Inter-residue Hydrogen Bonds Research Articles

Does Inter-Residue Hydrogen Bonding in β-(1→4)-Linked Disaccharides Influence Linkage Conformation in Aqueous Solution?

Two disaccharides, methyl β-d-galactopyranosyl-(1→4)-α-d-glucopyranoside (1) and methyl β-d-galactopyranosyl-(1→4)-3-deoxy-α-d-ribo-hexopyranoside (3), were prepared with selective 13C-enrichment to allow measurement of six trans-O-glycosidic J-couplings (2JCOC, 3JCOCH, and 3JCOCC) in each compound. Density functional theory (DFT) was used to parameterize Karplus-like equations that relate these J-couplings to either ϕ or ψ. MA'AT analysis was applied to both linkages to determine mean values of ϕ and ψ in each disaccharide and their associated circular standard deviations (CSDs). Results show that deoxygenation at C3 of 1 has little effect on both the mean values and librational motions of the linkage torsion angles. This finding implies that, if inter-residue hydrogen bonding between O3H and O5' of 1 is present in aqueous solution and persistent, it plays little if any role in dictating preferred linkage conformation. Hydrogen bonding may lower the energy of the preferred linkage geometry but does not determine it to any appreciable extent. Aqueous 1-μs MD simulation supports this conclusion and also indicates greater conformational flexibility in deoxydisaccharide 3 in terms of sampling several, conformationally distinct, higher-energy conformers in solution. The populations of these latter conformers are low (3-14%) and could not be validated by MA'AT analysis. If the MD model is correct, however, C3 deoxygenation does enable conformational sampling over a wider range of ϕ/ψ values, but linkage conformation in the predominant conformer is essentially identical in both 1 and 3.

PH Effects on the Conformations of Galacturonan in Solution: Conformational Transition and Loosening, Extension and Stiffness

Calorimetric (from both isothermal micro-calorimetry and DSC), chiro-optical, viscometric and rheological data on aqueous solutions of pectic acid and low-methoxyl pectin (LMP), published over decades from different laboratories, have been comparatively revisited. The aim was to arrive at a consistent and detailed description of the behavior of galacturonan as a function of pH, i.e., of the degree of charging (as degree of dissociation, α) of the polyanion. The previously hypothesized pH-induced transition from a 31 to a 21 helix was definitely confirmed, but it has been shown, for the first time, that the transition is always coupled with loosening/tightening effects brought about by an increase in charge. The latter property has a twofold effect: the former effect is a purely physical one (polyelectrolytic), which is always a loosening one. However, in the very low range of pH and before the beginning of the transition, an increase in charge tightens the 31 helix by strengthening an intramolecular—but inter-residue—hydrogen bond. The value of the enthalpy change of 31 → 21 transition—+0.59 kcal·mol−1—is bracketed by those provided by theoretical modeling, namely +0.3 and +0.8 kcal·mol−1; the corresponding entropy value is also positive: +1.84 cal·mole r.u.−1·K−1. The enthalpic and the entropic changes in chain loosening amount only to about 23% of the corresponding 31 → 21 changes, respectively. Much like poly(galacturonic acid), the 31 conformation of LMP also stiffens on passing from pH = 2.5 to 3.0, to then start loosening and transforming into the 21 one on passing to pH = 4.0. Lowering the pH of a salt-free aqueous solution of LMP down to 1.6 brings about a substantial chain–chain association, which is at the root of the interchain junctions stabilizing the acid pH gels, in full agreement with the rheological results. A comparison of the enthalpic data reveals that, at 85 °C, LMP in acidic pH conditions has lost its initial order by about 2.3 times more than pectic acid brought from low charging to full neutralization (at α = 1.0) at 25 °C. A proper combination of experiments (enthalpic measurements) and theory (counterion condensation polyelectrolyte theory) succeeded in demonstrating, for the first time ever, a lyotropic/Hofmeister effect of the anion perchlorate in stabilizing the more disordered form of the 21 helix of galacturonan. The viscometric results in water showed that the 31 helix is capable of forming longer rheologically cooperative units compared with the 21 helix. Extrapolation to infinite ionic strength confirmed that, once all electrostatic interactions are cancelled, the elongation of the two helical forms is practically the same. At the same time, however, they indicated that the flexibility of the two-fold helix is more than fifteen times larger than that of the three-fold one. The result is nicely corroborated by a critical revisiting of 23Na relaxation experiments.

Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents

All-atom MD simulations provide the atomic details of glycan structure in solution, but extensive sampling is required for simulating the transition between rotameric states. For carbohydrate modeling, the motions of the glycosidic linkages in a glycan are often sampled well on the sub-μs time scale. Consequently, simulations of large glycans or glycoconjugates in aqueous environments are very challenging at the atomistic level because of a huge number of water molecules, which eventually slows down the conformational sampling. An alternative to the all-atom approach is the multiscale simulation, where the glycan is in all-atom form while the solvent is treated implicitly. Here we present a comparative analysis of the implicit model with the currently used explicit model using Gaussian accelerated molecular dynamics (GaMD). Here we used a hybrid N-glycan to investigate the accuracy of the implicit solvent model. Estimating several structural parameters, namely dihedral torsional angles, puckering angles, and end-to-end distances, yields a complete classification of structural space in both solvent models. Both solvent models displayed similar conformations at the monosaccharide level, whereas minor differences were observed in the global conformation. The only major difference was observed in the inter-residue hydrogen bonds, which increased by 2-fold in the explicit solvent model. Detailed analysis of structural parameters established a balanced trade-off between the computational speed and accuracy for studying long-chain glycan molecules in an implicit solvent.

Potential Foldamers Based on an ortho-Terphenyl Amino Acid.

We describe the synthesis and characterization of a new class of oligomers built from a terphenyl-based amino acid. These oligomeric amides are of interest because the adoption of specific conformations could potentially be driven by the coordinated formation of inter-residue hydrogen bonds and aromatic interactions. Although high-resolution structural data have proven inaccessible, circular dichroism and nuclear magnetic resonance studies suggest that the new oligomers fold concomitantly with discrete self-association in chloroform.

Prediction of procarbazine adsorption on the hydroxyethyl cellulose: A density functional theory study

An extensive isomer search was performed to investigate the adsorption configurations of procarbazine on the hydroxyethyl cellulose (HEC) at M06-2X/6–31++G(d,p) level of theory. The adsorption of procarbazine on the HEC is exergonic (ΔGads < 0) with the formation of three inter-residue hydrogen bonds. Considering water, Gibs free energy of procarbazine adsorption on HEC decreases in comparison to the gas phase. The NBO and AIM analyses confirmed the formation of three inter-residue hydrogen bonds based on delocalization interactions and bond critical points such as electron density and its laplacian. Among the inter-residue hydrogen bonds, the largest values of delocalization energy E(2) (2.87 kcal/mol) and electron density (0.0044 e) were obtained for O-H1…N1H followed by those for C-H3…O3 = C and N-H2…O2-H. The results indicated that adsorption of procarbazine on the HEC led to a decrease in the HOMO-LUMO gap (~29%) and an increase in electrophilicity value (~64%) with respect to the hydroxyethyl cellulose.

Burkholderia cenocepacia H111 Produces a Water-Insoluble Exopolysaccharide in Biofilm: Structural Determination and Molecular Modelling.

Biofilms are a multicellular way of life, where bacterial cells are close together and embedded in a hydrated macromolecular matrix which offers a number of advantages to the cells. Extracellular polysaccharides play an important role in matrix setup and maintenance. A water-insoluble polysaccharide was isolated and purified from the biofilm produced by Burkholderia cenocepacia strain H111, a cystic fibrosis pathogen. Its composition and glycosidic linkages were determined using Gas–Liquid Chromatography–Mass Spectrometry (GLC–MS) on appropriate carbohydrate derivatives while its complete structure was unraveled by 1D and 2D NMR spectroscopy in deuterated sodium hydroxide (NaOD) aqueous solutions. All the collected data demonstrated the following repeating unit for the water-insoluble B. cenocepacia biofilm polysaccharide: [3)-α-d-Galp-(1→3)-α-d-Glcp-(1→3)-α-d-Galp-(1→3)-α-d-Manp-(1→]n Molecular modelling was used, coupled with NMR Nuclear Overhauser Effect (NOE) data, to obtain information about local structural motifs which could give hints about the polysaccharide insolubility. Both modelling and NMR data pointed at restricted dynamics of local conformations which were ascribed to the presence of inter-residue hydrogen bonds and to steric restrictions. In addition, the good correlation between NOE data and calculated interatomic distances by molecular dynamics simulations validated potential energy functions used for calculations.

