Hexopyranose Ring Research Articles

Molecular dynamics simulations of hexopyranose ring distortion in different force fields

Abstract The four classical, biomolecular force fields designed to study hexopyranose-based carbohydrates (GROMOS 56a6CARBO/56a6CARBO_R, GROMOS 53a6GLYC, CHARMM and GLYCAM06) have been tested in the context of ring-inversion properties. These properties were evaluated for both unfunctionalized monomers of all hexopyranoses of the d series and for residues in a chain composed of uniform units connected by α(1→4) and β(1→4) glycosidic linkages. The results indicate that the tested force fields differ in their predictions of the ring-inversion properties of both monomers and residues in a chain. The comparison with the available experimental data and with the semi-empirical Angyal scheme reveals that, at the level of monomers, GROMOS 56a6CARBO, GROMOS 53a6GLYC and CHARMM correctly reproduce the ring-inversion free energies. However, due to the lack of analogous reference data we cannot state which force field is more or less accurate in the context of ring distortion of residues in a chain. Therefore, the use of ab initio potentials is recommended in the prospective, quantitative studies on the related subject.

Ring inversion properties of 1→2, 1→3 and 1→6-linked hexopyranoses and their correlation with the conformation of glycosidic linkages

Enhanced-sampling molecular dynamics simulations performed within the GROMOS 56a6CARBO_R force field were applied in order to elucidate ring-inversion properties of hexopyranose residues in a chain for the case of α(1→n) and β(1→n) glycosidic linkages (n = 2, 3 or 6). The results indicate that ring-inversion free energies calculated for residues in a chain are weakly correlated with those of corresponding monomers, except of the case of 1→6 linkages. This, in combination with the results for O1-methyl-hexopyranosides (Plazinski et al, 2016), suggests that both the type of functionalization (glycolysation vs. methylation) and the topology of glycosidic linkage play an important role in possible alterations of the hexopyranose ring flexibility. Additionally, the correlation of the ring shape with the preferred geometry of glycosidic linkages was investigated. The linkages of the 1→2, 1→3 and 1→6 types do not follow the trend found in the case of the 1→4 linkages, i.e. there is no correlation between the range of changes in the glycosidic linkage conformation and the topological orientation of the glycosidic oxygen atoms. Overall, the ring shape affects the glycosidic linkages of the 1→6 type to the least extent in comparison to the remaining ones.

Kinetic characteristics of conformational changes in the hexopyranose rings

The shape of the hexopyranose ring is an important factor which can influence the properties of carbohydrate molecules and affect their biological activity. Due to a limited availability of the experimental data, the conformational rearrangements (puckering) which occur within the pyranose rings are studied extensively by using various computational approaches. Contrary to the basic structural and energetic features characterizing the process of ring flexing, the kinetic and dynamics properties of puckering remain less recognized. We performed the first, molecular dynamics-based, systematic calculations aimed at description of the kinetic characteristics of the conformational changes in the rings of α-d- and β-d-glucopyranose molecules. The rate constants representing particular molecular events which comprise the chair–chair inversion are determined and analyzed in the context of the available experimental data. Furthermore, several various variables (e.g. transmission coefficients) and issues (e.g. memorylessness of the puckering process) are investigated and discussed. As several different parameter sets were used during the study (GROMOS 56A6CARBO, GLYCAM, GROMOS 53A6GLYC), the results provide the conclusion on the capability of the carbohydrate-dedicated force fields to describe the kinetic properties of pyranose ring flexing.

