Molecular Dynamics Approaches Dissect Molecular Mechanisms Underlying Methylene Blue–Glycosaminoglycan Interactions

Glycosaminoglycans (GAGs) are a class of periodic anionic linear polysaccharides involved in a number of biologically relevant processes in the extracellular matrix via interactions with various types of molecules including proteins, peptides and small organic molecules. The metachromatic dye methylene blue (MB) is a GAG binding agent. This molecule possesses a tricyclic, monocationic phenothiazine ring system, while the terminal methyl groups attached to the nitrogen atoms bear the most positive charges of the cation and, therefore, represent potential binding sites for negatively charged GAGs. In this study, we rigorously explored molecular mechanisms underlying these interactions for several GAG types: heparin, heparan and chondroitin sulfates. We found that GAG–MB interactions are predominantly electrostatically driven, with the particularly important role of sulfate groups. MB oligomeric stack formation was favored in the presence of GAGs. Furthermore, the impact of MB binding on the conformation of GAGs was also evaluated. The novel results allow for better quantitative analytics of GAG composition in the studied biochemical systems using MB dye as a GAG-specific marker. Our data add to the knowledge on small molecule–GAG interactions and could be potentially useful for novel developments in drug design and putative disease therapies in which GAGs are involved.     

Modeling large protein–glycosaminoglycan complexes using a fragment-based approach

Glycosaminoglycans (GAGs), a major constituent of the extracellular matrix, participate in cell-signaling by binding specific proteins. Structural data on protein–GAG interactions are crucial to understand and modulate these signaling processes, with potential applications in regenerative medicine. However, experimental and theoretical approaches used to study GAG–protein systems are challenged by GAGs high flexibility limiting the conformational sampling above a certain size, and by the scarcity of GAG-specific docking tools compared to protein–protein or protein–drug docking approaches. We present for the first time an automated fragment-based method for docking GAGs on a protein binding site. In this approach, trimeric GAG fragments are flexibly docked to the protein, assembled based on their spacial overlap, and refined by molecular dynamics. The method appeared more successful than the classical full-ligand approach for most of 13 tested complexes with known structure. The approach is particularly promising for docking of long GAG chains, which represents a bottleneck for classical docking approaches applied to these systems. © 2019 Wiley Periodicals, Inc.     

Synthesis and distribution of glycosaminoglycans in human leukemic B- and T-cells and monocytes studied using specific enzymic treatments and high-performance liquid chromatography

Identification of glycosaminoglycans (GAGs) synthesized by three human leukaemic cell lines-Jurkat (T-cell leukaemia), Daudi (Burkitt's lymphoma, B-cell leukaemia) and THP-1 (acute monocytic leukemia)-and normal peripheral blood mononuclear cells (PBMC) and their distribution among cell membrane and culture medium were studied. GAGs were isolated using ion-exchange chromatography on DEAE-Sephacel and their composition and fine chemical structure were studied using high-performance liquid chromatography with radiochemical detection. All cell lines synthesize chondroitin sulphate (CS) and heparan sulphate (HS) in both cell membrane and culture medium. No hyaluronan was detected using treatment with specific lyases and highly sensitive HPLC methodology. CS is the major secreted GAG in all cell lines tested and the major cell retained GAG in Jurkat and Daudi. HS is the major GAG in the cell membrane of THP-1. The amounts of distinct GAGs synthesized by all cancer cell lines differ from those produced by normal PBML indicating a major role of GAGs in malignant transformation of human lymphocytes and monocytes.     

UPLC-MS/MS detection of disaccharides derived from glycosaminoglycans as biomarkers of mucopolysaccharidoses

