Calcium chondroitin 4-sulfate: molecular conformation and organization of polysaccharide chains in a proteoglycan

The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans

The increasing recognition of the biochemical importance of glycosaminoglycans (GAGs) has in recent times made them the center of attention of recent research investigations. It became evident that subtle conformational factors play an important role in determining the relationship between the chemical composition of GAGs and their activity. Therefore, a thorough understanding of their structural flexibility is needed, which is addressed in this work by means of all-atom molecular dynamics (MD) simulations. Four major GAGs with different substitution patterns, namely hyaluronic acid as unsulphated GAG, heparan-6-sulphate, chondroitin-4-sulphate, and chondroitin-6-sulphate, were investigated to elucidate the influence of sulphation on the dynamical features of GAGs. Moreover, the effects of increasing NaCl and KCl concentrations were studied as well. Different structural parameters were determined from the MD simulations, in combination with a presentation of the free energy landscape of the GAG conformations, which allowed us to unravel the conformational fingerprints unique to each GAG. The largest effects on the GAG structures were found for sulphation at position 6, as well as binding of the metal ions in the absence of chloride ions to the carboxylate and sulphate groups, which both increase the GAG conformational flexibility.

Combinatorial Virtual Library Screening Study of Transforming Growth Factor-β2-Chondroitin Sulfate System

Transforming growth factor-beta (TGF-β), a member of the TGF-β cytokine superfamily, is known to bind to sulfated glycosaminoglycans (GAGs), but the nature of this interaction remains unclear. In a recent study, we found that preterm human milk TGF-β2 is sequestered by chondroitin sulfate (CS) in its proteoglycan form. To understand the molecular basis of the TGF-β2-CS interaction, we utilized the computational combinatorial virtual library screening (CVLS) approach in tandem with molecular dynamics (MD) simulations. All possible CS oligosaccharides were generated in a combinatorial manner to give 24 di- (CS02), 192 tetra- (CS04), and 1536 hexa- (CS06) saccharides. This library of 1752 CS oligosaccharides was first screened against TGF-β2 using the dual filter CVLS algorithm in which the GOLDScore and root-mean-square-difference (RMSD) between the best bound poses were used as surrogate markers for in silico affinity and in silico specificity. CVLS predicted that both the chain length and level of sulfation are critical for the high affinity and high specificity recognition of TGF-β2. Interestingly, CVLS led to identification of two distinct sites of GAG binding on TGF-β2. CVLS also deduced the preferred composition of the high specificity hexasaccharides, which were further assessed in all-atom explicit solvent MD simulations. The MD results confirmed that both sites of binding form stable GAG-protein complexes. More specifically, the highly selective CS chains were found to engage the TGF-β2 monomer with high affinity. Overall, this work present key principles of recognition with regard to the TGF-β2-CS system. In the process, it led to the generation of the in silico library of all possible CS oligosaccharides, which can be used for advanced studies on other protein-CS systems. Finally, the study led to the identification of unique CS sequences that are predicted to selectively recognize TGF-β2 and may out-compete common natural CS biopolymers.

Sulfation and Calcium Favor Compact Conformations of Chondroitin in Aqueous Solutions

The effects of sulfation and calcium cations (Ca²⁺) on the atomic-resolution conformational properties of chondroitin carbohydrate polymers in aqueous solutions are not well studied owing to experimental challenges. Here, we compare all-atom explicit-solvent molecular dynamics simulations results for pairs of O-type (nonsulfated) and A-type (GlcNAc 4-O-sulfated) chondroitin 20-mers in 140 mM NaCl with and without Ca²⁺ and find that both sulfation and Ca²⁺ favor more compact polymer conformations. We also show that subtle differences in force-field parametrization can have dramatic effects on Ca²⁺ binding to chondroitin carboxylate and sulfate functional groups and thereby determine Ca²⁺-mediated intra- and interstrand association. In addition to providing an atomic-resolution picture of the interaction of Ca²⁺ with sulfated and nonsulfated chondroitin polymers, the molecular dynamics data emphasize the importance of careful force-field parametrization to balance ion-water and ion-chondroitin interactions and suggest additional parametrization efforts to tune interactions involving sulfate.

GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans

Glycosaminoglycans (GAGs) are complex linear polysaccharides. GAG-DB is a curated database that classifies the three-dimensional features of the six mammalian GAGs (chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate) and their oligosaccharides complexed with proteins. The entries are structures of GAG and GAG-protein complexes determined by X-ray single-crystal diffraction methods, X-ray fiber diffractometry, solution NMR spectroscopy, and scattering data often associated with molecular modeling. We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. Special attention was devoted to the description of the bound glycan ligands using simple graphical representation and numerical format for cross-referencing to other databases in glycoscience and functional data. GAG-DB provides detailed information on GAGs, their bound protein ligands, and features their interactions using several open access applications. Binding covers interactions between monosaccharides and protein monosaccharide units and the evaluation of quaternary structure. GAG-DB is freely available.

