4C1 Chair Conformation Research Articles

Enzymatic C4-Epimerization of UDP-Glucuronic Acid: Precisely Steered Rotation of a Transient 4-Keto Intermediate for an Inverted Reaction without Decarboxylation.

UDP-glucuronic acid (UDP-GlcA) 4-epimerase illustrates an important problem regarding enzyme catalysis: balancing conformational flexibility with precise positioning. The enzyme coordinates the C4-oxidation of the substrate by NAD+ and rotation of a decarboxylation-prone β-keto acid intermediate in the active site, enabling stereoinverting reduction of the keto group by NADH. We reveal the elusive rotational landscape of the 4-keto intermediate. Distortion of the sugar ring into boat conformations induces torsional mobility in the enzyme's binding pocket. The rotational endpoints show that the 4-keto sugar has an undistorted 4 C1 chair conformation. The equatorially placed carboxylate group disfavors decarboxylation of the 4-keto sugar. Epimerase variants lead to decarboxylation upon removal of the binding interactions with the carboxylate group in the opposite rotational isomer of the substrate. Substitutions R185A/D convert the epimerase into UDP-xylose synthases that decarboxylate UDP-GlcA in stereospecific, configuration-retaining reactions.

Adsorption of Emerging Munitions Contaminants on Cellulose Surface: A Combined Theoretical and Experimental Investigation

This manuscript reports results of an integrated theoretical and experimental investigation of adsorption of two emerging contaminants (DNAN and FOX-7) and legacy compound TNT on cellulose surface. Cellulose was modeled as trimeric form of the linear chain of 1→4 linked of β-D-glucopyranos in (4)C1 chair conformation. Geometries of modeled cellulose, munitions compounds and their complexes were optimized at the M06-2X functional level of Density Functional Theory using the 6-31G(d,p) basis set in gas phase and in water solution. The effect of water solution was modeled using the CPCM approach. Nature of potential energy surfaces was ascertained through harmonic vibrational frequency analysis. Interaction energies were corrected for basis set superposition error and the 6-311G(d,p) basis set was used. Molecular electrostatic potential mapping was performed to understand the reactivity of the investigated systems. It was predicted that adsorbates will be weakly adsorbed on the cellulose surface in water solution than in the gas phase.

Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. family GH3 β-D-glucosidases.

The industrial conversion of cellulosic plant biomass into useful products such as biofuels is a major societal goal. These technologies harness diverse plant degrading enzymes, classical exo- and endo-acting cellulases and, increasingly, cellulose-active lytic polysaccharide monooxygenases, to deconstruct the recalcitrant β-D-linked polysaccharide. A major drawback with this process is that the exo-acting cellobiohydrolases suffer from severe inhibition from their cellobiose product. β-D-Glucosidases are therefore important for liberating glucose from cellobiose and thereby relieving limiting product inhibition. Here, the three-dimensional structures of two industrially important family GH3 β-D-glucosidases from Aspergillus fumigatus and A. oryzae, solved by molecular replacement and refined at 1.95 Å resolution, are reported. Both enzymes, which share 78% sequence identity, display a three-domain structure with the catalytic domain at the interface, as originally shown for barley β-D-glucan exohydrolase, the first three-dimensional structure solved from glycoside hydrolase family GH3. Both enzymes show extensive N-glycosylation, with only a few external sites being truncated to a single GlcNAc molecule. Those glycans N-linked to the core of the structure are identified purely as high-mannose trees, and establish multiple hydrogen bonds between their sugar components and adjacent protein side chains. The extensive glycans pose special problems for crystallographic refinement, and new techniques and protocols were developed especially for this work. These protocols ensured that all of the D-pyranosides in the glycosylation trees were modelled in the preferred minimum-energy (4)C1 chair conformation and should be of general application to refinements of other crystal structures containing O- or N-glycosylation. The Aspergillus GH3 structures, in light of other recent three-dimensional structures, provide insight into fungal β-D-glucosidases and provide a platform on which to inform and inspire new generations of variant enzymes for industrial application.