Mucopolysaccharidoses (MPSs) are a group of disorders resulting from primary defects in lysosomal enzymes involved in the degradation of glycosaminoglycans (GAGs). Depending on the specific enzyme defect, the catabolism of one or more GAGs is blocked leading to accumulation in tissues and biological fluids. GAG measurements are important for high-risk screening, diagnosis, monitoring treatment efficacy, and patient follow up. The dimethylmethylene blue (DMB) spectrophotometric method commonly used in most biochemical genetics laboratories relies on a non-specific total GAG analysis which has led to false positive results, and even false negative results (mainly for MPS III and IV patients). The main objective of our project was to devise and validate a reliable tandem mass spectrometry multiplex analysis for the urine quantitation of four GAGs (dermatan sulfate (DS), heparan sulfate (HS), keratan sulfate (KS), and chondroitin sulfate (CS)) for an eventual technological transfer to the clinic. The developed methodology is rapid (7 min) and our results showed good intraday and interday precision (RSDs ≤ 8.7%) and accuracy (Biases range: −12.0%–18.4%). Linearity was good (r² > 0.995) for DS, HS, CS, and KS calibration curves. In comparison with the DMB spectrophotometric method, this multiplex tandem mass spectrometry method allows GAG fractionation, thus a differentiation of MPS types, except for MPS I and II which are characterized by the same GAG profile. The devised method is a useful and reliable tool for diagnosis of MPS patients, as well as their monitoring and follow up, as shown by longitudinal studies.     

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. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

High-performance liquid chromatographic analysis of g;ycosaminoglycan-derived oligosaccharides

High-performance liquid chromatography of glycosaminoglycan (GAG)-derived oligosaccharides has been employed for structural analysis and measurement of hyaluronan, chondroitin sulphate, dermatan sulphate, keratan sulphate, herapan sulphate and heparin. Recent developments in the separation and detection of unsaturated dissacharides and oligosaccharides derived from GAGs by enzyme or chemical degradation are reviewed.     

Quantitative analysis of sulphated glycosaminoglycans content of Malaysian sea cucumber Stichopus hermanni and Stichopus vastus

Stichopus hermanni and Stichopus vastus are sea cucumber species from the Stichopodidae family within the coastal waters of Malaysia. The integument of these invertebrates is hypothesised to contain abundant glycosaminoglycans (GAGs). GAGs are divided into non-sulphated and sulphated GAGs. Sulphated GAGs have various chemico-biological functions that are beneficial to humans. This study quantitatively analysed N-, O-sulphated and total sulphated GAG content from three different anatomical regions (integument, internal organs and coelomic fluid) of S. hermanni and S. vastus. The integument revealed the highest content of total, O- and N-sulphated GAGs, followed by the internal organs and the coelomic fluid for both species of sea cucumbers. The percentage division of O- and N-sulphated GAGs suggested that anatomical parts of both species showed higher levels of O-sulphated GAGs compared to N-sulphated GAGs. In conclusion, these findings indicate that the integument body wall of S. hermanni and S. vastus is a rich source of sulphated GAGs.     

Structural insights into biological roles of protein-glycosaminoglycan interactions

The extracellular environment is largely comprised of complex polysaccharides, which were historically considered inert materials that hydrated the cells and contributed to the structural scaffolds. Recent advances in development of sophisticated analytical techniques have brought about a dramatic transformation in understanding the numerous biological roles of these complex polysaccharides. Glycosaminoglycans (GAGs) are a class of these polysaccharides, which bind to a wide variety of proteins and signaling molecules in the cellular environment and modulate their activity, thus impinging on fundamental biological processes. Despite the importance of GAGs modulating biological functions, there are relatively few examples that demonstrate specificity of GAG-protein interactions, which in turn define the structure-function relationships of these polysaccharides. Focusing on heparin/heparan (HSGAGs) and chondroitin/dermatan sulfate (CSGAGs), this review provides structural insights into the oligosaccharide-protein interactions and discusses some key and challenging aspects of understanding GAG structure-function relationships.     

Effect of Immobilized Thiolated Glycosaminoglycans on Fibronectin Adsorption and Behavior of Fibroblasts

Glycosaminoglycans (GAGs) chondroitin sulfate, heparin, hyaluronan, and sulfated hyaluronan are lower and higher thiolated to enable a one?step covalent modification of gold or vinyl?terminated surfaces. Measurements of water contact angle and zeta potentials reveal that sulfated GAG?modified surfaces are more wettable and possess a negative surface potential. Additionally, higher thiolated GAGs (tGAGs) exhibit increased wettability and higher surface roughness. Fibronectin (FN) adsorption increases with sulfation degree of tGAGs. The tGAG?functionalized surfaces with higher degree of sulfation promote fibroblast adhesion most under serum‐free conditions. The preadsorption of FN allows for more cell adhesion on tGAG surfaces. Metabolic activity measurements show that cell growth is enhanced for tGAGs up to a certain thiolation degree. Overall, thiolation of GAGs does not hamper their bioactivity toward proteins and cells, which make them highly interesting for biomimetic surface modification of implants and tissue engineering scaffolds.     

