Building Up Key Segments of N-Glycans in the Gas Phase: Intrinsic Structural Preferences of the α(1,3) and α(1,6) Dimannosides

Mixing water, sugar, and lipid: Conformations of isolated and micro-hydrated glycolipids in the gas phase

Both sugars and lipids are important biomolecular building blocks with exceptional conformational flexibility and adaptability to their environment. Glycolipids bring together these two molecular components in the same assembly and combine the complexity of their conformational landscapes. In the present study, we have used selective double resonance vibrational spectroscopy, in combination with a computational approach, to explore the conformational preferences of two glycolipid models (3-0-acyl catechol and guaiacol α-D-glucopyranosides), either fully isolated in the gas phase or controlled interaction with a single water molecule. We could identify the preferred conformation and structures of the isolated and micro-hydrated species and evidence of the presence of a strong water pocket, which may influence the conformational flexibility of such systems, even in less controlled environments.

Gas Phase Conformation of Trisaccharides and Core Pentasaccharide: A Three-Step Tree-Based Sampling and Quantum Mechanical Computational Approach

As an important component of N-linked glycoproteins, the core pentasaccharide is highly crucial to the potential application prospect of glycoprotein. However, the gas phase conformation study is a challenging one due to the size and complexity of the molecule, together with the necessity to rely on quantum chemistry modeling for relevant energetics and structures. In this paper, the structures of the trisaccharides and core pentasaccharides in N-linked glycans in the gas phase were constructed by a three-step tree-based (TSTB) sampling. Since single point energies of all the conformers are calculated at the temperature of zero, it is necessary to evaluate the stability at a high temperature. We calculate the Gibbs free energies using the standard thermochemistry model (T = 298.15 K). For trimannose, the energetic ordering at 298.15 K can be strongly changed compared to 0 K. Moreover, two structures of trimannose with high energies at 0 K are considered to provide a much better match of IR vibration signatures with the low Gibbs free energies. On this basis, the core pentasaccharide was constructed in three ways. The building configurations of core pentasaccharide were optimized to obtain reasonable low-energy stable conformers. Fortunately, the lowest-energy structure of core pentasaccharide is eventually the minimum at 0 K and 298.15 K. Furthermore, spectrum analysis of core pentasaccharide was carried out. Although poorly resolved, its contour from the experiment was in qualitative correspondence with the computed IR spectrum associated with its minimum free energy structure. A large number of strongly and weakly hydrogen-bonded hydroxyl and acetylamino groups contribute to a highly congested set of overlapping bands. Compared with traditional conformation generators, the TSTB sampling is employed to efficiently and comprehensively obtain preferred conformers of larger saccharides with lower energy.

Exploring the interaction sites in glucose and galactose using phenol as a probe

Sugars, together with amino acids and nucleobases, are the fundamental building blocks of a cell. They are involved in many fundamental processes and they especially play relevant roles as part of the immune system. The latter is connected to their ability to establish a collection of intermolecular interactions, depending on the position of their hydroxyl groups. Here we explore how the position of the OH in C4, the anomeric conformation and the nature substituent affect the interaction with phenol, which serves as a probe of the preferred site for the interaction. Using mass-resolved excitation spectroscopy and density functional calculations, we unravel the structure of the dimers and compare their conformation with those found for similar systems. The main conclusion is that the hydroxymethyl group has a very strong influence, guiding the whole aggregation process and that the position of the substituent in C4 has a stronger influence on the final structure of the dimer than the anomeric conformation.

Limitations in the description of conformational preferences of C-disaccharides: The (1 → 3)-C-mannobiose case

