A refined model for N-acetyl-α-D-glucosamine

Development of an Amino Sugar-Based Supramolecular Hydrogelator with Reduction Responsiveness

Stimuli-responsive supramolecular hydrogels are a newly emerging class of aqueous soft materials with a wide variety of bioapplications. Here we report a reduction-responsive supramolecular hydrogel constructed from a markedly simple low-molecular-weight hydrogelator, which is developed on the basis of modular molecular design containing a hydrophilic amino sugar and a reduction-responsive nitrophenyl group. The hydrogel formation ability differs significantly between glucosamine- and galactosamine-based self-assembling molecules, which are epimers at the C4 position, and only the glucosamine-based derivative can act as a hydrogelator.

Glycosidic linkage, N-acetyl side-chain, and other structural properties of methyl 2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-β-D-mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2-acetamido-2-deoxy-β-D-glycopyranosyl-(1→4)-β-D-mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono- and disaccharides bearing N-acetyl side-chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C-N (amide) and C-O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N-H hydrogen. Relative to N-acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen-bond acceptor display elongated C-O and shortened C-N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C-N and C-O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis-trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter-residue hydrogen bonding and some bond angles in or proximal to β-(1→4) O-glycosidic linkages on linkage torsion angles φ and ψ. Hypersurfaces correlating φ and ψ with the linkage C-O-C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.

Is N-acetyl-D-glucosamine a rigid 4C1 chair?

Understanding microsecond-timescale dynamics is crucial to establish three-dimensional (3D) structure-activity relationships in sugars but has been intractable to experiments and simulations. As a consequence, whether arguably the most important chemical scaffold in glycobiology, N-acetyl-d-glucosamine (GlcNAc), deviates from a rigid (4)C(1) chair is unknown. Here, conformer populations and exchange kinetics were quantified from the longest aqueous carbohydrate simulations to date (0.2 ms total) of GlcNAc, four derivatives from heparan sulfate and their methylglycosides. Unmodified GlcNAc took 3-5 μs to reach a conformational equilibrium, which comprised a metastable (4)C(1) chair that underwent (4)C(1) ↔ (1)C(4) transitions at a predicted forward rate of 0.8 μs(-1) with an average (1)C(4)-chair lifetime of 3 ns. These predictions agree with high-resolution crystallography and nuclear magnetic resonance but not with the hypothesis that GlcNAc is a rigid (4)C(1) chair, concluded from previous experimental analyses and non-aqueous modeling. The methylglycoside was calculated to have a slower forward rate (0.3 μs(-1)) and a more stable (4)C(1) conformer (0.2 kcal mol(-1)), suggesting that pivotal 3D intermediates (particularly (2)S(O), (1)S(5) and B(2,5)) increased in energy, and water was implicated as a major cause. Sulfonation (N-, 3-O and 6-O) significantly augmented this effect by blocking pseudorotation, but did not alter the rotational preferences of hydroyxl or hydroxymethyl groups. We therefore propose that GlcNAc undergoes puckering exchange that is dependent on polymerization and sulfo substituents. Our analyses, and 3D model of the equilibrium GlcNAc conformer in water, can be used as dictionary data and present new opportunities to rationally modify puckering and carbohydrate bioactivity, with diverse applications from improving crop yields to disease amelioration.

Methyl 2-acetamido-2-deoxy-β-D-glucopyranoside dihydrate and methyl 2-formamido-2-deoxy-β-D-glucopyranoside

Methyl 2-acetamido-2-deoxy-β-D-glucopyranoside (β-GlcNAcOCH(3)), (I), crystallizes from water as a dihydrate, C(9)H(17)NO(6)·H(2)O, containing two independent molecules [denoted (IA) and (IB)] in the asymmetric unit, whereas the crystal structure of methyl 2-formamido-2-deoxy-β-D-glucopyranoside (β-GlcNFmOCH(3)), (II), C(8)H(15)NO(6), also obtained from water, is devoid of solvent water molecules. The two molecules of (I) assume distorted (4)C(1) chair conformations. Values of φ for (IA) and (IB) indicate ring distortions towards B(C2,C5) and (C3,O5)B, respectively. By comparison, (II) shows considerably more ring distortion than molecules (IA) and (IB), despite the less bulky N-acyl side chain. Distortion towards B(C2,C5) was observed for (II), similar to the findings for (IA). The amide bond conformation in each of (IA), (IB) and (II) is trans, and the conformation about the C-N bond is anti (C-H is approximately anti to N-H), although the conformation about the latter bond within this group varies by ~16°. The conformation of the exocyclic hydroxymethyl group was found to be gt in each of (IA), (IB) and (II). Comparison of the X-ray structures of (I) and (II) with those of other GlcNAc mono- and disaccharides shows that GlcNAc aldohexopyranosyl rings can be distorted over a wide range of geometries in the solid state.