The influence of the hexopyranose ring geometry on the conformation of glycosidic linkages investigated using molecular dynamics simulations

The conformation of the carbohydrate molecules is a subject of many theoretical and experimental studies. The different timescales associated with the particular degrees of freedom hinder the progress in both those fields. The present paper reports the results of computational studies aimed at elucidating and characterizing the potential correlations between the two main structural determinants of the carbohydrate structure, i.e. the ring conformation and the orientation of the glycosidic bonds (expressed in terms of the ϕ and ψ glycosidic dihedral angles). The free energy landscapes computed for 16 different oligomers composed of unsubstituted, 1,4-linked hexopyranose residues allowed for a detailed insight into how the ring geometry affects the glycosidic linkage conformation. The factor of main importance appeared to be the local changes of the chain length induced by the ring conformational rearrangements. This effect is important mainly for the carbohydrate chains exploiting the glycosidic bonds of uniform orientation with respect to the ring (i.e. either exclusively axially or exclusively equatorially oriented). The shape of the ring may affect the (ϕ,ψ) free energy maps but only if the population of the alternative ring conformers is relatively high and (at the same time) the presence of such conformers is associated with the significant shifts of the favorable ϕ and ψ values.

The dynamics of the conformational changes in the hexopyranose ring: a transition path sampling approach

The transition paths corresponding to the conformational rearrangements in the ring of hexapyranose (α-d- and β-d-glucose) molecules were described by applying the transition path sampling method.

GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates.

An improved parameter set for explicit-solvent simulations of carbohydrates (referred to as GROMOS 53A6GLYC) is presented, allowing proper description of the most stable conformation of all 16 possible aldohexopyranose-based monosaccharides. This set includes refinement of torsional potential parameters associated with the determination of hexopyranose rings conformation by fitting to their corresponding quantum-mechanical profiles. Other parameters, as the rules for third and excluded neighbors, are taken directly from the GROMOS 53A6 force field. Comparisons of the herein presented parameter set to our previous version (GROMOS 45A4), the GLYCAM06 force field, and available NMR data are presented in terms of ring puckering free energies, conformational distribution of the hydroxymethyl group, and glycosidic linkage geometries for 16 selected monosaccharides and eight disaccharides. The proposed parameter modifications have shown a significant improvement for the above-mentioned quantities over the two tested force fields, while retaining full compatibility with the GROMOS 53A6 and 54A7 parameter sets for other classes of biomolecules.

Structure and stability of Li(I) and Na(I) – Carboxylate, sulfate and phosphate complexes

DFT was used to investigate molecular structure and metal affinity of the systems CH 3CO 2M ( 1), CH 3–O–SO 3M ( 2), CH 3–NH–SO 3M ( 3), (CH 3–O–PO 3M) − ( 4), CH 3–O–PO 3M 2 ( 5), CH 3–O–(CH 3)PO 2M ( 6), and 1,4-DiOMe IdoA-2SM 2 ( 7; 2S o conformation) (M = Li + and Na +), respectively. Interaction enthalpies, entropies and Gibbs energies of the metal-coordinated systems were determined on the B3LYP/6-311+G(d,p) level. The computed Gibbs energies, Δ G o , of the isolated systems 1– 7 are negative and span a rather broad energy interval (from −500 to −1500 kJ mol −1). The lithium and sodium binding enthalpies and Gibbs energies of a series of phosphate, carboxylate, N-, and O-sulfate anions indicate that multidentate chelation plays an important role in the binding. In particular, the glycosaminoglycan structural unit of heparin 1,4-DiOMe IdoA-2SM 2 (M = Li + and Na +) with coordinating groups in the hexopyranose ring exhibits enhanced metal ion binding energies. Computations that include the effect of solvation showed that in water the relative stability of Li +⋯Ligand and Na +⋯Ligand ionic bonds is rapidly diminished. The computed interaction Gibbs energy in water is small, slightly negative and/or positive, i.e. destabilizing. Thus in water, both contact ion pairs and solvent-separated ion pairs may coexist.

Glycosidase inhibitors as conformational transition state analogues

A method for estimating the conformational similarity between hexopyranose rings is presented and used to probe the behaviour of various glycosyl hydrolase inhibitors as conformational transition state analogues.