Conformational preferences of two C-glycosyl analogues of Manp-(1 → 3)-Manp, were studied using a combined method of theoretical and experimental chemistry. Molecular dynamics was utilized to provide conformational behavior along C-glycosidic bonds of methyl 3-deoxy-3-C-[(α-d-mannopyranosyl)methyl]-α-d- and l-mannopyranosides. The OPLS2005 and Glycam06 force fields were used. Simulations were performed with explicit water (TIP3P) and methanol. Results were compared with a complete conformational scan at the MM4 level with the dielectric constant corresponding to methanol. In order to verify predicted conformational preferences, vicinal ³J_HH NMR coupling constants were calculated by the Karplus equation on simulated potential energy surfaces (PES). A set of new parameters for the Karplus equation was also designed. Predicted ³J_HH were compared with experimental data. We also used reverse methodology, in which the ³J_HH coupling constants were calculated at the DFT level for each family of (ϕ, ψ)-conformers separately and then experimental values were decomposed onto calculated ³J_HH couplings in order to obtain experimentally derived populations of conformers. As an alternative method of evaluation of preferred conformers, analysis of sensitive ¹³C chemical shifts was introduced. We were able to thoroughly discuss several fundamental issues in predictions of preferred conformers of C-saccharides, such as the solvent effect, reliability of the force field, character of empirical Karplus equation or applicability of NMR parameters in predictions of conformational preferences in general.

Molecular gels in the gas phase? Gelator-gelator and gelator-solvent interactions probed by vibrational spectroscopy

Benzylidene glucose (BzGlc) is a member of the benzylidene glycoside family. These molecules have the ability to form molecular physical gels. These materials are formed when gelator molecules create a non-covalently bound frame where solvent molecules are trapped. Since the gel formation process and its properties are determined by the subtle balance between non-covalent forces, it is difficult to anticipate them. Quantitative and qualitative understanding of the gelator-gelator and gelator-solvent interactions is needed to better control these materials for important potential applications. We have used gas phase vibrational spectroscopy and theoretical chemistry to study the conformational choices of BzGlc, its dimer and the complexes it forms with water or toluene. To interpret the vibrational spectra we have used the dispersion corrected functional B97D which we have calibrated for the calculation of OH stretching frequencies. Even at the most basic molecular level, it is possible to interrogate a large range of non-covalent interactions ranging from OH → OH hydrogen bonding, to OH → π, and CH → π, all being at the center of gel properties at the macroscopic level.

Distinguishing isobaric phosphated and sulfated carbohydrates by coupling of mass spectrometry with gas phase vibrational spectroscopy

An original application of the coupling of mass spectrometry with vibrational spectroscopy, used for the first time to discriminate isobaric bioactive saccharides with sulfate and phosphate functional modifications, is presented. Whereas their nominal masses and fragmentation patterns are undifferentiated by sole mass spectrometry, their distinctive OH stretching modes at 3595 cm(-1) and 3666 cm(-1), respectively, provide a reliable spectroscopic diagnostic for distinguishing their sulfate or phosphate functionalization. A detailed analysis of the 6-sulfated and 6-phosphated d-glucosamine conformations is presented, together with theoretical scaled harmonic spectra and anharmonic spectra (VPT2 and DFT-based molecular dynamics simulations). Strong anharmonic effects are observed in the case of the phosphated species, resulting in a dramatic enhancement of its phosphate diagnostic mode.

A tree-step computational approach to simplify conformational determination of cellobiose and lactose

Great theoretical attentions have been paid on the conformational preference of individual molecular building blocks of carbohydrates because it is helpful for assignments of the experimental signals and explorations of the biological implications. A tree-step approach is applied here to simplify the conformational determination of phenyl β-cellobioside and benzyl β-lactoside, for which 35 and 23 initial structures are built, respectively. After the high-level calculations, low-energy conformers are determined and then compared with previous experimental and theoretical results. The low-energy conformers are reconstructed in our work for both cellobiose and lactose and the results show a quantitative agreement between the experimental signature and the predicted IR vibration assignment. In addition, two low-energy conformers, which are predicted in our work, have not been reported by the previous work using the traditional method. The tree-step computational approach provides an alternative timesaving and accurate method to focus on determining the preferred conformations of disaccharides.