Perspective on computational simulations of glycosaminoglycans

Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.

Effects of sulfation and the environment on the structure of chondroitin sulfate studied via Raman optical activity

Raman optical activity reflects differences in the secondary structure of chondroitin caused by its sulfation.

The derivatization and antitumor mechanisms of polysaccharides

At present, the polysaccharide antitumor research is focused on how to further improve the antitumor activity of polysaccharides. The structural modification of polysaccharides can enhance their antitumor activity to a certain extent. The antitumor mechanisms of polysaccharide derivatives mainly contain the inducing apoptosis of tumor cells, effecting on the cycle of tumor cells, enhancing the antioxidant activity of organism, activating the body's immune response and inhibiting the tumor angiogenesis. Herein, the common methods of polysaccharide modification, such as sulfation, carboxymethylation, phosphorylation and acetylation, were summarized. At the same time, the effects of chemical modification of polysaccharides on their antitumor mechanisms and activity were analyzed and discussed.

Effect of the chelation of metal cation on the antioxidant activity of chondroitin sulfates

The antioxidant potencies of chondroitin sulfates (CSs) from shark cartilage, salmon cartilage, bovine trachea, and porcine intestinal mucosa were compared by three representative methods for the measurement of the antioxidant activity; DPPH radical scavenging activity, superoxide radical scavenging activity, and hydroxyl radical scavenging activity. CSs from salmon cartilage and bovine trachea showed higher potency in comparison with CSs from shark cartilage and porcine intestinal mucosa. Next, CS from salmon cartilage chelating with Ca2+, Mg2+, Mn2+, or Zn2+ were prepared, and their antioxidant potencies were compared. CS chelating with Ca2+ or Mg2+ ions showed rather decreased DPPH radical scavenging activity in comparison with CS of H+ form. In contrast, CS chelating with Ca2+ or Mg2+ ion showed remarkably enhanced superoxide radical scavenging activity than CS of H+ or Na+ form. Moreover, CS chelating with divalent metal ions, Ca2+, Mg2+, Mn2+, or Zn2+, showed noticeably higher hydroxyl radical scavenging activity than CS of H+ or Na+ form. The present results revealed that the scavenging activities of, at least, superoxide radical and hydroxyl radical were enhanced by the chelation with divalent metal ions.

Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides

Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide -4GlcAβ1-3GalNAcβ1-, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic "backbone" has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1-3 glycosidic linkage and (ϕ2, ψ2) about the β1-4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high-resolution, high-precision free energies of CS disaccharides as a function of all possible backbone geometries. All 10 disaccharides (β1-3 vs β1-4 linkage × five different sulfation patterns) were studied; additionally, ion effects were investigated by considering each disaccharide in the presence of either neutralizing sodium or calcium cations. GlcAβ1-3GalNAc disaccharides have a single, broad, thermodynamically important free-energy minimum, whereas GalNAcβ1-4GlcA disaccharides have two such minima. Calcium cations but not sodium cations bind to the disaccharides, and binding is primarily to the GlcA -COO(-) moiety as opposed to sulfate groups. This binding alters the glycan backbone thermodynamics in instances where a calcium cation bound to -COO(-) can act to bridge and stabilize an interaction with an adjacent sulfate group, whereas, in the absence of this cation, the proximity of a sulfate group to -COO(-) results in two like charges being both desolvated and placed adjacent to each other and is found to be destabilizing. In addition to providing information on sulfation and cation effects, the present results can be applied to building models of CS polymers and as a point of comparison in studies of CS polymer backbone dynamics and thermodynamics.

Proteoglycans and their heterogeneous glycosaminoglycans at the atomic scale

Proteoglycan spatiotemporal organization underpins extracellular matrix biology, but atomic scale glimpses of this microarchitecture are obscured by glycosaminoglycan size and complexity. To overcome this, multimicrosecond aqueous simulations of chondroitin and dermatan sulfates were abstracted into a prior coarse-grained model, which was extended to heterogeneous glycosaminoglycans and small leucine-rich proteoglycans. Exploration of relationships between sequence and shape led to hypotheses that proteoglycan size is dependent on glycosaminoglycan unit composition but independent of sequence permutation. Uronic acid conformational equilibria were modulated by adjacent hexosamine sulfonation and iduronic acid increased glycosaminoglycan chain volume and rigidity, while glucuronic acid imparted chain plasticity. Consequently, block copolymeric glycosaminoglycans contained microarchitectures capable of multivalent binding to growth factors and collagen, with potential for interactional synergy at greater chain number. The described atomic scale views of proteoglycans and heterogeneous glycosaminoglycans provide structural routes to understanding their fundamental signaling and mechanical biological roles and development of new biomaterials.