Side Chain Hydrogen-Bonding Interactions within Amyloid-like Fibrils Formed by the Low-Complexity Domain of FUS: Evidence from Solid State Nuclear Magnetic Resonance Spectroscopy.

In aqueous solutions, the 214-residue low-complexity domain of the FUS protein (FUS-LC) is known to undergo liquid-liquid phase separation and also to self-assemble into amyloid-like fibrils. In previous work based on solid state nuclear magnetic resonance (ssNMR) methods, a structural model for the FUS-LC fibril core was developed, showing that residues 39-95 form the fibril core. Unlike fibrils formed by amyloid-β peptides, α-synuclein, and other amyloid-forming proteins, the FUS-LC core is largely devoid of purely hydrophobic amino acid side chains. Instead, the core-forming segment contains numerous hydroxyl-bearing residues, including 18 serines, six threonines, and eight tyrosines, suggesting that the FUS-LC fibril structure may be stabilized in part by inter-residue hydrogen bonds among side chain hydroxyl groups. Here we describe ssNMR measurements, performed on 2H,15N,13C-labeled FUS-LC fibrils, that provide new information about the interactions of hydroxyl-bearing residues with one another and with water. The ssNMR data support the involvement of specific serine, threonine, and tyrosine residues in hydrogen-bonding interactions. The data also reveal differences in hydrogen exchange rates with water for different side chain hydroxyl groups, providing information about solvent exposure and penetration of water into the FUS-LC fibril core.

Human Rhinovirus Inhibition Through Capsid "Canyon" Perturbation: Structural Insights into The Role of a Novel Benzothiophene Derivative.

The challenge in targeting human rhinoviruses (HRV) over the years has been attributed to the wide variety in HRV serotypes. Nonetheless, the search for therapeutic agents against HRV continues unabated. These efforts have been augmented by the recent discovery of the novel benzothiophene derivative shown to inhibit HRV viral replication. Bound to subtype HRV-B14, the compound showed similar inhibitory activity as Pleconaril, a known capsid inhibitor. However, the molecular and structural basis of this inhibition remains unclear. In this in silico report, residue interaction network analysis revealed that the binding of the benzothiophene derivative into the "canyon" region of the active site of HRV-B14 distorts its initially extensively networked and compact residue profile. This was characterized by fewer inter-residue hydrogen bonds, reduced van der Waals interactions, and increased residue flexibility. Interestingly, however, the binding of this benzothiophene derivative decreased the flexibility of the north-south wall around the canyon region possibly impeding the "breathing motion" of HRV-B14, hence its inhibition. Atomistic insights also revealed the cruciality of Tyr152 toward inhibitor binding at HRV-B14. This was justified by the amino acid's high intermolecular interaction with both inhibitors. Findings provide important structural insights in the inhibitory activity the novel benzothiophene derivative, and reaffirm its promising potential as an alternative capsid inhibitor toward common cold therapy upon further experimental validation.

Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights

The PR20 HIV-1 protease, a variant with 20 mutations, exhibits high levels of multi-drug resistance; however, to date, there has been no report detailing the impact of these 20 mutations on the conformational and drug binding landscape at a molecular level. In this report, we demonstrate the first account of a comprehensive study designed to elaborate on the impact of these mutations on the dynamic features as well as drug binding and resistance profile, using extensive molecular dynamics analyses. Comparative MD simulations for the wild-type and PR20 HIV proteases, starting from bound and unbound conformations in each case, were performed. Results showed that the apo conformation of the PR20 variant of the HIV protease displayed a tendency to remain in the open conformation for a longer period of time when compared to the wild type. This led to a phenomena in which the inhibitor seated at the active site of PR20 tends to diffuse away from the binding site leading to a significant change in inhibitor–protein association. Calculating the per-residue fluctuation (RMSF) and radius of gyration, further validated these findings. MM/GBSA showed that the occurrence of 20 mutations led to a drop in the calculated binding free energies (ΔGbind) by ~25.17 kcal/mol and ~5 kcal/mol for p2-NC, a natural peptide substrate, and darunavir, respectively, when compared to wild type. Furthermore, the residue interaction network showed a diminished inter-residue hydrogen bond network and changes in inter-residue connections as a result of these mutations. The increased conformational flexibility in PR20 as a result of loss of intra- and inter-molecular hydrogen bond interactions and other prominent binding forces led to a loss of protease grip on ligand. It is interesting to note that the difference in conformational flexibility between PR20 and WT conformations was much higher in the case of substrate-bound conformation as compared to DRV. Thus, developing analogues of DRV by retaining its key pharmacophore features will be the way forward in the search for novel protease inhibitors against multi-drug resistant strains.