Vibrational analysis of N-acetyl-alpha-D-glucosamine and beta-D-glucuronic acid

Infrared spectra of solid and aqueous solutions of N-acetyl-alpha-D-glucosamine and beta-D-glucuronic acid have been investigated by means of Fourier transform infrared (FT-IR) spectroscopy and quantum chemical density functional theory (DFT) calculations. The errors of the computed harmonic force field were corrected according to the scaled quantum mechanical (SQM) method of Pulay, with scale factors partly from the literature and partly developed here. Scale factors for the hydrogen-bonded OH groups were determined by SQM treatment of ethylene glycol. The IR spectra and test computations revealed that beta-D-glucuronic acid is present as a dimer, formed by hydrogen-bonding between the COOH groups, in the solid phase. On the basis of the calculated results, 64 and 56 bands in the 4000-50 cm(-1) range of the FT-IR spectra have been assigned for N-acetyl-alpha-D-glucosamine and beta-D-glucuronic acid, respectively.

TIP5P-Consistent Treatment of Electrostatics for Biomolecular Simulations

The inclusion of zero-mass point charges around electronegative atoms, such as oxygen, within molecular mechanical force fields is known to improve hydrogen-bonding directionality. In parallel, inclusion of lone-pairs (LPs) in the TIP5P water model increased its ability to reproduce both gas-phase and condensed-phase properties over its non-LP predecessor, TIP3P. Currently, most biomolecular parameter sets compute partial atomic charges via fitting of the classical molecular electrostatic potential (MEP) to the quantum mechanical MEP. Application of this methodology to optimize lone-pair description is therefore consistent with the current approach to modeling electrostatics and is straightforward to implement. Here, we present an atom-type specific lone-pair model, which leads to the most optimal LP placement for each atom type, and, notably, results in reproduction of the lone-pair description present in TIP5P. Carbohydrates are rich in hydroxyl groups, and development of a lone-pair inclusive carbohydrate force field for use with a lone-pair containing water model, such as TIP5P, ensures the compatibility between these two models. Implementation of this lone-pair model improves the geometry and energetics for a series of hydrogen-bonded clusters and the properties of several small molecule crystals over the non-LP containing force field.

Density functional study of the conformational space of 4C1 D-glucuronic acid

The conformational space of (4)C(1) alpha- and beta-d-glucuronic acid was scanned by HF/3-21G(p) calculations followed by optimization of the 15 most stable structures for each, using the B3LYP density functional theory method in conjunction with a diffuse polarized valence triple-zeta basis set. We found a general preference of the alpha anomers in the isolated molecules in agreement with the large endo-anomeric hyperconjugation effects in these structures. From the other intramolecular interactions (exo-anomeric hyperconjugation, hydrogen-bonding, dipole-dipole, and steric interactions), the effect of the hydrogen bonding is the most pronounced and plays a major role in determining the stability order within the alpha and beta series. The most stable conformer of both alpha and beta (4)C(1) d-glucuronic acid is the structure with the maximum number (5) of intramolecular hydrogen bonds. Introduction of solvent (water) effects by the SCI-PCM model resulted in two characteristic changes of the energetic properties: the gas-phase stability order changed considerably, and the energy range of the 15 most stable conformers decreased from 30 to 15 kJ/mol. The geometrical parameters reflect well the superimposed effects of hyperconjugation and hydrogen-bonding interactions. Most characteristics are the variations of the C-O bond distances (within a range of 0.04 A) upon the combined intramolecular effects.

