Flexibility Of Glycosidic Linkages Research Articles

Understanding Conformational Properties and Role of Hydrogen Bonds in Glycosaminoglycans-Interleukin8 Complexes in Aqueous Medium by Molecular Dynamics Simulation.

Atomistic molecular dynamics simulations were performed under ambient conditions to explore the conformational features and binding affinities of hexameric glycosaminoglycans (GAGs) with chemokine Interleukin8 (IL8) in an aqueous medium. We tried to understand the role of hydrogen bonds (HBs) involving conserved water in mediating the interactions. The Luzar-Chandler model was adopted to study the kinetics of HB breaking and formation concerning different water-mediated HBs. The conformational flexibilities of bound GAGs are due to the flexible glycosidic linkages than the occasional/rare ring pucker conformation. The free energy landscape constructed with ϕ, and ψ, depicted that different conformational minima associated with the glycosidic linkage flexibility of the GAGs in bound states are separated by energy barriers. The binding affinities of IL8 towards GAGs are favored through the electrostatic and non-polar solvation interactions. 4-different types of conserved water were explored in the solvent-mediated binding of GAGs with IL8. The average lifetime of the IL8-GAG direct HB pairs was ∼ten times less than the IL8-GAG-shared water HBs. This is due to the rapid establishment of HB breaking and reformation kinetics involving water of a shared layer. We find that despite the highly negatively charged surface of GAGs, the IL8 surface populated by non-cationic amino acids could serve as a promising binding site in addition to the cationic surface of the protein.

Adsorption of hyaluronan saccharides on the surface of a single walled carbon nanotube. A computational study

Adsorption of β-d-glucopyranuronic acid (GlcA), N-acetyl-β-d-glucosamine (GlcNAc), two disaccharides composed of GlcA and GlcNAc and hyaluronic acid (HA) on single walled carbon nanotube (CNT) was studied using molecular dynamics simulations based on the GLYCAM-06j force field and quantum chemical approach based on DFT method and ωB97X-D functional. It was found that both monosaccharides adsorb on the (17,0) single walled carbon nanotube with adsorption energy strongly dependent on the number of molecules. Single molecule adsorption was stable only for GlcNAc molecule while the GlcA molecule revealed energetically quite complex picture involving the assumption of energy barrier for desorption. Hetero-disaccharides composed of GlcNAc and GlcA revealed stable surface layers. Most uniform surface layer with highly specific orientation towards surface was found for GlcNAc. Adsorption of monosaccharides weakly affects their conformation: disaccharides display only moderate reduction in the flexibility of glycosidic linkages but oligosaccharides can be more significantly deformed, exhibiting conformationally-locked kinks along the chain that impose tighter CNT-HA contact. Results from quantum chemical studies concerning conformation and energetics of monosaccharides adsorption on the same CNT type are consistent with molecular dynamics studies based on the GLYCAM-06j force field at the limit of absolute zero temperature.

Glycosidic linkage flexibility: The ψ torsion angle has a bimodal distribution in α-L-Rhap-(1→2)-α-L-Rhap-OMe as deduced from 13C NMR spin relaxation.

The molecular dynamics (MD) computer simulation technique is powerful for the investigation of conformational equilibrium properties of biomolecules. In particular, free energy surfaces of the torsion angles (those degrees of freedom from which the geometry mostly depends) allow one to access conformational states, as well as kinetic information, i.e., if the transitions between conformational states occur by simple jumps between wells or if conformational regions close to these states also are populated. The information obtained from MD simulations may depend substantially on the force field employed, and thus, a validation procedure is essential. NMR relaxation data are expected to be highly sensitive to the details of the torsional free energy surface. As a case-study, we consider the disaccharide α-l-Rhap-(1 → 2)-α-l-Rhap-OMe that features only two important torsion angles, ϕ and ψ, which define the interglycosidic orientation of the sugar residues relative to each other, governed mainly by the exo-anomeric effect and steric interactions, respectively. In water, a ψ- state is preferred, whereas in DMSO, it is a ψ+ state, suggesting inherent flexibility at the torsion angle. MD simulations indicated that bistable potentials describe the conformational region well. To test whether a unimodal distribution suffices or if a bimodal distribution better represents molecular conformational preferences, we performed an alchemical morphing of the torsional free energy surface and computed T1, T2, and NOE13C NMR relaxation data that were compared to experimental data. All three NMR observables are substantially affected by the morphing procedure, and the results strongly support a bimodal Boltzmann equilibrium density with a major and a minor conformational state bisected at ψ ≈ 0°, in accord with MD simulations in an explicit solvent.