Performance of four different force fields for simulations of dipeptide conformations: GlyGly, GlyGly-, GlyGly · Cl-, GlyGly · Na+ and GlyGly · (H2O)2

Monte-Carlo conformational searches with four kinds of force fields (AMBER94, MM3*, MMFFs, and OPLS-2005) were performed on glycylglycine (GlyGly), deprotonated glycylglycine (GlyGly(-)), glycylglycine chloride anion complex (GlyGly · Cl(-)), glycylglycine sodium cation complex (GlyGly · Na(+)) and glycylglycine dihydrate [GlyGly · (H2O)2]. Combined with Hartree-Fock (HF) and second-order Møller-Plesset (MP2) optimizations, conformations within an energy of 20 kJ mol(-1) were predicted. After MP2 calculations, the geometries and relative energies of the predicted structures were the same regardless of the force field used. Therefore, the performance of different force fields reflects mainly the conformational search process. For GlyGly, there was practically no difference among the four force fields. Due to the complex hydrogen bonding network when involving water, the total number of resulting conformers for GlyGly · (H2O)2 increased drastically. Moreover, the MMFFs force field fared best in finding the global minimum compared to the remaining three force fields. In describing hydrogen bonded and inter-molecular complexes, we recommend application of the MMFFs and AMBER94 force fields. Furthermore, the MMFFs and OPLS-2005 force fields have a good description of electrostatic interactions. This work will contribute to helping the reader make an optimal choice of force field, taking into account the latter's strengths and limitations.

Synthetic mimics of carbohydrate-based anticancer vaccines: preparation of carbohydrate polymers bearing unimolecular trivalent carbohydrate ligands by controlled living radical polymerization

Under the conditions of nitroxide-mediated polymerizations, novel carbohydrate polymers bearing unimolecular trivalent carbohydrate ligands could be achieved through a living radical process.

Carbohydrates

Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).

'Naked' and hydrated conformers of the conserved core pentasaccharide of N-linked glycoproteins and its building blocks

N-glycosylation of eukaryotic proteins is widespread and vital to survival. The pentasaccharide unit -Man3GlcNAc2- lies at the protein-junction core of all oligosaccharides attached to asparagine side chains during this process. Although its absolute conservation implies an indispensable role, associated perhaps with its structure, its unbiased conformation and the potential modulating role of solvation are unknown; both have now been explored through a combination of synthesis, laser spectroscopy, and computation. The proximal -GlcNAc-GlcNAc- unit acts as a rigid rod, while the central, and unusual, -Man-β-1,4-GlcNAc- linkage is more flexible and is modulated by the distal Man-α-1,3- and Man-α-1,6- branching units. Solvation stiffens the 'rod' but leaves the distal residues flexible, through a β-Man pivot, ensuring anchored projection from the protein shell while allowing flexible interaction of the distal portion of N-glycosylation with bulk water and biomolecular assemblies.

Predicting the preferred conformations of luteolin-4'-O-β-D-glucoside in gas phase: a comparison of two computational approaches

A tree-step computational approach has been applied to determine the lowest-energy conformers of luteolin-4'-O-β-D-glucoside (L4'G). Fifty-seven starting structures of the L4'G have been built, and then by performing with density functional theory (DFT) optimizations and second-order Møller-Plesset (MP2) calculations, the preferred conformations of L4'G are predicted. In order to test the accuracy of the computational approach, a hybrid Monte-Carlo multiple minimum (MCMM)/quantum mechanical (QM) approach is applied to determine the favorable conformers of L4'G. The alternative classification is employed to put similar conformations into the same catalogue according to the dihedral angles among the luteolin rings, glycosidic dihedral angles, and the orientations of hydroxyl and hydroxymethyl groups. The low-energy conformations are located after the optimizations at the HF/6-31G(d) and B3LYP/6-311+G(d) levels. Compared with the hybrid MCMM/QM approach, the tree-step computational approach not only remains accurate but also saves a lot of computing resources.

Population distribution of flexible molecules from maximum entropy analysis using different priors as background information: application to the Φ, Ψ-conformational space of the α-(1-->2)-linked mannose disaccharide present in N- and O-linked glycoproteins

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.