Conformational interchange of a carbohydrate by mechanical compression at the air–water interface

Methyl xylopyranoside containing three 4-(pyrene-1-yl)benzoyl groups (PyXy) undergoes conformational interchange within a Langmuir monolayer upon mechanical compression. This xylose-type molecular machine PyXy was immobilized within two different matrix lipids, methyl stearate and methyl 2,3,4-tri-O-stearoyl-β-D-xylopyranoside, which respectively form rigid and soft monolayers. Structural properties of the monolayer were characterized by assessing the compressibility, compression modulus, and ideal limiting molecular area of PyXy, all of which were estimated from the π-A isotherm measurements. Only the rigid monolayer exhibited a transition to the condensed phase with a limiting molecular area of PyXy smaller than that of the cross-sectional area of the xylopyranose ring in its C1 chair conformation. This suggests conformational interchange of PyXy from the most stable (4)C1 (C1) form to the metastable (1)C4 (1C) form. Surface-reflective fluorescence spectroscopy of the monolayer was applied to detect excimer emission resulting from the face-to-face dimerization of pyrenes attached at the O-2 and O-4 positions of xylose. Fluorescence intensity of the excimer increased abruptly in the condensed region only when the rigid monolayer was applied. These results indicate that the rigidity of the matrix monolayer is a critical aspect of the precise manipulation of molecular machines at interfaces. Consequently, this study demonstrates that including a molecular machine into a rigid lipid matrix is a promising means for the preparation of a novel nanoassembly with dynamic functionalities variable depending on a mechanical stimulus.

A Novel Transition-state Analogue for Lysozyme, 4-O-β-Tri-N-acetylchitotriosyl Moranoline, Provided Evidence Supporting the Covalent Glycosyl-enzyme Intermediate*

4-O-β-Di-N-acetylchitobiosyl moranoline (2) and 4-O-β-tri-N-acetylchitotriosyl moranoline (3) were produced by lysozyme-mediated transglycosylation from the substrates tetra-N-acetylchitotetraose, (GlcNAc)4, and moranoline, and the binding modes of 2 and 3 to hen egg white lysozyme (HEWL) was examined by inhibition kinetics, isothermal titration calorimetry (ITC), and x-ray crystallography. Compounds 2 and 3 specifically bound to HEWL, acting as competitive inhibitors with Ki values of 2.01 × 10(-5) and 1.84 × 10(-6) m, respectively. From ITC analysis, the binding of 3 was found to be driven by favorable enthalpy change (ΔHr°), which is similar to those obtained for 2 and (GlcNAc)4. However, the entropy loss (-TΔSr°) for the binding of 3 was smaller than those of 2 and (GlcNAc)4. Thus the binding of 3 was found to be more favorable than those of the others. Judging from the Kd value of 3 (760 nm), the compound appears to have the highest affinity among the lysozyme inhibitors identified to date. X-ray crystal structure of HEWL in a complex with 3 showed that compound 3 binds to subsites -4 to -1 and the moranoline moiety adopts an undistorted (4)C1 chair conformation almost overlapping with the -1 sugar covalently bound to Asp-52 of HEWL (Vocadlo, Davies, G. J., Laine, R., and Withers, S. G. (2001) Nature 412, 835-838). From these results, we concluded that compound 3 serves as a transition-state analogue for lysozyme providing additional evidence supporting the covalent glycosyl-enzyme intermediate in the catalytic reaction.