Molecular and crystal structure of N-(2-deoxy-D-aldohexos-2-yl)-glycines (Heyns compounds)

Heyns compounds, 2-carboxymethylamino-2-deoxy-D-glucose (1), -mannose (2), and -galactose (3), were prepared by N-carboxymethylation of the corresponding hexosamines and 1 was also prepared via the reaction of D-fructose with glycine. Both 1 and 3 crystallize from aqueous solutions as zwitterions in the alpha-pyranose form and in the 4C1 conformation. Crystalline 1 is nearly isostructural to N-acetylglucosamine, forming stacks of molecules with infinite chains of homodromic hydrogen bonds along the stacks. For both 1 and 3, all hydroxyl, ammonium, and carboxyl groups are involved in intermolecular hydrogen-bonding, and an intramolecular hydrogen bond in 3 is formed via interaction of the ammonium and carboxyl groups. 1H and 13C NMR spectra (D2O solutions) indicate that all of the compounds are conformationally unstable, and that the major form present in D2O solution at 25 degrees C is the 4C1 alpha-pyranose form, with the 4C1 beta-pyranose form present in lesser amounts. In addition, for solutions of 2 and 3, considerable amounts of alpha- and beta-furanose forms are present and exist in conformations favorable for a cis-relationship between the carboxymethylammonium and anomeric hydroxyl groups.

Application of two-dimensional NMR spectroscopy and molecular dynamics simulations to the conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of Streptococcus group A

This paper describes the use of a protocol for conformational analysis of oligosaccharide structures related to the cell-wall polysaccharide of Streptococcus group A. The polysaccharide features a branched structure with an L-rhamnopyranose (Rhap) backbone consisting of alternating alpha-(1-->2) and alpha-(1-->3) links and D-N-acetylglucosamine (GlcpNAc) residues beta-(1-->3)-connected to alternating rhamnose rings: [formula: see text] Oligomers consisting of three to six residues have been synthesized and nuclear magnetic resonance (NMR) assignments have been made. The protocol for conformational analysis of the solution structure of these oligosaccharides involves experimental and theoretical methods. Two-dimensional NMR spectroscopy methods (TOCSY, ROESY and NOESY) are utilized to obtain chemical shift data and proton-proton distances. These distances are used as constraints in 100 ps molecular dynamics simulations in water using QUANTA and CHARMm. In addition, the dynamics simulations are performed without constraints. ROE build-up curves are computed from the averaged structures of the molecular dynamics simulations using the CROSREL program and compared with the experimental curves. Thus, a refinement of the initial structure may be obtained. The alpha-(1-->2) and the beta-(1-->3) links are unambiguously defined by the observed ROE cross peaks between the A-B',A'-B and C-B,C'-B' residues, respectively. The branch-point of the trisaccharide CBA' is conformationally well-defined. Assignment of the conformation of the B-A linkage (alpha-(1-->3)) was problematic due to TOCSY relay, but could be solved by NOESY and T-ROESY techniques. A conformational model for the polysaccharide is proposed.

13C NMR studies of wheat germ agglutinin interactions with N-acetylglucosamine at a magnetically oriented bilayer surface

The orientation of synthetic 13C-labeled glycolipid receptors and their interaction with the plant lectin wheat germ agglutinin have been studied in an oriented membrane system using NMR spectroscopy. A series of 2-[1,2-13C2]acetamido-2-deoxy-beta-D-glucopyranosides were synthesized with between zero and four hydrophilic ethoxy units between the headgroup and an alkyl chain which anchors the receptors in the bilayers. The chemical shift anisotropy of the 13C carbonyl and a 13C-13C dipolar coupling between the labeled carbons provide information about the orientation and dynamics of the receptor headgroup in oriented membrane systems. It was found that the headgroups of the receptors with two, three, or four ethoxy units appeared isotropic when incorporated in the oriented bilayers, but those of the receptors with zero or one ethoxy units were significantly ordered by the bilayers. The average orientations consistent with measured spectral parameters were determined for the receptors with zero and one ethoxy units and were found to coincide with low-energy conformations from molecular modeling. When the plant lectin wheat germ agglutinin was added to the sample, only the receptors with two, three, or four ethoxy units separating the headgroup from the alkyl chain showed evidence of binding by the lectin. Although the 13C-labeled resonances broadened when the protein bound, no changes in dipolar couplings or chemical shift anisotropies could be detected, suggesting that the motion of the headgroup was slowed by protein binding, but average orientation and overall order changed little. Competition studies demonstrated that none of the lectin/receptor complexes are more stable than the complex of the lectin and N-acetylglucosamine in solution. These results suggest that the membrane does not stabilize the interactions of wheat germ agglutinin with these cell-surface receptors. Furthermore, molecular modeling demonstrates that the zero- and one-spacer receptors may not bind wheat germ agglutinin because the orientations of the N-acetyl groups in these receptors would result in significant steric contacts between the lectin/receptor complex and the membrane.