Blood Group B Galactosyltransferase: Insights into Substrate Binding from NMR Experiments

The biosynthesis of human blood group B antigens is accomplished by a highly specific galactosyltransferase (GTB). On the basis of NMR experiments, we propose a "molecular tweezers mechanism" that accounts for the exquisite stereoselectivity of donor substrate selection. Transferred NOE experiments for the first time reveal the bioactive conformation of the donor substrate UDP-galactose (UDP-Gal) and of its enzymatically inactive analogue, UDP-glucose (UDP-Glc). Both bind to GTB in a folded conformation that is sparsely populated in solution, whereas acceptor ligands bind in a conformation that predominates in solution. The bound conformations of UDP-Gal and UDP-Glc are identical within experimental error. Therefore, GTB must discriminate between the two activated sugars on the basis of a hitherto unknown transition state that can only be formed in the case of UDP-Gal. A full relaxation and exchange matrix analysis of STD NMR experiments reveals that acceptor substrates dissociate significantly faster (k(off) > 100 Hz) from the binding pocket than donor substrates (k(off) approximately 10 Hz). STD NMR experiments also directly show that proper recognition of the hexopyranose rings of the UDP sugars requires bivalent metal cations. At the same time, this analysis furnishes the complete three-dimensional structure of the enzyme with its bound donor substrate UDP-Gal on the basis of a prior crystal structure analysis. We propose that, upon acceptor binding, GTB uses the Asp 302 and Glu 303 side chains as "molecular tweezers" to promote bound UDP-Gal but not UDP-Glc into a transition state that leads to product formation.

Mechanistic implications of Escherichia coli galactokinase structure-based engineering.

Engineering GalK: The Escherichia coli galactokinase GalK has been engineered in its active site. The amino acid exchanges Y223F and Y223W broadened the sugar-substrate spectrum to include, among others, 4-deoxy-D-galactose. This finding suggests that the role of Y223 is not primarily hydrogen bonding but rather a hydrophobic stacking to secure the hexopyranose ring in the active site.

Further Evidence for the Critical Role of a Non-Chair Conformation of L-Iduronic Acid in the Activation of Antithrombin

L-iduronic acid, a conformationally flexible monosaccharide, imparts a remarkable protein adaptability to the glycosaminoglycans heparin, heparan sulfate, and dermatan sulfate. The pentasaccharide representing the antithrombin binding site of heparin contains one such L-iduronic acid residue, the conformation of which has been suspected for a long time to be a critical factor in the interaction with antithrombin. We have recently synthesized pentasaccharides containing an L-iduronic acid residue conformationally forced to exist within a restricted arc (2S0 ⇄ 2,5B ⇄ 5S1) of the overall pseudorotational circle. We could thus demonstrate that the 2S0 conformation is adopted upon binding to the protein. In the present work, we now describe the synthesis of a similar pentasaccharide containing a slightly more flexible L-iduronic acid unit with a three-atom bridge between C-2 and C5 of the hexopyranose ring. This pentasaccharide is a better activator of AT-III with respect to blood coagulation factor Xa inhibition. These results confirm that L-iduronic acid adopts an unusual non-chair conformation close to 2S0 and clearly explains how the unique conformational behavior of L-iduronic acid is the key to heparin’s interaction with AT-III. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)

Spectral Editing of Carbon Thirteen Hexopyranose Ring Nuclei by One-Dimensional NMR Extended Distortionless Enhancement by Polarization Transfer Experiments

This paper reports application of the one-dimensional 13C NMR “extended” distortionless enhancement by polarization transfer (DEPT) editing method to the determination of hexopyranose ring 13C nuclei. Relative spatial arrangements of the vicinal protons in the local environment of a skeletal carbon atom are determined from the signs of intensity modulation profiles and connected with their specific positions in the ring. In combination with a computer simulation program, the “extended” DEPT sequence allows the straightforward and unambiguous assignment of the hexopyranose ring carbon atoms.

Mutational analysis at Asn-41 in peanut agglutinin. A residue critical for the binding of the tumor-associated Thomsen-Friedenreich antigen.