Epithelial glucose transport by lobster antennal gland

Transport of d-[3H]glucose into lobster (Homarus americanus) brush-border membrane vesicles (BBMVs) prepared by Mg2+ precipitation from antennal gland labyrinth-coelomosac tissue was examined. Influx of d-glucose occurred primarily by a phlorizin-sensitive, Na+-dependent carrier similar to that found in vertebrate renal epithelium. An inwardly directed Na+ gradient drove concentrative d-glucose uptake, whereas similar gradients of Li+ and K+ did not. Stimulation by the Na+ gradient was further enhanced by the imposition of an inside-negative potential difference and also by increases in the pH of the vesicle and incubation media. An analysis of cis inhibition of d-glucose uptake by a number of sugars and sugar derivatives indicated that the transporter requires (a) that the sugar substrate be a d-pyranose in the C1 chair conformation and (b) that the hydroxyl groups at C2 and C3 of the ring be unmodified and equatorial. Apparent kinetic parameters for glucose uptake were determined under zero-trans, short-circuited conditions. Maximal influx of d-glucose into vesicles was estimated to be 96 pmol mg-1 protein s-1. Half-maximal influx was determined to occur at 0.20 mmol l-1 d-glucose. The relationship between external Na+ concentration and glucose influx was sigmoidal, and the stoichiometry of Na+-dependent glucose transport found to be 3 Na+:1 glucose using the static head method.

Three‐Dimensionnal structures of complexes of Lathyrus ochrus isolectin I with glucose and mannose: Fine specificity of the monosaccharide‐binding site

The structure of the methyl-alpha-D-mannopyranoside-LOL I complex has been solved by the molecular replacement method using the refined saccharide-free LOL I coordinates as starting model. The methyl-alpha-D-mannopyranoside-LOL I complex was refined by simulated annealing using the program X-PLOR. The final R-factor value is 0.182 [Fo greater than 1 sigma(Fo)]. The isostructural methyl-alpha-D-glucopyranoside-LOL I complex was refined by X-Ray coupled energy minimization using the methyl-alpha-D-mannopyranoside-LOL I structure as a starting model to an R factor of 0.179 (all data). In both crystal forms, each dimer binds two molecules of sugar in pockets found near the calcium ions. The two saccharide moieties, which are in the C1 chair conformation, establish the same hydrogen bond pattern with the lectin. However, the van der Waals contacts are different between the O2, C2, C6, and O6 atoms of the two molecules and the backbone atoms of residues 208-211. Mannose, due to its axial C2 conformation, encloses the backbone atoms of the protein in a clamplike way. Van der Waals energy calculations suggest that this better complementarity of the mannoside molecule with the lectin could explain its higher affinity for isolectin I.

1,5-Anhydro-D-glucitol—A novel type of sugar in the human organism

1,5-Anhydroglucitol is a six-carbon chain monosaccharide in C1-chair conformation with an oxygen ring in pyran position. The compound is a component of normal human blood serum. The concentration in serum fluctuates within a narrow range in a normal population. Very low serum concentrations are found in patients with diabetes mellitus. In insulin-dependent (type 1) diabetes with a long history of disease the concentration of 1,5-anhydroglucitol remains low in spite of improvement of glycaemic control by intensification of treatment, whereas in non-insulin dependent (type 2) diabetes the concentration gradually increases towards normal levels concomitantly with improvement in glycaemic control. The serum 1,5-anhydroglucitol concentration may be useful as an indicator of glycaemic control in patients with non-insulin dependent diabetes. Urinary excretion of 1,5-anhydroglucitol in normal subjects is very low inferring that the compound is efficiently reabsorbed by tubular cells. During glucosuria, induced by glucose tolerance test in human or streptozotocin administration in rats the 1,5-anhydroglucitol excretion is temporarily increased, which may be attributable to a competition between 1,5-anhydroglucitol and glucose for renal tubular transporters. Data so far obtained indicate that 1,5-anhydroglucitol may be either actively or passively transported through the cell membrane, depending on the cell type. Gas-liquid chromatography is the method of choice in the measurement of the low concentrations of 1,5-anhydroglucitol present in biological samples.

The structure of the saccharide-binding site of concanavalin A.