ChemInform Abstract: Synthesis and Conformational Analysis of Cyclic Homooligomers from Pyranoid ε‐Sugar Amino Acids.

New pyranoid e-sugar amino acids were designed as building blocks, in which the carboxylic acid and the amine groups were placed in positions C2 and C3 with respect to the tetrahydropyran oxygen atom. By using standard solution-phase coupling procedures, cyclic homooligomers containing pyranoid e-sugar amino acids were synthesized. Conformation analysis was performed by using NMR spectroscopic experiments, FTIR spectroscopic studies, X-ray analysis, and a theoretical conformation search. These studies reveal that the presence of a methoxy group in the position C4 of the pyran ring produces an important structural change in the cyclodipeptides. When the methoxy groups are present, the structure collapses through interresidue hydrogen bonds between the oxygen atoms of the pyran ring and the amide protons. However, when the cyclodipeptide lacks the methoxy groups, a U-shape structure is adopted, in which there is a hydrophilic concave face with four oxygen atoms and two amide protons directed toward the center of the cavity. Additionally, we found important evidence of the key role played by weak electrostatic interactions, such as the five-membered hydrogen-bonded pseudocycles (C5) between the amide protons and the ether oxygen atoms, in the conformation equilibrium of the macrocycles and in the cyclization step of the cyclic tetrapeptides.

Synthesis and Conformational Analysis of Cyclic Homooligomers from Pyranoid ε‐Sugar Amino Acids

New pyranoid ε-sugar amino acids were designed as building blocks, in which the carboxylic acid and the amine groups were placed in positions C2 and C3 with respect to the tetrahydropyran oxygen atom. By using standard solution-phase coupling procedures, cyclic homooligomers containing pyranoid ε-sugar amino acids were synthesized. Conformation analysis was performed by using NMR spectroscopic experiments, FTIR spectroscopic studies, X-ray analysis, and a theoretical conformation search. These studies reveal that the presence of a methoxy group in the position C4 of the pyran ring produces an important structural change in the cyclodipeptides. When the methoxy groups are present, the structure collapses through interresidue hydrogen bonds between the oxygen atoms of the pyran ring and the amide protons. However, when the cyclodipeptide lacks the methoxy groups, a U-shape structure is adopted, in which there is a hydrophilic concave face with four oxygen atoms and two amide protons directed toward the center of the cavity. Additionally, we found important evidence of the key role played by weak electrostatic interactions, such as the five-membered hydrogen-bonded pseudocycles (C5) between the amide protons and the ether oxygen atoms, in the conformation equilibrium of the macrocycles and in the cyclization step of the cyclic tetrapeptides.

Methyl 4-O-β-D-mannopyranosyl β-D-xylopyranoside

Methyl β-D-mannopyranosyl-(1→4)-β-D-xylopyranoside, C(12)H(22)O(10), (I), crystallizes as colorless needles from water, with two crystallographically independent molecules, (IA) and (IB), comprising the asymmetric unit. The internal glycosidic linkage conformation in molecule (IA) is characterized by a ϕ' torsion angle (O5'(Man)-C1'(Man)-O1'(Man)-C4(Xyl); Man is mannose and Xyl is xylose) of -88.38 (17)° and a ψ' torsion angle (C1'(Man)-O1'(Man)-C4(Xyl)-C5(Xyl)) of -149.22 (15)°, whereas the corresponding torsion angles in molecule (IB) are -89.82 (17) and -159.98 (14)°, respectively. Ring atom numbering conforms to the convention in which C1 denotes the anomeric C atom, and C5 and C6 denote the hydroxymethyl (-CH(2)OH) C atom in the β-Xylp and β-Manp residues, respectively. By comparison, the internal glycosidic linkage in the major disorder component of the structurally related disaccharide, methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside), (II) [Zhang, Oliver & Serriani (2012). Acta Cryst. C68, o7-o11], is characterized by ϕ' = -85.7 (6)° and ψ' = -141.6 (8)°. Inter-residue hydrogen bonding is observed between atoms O3(Xyl) and O5'(Man) in both (IA) and (IB) [O3(Xyl)...O5'(Man) internuclear distances = 2.7268 (16) and 2.6920 (17) Å, respectively], analogous to the inter-residue hydrogen bond detected between atoms O3(Xyl) and O5'(Gal) in (II). Exocyclic hydroxymethyl group conformation in the β-Manp residue of (IA) is gauche-gauche, whereas that in the β-Manp residue of (IB) is gauche-trans.