Quantum Chemistry Meets Deep Learning for Complex Carbohydrate and Glycopeptide Species I

Abstract Carbohydrate complexes are crucial in many various biological and medicinal processes. The impacts of N-acetyl on the glycosidic linkage flexibility of methyl β-D-glucopyranose, and of the glycoamino acid β-D-glucopyranose-asparagine are poorly understood at the electronic level. Furthermore, the effect of D- and L-isomers of asparagine in the complexes of N-acetyl-β-D-glucopyranose-(L)-asparagine and N-acetyl-β-D-glucopyranose-(D)-asparagine is unknown. In this study, we performed density functional theory calculations of methyl β-D-glucopyranose, methyl N-acetyl-β-D-glucopyranose, and of glycoamino acids β-D-glucopyranose-asparagine, N-acetyl-β-D-glucopyranose-(L)-asparagine and N-acetyl-β-D-glucopyranose-(D)-asparagine for studying their linkage flexibilities, total solvated energies, thermochemical properties and intra-molecular hydrogen bond formations in an aqueous solution environment using the COnductor-like Screening MOdel (COSMO) for water. We linked these density functional theory calculations to deep learning via estimating the total solvated energy of each linkage torsional angle value. Our results show that deep learning methods accurately estimate the total solvated energies of complex carbohydrate and glycopeptide species and provide linkage flexibility trends for methyl β-D-glucopyranose, methyl N-acetyl-β-D-glucopyranose, and of glycoamino acids β-D-glucopyranose-asparagine, N-acetyl-β-D-glucopyranose-(L)-asparagine and N-acetyl-β-D-glucopyranose-(D)-asparagine in agreement with density functional theory results. To the best of our knowledge, this study represents the first application of density functional theory along with deep learning for complex carbohydrate and glycopeptide species in an aqueous solution medium. In addition, this study shows that a few thousands of optimization frames from DFT calculations are enough for accurate estimations by deep learning tools.

Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study.

The inherent flexibility of carbohydrates is dependent on stereochemical arrangements, and characterization of their influence and importance will give insight into the three-dimensional structure and dynamics. In this study, a β-(1→4)/β-(1→3)-linked glucosyl decasaccharide is experimentally investigated by synchrotron small-angle X-ray scattering from which its radius of gyration (Rg) is obtained. Molecular dynamics (MD) simulations of the decasaccharide show four populated states at each glycosidic linkage, namely, syn- and anti-conformations. The calculated Rg values from the MD simulation reveal that in addition to syn-conformers the presence of anti-ψ conformational states is required to reproduce experimental scattering data, unveiling inherent glycosidic linkage flexibility. The CHARMM36 force field for carbohydrates thus describes the conformational flexibility of the decasaccharide very well and captures the conceptual importance that anti-conformers are to be anticipated at glycosidic linkages of carbohydrates.

A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility.

The macromolecular conformation of the constituent polysaccharides in lignocellulosic biomass influences their supramolecular interactions, and therefore their function in plants and their performance in technical products. The flexibility of glycosidic linkages from the backbone of hemicelluloses was studied by evaluating the conformational freedom of the φ and ψ dihedral angles using molecular dynamic simulations, additionally selected molecules were correlated with experimental data by nuclear magnetic resonance spectroscopy. Three types of β-(1→4) glycosidic linkages involving the monosaccharides (Glcp, Xylp and Manp) present in the backbone of hemicelluloses were defined. Different di- and tetrasaccharides with combinations of such sugar monomers from hemicelluloses were simulated, and free energy maps of the φ - ψ space and hydrogen-bonding patterns were obtained. The glycosidic linkage between Glc-Glc or Glc-Man (C-type) was the stiffest with mainly one probable conformation; the linkage from Man-Man or Man-Glc (M-type) was similar but with an increased probability for an alternative conformation making it more flexible, and the linkage between two Xyl-units (X-type) was the most flexible with two almost equally populated conformations. Glycosidic linkages of the same type showed essentially the same conformational space in both disaccharides and in the central region of tetrasaccharides. Different probabilities of glycosidic linkage conformations in the backbone of hemicelluloses can be directly estimated from the free energy maps, which to a large degree affect the overall macromolecular conformations of these polymers. The information gained contributes to an increased understanding of the function of hemicelluloses both in the cell wall and in technical products.