Conformational choice and selectivity in singly and multiply hydrated monosaccharides in the gas phase

Factors governing hydration, regioselectivity and conformational choice in hydrated carbohydrates have been examined by determining and reviewing the structures of a systematically varied set of singly and multiply hydrated monosaccharide complexes in the gas phase. This has been achieved through a combination of experiments, including infrared ion-depletion spectroscopy conducted in a supersonic jet expansion, and computation through molecular mechanics, density functional theory (DFT) and ab initio calculations. New spectroscopic and/or computational results obtained for the singly hydrated complexes of phenyl beta-D-mannopyranoside (beta-D-PhMan), methyl alpha-D-gluco- and alpha-D-galactopyranoside (alpha-D-MeGlc and alpha-D-MeGal), when coupled with those reported earlier for the singly hydrated complexes of alpha-D-PhMan, beta-D-PhGlc and beta-D-PhGal, have created a comprehensive data set, which reveals a systematic pattern of conformational preference and binding site selectivity, driven by the provision of optimal, co-operative hydrogen-bonded networks in the hydrated sugars. Their control of conformational choice and structure has been further revealed through spectroscopic and/or computational investigations of a series of multiply hydrated complexes; they include beta-D-PhMan.(H2O)2,3, which has an exocyclic hydroxymethyl group, and the doubly hydrated complex of phenyl alpha-L-fucopyranoside, alpha-L-PhFuc.(H2O)2, which does not. Despite the very large number of potential structures and binding sites, the choice is highly selective with binding invariably "focussed" around the hydroxymethyl group (when present). In beta-D-PhMan.(H2O)2,3, the bound water molecules are located exclusively on its polar face and their orientation is dictated by the (perturbed) conformation of the carbohydrate to which they are attached. The possible operation of similar rules governing the structures of hydrogen-bonded protein-carbohydrate complexes is proposed.

Conformational preferences of an amyloidogenic peptide: IR spectroscopy of Ac-VQIVYK-NHMe

The (306)VQIVYK(311) sequence in the tau peptide is essential for the formation of intracellular amyloid fibrils related to Alzheimer's disease, where it forms interdigitating cross-beta-structures. The inherent conformational preferences of the capped hexapeptide Ac-VQIVYK-NHMe were characterized in the gas phase. IR/UV double-resonance spectroscopy of the peptide isolated in a cold molecular beam was used to probe the conformation of the neutral peptide. The influence of protonation at the lysine side chain was investigated at 298 K by characterizing the protonated peptide ion, Ac-VQIVYK(H(+))-NHMe, with IRMPD spectroscopy in the fingerprint and amide I/II band region in an FTICR mass spectrometer. The conformations for both neutral and protonated peptides were predicted by an extensive conformational search procedure followed by cluster analysis and then DFT calculations. Comparison of the experimental and computed IR spectra, with consideration of the relative energies, was used to assign the dominant conformations observed. The neutral peptide adopts a beta-hairpin-like conformation with two loosely extended peptide chains, demonstrating the preference of the sequence for extended beta-strand-like structures. In the protonated peptide, the lysine NH3(+) disrupts this extended conformation by binding to the backbone and induces a transition to a random-coil-like structure.

NMR study of hydroxy protons of di- and trimannosides, substructures of Man-9

The chemical shifts, temperature coefficients and inter-residual rotating-frame Overhauser effect (ROE)s for the hydroxy protons of some alpha-(1,2)-, alpha-(1,3)- and alpha-(1,6)-linked di- and trimannosides have been measured for samples in 85% H2O/15% acetone-d6 solution. These mannosides, Manalpha(1-->2)ManalphaOMe (1) Manalpha(1-->3)ManalphaOMe (2), Manalpha(1-->6)ManalphaOMe (3), Manalpha(1-->2)Manalpha(1-->2)ManalphaOMe (4), Manalpha(1-->2)Manalpha(1-->3)ManalphaOMe (5), Manalpha(1-->2)Manalpha(1-->6)ManalphaOMe (6) and Manalpha(1-->3)[Manalpha1-->6]ManalphaOMe (7), are substructures of the N-glycan Man-9. The NMR data show that the hydration of each individual hydroxyl group in the di- and trisaccharides is very similar to the hydration of the corresponding hydroxyl in the monomeric methyl alpha-D-mannoside. No hydrogen-bond interactions were found to stabilize the conformations of the alpha-(1,2)- and alpha-(1,6)-linkages and the chemical shifts for the hydroxy proton resonances of the alpha-(1,6)-linkage indicated high-conformational flexibility. For the alpha-(1,3)-linkage, however, the downfield shift for the signal of O(2)H of the 3-substituted residue together with the ROE between this proton and H5' on the next residue suggest some weak inter-residue interactions.