Fucosylated chondroitin sulfates from the body wall of the sea cucumber Holothuria forskali: conformation, selectin binding, and biological activity

Fucosylated chondroitin sulfate (fCS) extracted from the sea cucumber Holothuria forskali is composed of the following repeating trisaccharide unit: → 3)GalNAcβ4,6S(1 → 4) [FucαX(1 → 3)]GlcAβ(1 →, where X stands for different sulfation patterns of fucose (X = 3,4S (46%), 2,4S (39%), and 4S (15%)). As revealed by NMR and molecular dynamics simulations, the fCS repeating unit adopts a conformation similar to that of the Le(x) blood group determinant, bringing several sulfate groups into close proximity and creating large negative patches distributed along the helical skeleton of the CS backbone. This may explain the high affinity of fCS oligosaccharides for L- and P-selectins as determined by microarray binding of fCS oligosaccharides prepared by Cu(2+)-catalyzed Fenton-type and photochemical depolymerization. No binding to E-selectin was observed. fCS poly- and oligosaccharides display low cytotoxicity in vitro, inhibit human neutrophil elastase activity, and inhibit the migration of neutrophils through an endothelial cell layer in vitro. Although the polysaccharide showed some anti-coagulant activity, small oligosaccharide fCS fragments had much reduced anticoagulant properties, with activity mainly via heparin cofactor II. The fCS polysaccharides showed prekallikrein activation comparable with dextran sulfate, whereas the fCS oligosaccharides caused almost no effect. The H. forskali fCS oligosaccharides were also tested in a mouse peritoneal inflammation model, where they caused a reduction in neutrophil infiltration. Overall, the data presented support the action of fCS as an inhibitor of selectin interactions, which play vital roles in inflammation and metastasis progression. Future studies of fCS-selectin interaction using fCS fragments or their mimetics may open new avenues for therapeutic intervention.

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides

Background

Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D) structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol.

Description

PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s) and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s) (when applicable), experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI). It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available.

Conclusion

PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available via the web-interface utilizing the search engine and can be accessed at http://polysac3db.cermav.cnrs.fr.

How specific is Plasmodium falciparum adherence to chondroitin 4-sulfate?

Plasmodium falciparum infection during pregnancy results in the sequestration of infected red blood cells (IRBCs) in the placenta, contributing to pregnancy associated malaria (PAM). IRBC adherence is mediated by the binding of a variant Plasmodium falciparum erythrocyte binding protein 1 named VAR2CSA to the low sulfated chondroitin 4-sulfate (C4S) proteoglycan (CSPG) present predominantly in the intervillous space of the placenta. IRBC binding is highly specific to the level and distribution of 4-sulfate groups in C4S. Given the strict specificity of IRBC-C4S interactions, it is better to use either placental CSPG or CSPGs bearing structurally similar C4S chains in defining VAR2CSA structural architecture that interact with C4S, evaluating VAR2CSA constructs for vaccine development or studying structure-based inhibitors as therapeutics for PAM.

Atomistic insight into chondroitin-6-sulfate glycosaminoglycan chain through quantum mechanics calculations and molecular dynamics simulation

Chondroitin-6-sulfate (C6S) is a glycosaminoglycan (GAG) constituent in the extracellular matrix, which participates actively in crucial biological processes, as well as in various pathological conditions, such as atherosclerosis and cancer. Molecular interactions involving the C6S chain are therefore of considerable interest. A computational model for atomistic simulation was built. This work describes the design and validation of a force field for a C6S dodecasaccharide chain. The results of an extensive molecular dynamics simulation performed with the new force field provide a novel insight into the structure and dynamics of the C6S chain. The intramolecular H-bonds in the disaccharide linkage region are suggested to play a major role in determining the chain structural dynamics. Moreover, the unravelling of an additional H-bond involving the sulfate groups in C6S is interesting as changes in sulfation have been claimed to be an important factor in several diseases. The force field will prove useful for future studies of crucial interactions between C6S and various nanoassemblies. It can also be used as a basis for modeling of other GAGs.

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-structure at the atomic level is unclear. To address this, we have purified homogenous oligosaccharides of unsulfated chondroitin (with and without (15)N-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 beta(1-->3) glycosidic linkage. The unsulfated chondroitin bond geometry differs slightly from hyaluronan by rotation about the beta(1-->3) psi dihedral (as previously predicted by simulation), while the beta(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.