Conformational Dynamics of a Central Trisaccharide Fragment of the LeaLex Tumor Associated Antigen Studied by NMR Spectroscopy and Molecular Dynamics Simulations

AbstractCertain carbohydrate structures are recognized as cancer antigens, and identification of these and relevant epitopes are essential in fighting the disease. The trisaccharide β‐D‐GlcpNAc‐(1→3)‐β‐D‐Galp‐(1→4)‐β‐D‐GlcpNAc‐OMe represents a model for the central region of the LeaLex hexasaccharide and it has herein been investigated by 1D 1H,1H‐NOESY experiments to obtain effective interresidue proton–proton distances as well as by 2D J‐HMBC experiments to determine transglycosidic 3JCH coupling constants. Molecular dynamics (MD) simulations using explicit water as solvent and three different carbohydrate force fields, namely, GLYCAM06, PARM22/SU01, and CHARMM2011, were employed for the interpretation of experimental data. Overall, the force field based MD simulations are able to reproduce the experimental data and the ψ torsion angle at the β‐(1→3)‐linkage is concluded to be flexible. In addition, different minor states were present for the three force fields with either anti‐ψ or non‐exo‐anomeric conformations. Transitions between the exo‐anomeric and the non‐exo‐anomeric conformations for the φ torsion angle at the β‐(1→4)‐linkage in one of the MD simulations were analyzed in detail. It was found that hydrogen‐bonding water molecules, interresidue hydrogen bonds and the transitions between antiperiplanar and synperiplanar conformations for the τH torsion angle of an N‐acetyl group were all essential in the description of the glycosidic transition process. In particular, the transition of τH may be a general way of regulating other transitions into less populated but biologically important conformational regions.

Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution

The introduction of bisecting GlcNAc and core fucosylation in N-glycans is essential for fine functional regulation of glycoproteins. In this paper, the effect of these modifications on the conformational properties of N-glycans is examined at the atomic level by performing replica-exchange molecular dynamics (REMD) simulations. We simulate four biantennary complex-type N-glycans, namely, unmodified, two single-substituted with either bisecting GlcNAc or core fucose, and disubstituted forms. By using REMD as an enhanced sampling technique, five distinct conformers in solution, each of which is characterized by its local orientation of the Manα1-6Man glycosidic linkage, are observed for all four N-glycans. The chemical modifications significantly change their conformational equilibria. The number of major conformers is reduced from five to two and from five to four upon the introduction of bisecting GlcNAc and core fucosylation, respectively. The population change is attributed to specific inter-residue hydrogen bonds, including water-mediated ones. The experimental NMR data, including nuclear Overhauser enhancement and scalar J-coupling constants, are well reproduced taking the multiple conformers into account. Our structural model supports the concept of "conformer selection", which emphasizes the conformational flexibility of N-glycans in protein-glycan interactions.

Disorder and conformational analysis of methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside

Methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside, C(12)H(22)O(10), (II), crystallizes as colorless needles from water with positional disorder in the xylopyranosyl (Xyl) ring and no water molecules in the unit cell. The internal glycosidic linkage conformation in (II) is characterized by a φ' torsion angle (C2'(Gal)-C1'(Gal)-O1'(Gal)-C4(Xyl)) of 156.4 (5)° and a ψ' torsion angle (C1'(Gal)-O1'(Gal)-C4(Xyl)-C3(Xyl)) of 94.0 (11)°, where the ring atom numbering conforms to the convention in which C1 denotes the anomeric C atom, and C5 and C6 denote the hydroxymethyl (-CH(2)OH) C atoms in the β-Xyl and β-Gal residues, respectively. By comparison, the internal linkage conformation in the crystal structure of the structurally related disaccharide, methyl β-lactoside [methyl β-D-galactopyranosyl-(1→4)-β-D-glucopyranoside], (III) [Stenutz, Shang & Serianni (1999). Acta Cryst. C55, 1719-1721], is characterized by φ' = 153.8 (2)° and ψ' = 78.4 (2)°. A comparison of β-(1→4)-linked disaccharides shows considerable variability in both φ' and ψ', with the range in the latter (~38°) greater than that in the former (~28°). Inter-residue hydrogen bonding is observed between atoms O3(Xyl) and O5'(Gal) in the crystal structure of (II), analogous to the inter-residue hydrogen bond detected between atoms O3(Glc) and O5'(Gal) in (III). The exocyclic hydroxymethyl conformations in the Gal residues of (II) and (III) are identical (gauche-trans conformer).

