Molecular transforms of kappa carrageenan and furcellaran from mixed gel systems

X-ray fibre diffraction studies of furcellaran-carob, furcellaran-tara, and furcellaran-konjac mannan mixed gels have failed to reveal any evidence for the predicted intermolecular binding between the algal polysaccharide helix and the galactomannan or glucomannan (konjac) mannan). In the absence of such interactions, mixed gels of kappa carrageenan-konjac mannan and furcellaran-konjac mannan, have been used to obtain good quality molecular transforms of the kappa carrageenan and furcellaran molecules in an oriented nematic liquid crystalline form. Analyses of the pattern support double helix structures with threefold symmetry with helix pitch of 2.5 nm. The absence of a 0.83 nm meridional in kappa carrageenan necessitates zero axial translation from the exact half-stagger position, contrary to the model building prediction. An axial translation from half-stagger is necessary for furcellaran.     

Molecular structures for microbial polysaccharides: conformation of the Klebsiella serotype K25 capsular polysaccharide

Fibre type X-ray diffraction patterns have been obtained from oriented, semi-crystalline films prepared from the sodium salt of the capsular polysaccharide of Klebsiella serotype K25. This molecule has a tetrasaccharide repeating structure consisting of a disaccharide backbone and a disaccharide side chain. The backbone contains a di-equatorially 1,4 linked β-d-glucose residue followed by a di-equatorially 1,3 linked β-d-galactose residue. The side chain is attached to the axial O(4) position of the galactose residue and consists of a di-equaltorially 1,2 linked β-d-glucoronic acid with a β-d-glucose residue attached terminally. An interesting feature of the backbone linkage geometry of this polysaccharide is its similarity with those of the animal connective tissue polydisaccharides. Analysis of diffraction patterns gives rise to an extended three fold helical conformation with an axially projected advance per chemical repeat of 0.97 nm. Molecular models have been computer generated using least squares techniques to optimize interatomic contacts and simultaneously meet the observed helical parameters. A left handed helix with inter-residue stabilizing hydrogen bonds was found to be most favourable and comparison of this model with other relevant polysaccharide structures is male.     

X-ray diffraction patterns from chondroitin 4-sulphate, dermatan sulphate and heparan sulphate (Short Communication)

Ordered conformations from the sodium salts of chondroitin 4-sulphate, dermatan sulphate and heparan sulphate were observed by X-ray diffraction. Chondroitin 4-sulphate shows similar threefold helical character to that previously reported for chondroitin 6-sulphate and hyaluronates. Dermatan sulphate forms an eightfold helix with an axial rise per disaccharide of 0.93nm, which favours the l-iduronic acid moiety in the normal C1 chair form. The layer-line spacing and axial projection in heparan sulphate of 1.86nm favours a tetrasaccharide repeat with glycosidic linkages alternating β-d-(1→4) and α-d-(1→4).     

X-ray diffraction studies on the connective tissue polysaccharides. Molecular conformations of dermatan sulphate

Three distinct molecular conformations of the connective tissue polysaccharide dermatan sulphate have been observed by X-ray diffraction. These comprise an 8-fold type helix, a 3-fold helix and a 2-fold helix with disaccharide repeats projected onto the helix axis of 0.93 nm, 0.96 nm and 0.97 nm, respectively. The relative merits of the various 8-fold helices are discussed. The evidence favours the l-iduronic acid moiety to be in the Cl chair form for all three structures.     

X-ray-diffraction patterns from chondroitin 4-sulphate, dermatan sulphate and heparan sulphate

Ordered conformations from the sodium salts of chondroitin 4-sulphate, dermatan sulphate and heparan sulphate were observed by X-ray diffraction. Chondroitin 4-sulphate shows similar threefold helical character to that previously reported for chondroitin 6-sulphate and hyaluronates. Dermatan sulphate forms an eightfold helix with an axial rise per disaccharide of 0.93nm, which favours the l-iduronic acid moiety in the normal C1 chair form. The layer-line spacing and axial projection in heparan sulphate of 1.86nm favours a tetrasaccharide repeat with glycosidic linkages alternating beta-d-(1-->4) and alpha-d-(1-->4).     