Isolation and Characterization of Low Molecular Weight Glycosaminoglycans from Marine Mollusc Amussium pleuronectus (Linne) using Chromatography

The glycosaminoglycan (GAG) heparin is a polyanionic sulfated polysaccharide most recognized for its anticoagulant activity. In the present study, the GAGs were extracted from bivalve mollusc Amussium pleuronectus. The crude GAGs were fractionated by ion-exchange (DEAE-cellulose and Amberlite IRA-900 & 120) chromatography. The recovered active fractions (as determined by metachromatic assay) were confirmed by agarose gel electrophoresis and the active fractions were purified in Sephadex G-100 column. Fractionated and purified GAG molecular weight was determined through gradient polyacrylamide gel electrophoresis. The structural characterization of low molecular weight GAG was analyzed by Fourier transform infrared spectroscopy. The activated partial thromboplastin time of purified GAG is 95 IU/mg and has molecular weight 6,500–7,500 Da. The disaccharide compositional analysis on the GAG sample was sulfated like porcine intestinal mucosal heparan sulfate, and it contains equivalent amount of uronic acid and hexosamine. The results of this study suggest that the GAG from A. pleuronectus could be an alternative source of heparin.     

Proton nuclear magnetic resonance characterisation of glycosaminoglycans using chemometric techniques

Various types of glycosaminoglycans (GAGs) including heparins, chondroitin sulfates, dermatan sulfate and hyaluronic acid were studied from their proton nuclear magnetic resonance (1H NMR) spectra using chemometric techniques. Despite the complexity of the 1H NMR signals, data analysis using principal component analysis enabled the different GAG classes to be distinguished and permitted their classification according to their chemical structure. The analysis of the composition of the major disaccharide unit and other relevant chemical structures in the heparin samples was performed using partial least squares regression.     

Structural analysis of bikunin glycosaminoglycan

The structure of an intact glycosaminoglycan (GAG) chain of the bikunin proteoglycan (PG) was analyzed using a combined top-down and bottom-up sequencing strategy. PGs are proteins with one or more linear, high-molecular weight, sulfated GAG polysaccharides O-linked to serine or threonine residues. GAGs are often responsible for the biological functions of PGs, and subtle variations in the GAG structure have pronounced physiological effects. Bikunin is a serine protease inhibitor found in human amniotic fluid, plasma, and urine. Bikunin is posttranslationally modified with a chondroitin sulfate (CS) chain, O-linked to a serine residue of the core protein. Recent studies have shown that the CS chain of bikunin plays an important role in the physiological and pathological functions of this PG. While no PG or GAG has yet been sequenced, bikunin, the least complex PG, offers a compelling target. Electrospray ionization Fourier transform-ion cyclotron resonance mass spectrometry (ESI FTICR-MS) permitted the identification of several major components in the GAG mixture having molecular masses in a range of 5505-7102 Da. This is the first report of a mass spectrum of an intact GAG component of a PG. FTICR-MS analysis of a size-uniform fraction of bikunin GAG mixture obtained by preparative polyacrylamide gel electrophoresis, allowed the determination of chain length and number of sulfo groups in the intact GAGs.     

Heparin Binding by Murine Recombinant Prion Protein Leads to Transient Aggregation and Formation of RNA-Resistant Species