Transient hydrogen bonding in uniformly 13C,15N‐Labeled Carbohydrates in Water

We report NMR studies of transient hydrogen bonding in a polysaccharide (PS) dissolved in water without cosolvent at ambient temperature. The PS portion of the Escherichia coli O142 lipopolysaccharide is comprised of repeating pentasaccharide units of GalNAc (N-acetyl galactosamine), GlcNAc (N-acetyl glucosamine), and rhamnose in a 3:1:1 ratio, respectively. A 105-ns molecular dynamics (MD) simulation on one pentasaccharide repeat unit predicts transient inter-residue hydrogen bonds from the GalNAc NH groups in the PS. To investigate these predictions experimentally, the PS was uniformly ¹³C,¹⁵N enriched and the NH, carbonyl, C2, C4, and methyl resonances of the GalNAc and GlcNAc residues assigned using through-bond triple-resonance NMR experiments. Temperature dependence of amide NH chemical shifts and one-bond NH J couplings support that NH groups on two of the GalNAc residues are donors in transient hydrogen bonds. The remaining GalNAc and GlcNAc NHs do not appear to be donors from either temperature-dependent chemical shifts or one-bond NH J couplings. These results substantiate the presence of weak or partial hydrogen bonds in carbohydrates, and that MD simulations of repeating units in PSs provide insight into overall PS structure and dynamics.

Molecular Conformations in the Pentasaccharide LNF-1 Derived from NMR Spectroscopy and Molecular Dynamics Simulations

The conformational dynamics of the human milk oligosaccharide lacto-N-fucopentaose (LNF-1), α-L-Fucp-(1 → 2)-β-D-Galp-(1 → 3)-β-D-GlcpNAc-(1 → 3)-β-D-Galp-(1 → 4)-D-Glcp, has been analyzed using NMR spectroscopy and molecular dynamics (MD) computer simulations. Employing the Hadamard (13)C-excitation technique and the J-HMBC experiment, (1)H,(13)C trans-glycosidic J coupling constants were obtained, and from one- and two-dimensional (1)H,(1)H T-ROESY experiments, proton-proton cross-relaxation rates were determined in isotropic D(2)O solution. In the lyotropic liquid-crystalline medium consisting of ditetradecylphosphatidylcholine, dihexylphosphatidylcholine, N-cetyl-N,N,N-trimethylammonium bromide, and D(2)O, (1)H, (1)H and one-bond (1)H, (13)C residual dipolar couplings (RDCs), as well as relative sign information on homonuclear RDCs, were determined for the pentasaccharide. Molecular dynamics simulations with explicit water were carried out from which the internal isomerization relaxation time constant, τ(N), was calculated for transitions at the ψ torsion angle of the β-(1 → 3) linkage to the lactosyl group in LNF-1. Compared to the global reorientation time, τ(M), of ∼0.6 ns determined experimentally in D(2)O solution, the time constant for the isomerization relaxation process, τ(N(scaled)), is about one-third as large. The NMR parameters derived from the isotropic solution show very good agreement with those calculated from the MD simulations. The only notable difference occurs at the reducing end, which should be more flexible than observed by the molecular simulation, a conclusion in complete agreement with previous (13)C NMR relaxation data. A hydrogen-bond analysis of the MD simulation revealed that inter-residue hydrogen bonds on the order of ∼30% were present across the glycosidic linkages to sugar ring oxygens. This finding highlights that intramolecular hydrogen bonds might be important in preserving well-defined structures in otherwise flexible molecules. An analysis including generalized order parameters obtained from nuclear spin relaxation experiments was performed and successfully shown to limit the conformational space accessible to the molecule when the number of experimental data are too scarce for a complete conformational analysis.