Fibre-diffraction studies of the extracellular polysaccharide from Pseudomonas elodea

X-ray fibre diffraction techniques have been used to probe the structure of the microbial polysaccharide from Pseudomonas clodca (gellan gum). The polymer adopts a threefold helical structure with an axial repeat of 0.94 nm. The polymer form weak elastic thermoreversible gels and on deacetylation forms rigid brittle gels. Deacetylation has been shown to enhance crystallinity. Equatorial reflections index onto a trigonal unit cell (a=b=1.64 nm.     

Structural analysis of F18 fimbriae expressed by porcine toxigenic Escherichia coli

The F18 fimbriae expressed by porcine toxigenic Escherichia coli strains are 1- to 2-mm-long filaments that mediate the adhesion of the bacteria to enterocytes. The backbone of these fimbriae is built from a major structural 15.1-kDa protein, FedA. The structure of isolated negatively stained F18 fimbriae imaged by dark-field scanning transmission electron microscopy (STEM) was resolved to approximately 2 nm. Analyzing their helical symmetry showed the axially repeating units to alternate in a "zigzag" manner around the helical axis with an axial rise of 2.2 nm. Two repeating units give rise to the observed 4.3-nm helical repeat, which is practically identical to the pitch of the one-start helix formed. Additionally, an axially repeating pattern with a 27-nm spacing was found on rotary-shadowed fimbriae. Mass-per-length determination of unstained F18 fimbriae by STEM revealed the axially repeating unit to have a molecular mass of 25.4 kDa, indicating that it is a FedA monomer, with the difference in mass arising from the minor subunits, FedE and FedF. The presence of the latter two proteins might cause the observed 27-nm axial pattern.     

X-ray fibre diffraction study of conformational changes in hyaluronate induced in the presence of sodium,potassium and calcium cations

Hyaluronate purified from all cations by ion exchange chromatography was introduced to the cations sodium, potassium and calcium in a controlled way. The conformations formed in the presence of these ions were studied as a function of ionic strength, hydrogen ion activity, humidity and temperature using X-ray fibre diffraction. In sodium hyaluronate above pH 4.0 a contracted helix is found which approximates to a four-fold helix with an axial rise per disaccharide of 0.84 nm. There is no requirement for water molecules in the unit cell as the Na⁺ can be coordinate by the hyaluronate chains alone. On crystallizing hyaluronate below pH 4.0 an extended 2-fold helix with an axial rise per disaccharide of 0.98 nm is formed. In the presence of potassium above pH 4.0 a conformation similar, but not identical, to that of sodium was found where the helix backbone is again four-fold with an axial rise per disaccharide h=0.90 nm. To maintain the coordination of the potassium ion, four water molecule/disaccharide are required and on removal of these the conformation is destabilized going to a new helix where n = 4 and h = 0.97 nm. Below pH 4.0 the conformation is a contracted 4-fold helix with h = 0.82 nm. In this structure two antiparallel chains intertwine to form a double helix. The packing of the double helical units is stabilized by water molecules, the unit cell requiring 8 water molecules/disaccharide. Formation of the calcium hyaluronate complex above pH 3.5 yields a three-fold helix with h = 0.95 nm. The requirement for water in the unit cell to maintain full crystallinity is high, at 9 water molecules/disaccharide; however, on removal of this water, though the crystallinity is disrupted, the conformation remains constant. The acid form of calcium-hyaluronate yields an equivalent conformation to that of sodium under the same condition, i.e. a helix with n = 2, h = 0.98 nm. The presence of small quantities of calcium in what are otherwise potassium or sodium solutions of hyaluronate yield the 3-fold conformation for hyaluronate. Thus calcium has an important role to play in deciding the dominating conformation present in hyaluronate. The variety of conformations yielded by the different cations indicates a subtle interaction between hyaluronate and its environment, in which the balance between the cations will control to some degree the interactions between hyaluronate chains and thus affect the mechanical properties of the matrix which they form. The conformations of individual chains are all stabilized in varying degrees by intra-chain hydrogen bonds.     