Peanut agglutinin is a clinically important lectin due to its application in the screening of mature and immature thymocytes as well as in the detection of cancerous malignancies. The basis for these applications is the remarkably strong affinity of the lectin for the tumor-associated Thomsen-Friedenreich antigen (T-antigen) and more so due to its ability to distinguish T-antigen from its cryptic forms. The crystal structure of the complex of peanut agglutinin with T-antigen reveals the basis of this specificity. Among the contacts involved in providing this specificity toward T-antigen is the water-mediated interaction between the side chain of Asn-41 and the carbonyl oxygen of the acetamido group of the second hexopyranose ring of the sugar molecule. Site-directed mutational changes were introduced at this residue with the objective of probing the role of this residue in T-antigen binding and possibly engineering an altered species with increased specificity for T-antigen. Of the three mutants tested, i.e. N41A, N41D, and N41Q, the last one shows improved potency for recognition of T-antigen. The affinities of the mutants can be readily explained on the basis of the crystal structure of the complex and simple modeling. In particular, the change of asparagine to glutamine could lead to a direct interaction of the side chain with the sugar while at the same time retaining the water bridge. This study strengthens the theory that in lectins the nonprimary contacts generally made through water bridges are involved in imparting exquisite specificity.

The κ-carrageenase of P. carrageenovora Features a Tunnel-Shaped Active Site : A Novel Insight in the Evolution of Clan-B Glycoside Hydrolases

Background: κ-carrageenans are gel-forming, sulfated 1,3-α-1,4-β-galactans from the cell walls of marine red algae. The κ-carrageenase from the marine, gram-negative bacterium Pseudoalteromonas carrageenovora degrades κ-carrageenan both in solution and in solid state by an endoprocessive mechanism. This β-galactanase belongs to the clan-B of glycoside hydrolases. Results: The structure of P. carrageenovora κ-carrageenase has been solved to 1.54 Å resolution by the multiwavelength anomalous diffraction (MAD) method, using a seleno-methionine-substituted form of the enzyme. The enzyme folds into a curved β sandwich, with a tunnel-like active site cavity. Another remarkable characteristic is the presence of an arginine residue at subsite −1. Conclusions: The crystal structure of P. carrageenovora κ-carrageenase is the first three-dimensional structure of a carrageenase. Its tunnel-shaped active site, the first to be reported for enzymes other than cellulases, suggests that such tunnels are associated with the degradation of solid polysaccharides. Clan-B glycoside hydrolases fall into two subgroups, one with catalytic machinery held by an ancestral β bulge, and the other in which it is held by a regular β strand. At subsite −1, all of these hydrolases exhibit an aromatic amino acid that interacts with the hexopyranose ring of the monosaccharide undergoing catalysis. In addition, in κ-carrageenases, an arginine residue recognizes the sulfate-ester substituents of the β-linked κ-carrageenan monomers. It also appears that, in addition to the nucleophile and acid/base catalysts, two other amino acids are involved with the catalytic cycle, accelerating the deglycosylation step.

Synthesis and structural studies of anomeric 2,3,4,6-tetra- O-acetyl-5-thio- d-glucopyranosyl azides

Two methods are presented for the preparation of the α and β anomers of 2,3,4,6-tetra- O-acetyl-5-thio- d-glucopyranosyl azide. These methods are comparable in yield, but the one that converts a glucopyranosyl bromide into the azide is preferable because of easier purification. After chromatographic separation, the α and β anomers were analysed by NMR spectroscopy. The crystal and molecular structure of the β anomer was determined by X-ray diffraction. It crystallises in space group P2 1 [ a=11.729(3), b=7.305(3), c=11.363(3)Å, β=107.63(5)°, Z=2]. The hexopyranose ring of the β anomer assumes a 4 C 1 conformation and the orientation of the azido group is compatible with the requirements of the exo-anomeric effect. This geometry is compared to that of other similar structures.