A complex of concanavalin A with methyl alpha-D-mannopyranoside has been crystallized in space group P212121 with a = 123.9 A, b = 129.1 A and c = 67.5 A. X-ray diffraction intensities to 2.9 A resolution have been collected on a Xentronics/Nicolet area detector. The structure has been solved by molecular replacement where the starting model was based on refined coordinates of an I222 crystal of saccharide-free concanavalin A. The structure of the saccharide complex was refined by restrained least-squares methods to an R-factor value of 0.19. In this crystal form, the asymmetric unit contains four protein subunits, to each of which a molecule of mannoside is bound in a shallow crevice near the surface of the protein. The methyl alpha-D-mannopyranoside molecule is bound in the C1 chair conformation 8.7 A from the calcium-binding site and 12.8 A from the transition metal-binding site. A network of seven hydrogen bonds connects oxygen atoms O-3, O-4, O-5 and O-6 of the mannoside to residues Asn14, Leu99, Tyr100, Asp208 and Arg228. O-2 and O-1 of the mannoside extend into the solvent. O-2 is hydrogen-bonded through a water molecule to an adjacent asymmetric unit. O-1 is not involved in any hydrogen bond and there is no fixed position for its methyl substituent.

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.

The Crystal and Molecular Structure of Daphnin Dihydrate: 7-(β-d-Glucopyranosyloxy)-8-hydroxycoumarin Dihydrate

Abstract The title compound, C15H16O9·2H2O, crystallizes in orthorhombic space group P212121 with a=7.082(2), b=34.789(5), c=6.867(2) Å, and Z=4. The structure was solved by direct method and refined by least-squares to a final R of 0.038 based on 1841 observed reflections measured on a four-circle diffractometer. The coumarin ring is approximately planar and the torsion angle around the glucosidic C–O bond is 13.5°; this is much smaller than the corresponding value in 8-glucosyloxy-7-hydroxycoumarin, and causes considerable intramolecular repulsion around the glucosidic linkage. The valence angle of the oxygen atom linking the coumarin and glucose moieties is quite large, 118.5°. The glucopyranose portion is in a C1 chair conformation. Glucosidation at the 7-hydroxyl group brings about considerable decrease of the resonance system of the 7-hydroxylated coumarin moiety. Such an effect seems to play an important role in the transglucosidation of dihydroxycoumarin glucosides.

The Crystal and Molecular Structure of Daphnetin 8-β-d-Glucopyranoside Dihydrate Isolated from Daphne odora

Abstract The crystal structure of daphnetin 8-β-d-glucopyranoside dihydrate has been determined by the X-ray method. The crystal is monoclinic, space group P21, with the lattice parameters a=7.773(1), b=22.478(5), c=4.715(1) Å, β=99.77(2)°, and Z=2. The structure was determined by the direct method and refined by least-squares to a final R of 0.041 for 2690 observed reflexions. The daphnetin moiety is approximately planar, and little effect from glucosylation is observed in the bond lengths and angles, compared with daphnetin itself. The glucopyranoside is in C1 chair conformation, with the ring torsion angles ranging from 48 to 66°. The anomeric C–O bond is twisted by 78.2° against the coumarin plane, which is the largest value in aromatic glycopyranosides so far reported and which is concomitant with a small valence angle, 114.4°, at the oxygen atom linking the coumarin and the glucose group.

Topography of cyclodextrin inclusion complexes : Part II. The iodine-cyclohexa-amylose tetrahydrate complex; its molecular geometry and cage-type crystal structure