Structural Analysis of F18 Fimbriae Expressed by Porcine Toxigenic Escherichia coli

The F18 fimbriae expressed by porcine toxigenic Escherichia coli strains are 1- to 2-mm-long filaments that mediate the adhesion of the bacteria to enterocytes. The backbone of these fimbriae is built from a major structural 15.1-kDa protein, FedA. The structure of isolated negatively stained F18 fimbriae imaged by dark-field scanning transmission electron microscopy (STEM) was resolved to approximately 2 nm. Analyzing their helical symmetry showed the axially repeating units to alternate in a “zigzag” manner around the helical axis with an axial rise of 2.2 nm. Two repeating units give rise to the observed 4.3-nm helical repeat, which is practically identical to the pitch of the one-start helix formed. Additionally, an axially repeating pattern with a 27-nm spacing was found on rotary-shadowed fimbriae. Mass-per-length determination of unstained F18 fimbriae by STEM revealed the axially repeating unit to have a molecular mass of 25.4 kDa, indicating that it is a FedA monomer, with the difference in mass arising from the minor subunits, FedE and FedF. The presence of the latter two proteins might cause the observed 27-nm axial pattern.     

Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains

Carbohydrate recognition is central to the biological and industrial exploitation of plant structural polysaccharides. These insoluble polymers are recalcitrant to microbial degradation, and enzymes that catalyze this process generally contain non-catalytic carbohydrate binding modules (CBMs) that potentiate activity by increasing substrate binding. Agarose, a repeat of the disaccharide 3,6-anhydro-alpha-L-galactose-(1,3)-beta-D-galactopyranose-(1,4), is the dominant matrix polysaccharide in marine algae, yet the role of CBMs in the hydrolysis of this important polymer has not previously been explored. Here we show that family 6 CBMs, present in two different beta-agarases, bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide. The crystal structure of one of these modules Aga16B-CBM6-2, in complex with neoagarohexaose, reveals the mechanism by which the protein displays exquisite specificity, targeting the equatorial O4 and the axial O3 of the anhydro-L-galactose. Targeting of the CBM6 to the non-reducing end of agarose chains may direct the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases where the matrix polysaccharide is likely to be more amenable to further enzymic hydrolysis.     

Comparative study of carrageenans from reproductive and sterile forms of <Emphasis Type="Italic">Tichocarpus crinitus</Emphasis> (Gmel.) Rupr (Rhodophyta,Tichocarpaceae)

A comparative study of the structure and properties of the sulfated polysaccharides (carrageenans) isolated from the vegetative and reproductive forms of the red alga Tichocarpus crinitus was performed. The polysaccharides were separated into the gelling (KCl-insoluble) and non-gelling (KCl-soluble) fractions by precipitation with 4% KCl. The total content of polysaccharides extracted from the reproductive form of the alga was 1.8-fold more than that extracted from the vegetative form, and in the first case, the gelling polysaccharides mostly accumulated. The gelling polysaccharides from the vegetative form have the highest molecular weight (354 kD). According to the results of FT-IR and 13C-NMR spectroscopy, the gelling polysaccharide fractions from both forms are kappa/beta carrageenans. The differences concern the content of the kappa- and beta-disaccharide units and the presence of a small content of the sulfated disaccharide segments (precursors of the kappa-carrageenans) in the polysaccharide from the reproductive form of the alga. The non-gelling polysaccharide fractions from both forms of the plant are mixtures of sulfated galactans with a low content of 3,6-anhydrogalactose.     

Acetan:glucomannan interactions--a molecular modeling study

X-ray fiber diffraction patterns from deacylated acetan and glucomannan (konjac mannan) blends are diagnostic of good orientation and modest polycrystallinity. The meridional reflection on the sixth layer line suggests that the binary complex is a 6-fold helix of pitch 55.4 A. A molecular modeling study incorporating this information reveals that a double helix in which one strand is acetan and the other glucomannan is stereochemically feasible. While the backbone and side groups are sufficiently flexible to allow the chains to associate with the same or opposite polarity, the parallel model is superior in terms of unit cell packing. The results are compatible with the observed synergy; namely the weak gelation behavior of the complex. The molecular model can be generalized for the binary system when acetan is replaced by xanthan or glucomannan by galactomannan.     