Exploring N-Glycan Conformers: Assessment of Enhanced Sampling Algorithms

N-glycans (oligosaccharides linked to proteins via the side chain of asparagine) play an important role in protein folding control, cell adhesion, organism immune response, etc. The functional versatility comes from structural variety and the inherit flexibility of glycosidic linkages. Each N-glycan has several co-existing conformers posing a challenge for experimental characterisation and computational modelling. In this work, we assess the enhanced sampling capabilities of the replica-exchange MD (REMD) and metadynamics (MTD). While REMD has been used in the previous studies of N-glycans, it is the first application of MTD, as we know. Our proposed approach is based on the multi-replica MTD, where some degrees of freedom are biased explicit by the MTD procedure and the others implicitly by using replicas at higher temperatures. In addition, we apply the replica state exchange MTD (RSE-MTD), our proposed enhancement to increase replica exchange efficiency. Finally, the methods have been tested on Bi9, a biantennary complex-type N-glycan. We demonstrate that REMD, following a protocol from the previous studies, fails to provide consistent results, in contrast, our MTD approach enhances sampling along the critical collective variables and ensures converged results. The estimated conformer populations of Bi9 are in agreement with the experimental results obtained from the NMR pseudo-contact shift (PCS) measurements.

Studies on the conformational flexibility of α-l-rhamnose-containing oligosaccharides using 13C-site-specific labeling, NMR spectroscopy and molecular simulations: implications for the three-dimensional structure of bacterial rhamnan polysaccharides

Bacterial polysaccharides are comprised of a variety of monosaccharides, L-rhamnose (6-deoxy-L-mannose) being one of them. This sugar is often part of α-(1 → 2)- and/or α-(1 → 3)-linkages and we have therefore studied the disaccharide α-L-Rhap-(1 → 2)-α-L-Rhap-OMe to obtain information on conformational preferences at this glycosidic linkage. The target disaccharide was synthesized with (13)C site-specific labeling at C1' and at C2', i.e., in the terminal group. 2D (1)H,(13)C-HSQC-HECADE and (1)H,(13)C-J-HMBC NMR experiments, 1D (13)C and (1)H NMR spectra together with total line-shape analysis were used to extract conformationally dependent hetero- and homonuclear spin-spin coupling constants. This resulted in the determination of (2)J(C2',H1'), (3)J(C1',C1), (3)J(C1',C3), (3)J(C2',C2), (2)J(C1',C2), (1)J(C1',C2'), and (1)J(C1',H1'). These data together with previously determined J(CH) and (1)H,(1)H NOEs result in fourteen conformationally dependent NMR parameters that are available for analysis of glycosidic linkage flexibility and conformational preferences. A 100 ns molecular dynamics (MD) simulation of the disaccharide with explicit water molecules as solvent showed a major conformational state at φ(H)≈ 40° and ψ(H)≈-35°, consistent with experimental NMR data. In addition, MD simulations were carried out also for α-L-Rhap-(1 → 3)-α-L-Rhap-OMe and a rhamnan hexasaccharide. The gathered information on the oligosaccharides was used to address conformational preferences for a larger structure, a 2- and 3-linked nonasaccharide, with implications for the 3D structure of rhamnan polysaccharides, which should be regarded as flexible polymers.

The role of water in the design of glycosidic linkage flexibility

In this paper we show how a variety of computational methods are used to understand the role that water plays in the solution conformational dynamics of carbohydrates. A comparison is made between maltose and a designed disaccharide (α-D-Glc-NAc-(1→4)-β-D-Glc-3-NH2) in which the cross glycosidic linkage hydrogen bonds have been significantly strengthened. However, despite the stronger intramolecular hydrogen bonds in the maltose derivative, the correlation times for glycosidic dihedral angle fluctuations are approximately the same for the two sugars. Upon investigation of the water in the first hydration shells for the two disaccharides, high water probability densities were found between the functional groups straddling the glycosidic linkage that bonds the two monosaccharides together. This probability density corresponds to single water molecules forming bridging hydrogen bonds between the functional groups on either side of the linkage for periods of 3.66 ps in the case of maltose and 8.36 ps in the case of the amine derivative. Ab initio studies of saccharide structure interaction with single water molecules reveal that these intermolecular (sugar-solvent) hydrogen bonds are of similar strength to the intramolecular (sugar-sugar) hydrogen bonds. This combination of molecular dynamics and ab initio computational methods demonstrates that increasing the internal hydrogen bond strength in oligosaccharides does not lead to significantly slower internal molecular motion of these sugars in solution. The intermolecular hydrogen bonds formed with water compete equally with the intramolecular hydrogen bonds in the sugar. This result has important implications when considering hydrophobic versus hydrophilic effects in glycoproteins.