Methyl β-D-galactopyranosyl-(1→4)-β-D-allopyranoside tetrahydrate

The title compound, C13H24O11·4H2O, (I), crystallized from water, has an inter­nal glycosidic linkage conformation having φ′ (O5Gal—C1Gal—O1Gal—C4All) = −96.40 (12)° and ψ′ (C1Gal—O1Gal—C4All—C5All) = −160.93 (10)°, where ring-atom numbering conforms to the convention in which C1 denotes the anomeric C atom, C5 the ring atom bearing the exocyclic hydroxymethyl group, and C6 the exocyclic hy­droxy­methyl (CH2OH) C atom in the βGalp and βAllp residues. Inter­nal linkage conformations in the crystal structures of the structurally related disaccharides methyl β-lactoside [methyl β-d-galactopyranosyl-(1→4)-β-d-gluco­pyran­oside] methanol solvate [Stenutz, Shang & Serianni (1999). Acta Cryst. C55, 1719–1721], (II), and methyl β-cello­bioside [methyl β-d-gluco­pyran­osyl-(1→4)-β-d-gluco­pyran­oside] methanol solvate [Ham & Williams (1970). Acta Cryst. B26, 1373–1383], (III), are characterized by φ′ = −88.4 (2)° and ψ′ = −161.3 (2)°, and φ′ = −91.1° and ψ′ = −160.7°, respectively. Inter-residue hydrogen bonding is observed between O3Glc and O5Gal/Glc in the crystal structures of (II) and (III), suggesting a role in determining their preferred linkage conformations. An analogous inter-residue hydrogen bond does not exist in (I) due to the axial orientation of O3All, yet its inter­nal linkage conformation is very similar to those of (II) and (III).

A 3D-structural model of unsulfated chondroitin from high-field NMR: 4-sulfation has little effect on backbone conformation

The glycosaminoglycan chondroitin sulfate is essential in human health and disease but exactly how sulfation dictates its 3D-strucutre at the atomic level is unclear. To address this, we have purified homogenous oligosaccharides of unsulfated chondroitin (with and without 15N-enrichment) and analysed them by high-field NMR to make a comparison published chondroitin sulfate and hyaluronan 3D-structures. The result is the first full assignment of the tetrasaccharide and an experimental 3D-model of the hexasaccharide (PDB code 2KQO). In common with hyaluronan, we confirm that the amide proton is not involved in strong, persistent inter-residue hydrogen bonds. However, in contrast to hyaluronan, a hydrogen bond is not inferred between the hexosamine OH-4 and the glucuronic acid O5 atoms across the β(1→3) glycosidic linkage. The unsulfated chondroitin bond geometry differs slightly from hyaluronan by rotation about the β(1→3) ψ dihedral (as previously predicted by simulation), while the β(1→4) linkage is unaffected. Furthermore, comparison shows that this glycosidic linkage geometry is similar in chondroitin-4-sulfate. We therefore hypothesise that both hexosamine OH-4 and OH-6 atoms are solvent exposed in chondroitin, explaining why it is amenable to sulfation and hyaluronan is not, and also that 4-sulfation has little effect on backbone conformation. Our conclusions exemplify the value of the 3D-model presented here and progress our understanding of glycosaminoglycan molecular properties.

Conformational Analysis of Trimannoside and Bisected Trimannoside Using Aqueous Molecular Dynamics Simulations

The conformational properties of oligosaccharides are important to understand carbohydrate-protein interactions. A trimannoside, methyl 3,6-di-O-(<TEX>$\alpha$</TES>-D-Man)-<TEX>$\alpha$</TES>-D-Man (TRIMAN) is a basic unit of N-linked oligosaccharides. This TRIMAN moiety was further modified by GlcNAc (BISECT), which is important to biological activity of N-glycan. To characterize the trimannoside and its bisecting one we performed a molecular dynamics simulation in water. The resulting models show the conformational transition with two major and minor conformations. The major conformational transition results from the <TEX>$\omega$</TEX> angle transition; another minor transition is due to the <TEX>$\psi$</TEX> angle transition of <TEX>$\alpha$</TES> (1 <TEX>$\rightarrow$</TEX> 6) linkage. The introduction of bisecting GlcNAc on TRIMAN made the different population of the major and minor conformations of the TRIMAN moiety. Omega (<TEX>$\omega$</TEX>) angle distribution is largely changed and the population of gt conformation is increased in BISECT oligosaccharide. The inter-residue hydrogen bonds and water bridges via bisecting GlcNAc residue make alterations on the local and overall conformation of TRIMAN moiety. These changes of conformational distribution for TRIMAN moiety can affect the overall conformation of N-glycan and the biological activity of glycoprotein.