Crystal structure of (Gly-Pro-Hyp)(9) : implications for the collagen molecular model

Collagens have long been believed to adopt a triple‐stranded molecular structure with a 10/3 symmetry (ten triplet units in three turns) and an axial repeat of 29 Å. This belief even persisted after an alternative structure with a 7/2 symmetry (seven triplet units in two turns) with an axial repeat of 20 Å had been proposed. The uncertainty regarding the helical symmetry of collagens is attributed to inadequate X‐ray fiber diffraction data. Therefore, for better understanding of the collagen helix, single‐crystal analyses of peptides with simplified characteristic amino acid sequences and similar compositions to collagens have long been awaited. Here we report the crystal structure of (Gly‐Pro‐Hyp)₉ peptide at a resolution of 1.45 Å. The repeating unit of this peptide, Gly‐Pro‐Hyp, is the most typical sequence present in collagens, and it has been used as a basic repeating unit in fiber diffraction analyses of collagen. The (Gly‐Pro‐Hyp)₉ peptide adopts a triple‐stranded structure with an average helical symmetry close to the ideal 7/2 helical model for collagen. This observation strongly suggests that the average molecular structure of collagen is not the accepted Rich and Crick 10/3 helical model but is a 7/2 helical conformation. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 607–616, 2012.     

Hyaluronic acid: molecular conformations and interactions in two sodium salts.

A detailed structure for the tetragonal form (a = b = 0.989 nm, c, fibre axis, = 3.394 nm) of sodium hyaluronate has been obtained by analysing X-ray fibre diffraction data using new molecular modelling techniques. Two polysaccharide chains pass through each unit cell, one at the corner and one at the centre. The chains are anti-parallel to one another. Each chain is a left-handed, 4-fold helix of disaccharide units. There are intramolecular hydrogen bonds stabilising each glycosidic linkage. Octahedrally co-ordinated sodium ions link, by O … Na⁺ … O bridges, neighbouring polysaccharide chains that are further linked by hydrogen bonds. No double-helix model (as originally proposed for this structure) has been found to be free of unacceptable non-bonded contacts or to fit the diffraction intensities as closely.The tetragonal form, which is stable at zero relative humidity, contains no detectable water molecules. At higher relative humidities a related orthorhombic form is observed in which only the a dimension of the lattice is different (a = 1.153 nm, b = 0.989 nm, c = 3.386 nm). In this form the hyaluronate helix is 2-fold with tetrasaccharide units conformationally similar to the 4-fold helix of the tetragonal form. The Na⁺ … O binding and hydrogen bonds lost on expansion of the tetragonal lattice are all replaced in the orthorhombic structure by bridges through water molecules, four of which associated with each tetrasaccharide.     

Physicochemical characterization of an acetan variant secreted by Acetobacter xylinum strain CR1/4

Chemical mutagenesis has been used to produce mutants of Acetobacter xylinum NRRL B42 that are cellulose-negative and that produce variants of the acetan structure deficient in the side-chain sugar residues. The product of A. xylinum strain CR1/4 has been shown to possess a tetrasaccharide repeat unit with the side chain terminating in glucuronic acid. X-ray diffraction studies of oriented fibres suggest that the polysaccharide CR1/4 forms a fivefold helix with a pitch of 4.8 nm. Light-scattering studies on CR1/4 solutions suggest a molecular weight of 1.2 × 10⁶ with radii of gyration values of 86 nm (aqueous solution) and 67 nm (0.1 NaCl solution). The magnitude of the measured radii of gyration and the shape of the Holtzer plots suggest that CR1/4 can be described as a stiff coil. Preliminary differential scanning calorimetry data show melting behaviour consistent with order-disorder transitions of a charged helical structure. Rheological studies have revealed new synergistic interactions of CR1/4 with locus bean gum. Comparative studies of acetan and CR1/4 show that decreasing the length of the side chain enhances the solution viscosity.     

Conformational behavior of hyaluronan in relation to its physical properties as probed by molecular modeling

Hyaluronan (HA) is a linear charged polysaccharide whose structure is made up of repeating disaccharide units. Apparently conflicting reports have been published about the nature of the helical structure of HA in the solid state. Recent developments in the field of molecular modeling of polysaccharides offer new opportunities to reexamine the structural basis underlying the formation and stabilization of ordered structures and their interactions with counterions. The conformational spaces available and the low energy conformations for the disaccharide, trisaccharide, and tetrasaccharide segments of HA were investigated via molecular mechanics calculations using the MM3 force field. First, the results were used to access the configurational statistics of the corresponding polysaccharide. A disordered chain having a persistence length of 75 A at 25 degrees C is predicted. Then, the exploration of the stable ordered forms of HA led to numerous helical conformations, both left- and right-handed, having comparable energies. Several of these conformations correspond to the experimentally observed ones and illustrate the versatility of the polysaccharide. The double stranded helical forms have also been explored and theoretical structures have been compared to experimentally derived ones.     

