibria and dynamics are revealed by the method. In this Account, the salient features of MA'AT analysis are discussed, including some applications to conformational problems involving saccharides and peptides.

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.

Computational 1 H and 13 C NMR in structural and stereochemical studies

Present review outlines the advances and perspectives of computational ¹ H and ¹³ C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational ¹ H and ¹³ C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.

Nonconventional NMR Spin-Coupling Constants in Oligosaccharide Conformational Modeling: Structural Dependencies Determined from Density Functional Theory Calculations

Nonconventional NMR spin-coupling constants were investigated to determine their potential as conformational constraints in MA'AT modeling of the O-glycosidic linkages of oligosaccharides. Four (¹ J _C1',H1', ¹ J _C1',C2', ² J _C1',H2', and ² J _C2',H1') and eight (¹ J _C4,H4, ¹ J _C3,C4, ¹ J _C4,C5, ² J _C3,H4, ² J _C4,H3, ² J _C5,H4, ² J _C4,H5, and ² J _C3,C5) spin-couplings in methyl β-d-galactopyranosyl-(1→4)-β-d-glucopyranoside (methyl β-lactoside) were calculated using density functional theory (DFT) to determine their dependencies on O-glycosidic linkage C-O torsion angles, ϕ and ψ, respectively. Long-range ⁴ J _H1',H4 was also examined as a potential conformational constraint of either ϕ or ψ. Secondary effects of exocyclic (hydroxyl) C-O bond rotation within or proximal to these coupling pathways were investigated. Based on the findings of methyl β-lactoside, analogous J-couplings were studied in five additional two-bond O-glycosidic linkages [βGlcNAc-(1→4)-βMan, 2-deoxy-βGlc-(1→4)-βGlc, αMan-(1→3)-βMan, αMan-(1→2)-αMan, and βGlcNAc(1→2)-αMan] to determine whether the coupling behaviors observed in methyl β-lactoside were more broadly observed. Of the 13 nonconventional J-couplings studied, 7 exhibit properties that may be useful in future MA'AT modeling of O-glycosidic linkages, none of which involve coupling pathways that include the linkage C-O bonds. The findings also provide new insights into the general effects of exocyclic C-O bond conformation on the magnitude of experimental spin-couplings in saccharides and other hydroxyl-containing molecules.

MA'AT: A Web-Based Application to Determine Rotamer Population Distributions in Solution from Nuclear Magnetic Resonance Spin-Coupling Constants

A hybrid experimental-computational method to determine conformational equilibria of molecules in solution has been developed based on the use of redundant nuclear magnetic resonance (NMR) spin-spin coupling constants (spin-couplings; J-couplings), density functional theory (DFT) calculations, and circular statistics. The mathematics that underpins the method, known as MA'AT analysis, is presented, and key components of a computer program that applies this algorithm are discussed. The method was tested using single-state and multi-state models to identify the factors required to obtain reliable results, to establish the limitations of the method, and to highlight techniques to evaluate the uniqueness of solution.

MA'AT Analysis of Aldofuranosyl Rings: Unbiased Modeling of Conformational Equilibria and Dynamics in Solution

MA'AT analysis has been applied to methyl β-d-ribofuranoside (3) and methyl 2-deoxy-β-d-erythro-pentofuranoside (4) to demonstrate the ability of this new experimental method to determine multi-state conformational equilibria in solution. Density functional theory (DFT) was used to obtain parameterized equations for >20 NMR spin-coupling constants sensitive to furanose ring conformation in 3 and 4, and these equations were used in conjunction with experimental spin-couplings to produce unbiased MA'AT models of ring pseudorotation. These models describe two-state north-south conformational exchange consistent with results obtained from traditional treatments of more limited sets of NMR spin-couplings (e.g., PSEUROT). While PSEUROT, MA'AT, and aqueous molecular dynamics models yielded similar two-state models, MA'AT analysis gives more reliable results since significantly more experimental observables are employed compared to PSEUROT, and no assumptions are needed to render the fitting tractable. MA'AT models indicate a roughly equal distribution of north and south ring conformers of 4 in aqueous (²H₂O) solution compared to ∼80% north forms for 3. Librational motion about the mean pseudorotation phase angles P of the preferred north and south conformers of 3 in solution is more constrained than that for 4. The greater rigidity of the β-ribo ring may be caused by synergistic stereoelectronic effects and/or noncovalent (e.g., hydrogen-bonding) interactions in solution that preferentially stabilize north forms of 3. MA'AT analysis of oligonucleotides and other furanose ring-containing biomolecules promises to improve current experimental models of sugar ring behavior in solution and help reveal context effects on ring conformation in more complex biologically important systems.