Structural interactions in chondroitin 4-sulfate mediated adherence of Plasmodium falciparum infected erythrocytes in human placenta during pregnancy-associated malaria

Infection with Plasmodium falciparum during pregnancy results in the adherence of infected red blood cells (IRBCs) in placenta, causing pregnancy-associated malaria with severe health complications in mothers and fetuses. The chondroitin 4-sulfate (C4S) chains of very low sulfated chondroitin sulfate proteoglycans (CSPGs) in placenta mediate the IRBC adherence. While it is known that partially sulfated but not fully sulfated C4S effectively binds IRBCs, structural interactions involved remain unclear and are incompletely understood. In this study, structurally defined C4S oligosaccharides of varying sulfate contents and sizes were evaluated for their ability to inhibit the binding of IRBCs from different P. falciparum strains to CSPG purified from placenta. The results clearly show that, with all parasite strains studied, dodecasaccharide is the minimal chain length required for the efficient adherence of IRBCs to CSPG and two 4-sulfated disaccharides within this minimal structural motif are sufficient for maximal binding. Together, these data demonstrate for the first time that the C4S structural requirement for IRBC adherence is parasite strain-independent. We also show that the carboxyl group on nonreducing end glucuronic acid in dodecasaccharide motif is important for IRBC binding. Thus, in oligosaccharides containing terminal 4,5-unsaturated glucuronic acid, the nonreducing end disaccharide moiety does not interact with IRBCs due to the altered spatial orientation of carboxyl group. In such C4S oligosaccharides, 14-mer but not 12-mer constitutes the minimal motif for inhibition of IRBC binding to placental CSPG. These data have important implications for the development and evaluation of therapeutics and vaccine for placental malaria.

The crystal and molecular structures of a cathepsin K:chondroitin sulfate complex

Cathepsin K is the major collagenolytic enzyme produced by bone-resorbing osteoclasts. We showed earlier that the unique triple-helical collagen-degrading activity of cathepsin K depends on the formation of complexes with bone-or cartilage-resident glycosaminoglycans, such as chondroitin 4-sulfate (C4-S). Here, we describe the crystal structure of a 1:n complex of cathepsin K:C4-S inhibited by E64 at a resolution of 1.8 A. The overall structure reveals an unusual "beads-on-a-string"-like organization. Multiple cathepsin K molecules bind specifically to a single cosine curve-shaped strand of C4-S with each cathepsin K molecule interacting with three disaccharide residues of C4-S. One of the more important sets of interactions comes from a single turn of helix close to the N terminus of the proteinase containing a basic amino acid triplet (Arg8-Lys9-Lys10) that forms multiple hydrogen bonds either to the caboxylate or to the 4-sulfate groups of C4-S. Altogether, the binding sites with C4-S are located in the R-domain of cathepsin K and are distant from its active site. This explains why the general proteolytic activity of cathepsin K is not affected by the binding of chondroitin sulfate. Biochemical analyses of cathepsin K and C4-S mixtures support the presence of a 1:n complex in solution; a dissociation constant, K(d), of about 10 nM was determined for the interaction between cathepsin K and C4-S.

Towards a model of the mineral-organic interface in bone: NMR of the structure of synthetic glycosaminoglycan- and polyaspartate-calcium phosphate composites

We have synthesised three materials-chondroitin sulphate (ChS, a commercial product derived from shark cartilage and predominantly chondroitin-6-sulphate (Ch-6-S)) bound to pre-formed hydroxyapatite (HA, Ca(10)(PO(4))(6)(OH)(2)), HA formed in the presence of ChS and poly-Asp bound to pre-formed HA-to generate models for the mineral-organic interface in bone. The three materials have been investigated by (13)C cross polarisation magic-angle spinning (CPMAS) NMR, (13)C{(31)P} rotational echo double resonance (REDOR) and powder x-ray diffraction (XRD) in order to verify their composition and to determine the nature of their binding to HA. Our results show that for HA formed in the presence of Ch-6-S, all carbon atoms in the Ch-6-S having contact with mineral phosphate. We propose that HA in this case forms all around the Ch-6-S polymer rather than along one face of it as is more commonly supposed in cases of templating by organic molecules. However, Ch-6-S binding to pre-formed HA probably occurs via a surface layer of water on the mineral rather than to the mineral directly. In contrast, poly-Asp binds closely to the pre-formed HA surface and so is clearly able to displace at least some of the surface-bound water.

The SPASIBA force field for chondroitin sulfate: vibrational analysis of D-glucuronic and N-acetyl-D-galactosamine 4-sulfate sodium salts

Normal-mode analyses were carried out on the two components of the chondroitin 4-sulfate linear glycosaminoglycan, a copolymer implying alternate D-glucuronate beta-(1-->3) and N-acetyl-D-galactosamine 4-sulfate beta-(1-->4) (hereafter named D-galactosamine 4-sulfate) residues. Scaled quantum mechanical calculations (SQM) using the density functional theory approach at different levels of theory (B3LYP/6-31G** and B3LYP/6-31++G**) were performed to obtain correct vibrational assignments. The SPASIBA empirical force field parameters were then obtained from both theoretical predictions and observed IR and Raman data. It is shown that calculations including diffuse functions at the B3LP/6-31++G** level and the introduction of the Na+ counterion are necessary to give correct assignments of the CO2- symmetric (nu(s)) and antisymmetric (nu(a)) stretching modes for the glucuronic carboxylate residue.