Molecular modelling of bacterial deep rough mutant lipopolysaccharide of Escherichia coli

Molecular modelling techniques have been applied to compute the conformation accessible to bacterial deep rough lipopolysaccharide of Escherichia coli (Re-LPS). Analyses of the results showed that the models typically exhibit a tilt of the diglucosamine backbone with respect to the membrane normal of 53 +/- 7 degrees while both the glucosamine ring planes are oriented approximately parallel to the membrane normal. Different models were found to show compact and elongated types of acyl chain arrangements, both producing anisotropic lateral dimensions of the models of 1.0-1.1 nm and 1.7-2.0 nm for the shorter and the longer side, respectively. The conformationally allowed range of the isolated dOclA(alpha-2-4)dOclA disaccharide (dOclA = 3-deoxy-D-mannooctulosonic acid) was found to be extremely limited. It appeared that the dOclA disaccharide (dOclA)2 is centred at the top of the Re-LPS molecule preferring two orientations stabilized by hydrogen bonds involving only one phosphate group of the lipid A moiety at a time. The effect of charges on the Re-LPS conformations has been studied in separate calculations. From these calculations it was obvious that charges have no significant effects on the conformations of the isolated lipid A and (dOclA)2 moieties. However, it was found that the orientation of (dOclA)2 with respect to the lipid A part is highly sensitive to charges, i.e. in the charged models the proximity of phosphate and carboxyl groups is prevented by strong electrostatic repulsion between these negatively charged groups. In order to rationalize the acyl chain packing of the models, a simple geometrical model which correlates the tilt of the diglucosamine backbone with the energically favoured close packing of the acyl chains is proposed. Furthermore, the possibility of a chelate-like complexation of divalent cations and its contribution to head group mobility is discussed.

Crystal structure of hexameric haemocyanin from Panulirus interruptus refined at 3.2 A resolution

The use of non-crystallographic symmetry restraints in the refinement of the haemocyanin hexamer from Panulirus interruptus at 3.2 A resolution has resulted in a final model with a very reasonable geometry and a crystallographic R-factor of 20.1%, using 59,193 observed structure factor amplitudes between 8.0 and 3.2 A. The mean co-ordinate error is approximately 0.35 A. The six subunits appear to be related by symmetry operations that differ slightly from 32 point group symmetry. The six subunits have essentially maintained the same structure. The hexamer, with point group 32, is best described as a trimer of "tight dimers". The contacts between the subunits in such a dimer are more numerous, and better conserved during evolution than contacts in a trimer. The interface of a tight dimer is separated by an internal cavity into two "contact areas". The contact area nearest to the centre of the hexamer is most extensive and consists mainly of residues that are quite conserved among arthropodan haemocyanins. All these residues are provided by the second domain of each subunit. Hence, this second domain may play a crucial role in the allosteric functioning of this oxygen transport protein. The dinuclear copper oxygen-binding site resides in the centre of domain 2. This oxygen-binding centre is not fully accessible from the solvent. Three large cavities occur, however, within each subunit at the interfaces of the three domains. All three cavities contain ordered water molecules, and two of them are accessible from the surrounding solvent. These cavities may play a role in facilitating fast movement of dioxygen towards the binding site, which is situated in a highly conserved, rather hydrophobic core. A detailed definition of the geometry of the copper site is, of course, not possible at the limited resolution of 3.2 A. Nevertheless, it is possible to conclude that each copper is co-ordinated by two, more or less tightly bound, histidine ligands and one more distant histidine residue. The six histidine residues utilize their N epsilon atoms for copper co-ordination, while their N delta atoms are engaged in hydrogen bonds with conserved residues or water molecules. The two distant histidine ligands are located in apical positions and are on opposite sides with respect to the plane approximately defined by the four more tightly bound histidine ligands and the two copper ions. The copper-to-copper distance is 3.5 to 3.6 A in four of the subunits, but this distance deviates considerably in two others.(ABSTRACT TRUNCATED AT 400 WORDS)

The conformation of core oligosaccharides from Escherichia coli and Salmonella typhimurium lipopolysaccharides as predicted by semi-empirical calculations

The preferred conformation of the hexose and heptose regions of core saccharides from Enterobacteriaceae lipopolysaccharides was calculated. The Hard Sphere Exo Anomeric (HSEA) approach was used and the minimum energy conformation of the Salmonella typhimurium and Escherichia coli R1, R2, R3, R4 and K12 cores calculated. The results indicate that most of the cores are sterically crowded, with small degrees of freedom, and that the hexose and heptose parts form two separate regions. The core structures exhibit a 'front'-side and a 'back'-side, the former being similar for all the structures and the latter being characteristic for each core type.