Structure effects on isomerization pathways and vibrational spectra of epoxysaccharides: a numerical study

Results of a comparative analysis of conformational possibilities of the hexopyranose ring of six epoxysaccharides differing from each other by the position of the oxirane ring within the limits of the hexapyranose ring and having different orientations of substituents and different positions of the oxirane ring with respect to the skeleton plane of the molecules are presented. Numerical simulations based on the Wiberg and Boyd method made it possible to determine all the stationary forms in which anhydropyranose rings can exist. The effect of various structural factors on the character of conformational transformations, heights of transition barriers, and the energy of stationary forms has been investigated. Normal vibrational modes of the stationary forms of the compounds were calculated using molecular mechanics. Based on results of our simulations, we predict a strong effect of steric factors on the vibrational spectra of sugar epoxides.

Vibrational spectra and stereoisomerism of the hexopyranose ring in epoxysaccharides

Investigation of the potential surface of methyl 2,3-anhydro-2,3,4-trideoxy-β-D-lyxohexopyranoside has shown that the molecule has seven conformers with different frameworks. A comparative analysis of the calculated frequencies, forms, and PED of normal vibrations of the seven conformers allowed us to follow the frequency shifts of similar modes, which depend on the geometry of the epoxysaccharide framework. In the high-frequency region of the vibration spectrum, PED has considerable contributions from the deformation vibrations of methine and methylene (CCH, OCH) groups, and we can clearly observe a dependence of the frequency shift on the geometry of the ring at the site where vibrating groups are localized. The vibrations that have predominant contributions to PED from the C−O stretching vibrations depend on the overall geometry of the molecule. In the low-frequency region (below 700 cm−1), skeletal deformation modes appear. Apart from the common dominant forms of vibrations, each conformer is characterized by individual “deviations” that depend on the conformation of the hexopyranose ring as a whole. The frequency shifts in this case can be 100 cm−1 or higher.

Vibrational spectra and stereoisomerism of the hexopyranose cycle in epoxysaccharides

Investigation of the potential surface of methyl 2,3-anhydro-2,3,4-trideoxy-β-D-lyxohexopyranoside has shown that the molecule has seven conformers with different frameworks. A comparative analysis of the calculated frequencies, forms, and PED of normal vibrations of the seven conformers allowed us to follow the frequency shifts of similar modes, which depend on the geometry of the epoxysaccharide framework. In the high-frequency region of the vibration spectrum, PED has considerable contributions from the deformation vibrations of methine and methylene (CCH, OCH) groups, and we can clearly observe a dependence of the frequency shift on the geometry of the ring at the site where vibrating groups are localized. The vibrations that have predominant contributions to PED from the C−O stretching vibrations depend on the overall geometry of the molecule. In the low-frequency region (below 700 cm−1), skeletal deformation modes appear. Apart from the common dominant forms of vibrations, each conformer is characterized by individual “deviations” that depend on the conformation of the hexopyranose ring as a whole. The frequency shifts in this case can be 100 cm−1 or higher.

Determination of proton-proton distances in 2-acetamido-2-deoxy monosaccharides from 1H NMR relaxation measurements in solution

Determination of selective and biselective 1H spin-lattice relaxation rates combined with steady-state and transient 1H 1H NOE data allowed calculation of intramolecular proton-proton distances in 2-acetamido-2-deoxy- d-glucosides ( 1a an 1b), 2-acetamido-2-deoxy- d-mannoses ( 5a and 5b) and their acetylated derivatives. These measurements were supplemented by DESERT studies using derivatives selectively labeled by 2H at position 2. These distance data are in good correlation with literature values obtained by X-ray crystallography. Interproton distance measurements allow the determination of relative configurations, including that of the anomeric carbon, in hexopyranose rings in cases where other methods, like those based on scalar coupling constants, fail.

Using an oval to represent carbohydrates with hexopyranose rings

An shorthand alternative to representing hexopyranose rings using chair conformation structures.