Structure and composition of the septal nacreous layer of Nautilus macromphalus L. (Mollusca, Cephalopoda)

The nacreous layer of Mollusca is the best-known aragonitic structure and is the usual model for biomineralization. However, data are based on less than 10 species. In situ observations of the septal nacreous layer of the cephalopod Nautilus shell has revealed that the tablets are composed of acicular laths. These laths are composed of round nanograins surrounded by an organic sheet. No hole has been observed in the decalcified interlamellar membranes. A set of combined analytical data shows that the organic matrices extracted from the nacreous layer are glycoproteins. In both soluble and insoluble matrices, S amino acids are rare and the soluble organic matrices have a higher sulfated sugar content than the insoluble matrices. It is possible that the observed differences in the structure and composition of the nacreous layers of the outer wall and septa of the Nautilus shell have a dual origin: evolution and functional adaptation. However, we have no appropriate data as yet to answer this question.

A coarse-grained molecular model for glycosaminoglycans: application to chondroitin, chondroitin sulfate, and hyaluronic acid

A coarse-grained molecular model is presented for the study of the equilibrium conformation and titration behavior of chondroitin (CH), chondroitin sulfate (CS), and hyaluronic acid (HA)-glycosaminoglycans (GAGs) that play a central role in determining the structure and biomechanical properties of the extracellular matrix of articular cartilage. Systematic coarse-graining from an all-atom description of the disaccharide building blocks retains the polyelectrolytes' specific chemical properties while enabling the simulation of high molecular weight chains that are inaccessible to all-atom representations. Results are presented for the characteristic ratio, the ionic strength-dependent persistence length, the pH-dependent expansion factor for the end-to-end distance, and the titration behavior of the GAGs. Although 4-sulfation of the N-acetyl-D-galactosamine residue is found to increase significantly the intrinsic stiffness of CH with respect to 6-sulfation, only small differences in the titration behavior of the two sulfated forms of CH are found. Persistence length expressions are presented for each type of GAG using a macroscopic (wormlike chain-based) and a microscopic (bond vector correlation-based) definition. Model predictions agree quantitatively with experimental conformation and titration measurements, which support use of the model in the investigation of equilibrium solution properties of GAGs.

Static material properties of the tectorial membrane: a summary

The tectorial membrane (TM) is a polyelectrolyte gel. Hence, its chemical, electrical, mechanical, and osmotic properties are inextricably linked. We review, integrate, and interpret recent findings on these properties in isolated TM preparations. The dimensions of the TM in alligator lizard, chick, and mouse are sensitive to bath ion concentrations of constituents normally present in the cochlear fluids - an increase in calcium concentration shrinks the TM, and an increase in sodium concentration swells the TM in a manner that depends competitively on the calcium concentration. The sodium-induced swelling is specific; it does not occur with other alkali metal cations. We interpret these findings as due to competitive binding of sodium and calcium to TM macromolecules which causes a change in their conformation that leads to a change in mechanical properties. In mouse TM, decreasing the bath pH below 6 or increasing it above 7 results in swelling of the TM. Electric potential measurements are consistent with the notion that the swelling is caused by a pH-driven increase in positive fixed charge at low pH and an increase in the magnitude of the negative fixed charge at high pH which is consistent with the known protonation pattern of TM macromolecules. Increasing the osmotic pressure of the bathing solution with polyethylene glycol shrinks the TM and decreasing the ionic strength of the bathing solution swells the TM. Both results are qualitatively consistent with predictions of a polyelectrolyte gel model of the TM.

Conformational behavior of chondroitin and chondroitin sulfate in relation to their physical properties as inferred by molecular modeling

Chondroitin and chondroitin sulfates belong to the family of glycosaminoglycans. They are most widely distributed in animal tissues, where they are involved in structural functions and in cell-cell communication. Their basic structures consist of a disaccharidic repeating unit of beta-D-glucuronic acid (GlcA) and 2-acetamido-2-deoxy-beta-D-galactose (GalNAc), this latter being sulfated at different positions. Molecular mechanics has been applied to calculate the adiabatic energy maps for each of the constituting disaccharides of chondroitin, chondroitin 4-sulfate, and chondroitin 6-sulfate using the MM3 force field. Based on these maps, higher levels of structural organization have been simulated. On one hand, the disordered state is studied through a Metropolis-based algorithm; the resulting chains present a behavior of semirigid polymers, with an order of stiffness: chondroitin 4-sulfate > chondroitin > chondroitin 6-sulfate. On the other hand, the exploration of the stable ordered forms leads to numerous helical conformations of comparable energies. Several of these conformations correspond to the experimentally observed ones. The ability of coordination with cations has also been explored, resulting in a preferential stereospecificity for calcium ions when compared to sodium ions.