Intermolecular nuclear Overhauser effect and atomic pair potential approaches to wheat germ agglutinin-sugar binding

The detailed binding mechanism of wheat germ agglutinin (WGA) with N-acetylglucosamine (GlcNAc) was investigated using intermolecular 1H-1H nuclear Overhauser effect (NOE) and atomic pair potential (APP) calculations. Negative NOE was observed on the 1H spectrum of 1-O-methyl derivative of GlcNAc in a solution containing WGA, when the aromatic region of the WGA spectrum was irradiated. Analyses of the time dependence of NOE revealed that H2 and the N-acetyl methyl protons of the sugar are in close proximity to the aromatic protons of WGA in the bound state. This was confirmed and further elucidated by the APP calculations. According to the calculation, the major binding force comes from a hydrogen-bonding between C3-OH of sugar and an acidic residue present in each of the two binding sites of WGA: Glu115 in site 1 and Asp29 in site 2. The binding is further assisted by the N-acetyl group which interacts with a few more polar amino acid residues in the binding sites. The optimized binding mode suggested by the APP calculations supports the NMR results in that H2 and a part of the N-acetyl methyl protons are within 4.5 A distance from protons of both Tyr64 and Tyr73 in site 1 and of Tyr159 in site 2.

1H- and 13C-n.m.r. assignments and conformational analysis of some monosaccharide and oligosaccharide substrate-analogues of lysozyme

The 1H- and 13C-n.m.r. spectra of solutions of GlcNAc, beta-GlcNAc-(1----4)-GlcNAc, and beta-GlcNAc-(1----4)-beta-GlcNAc-(1----4)-GlcNAc in D2O at 50 degrees are interpreted in terms of the conformations, using a combination of 1D- and 2D-n.m.r. spectroscopy and spectra simulation techniques. Two preferred orientations of the hydroxymethyl group were found for each of these saccharides. The conformations have been compared with those found from X-ray crystallographic data and conformational energy calculations.

Structural studies on the bacterial cell wall peptidoglycan pseudomurein. I. Conformational energy calculations on the glycan strands in C1 conformation and comparison with murein

Conformational energy calculations have been used to explore the conformations which may be realized for the sugar moiety of murein and pseudomurein. For the building blocks of the pseudomurein sugar strands, i.e. for the monosaccharides beta-D-N-acetylglucosamine (NAG) and alpha-L-N-acetyltalosaminuronic acid (NAT), both in C1 ring conformation, as well as for their 1,3 and 1,4 linked disaccharides, the favoured conformations were obtained. The helical parameters of sugar strands of both linkage types, which describe the regular structure of the corresponding polysaccharides, poly-(1,3-NAT-NAG) and poly-(1,4-NAT-NAG), were calculated. Both types of polysaccharides poly-(NAG-NAT) considered in this study favoured extended conformations, which in the case of 1,3 linked polymers showed less gain of length per saccharide unit compared to 1,4 linked poly-(NAG-NAT) residues. For a 1,3 linked sugar moiety of pseudomurein every pair of neighbouring peptides attached to glycan chain pointed in favoured conformations approximately to opposite sides of the strands, whereas in a 1,4 linked poly-(NAG-NAT) the peptides protruded approximately to the same side of the glycan moiety. A comparison between pseudomurein and murein revealed that the sugar moieties of both peptidoglycans have similar features in respect to their overall structure, i.e. both favoured more or less extended structures. In contrast to these data the shapes of the resulting polysaccharide moieties were remarkably different. In poly-(1,3-NAG-NAT) the glycan chains possessed a zig-zag-like arrangement, whereas for glycan chains of the murein type relatively flat structures were preferred. These remaining differences in the conformational arrangement between both peptidoglycans depend strongly on the C1 chair conformation of NAT. It is, therefore, attractive to speculate about an hypothetical pseudomurein sugar chain configuration comprising beta-L-N-acetyltalosaminuronic acid in its 1C conformation.