The glycosidic linkage flexibility and time-scale similarity hypotheses

In this paper, the framework surrounding two hypotheses is described: 1. (1) that glycosidic linkages of carbohydrates can be inherently flexible and thus undergo significant torsional motions in solution; 2. (2) that internal and overall motions of disaccharides occur on similar time-scales. A brief summary is provided of the current position of the experimental and theoretical data with respect to these hypotheses. An analysis of glycosidic linkage conformational flexibility in terms of linkage density functions is presented. Statistical indices for the evaluation and ranking of linkage flexibility are developed. Conformational sampling of glycosidic linkages using Monte Carlo sampling based on linkage distributions is described. Time-scale similarity is examined by comparing interproton correlation functions with respect to the laboratory frame and different internal coordinate frames, and the relative dependence of the time-scales on the system temperature is analysed. Finally, it is suggested that, instead of the traditional “lock-and-key” viewpoint, we should consider the paradigm that carbohydrates may be viewed as a “bunch of keys”.

Assessing glycosidic linkage flexibility: conformational analysis of the repeating trisaccharide unit of Aeromonas salmonicida.

A detailed conformational analysis was performed for the synthetic branched trisaccharide beta-D-ManNAc-(1-->4)-[alpha-D-Glc-(1-->3)]-L-Rha 1 which represents the repeating unit of the O-antigenic polysaccharide of Aeromonas salmonicida. The study was based on 26 experimental NOE curves from 1D transient NOE experiments, employing Gaussian-shaped inversion pulses at 600 MHz. Eight of the NOE curves were interglycosidic and thus useful for an analysis of glycosidic linkage orientations. Metropolis Monte Carlo (MMC) simulations and minimum-energy calculations with the program GEGOP were used to obtain theoretical NOE curves which were compared to the experimental ones. MMC simulations with different temperature parameters of 310, 600, 900 and 2000 K allowed identification of NOEs which are sensitive towards different conformation distributions--not only different conformations--at both glycosidic linkages in 1. A comparison of trisaccharide 1 with the constituent disaccharides beta-D-ManNAc-(1-->4)-L-Rha 2 and alpha-D-Glc-(1-->3)-L-Rha 3 revealed effects of branching on glycosidic linkage flexibility. A quantitative evaluation was facilitated by the introduction of entropy-related flexibility parameters. Our study indicates a notable restriction of flexibility, especially at the (1-->3) linkage in 1. Although overall flexibility in 1 is reduced as compared to the constituent disaccharides 2 and 3, it cannot be neglected altogether. In summary, combined transient NOE experiments and MMC simulations provide a simple approach to analyse glycosidic linkage flexibility.

Conformation and circular dichroism of oligosaccharides and model glycosides containing neuraminic acid (5-acetamido-3,5-dideoxy-D-glycero-D-galacto-nonulopyranosonic acid) residues

C.d. spectra have been recorded for N-acetylneuraminic acid, a widely occurring component of glycoproteins and glycolipids of animal cells and tissues, as well as for some of its synthetic and naturally occurring glycosides and related compounds. Principal spectral features are systemised in terms of the accessible chromophores, and the geometry and flexibility of glycosidic linkages. The main c.d. band, centred below 200 nm, is attributed to the acetamido group, and shows little structural or conformational sensitivity. Smaller spectral features at higher wavelength (around 225 nm) arise from the n→π* transition of the carboxy chromophore, and provide a convenient index of glycosidic configuration and conformation. Thus α-linked glycosides of N-acetylneuraminic acid show a negative band, while β-glycosides give rise to a positive peak. In both cases the magnitude of the band is increased by restricted mobility. The planar symmetry rule developed by Listowsky is even more successful in predicting the sign of observed optical activity in sterically unambiguous fused ring lactone systems than the earlier and more complex lactone sector rule. Application of the planar rule provides a satisfactory unified interpretation of the observed c.d. behaviour of the carboxy chromophore of N-acetylneuraminic acid and its derivatives, in terms of established conformational principles. C.d. of the tetrasaccharide glycitol derived from the major cell surface glycoprotein of human erythrocytes, shows perturbations additional to those that occur between adjacent residues in the covalent sequence, suggesting that non-bonded interactions between branches of glycoproteins can be relevant to their tertiary structure.