Soluble organic matrices of the calcitic prismatic shell layers of two Pteriomorphid bivalves. Pinna nobilis and Pinctada margaritifera

The calcitic prisms of the shells of two bivalves, Pinna and Pinctada, are considered simple prisms according to some morphological and mineralogical characteristics. Scanning electron microscopic and atomic force microscopic studies show that the microstructures and nanostructures of these two shells are different. Pinna prisms are monocrystalline, whereas Pinctada prisms are not. Moreover, intraprismatic membranes are present only in the Pinctada prisms. The soluble organic matrices extracted from these prisms are acidic, but their bulk compositions differ. Ultraviolet and infrared spectrometries, fluorescence, high pressure liquid chromatography, and electrophoresis show that the sugar-protein ratios and the molecular weights are different. Sulfur is mainly associated with acidic sulfated sugars, not with amino acids, and the role of acidic sulfated sugars is still underestimated. Thus, the simple prism concept is not a relevant model for the biomineralization processes in the calcitic prismatic layer of mollusk shells.

Comparison of the soluble matrices of the calcitic prismatic layer of Pinna nobilis (Mollusca, Bivalvia, Pteriomorpha)

The calcitic prisms of the outer layer of the shell of Pinna nobilis, surrounded by thick organic walls, contain a soluble intracrystalline matrix. The structure and composition of the outer interprismatic walls are not well known. The current viewpoint is they are composed of an insoluble matrix. Another thick organic structure, the interlamellar sheet of the nacreous layer, is composed of insoluble and soluble matrices. The composition of two sets of soluble organic matrices from the calcitic layer of Pinna nobilis, extracted with and without the organic walls are compared. According to the various analyses (SEM and AFM, UV and FTIR spectrometry, HPLC, electrophoreses, XANES), the main characteristics of the two matrices are similar, but not identical. Thus, the organic walls contain soluble components. However, the three-layered structure of the interlamellar sheet of the nacreous layer has not been observed.

Effect of calcium ions on the organization of iota-carrageenan helices: an X-ray investigation

X-ray fiber diffraction analysis confirms that calcium iota-carrageenan forms a threefold, right-handed, half-staggered, parallel, double helix of pitch 26.42 A stabilized by interchain hydrogen bonds. According to the detailed structural results, three helices are packed in a trigonal unit cell (a=23.61 and c=13.21 A). Strong interactions between the sulfate groups of neighboring helices, mediated by calcium ions and water molecules, are responsible for stabilizing the three-dimensional structure.

Glycosaminoglycan conformation: do aqueous molecular dynamics simulations agree with x-ray fiber diffraction?

Glycosaminoglycan-protein interactions are biologically important and require an appreciation of glycan molecular shape in solution, which is presently unavailable. In previous studies we found strong similarity between aqueous molecular dynamics (MD) simulations and published x-ray diffraction refinements of hyaluronan. We have applied a similar approach here to chondroitin and dermatan, attempting to clarify some of the issues raised by the x-ray diffraction literature relating to chondroitin and dermatan sulfate. We predict that chondroitin has the same beta(1-->4) linkage conformation as hyaluronan, and that their average beta(1-->3) conformations differ. This is explained by changes in hydrogen-bonding across this linkage, resulting from its axial hydroxyl, causing a different sampling of left-handed helices in chondroitin (2.5- to 3.5-fold) as compared with hyaluronan (3.0- to 4.0-fold). Few right-handed helices, which lack intramolecular hydrogen-bonds, were sampled during our MD simulations. Thus, we propose that the 8-fold helix observed in chondroitin-6-sulfate, represented in the literature as an 8(3) helix (right-handed), though it has never been refined, is more likely to be 8(5) (left-handed) helix. Molecular dynamics simulations implied that (4)C(1) and (2)S(O), but not (1)C(4), forms of iduronate could be used in refinements of dermatan x-ray fiber diffraction patterns. Current models of 8-fold dermatan sulfate chains containing (4)C(1) iduronate refine to right-handed helices, which possess no intramolecular hydrogen-bonds. However, MD simulations predict that models containing (2)S(O) iduronate could provide better (8(5) helix) starting structures for refinement. Thus, the 8-fold dermatan sulfate refinement (8(3) helix) could be in error.

Adsorption of chondroitin-4-sulphate and heparin onto hydroxyapatite--effect of bovine serum albumin

The adsorption of chondroitin-4-sulphate (C4S) and heparin onto hydroxyapatite (HA) has been studied in the absence and presence of bovine serum albumin (BSA). Isotherm data at pH 6.8 have shown that BSA in solution has no effect on C4S adsorption, whereas heparin affinity and adsorption decrease. These data suggest that C4S and BSA bind to different calcium sites on the HA surface. Heparin and BSA may compete for the same calcium sites, or alternatively form heparin-BSA complexes leading to less binding due to steric effects. Evidence of an interaction between heparin and BSA in solution has been shown in this study, there being negligible interaction for C4S. BSA adsorption from solution onto HA decreases with increasing C4S/heparin solution concentration, which may be due to glycosaminoglycan-induced conformational change of BSA from a compact to an extended structure. For the HA precoated with BSA, both C4S and heparin adsorption decrease above a certain solution concentration. A possible explanation is that precoated BSA masks binding sites for the C4S/heparin. The percentage of BSA desorbed from the precoated HA in the presence of C4S and heparin is < 10% and < 30% respectively, indicating that BSA is strongly bound to the HA surface.