Carbohydrate Force Fields: The Role of Small Partial Atomic Charges in Preventing Conformational Collapse

Although the quality of current additive all-atom force fields for carbohydrates has been demonstrated in many applications, occasional significant differences reported for the hydrodynamic behavior of specific polysaccharides modeled with different force fields is a cause for concern. In particular, irreversible conformational collapse has been noted for some polysaccharide simulations with the GLYCAM06j force field. Here, we investigate the cause of this phenomenon through comparative simulations of a range of saccharides with both the GLYCAM06j and the CHARMM36 carbohydrate force fields. We find that conformational collapse in GLYCAM06j occurs for saccharide chains containing the deoxy sugar α-l-rhamnose after relatively long simulation intervals. Further, we explore the mechanism of conformational collapse and show that this phenomenon arises because of the anomalous low energy in GLYCAM06j (as compared to quantum mechanical calculations) of a specific orientation of α-l-Rha to α-l-Rha glycosidic linkages, which are subsequently sustained by intramolecular interactions in the saccharide chain. We identify the lack of partial charges on aliphatic hydrogens in GLYCAM as the source of this anomaly, demonstrating that addition of small partial atomic charges on the aliphatic protons in rhamnose removes the conformational collapse phenomenon. This work reveals the large cumulative impact that small partial charges may have on the dynamic behavior of polysaccharides and indicates that future reparameterization of the GLYCAM06j force field should investigate the addition of partial charges on all aliphatic hydrogens.

Rationalizing the Stereoelectronic Influence of Interglycosidic Bond Conformations on the Reactivity of 1,4-O-Linked Disaccharide Donors

Disaccharide donors are key precursors in convergent glycan synthesis strategies. Unexpectedly, we observed that disaccharide thioglycosyl donors containing 1,4-O-linked α-glycosidic bonds are much more reactive than their β-analogues with the same protecting group pattern. Herein, we rationalized that such a difference in their reactivity is attributed to the conformation of the 1,4-O-interglycosidic bond which is controlled by anomeric and exo-anomeric effects. Moreover, the conformational preferences of these donors are dictated by the dihedral angles ϕ and ψ of their interglycosidic linkages and the torsional angle ω of their side chain along the C5-C6 bond. This fundamental research clarifies how the long-range stereoelectronic effects from the nonreducing end sugar can influence the reactivity of the leaving group at the reducing end and the behavior of disaccharide donors thereof.

O-Methylation in Carbohydrates: An NMR and MD Simulation Study with Application to Methylcellulose

Methylated carbohydrates are important from both biological and technical perspectives. Specifically, methylcellulose is an interesting cellulose derivative that has applications in foods, materials, cosmetics, and many other fields. While the molecular dynamics simulation technique has the potential for both advancing the fundamental understanding of this polymer and aiding in the development of specific applications, a general drawback is the lack of experimentally validated interaction potentials for the methylated moieties. In the present study, simulations using the GROMOS 56 carbohydrate force field are compared to NMR spin–spin coupling constants related to the conformation of the exocyclic torsion angle ω in d-glucopyranose and derivatives containing a 6-O-methyl substituent and a ¹³C-isotopologue thereof. A ³J_CC Karplus-type relationship is proposed for the C5–C6–O6–C_Me torsion angle. Moreover, solvation free energies are compared to experimental data for small model compounds. Alkylation in the form of 6-O-methylation affects exocyclic torsion only marginally. Computed solvation free energies between nonmethylated and methylated molecules were internally consistent, which validates the application of these interaction potentials for more specialized purposes.

Automated Quantification of Hydroxyl Reactivities: Prediction of Glycosylation Reactions

The stereoselectivity and yield in glycosylation reactions are paramount but unpredictable. We have developed a database of acceptor nucleophilic constants (Aka) to quantify the nucleophilicity of hydroxyl groups in glycosylation influenced by the steric, electronic and structural effects, providing a connection between experiments and computer algorithms. The subtle reactivity differences among the hydroxyl groups on various carbohydrate molecules can be defined by Aka, which is easily accessible by a simple and convenient automation system to assure high reproducibility and accuracy. A diverse range of glycosylation donors and acceptors with well-defined reactivity and promoters were organized and processed by the designed software program "GlycoComputer" for prediction of glycosylation reactions without involving sophisticated computational processing. The importance of Aka was further verified by random forest algorithm, and the applicability was tested by the synthesis of a Lewis A skeleton to show that the stereoselectivity and yield can be accurately estimated.