N-Acetyl Side-Chain Conformation in Saccharides: Solution Models Obtained from MA'AT Analysis

Geminal 13C-1H NMR Spin-Coupling Constants in Furanose Rings: New Empirical Correlations with Conformation

Density functional theory (DFT) calculations have been used to develop a new approach to interpreting geminal (two-bond) 2 J CCH NMR spin-coupling constants in saccharides containing aldofuranosyl (five-membered) rings. In the biologically important β-d-ribofuranosyl and 2-deoxy-β-d-ribofuranosyl (2-deoxy-β-d-erythro-pentofuranosyl) rings that were used as models, many of the 2 J CCH values associated with coupling pathways involving an endocyclic C-C bond depend linearly on P/π, a measure of ring conformation. In most cases, the endocyclic C-C bond is present in the coupling pathway. In other cases, the 2 J CCH value depends linearly on either an adjacent C-C bond torsion angle or shows no systematic relationship with any endocyclic C-C bond torsion angle. In the latter case, secondary (remote) structural effects, defined as those that primarily affect C-C or C-H bond lengths in the C-C-H coupling pathway, cause the 2 J CCH value to behave with less predictability. These effects apparently cancel and lead to linearity involving an adjacent C-C bond in some cases. These findings provide a new conceptual framework to understand and exploit the dependencies of geminal 13C-1H NMR spin-couplings on furanose ring conformation. They also reveal the effect of exocyclic C-O bond torsion angles on the magnitudes and signs of 2 J CCH values in saccharides, a complication that remains to be addressed before 2 J CCH values can be used quantitatively in single- and multi-state MA'AT modeling of redundant NMR J-values in furanosyl rings.

NMR spectroscopic studies of chitin oligomers - Resolution of individual residues and characterization of minor amide cis conformations

Chitin is the second most abundant biopolymer in nature after cellulose and is composed of N-acetylglucosamine (GlcNAc) connected via β(1 → 4)-glycosidic bonds. Despite its prominence in nature and diverse roles in pharmaceutical and food technological applications, there is still a need to develop methods to study structure and function of chitin and its corresponding oligomers. Efforts have been made to analyse chitin oligomers by NMR spectroscopy, but spectral overlap has prevented any differentiation between the interior residues. In this study, chitin oligomers up to hexaose with natural abundance of 15N were analysed with NMR spectroscopy in aqueous solution. Different 1H,15N-HSQC pulse sequences were evaluated to obtain the best resolution and sensitivity. Interior residues were resolved in the 15N dimension and detailed chemical shifts of amide proton and nitrogen are reported for the first time. Additionally, all oligomers were analysed for the presence of the amide cis form and its corresponding chemical shifts were assigned. This study exploits the information that can be obtained from chitin oligomers with NMR spectroscopy and depicts methods for detailed analysis of glycans containing oligomers of N-acetylglucosamine.

Physicochemical characteristics of chitosan molecules: Modeling and experiments

Chitosan, a biocompatible polysaccharide, finds a wide range of applications, inter alia as an antimicrobial agent, stabilizer of food products, cosmetics, and in the targeted delivery of drugs and stem cells. This work represents a comprehensive review of the properties of chitosan molecule and its aqueous solutions uniquely combining theoretical modeling and experimental results. The emphasis is on physicochemical aspects which were sparsely considered in previous reviews. Accordingly, in the first part, the explicit solvent molecular dynamics (MD) modeling results characterizing the conformations of chitosan molecule, the contour length, the chain diameter and the density are discussed. These MD data are used to calculate several parameters for larger chitosan molecules using a hybrid approach based on continuous hydrodynamics. The dependencies of hydrodynamic diameter, frictional ratio, radius of gyration, and intrinsic viscosity on the molar mass of molecules are presented and discussed. These theoretical predictions, comprising useful analytical solutions, are used to interpret and rationalize the extensive experimental data acquired by advanced experimental techniques. In the final part, the molecule charge, acid-base, and electrokinetic properties, comprising the electrophoretic mobility and the zeta potential, are reviewed. Future research directions are defined and discussed.