Enzymatic degradation of glycosaminoglycans

Glycosaminoglycans (GAGs) play an intricate role in the extracellular matrix (ECM), not only as soluble components and polyelectrolytes, but also by specific interactions with growth factors and other transient components of the ECM. Modifications of GAG chains, such as isomerization, sulfation, and acetylation, generate the chemical specificity of GAGs. GAGs can be depolymerized enzymatically either by eliminative cleavage with lyases (EC 4.2.2.-) or by hydrolytic cleavage with hydrolases (EC 3.2.1.-). Often, these enzymes are specific for residues in the polysaccharide chain with certain modifications. As such, the enzymes can serve as tools for studying the physiological effect of residue modifications and as models at the molecular level of protein-GAG recognition. This review examines the structure of the substrates, the properties of enzymatic degradation, and the enzyme substrate-interactions at a molecular level. The primary structure of several GAGs is organized macroscopically by segregation into alternating blocks of specific sulfation patterns and microscopically by formation of oligosaccharide sequences with specific binding functions. Among GAGs, considerable dermatan sulfate, heparin and heparan sulfate show conformational flexibility in solution. They elicit sequence-specific interactions with enzymes that degrade them, as well as with other proteins, however, the effect of conformational flexibility on protein-GAG interactions is not clear. Recent findings have established empirical rules of substrate specificity and elucidated molecular mechanisms of enzyme-substrate interactions for enzymes that degrade GAGs. Here we propose that local formation of polysaccharide secondary structure is determined by the immediate sequence environment within the GAG polymer, and that this secondary structure, in turn, governs the binding and catalytic interactions between proteins and GAGs.

The interaction of the vanadyl (IV) cation with chondroitin sulfate A

The interaction of VO2+ with the muchopolysaccharide chondroitin sulfate A (CSA) has been investigated by electron absorption spectroscopy and infrared measurements in aqueous solutions at different pH-values and ligand to metal ratios up to 6:1. The generation of a VO(CSA)2 species could be demonstrated. Coordination of the oxocation through the carboxylate group and the glycosidic oxygen of the D-glucuronate moieties is suggested. Infrared spectra of some poorly characterized solid VO/CSA complexes point to the same bonding characteristics. Preliminary results obtained at higher ligand to metal ratios suggest a different coordination behavior.

Ordered water in hydrated solid-state polysaccharide systems

Water molecules within a monolayer or so of macromolecular surfaces are often located in well-defined positions and have restricted mobility. These ordered water molecules play a role in stabilizing polysaccharide ordered structures and intermolecular interactions that are the basis of the rheological properties utilized in food systems. X-ray fiber diffraction can be used to determine the three-dimensional structures of polysaccharides in solid, but well-hydrated, polycrystalline fibers. In favorable cases, difference Fourier synthesis can be used to locate ordered water molecules in these systems, allowing one to visualize their functionally important interactions. These studies provide relevant evidence regarding water interactions in more hydrated systems and in solution. The functionality of ordered water in some polysaccharides used in food systems, as well as in some connective tissue glycosaminoglycans where the ordered water has been defined in considerable detail, as determined by fiber diffraction, is described in this chapter. These structures allow one to derive some general features of the role of ordered water in such systems.

Experimental mucopolysaccharidosis: preservation and ultrastructural visualization of intralysosomal glycosaminoglycans by use of the cationic dyes cuprolinic blue and toluidine blue

The cationic dyes Cuprolinic Blue (CB) and Toluidine Blue (TB) were used to preserve the intralysosomal storage material accumulating in tilorone-induced mucopolysaccharidosis. As shown in previous studies, the stored glycosaminoglycans (GAGs) are leached during the conventional fixation procedure, with the result that the lysosomes appear empty. In the present study, the liver, spleen, and cornea-conjunctiva of tilorone-treated rats were examined. The application of CB in the presence of 0.1 M or 0.3 M MgCl2 simultaneously with, or subsequently to the primary fixative yielded electron-dense precipitates within the storage lysosomes. When TB (0.1%) was added to the primary fixative, the storage lysosomes contained filamentous structures arranged in reticular patterns. With increasing TB concentrations (up to 1%) the lysosomes increasingly often showed apparently amorphous storage material which was continuous with the reticular filamentous structures. Similar ultrastructural patterns were obtained with GAG-TB complexes prepared in vitro. The intralysosomal storage material preserved by TB is interpreted as GAG-TB precipitates. In conclusion, the use of CB provides a method which allows direct cytochemical demonstration of the subcellular sites of GAG-storage. The use of TB represents an easy method to obtain electron micrographs pathognomonic of the mucopolysaccharidosis induced by tilorone and congeners. Either method may be helpful to detect this adverse drug effect at the subcellular level.