Salt dependence and ion specificity of the coil–helix transition of furcellaran

The conformational transition and the cation-binding properties of aqueous furcellaran (a gel-forming, low-sulfated polysaccharide of the carrageenan family) in various salts and salt mixtures was studied by optical rotation and by ¹³³Cs-nmr. The results were compared with theoretical predictions based on the Poisson–Boltzmann cell model (PBCM). The conformational transition of furcellaran occurs in a single step, which implies a nonblocklike distribution of sulfate groups along the polymer chain. The chloride salts of sodium, lithium, and tetramethylammonium are equally potent in inducing helix formation of furcellaran, indicating that these ions act by nonspecific electrostatic interactions. In contrast, the potassium and cesium ions specifically promote helix formation and aggregation (gelation) of furcellaran. The divalent calcium and magnesium ions are nonspecific, but more potent than the nonspecific monovalent ions in inducing helices. Anions differ in their capacity to stabilize the furcellaran helix in the sequence Cl^? < NO < Br^? < SCN^? < I^?. The iodide and thiocyanate anions impede aggregation and gel formation. ¹³³Cs-nmr chemical shifts indicate specific binding of cesium ions to the furcellaran helix. Thus, with respect to its ion specificity and ion-binding properties, furcellaran, with 0.6 sulfate group per repeating disaccharide, resembles κ-carrageenan (1 sulfate/disaccharide) but differs from ι-carrageenan (2 sulfates/disaccharide). The conformational transition temperatures of furcellaran are, however, generally higher than those of κ-carrageenan under comparable conditions, and in mixtures of the two polysaccharides, separate transitions still occur, indicating that no mixed helices are formed. The observed ion sensitivity and cation-binding properties of furcellaran agree with predictions, by the PBCM, for a K-carrageenan with a reduced charge density.     

X-ray diffraction data for (1→3)-α-d-glucan triacetate

The crystal structures of (1→3)-α-d-glucan triacetates were studied by X-ray diffraction measurements on fibre diagrams. The oriented films annealed in water at high temperature were of higher crystallinity and occurred as two crystalline polymorphs (GTA I and GTA II) depending on the samples and also the annealing temperature. All reflections in GTA I were indexed with a pseudo-orthorhombic unit cell with a = 1·753, b = 3·018 and c(fibre axis) = 1·205 nm. From the fibre repeat data coupled with the density data and the presence of only the (003) reflection on the meridian, an extended three-fold helical structure was proposed. Although some reflections in GTA II split from the layer lines, the basic unit cell was a monoclinic system with a = 1·685, b = 3·878, c (fibre axis) = 1·210 nm and γ = 112·2°. A similar three-fold structure to GTA I was proposed from the almost identical fibre repeat and the conformational analysis on (1→3)-α-d-glucan. It was concluded that, on acetylation, the d-glucan structure changed from the fully extended two-fold helix to the extended three-fold accompanied by some extent of chain shrinking.     

Formation and structure of 1-, 3- and 6+1-stranded helical cables of glutamine synthetase

Addition of millimolar concentrations of Co²⁺ to Escherichia coli glutamine synthetase induces aggregation along the 6-fold symmetry axes of the protein molecules, forming long strands. The strands subsequently aggregate laterally to form two types of helical cables, a large cable with six outer strands wrapped around a central strand (6+1-stranded cables) and a smaller cable in which three strands wrap around one another. Similar but less extensive aggregation is induced by other divalent metal cations: Cu²⁺, Ni²⁺ and Zn²⁺. The aggregates exhibit little enzymatic activity, and aggregation is completely reversible upon removal of Co²⁺ in the presence of millimolar Mn²⁺, including regeneration of nearly full enzyme activity.Each type of helical cable exists in a variety of related forms, which vary in their helical pitch: 6+1-stranded cables have 6-fold axial symmetry, and different specimens are observed with helical pitches from 320 to 540 nm; 3-stranded cables apparently do not have 3-fold axial symmetry and have pitches from 140 to 270 nm. The large variation in pitch for glutamine synthetase helical cables implies either a variation of the regions of intermolecular contacts of approximately 4–10 Å, or a movement of the bonding domains relative to the rest of the molecule by a similar amount.