Iodine-cyclohexa-amylose tetrahydrate [(C 6H 10O 5) 6 ·I 2·d4H 2O] crystallizes in the orthorhombic space-group P2 12 12 1, a  14.240 Å, b  36.014 Å, c  9.558 Å. The structure was solved by heavy-atom techniques and refined by least-squares methods to a conventional discrepancy index R  0.148 for the 2872 observed data. The six d-glucose residues are in the C1 chair conformation; the conformational angles vary in magnitude from 45 to 66°, the angles O(5)-C(5)-C(6)-O(6) are close to · 70°, and the six O(4) atoms are almost coplanar (r.m. s. displacement 0.13 Å). Only four of the six O(2) ⋯O(3) intramolecular hydrogen bonds have formed, which renders the molecule less symmetrical and more conical-shaped than in the previously determined α-cyclodextrin-potassium acetate complex. The iodine molecule is coaxial with the cyclohexa-amylose molecule. The I-I distance is a conventional 2.677 Å. Close interactions between the iodine atoms and the host molecule comprise carbon atoms C(5) and C(6) and oxygen atoms O(4), with interatomic distances all equal to or greater than van der Waals contacts. Intermolecular, almost-linear, short contacts O ⋯ I-I⋯O with I⋯O distances of 3.22 and 3.07 Å indicate attractive interaction. The molecules are arranged in herring-bone “cage-type” fashion, with the four water molecules as space-filling mediators; the structure is held together by an intricate network of hydrogen bonds.

Dermatan sulfate and chondroitin 6-sulfate conformations

X-ray diffraction patterns show that dermatan sulfate in oriented, crystalline films occurs as two or three or eight-fold helices. The two-fold helix has a greater axial rise per disaccharide residue [ h = 9.6 A ̊ ] than the corresponding chondroitin 6-sulfate helix [ h = 9.3 A ̊ ] . Three-fold dermatan sulfate and chondroitin 6-sulfate helices both have h = 9.5 A ̊ . Consequently the α-L-iduronate residues in dermatan sulfate helices have the C1 chair conformation like β-D-glucuronate in chondroitin 6-sulfate. Since the eight-fold dermatan sulfate helix has h = 9.3 A ̊ rather less than the eight-fold chondroitin 6-sulfate helix [ h = 9.8 A ̊ ] the possibility of α-L-iduronate 1C chairs cannot be ruled out for it. Computer methods have been used to produce molecular models. In these the polysaccharide chains are almost linear. Each backbone conformation can accommodate a variety of arrangements of charged side groups.

Structural components of alginic acid. I. The crystalline structure of poly-beta-D-mannuronic acid. Results of x-ray diffraction and polarized infrared studies.

AbstractA Structure determination of the naturally occuring marine algal polysaccharide poly‐β‐D‐mannuronic acid is described. The structure consists of 1e → 4e linked D‐mannuronic acid chains with the monosaccharide units in the C1 chair conformation. The X‐ray fiber diffraction photograph obtained from bundles of fibers prepared from Fucus vesiculosus has been indexed to an orthorhombic unit cell in which a =7.6 Å, b (fiber axis) = 10.4 Å, c = 8.6 Å, the unit cell containing two disaccharide chain segments with space group P212121.A sheet‐like structure involving one intra‐chain, one intra‐sheet, and one inter‐sheet hydrogen bond per monosaccharide is proposed. Features of the chain‐packing arrangement are compared with mannan.

Ionic polysaccharides. IV. Free-rotation dimensions for disaccharide polymers. Comparison with experiment for hyaluronic acid.

AbstractThe root‐mean‐square end‐to‐end distance has been calculated for a model allowing free rotation about glycoside bonds for the general case of polysaccharides having a disaccharide repeating unit. Numerical estimates are given for several naturally occurring structures based on an idealized pyranose unit in the C1 chair conformation. Extrapolation procedures which make use of the intrinsic viscosity [η] in good solvents to obtain unperturbed dimensions do not represent, data for hyaluronic acid very well, especially at low molecular weights. However, order‐of‐magnitude estimates suggest that this polymer behaves similarly to other polysaccharides, and probably has stiffer local structure than typical non‐ionic synthetic polymers. A double logarithmic plot of the product of [η] and M̄w, the weight‐average molecular weight, against the degree of polymerization in the range for M̄w of 104 to 2 × 104 permits a straight‐line fit of available data for all the glycosaminoglycans, including heparin and the chondroitin sulfates, as well as sodium carboxymethyl cellulose. This result suggests similarity of short‐chain hydrodynamic behavior of these polymers.