Cation movement in rat articular and non-articular cartilage and in isolated chondrocytes: calcium influx and efflux

1. Calcium ion influx varies between different types of young adult rat cartilage. Sternal cartilage accumulates significantly less Ca2+ than other cartilage types. 2. Influxes of Ca2+ into young adult and ageing tibial cartilage display no significant differences. 3. Efflux of Ca2+ from sternal and tibial cartilage resolves into exponential phases indicative of three compartments. Tracheal cartilage displays two compartment behaviour only. 4. Efflux of Ca2+ from isolated chondrocytes has different characteristics to cartilage efflux with the third slow compartment reduced. 5. Modification of Ca2+ efflux by lanthanum and barium is suggestive of an exchange of strongly bound extracellular calcium during the slow phase of the efflux from young adult tibial cartilage. 6. The metabolic inhibitor 2,4-dinitrophenol is without effect on the efflux of Ca2+ from tibial articular cartilage. 7. The degree of calcium binding exhibited during efflux depends upon cartilage type. Non-articular sternal cartilage binds calcium more strongly than articular tibial, both binding more strongly than non-articular tracheal cartilage. 8. In articular cartilage calcium binding shows an age-related increase.

Vacuum ultraviolet circular dichroism of keratan sulfate

The vacuum ultraviolet CD of keratan sulfate reveals an intense negative CD band at 171 nm. Its intensity can be rationalized with a recently proposed quadrant rule in terms of the acetamido group being slightly tilted toward the hexosaminidic linkage oxygen. The same structural feature accounts for the particularly intense negative n-pi CD band near 210 nm.

Binding of metal ions to polysaccharides. V. Potentiometric, spectroscopic, and viscosimetric studies of the binding of cations to chondroitin sulfate and chondroitin in neutral and acidic aqueous media

Binding of cations to chondroitin sulfate A and C, chondroitin, and D-glucuronate was investigated in neutral and acidic aqueous media using H+, Cu2+, and Na+ ion-specific electrodes, viscometry, electron spin resonance (esr), and ligand-field spectroscopy. Site binding to the carboxylate group and only electrostatic interaction with the sulfate group could describe the results well. The nitrogen atom of the N-acetyl group appeared not to be involved in bonding of cations to chondroitin(sulfate) systems. The interaction of the divalent metal ions follows the Irving-Williams series. The value of the electrostatic potential at the carboxylate group of chondroitin(sulfate), as experienced by a cation, was determined in dependence of cation bonding. It proved to be difficult to establish the composition of a complex of a metal ion with a polyion by means of a molar ratio curve.

Dermatan sulfate: molecular conformations and interactions in the condensed state

The molecular conformations and manner of aggregation has been determined for three allomorphs of the connective tissue polysaccharide dermatan sulfate by analysis of X-ray diffraction from oriented, polycrystalline fibers of sodium salts. One allomorph is unique among glycosaminoglycans in having right-handed (8(3)) helical chains. Two such chains pack antiparallel in a tetragonal unit cell (a = b = 1.267 nm, c = 7.353 nm) with P4(3)2(1)2 space group symmetry. The 3(2) chains of the second allomorph are organized in a trigonal unit cell (a = b = 1.460 nm, c = 2.823 nm, space group symmetry P3(2)21) containing two left-handed antiparallel polysaccharide molecules. (The chirality of this allomorph has been assumed to be the same as in other 3-fold glycosaminoglycan helices, since discrimination between 3(1) and 3(2) symmetries was found not to be possible.) The archiral 2(1) helices of the third allomorph, pack probably in an orthorhombic unit cell (a = 1.151 nm, b = 1.065 nm, c = 1.878 nm, space group symmetry P2(1)2(1)2(1)) that contains again two antiparallel polymer molecules. Each dermatan sulfate chain is stabilized intramolecularly by O3-O5 hydrogen bonds across the beta (1 leads to 4) linkage. There are two intermolecular hydrogen bonds per tetrasaccharide repeat in the tetragonal structure and two per disaccharide in the trigonal structure. Fourier difference syntheses indicated equivalents of four sodium ions per tetrasaccharide and two sodium ions per disaccharide in the tetragonal and trigonal structures, respectively. The cations are either partially or fully hydrated and link dermatan sulfate chains either intra- or intermolecularly by involving besides other polyanion oxygen atoms, carboxylate and sulfate oxygen atoms. The probable mode of packing in the orthorhombic structure indicates a pair of hydrogen bonds between adjacent antiparallel polysaccharide chains and suggests plausible cationic sites in the unit cell.