Probing the Role of Membrane in Neutralizing Activity of Antibodies Against Influenza Virus

Influenza poses a major health issue globally. Neutralizing antibodies targeting the highly conserved stem region of hemagglutinin (HA) of the influenza virus provide considerable protection against the infection. Using an array of advanced simulation technologies, we developed a high-resolution structural model of full-length, Fab-bound HA in a native viral membrane to characterize direct membrane interactions that govern the efficacy of the antibody. We reveal functionally important residues beyond the antibody's complementary-determining regions that contribute to its membrane binding. Mutagenesis experiments and infectivity assays confirm that deactivating the membrane-binding residues of the antibody decreases its neutralization activity. Therefore, we propose that the association with the viral membrane plays a key role in the neutralization activity of these antibodies. Given the rapid evolution of the influenza virus, the developed model provides a structural framework for the rational design and development of more effective therapeutic antibodies.

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.

Revealing the Structure of Sheer N-Acetylglucosamine, an Essential Chemical Scaffold in Glycobiology

We explored the conformational landscape of N-acetyl-α-d-glucosamine (α-GlcNAc), a fundamental chemical scaffold in glycobiology. Solid samples were vaporized by laser ablation, expanded in a supersonic jet, and characterized by broadband chirped pulse Fourier transform microwave spectroscopy. In the isolation conditions of the jet, three different structures of GlcNAc have been discovered. These are conclusively identified by comparing the experimental values of the rotational constants with those predicted by theoretical calculations. The conformational preferences are controlled by intramolecular hydrogen bond networks formed between the polar groups in the acetamido group and the hydroxyl groups and dominated in all cases by a strong OH···O═C interaction. We reported an exception to the gauche effect due to the enhanced stability observed for the Tg+ conformer. All the structures present the same disposition of the acetamido group, which explains the highly selective binding of N-acetylglucosamine with different amino acid residues. Thus, the comprehensive structural data provided here shall help to shed some light on the biological role of this relevant amino sugar.

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: Unbiased Multi-State Conformational Modeling of Exocyclic Hydroxymethyl Group Conformation in Methyl Aldohexopyranosides

MA'AT analysis (J. Chem. Inf. Model. 2022, 62, 3135-3141) has been applied to model exocyclic hydroxymethyl group conformation in methyl β-D-glucopyranoside (βGlcOMe), methyl β-D-galactopyranoside (βGalOMe), and methyl β-D-mannopyranoside (βManOMe) in an unbiased manner. Using up to eight NMR J-couplings sensitive to rotation about the C5-C6 bond (torsion angle ω), two-state models of ω were obtained that are qualitatively consistent with the relative populations of the gg, gt, and tg rotamers reported previously. MA'AT analysis gave consistent unbiased gt ⇌ tg models of ω in βGalOMe, with gt more populated than tg and mean values of ω for each population similar to those obtained from aqueous 1-μs MD simulation. Using different combinations of J-couplings had little effect on the βGalOMe model in terms of the mean values of ω and circular standard deviations (CSDs). In contrast, MA'AT analysis of ω in βGlcOMe and βManOMe produced more than one two-state model independent of the ensemble of J-values used in the analyses. These models were characterized by gg ⇌ gt conformer exchange as expected, but the mean values of ω in both conformers varied significantly in the different fits, especially for the gg rotamer. Constrained (biased) MA'AT analyses in which only staggered geometries about ω were allowed gave RMSDs slightly larger than those obtained from the unbiased fits, precluding an assignment of an unbiased model. It is unclear why MA'AT analysis gives consistent and predictable unbiased models of ω in βGalOMe but not in βGlcOMe and βManOMe. One possibility is that the distribution of ω in one or both of the gg and gt conformers in the latter does not conform to a von Mises function (i.e., is not Gaussian-like), but rather to a broad and/or flat distribution that cannot be fit by the current version of MA'AT. Nevertheless, the results of this study provide new evidence of the ability of MA'AT analysis to treat multi-state conformational exchange using only experimental NMR data, extending recent MA'AT applications to furanosyl ring pseudorotation (Biochemistry 2022, 61, 239-251).

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.