The conversion of cellular prion protein (PrP(C)) into the pathological conformer PrP(Sc) requires contact between both isoforms and probably also requires a cellular factor, such as a nucleic acid or a glycosaminoglycan (GAG). Little is known about the structural features implicit in the GAG-PrP interaction. In the present work, light scattering, fluorescence, circular dichroism, and nuclear magnetic resonance (NMR) spectroscopy were used to describe the chemical and physical properties of the murine recombinant PrP 23-231 interaction with low molecular weight heparin (LMWHep) at pH 7.4 and 5.5. LMWHep interacts with rPrP 23-231, thereby inducing transient aggregation. The interaction between murine rPrP and heparin at pH 5.5 had a stoichiometry of 2:1 (LMWHep:rPrP 23-231), in contrast to a 1:1 binding ratio at pH 7.4. At binding equilibrium, NMR spectra showed that rPrP complexed with LMWHep had the same general fold as that of the free protein, even though the binding can be indicated by significant changes in few residues of the C-terminal domain, especially at pH 5.5. Notably, the soluble LMWHep:rPrP complex prevented RNA-induced aggregation. We also investigated the interaction between LMWHep and the deletion mutants rPrP Δ51-90 and Δ32-121. Heparin did not bind these constructs at pH 7.4 but was able to interact at pH 5.5, indicating that this glycosaminoglycan binds the octapeptide repeat region at pH 7.4 but can also bind other regions of the protein at pH 5.5. The interaction at pH 5.5 was dependent on histidine residues of the murine rPrP 23-231. Depending on the cellular milieu, the PrP may expose different regions that can bind GAG. These results shed light on the role of GAGs in PrP conversion. The transient aggregation of PrP may explain why some GAGs have been reported to induce the conversion into the misfolded, scrapie conformation, whereas others are thought to protect against conversion. The acquired resistance of the complex against RNA-induced aggregation explains some of the unique properties of the PrP interaction with GAGs.     

Electron-induced dissociation of glycosaminoglycan tetrasaccharides

Electron detachment dissociation (EDD) Fourier transform mass spectrometry has recently been shown to be a powerful tool for examining the structural features of sulfated glycosaminoglycans (GAGs). The characteristics of GAG fragmentation by EDD include abundant cross-ring fragmentation primarily on hexuronic acid residues, cleavage of all glycosidic bonds, and the formation of even- and odd-electron product ions. GAG dissociation by EDD has been proposed to occur through the formation of an excited species that can undergo direct decomposition or ejects an electron and then undergoes dissociation. In this work, we perform electron-induced dissociation (EID) on singly charged GAGs to identify products that form via direct decomposition by eliminating the pathway of electron detachment. EID of GAG tetrasaccharides produces cleavage of all glycosidic bonds and abundant cross-ring fragmentation primarily on hexuronic acid residues, producing fragmentation similar to EDD of the same molecules, but distinctly different from the products of infrared multiphoton dissociation or collisionally activated decomposition. These results suggest that observed abundant fragmentation of hexuronic acid residues occurs as a result of their increased lability when they undergo electronic excitation. EID fragmentation of GAG tetrasaccharides results in both even- and odd-electron products. EID of heparan sulfate tetrasaccharide epimers produces identical fragmentation, in contrast to EDD, in which the epimers can be distinguished by their fragment ions. These data suggest that for EDD, electron detachment plays a significant role in distinguishing glucuronic acid from iduronic acid.     

Expedient Synthesis of Core Disaccharide Building Blocks from Natural Polysaccharides for Heparan Sulfate Oligosaccharide Assembly

The complex sulfation motifs of heparan sulfate glycosaminoglycans (HS GAGs) play critical roles in many important biological processes. However, an understanding of their specific functions has been hampered by an inability to synthesize large numbers of diverse, yet defined, HS structures. Herein, we describe a new approach to access the four core disaccharides required for HS/heparin oligosaccharide assembly from natural polysaccharides. The use of disaccharides rather than monosaccharides as minimal precursors greatly accelerates the synthesis of HS GAGs, providing key disaccharide and tetrasaccharide intermediates in about half the number of steps compared to traditional strategies. Rapid access to such versatile intermediates will enable the generation of comprehensive libraries of sulfated oligosaccharides for unlocking the “sulfation code” and understanding the roles of specific GAG structures in physiology and disease.     

Fibronectin and proteoglycans as determinants of cell-substratum adhesion.

When normal or SV40-transformed Balb/c 3T3 cells are treated with the Ca++-specific chelator EGTA, they round up and pull away from their footpad adhesion sites to the serum-coated tissue culture substrate, as shown by scanning electron microscope studies. Elastic membranous retraction fibers break upon culture agitation, leaving adhesion sites as substrate-attached material (SAM) (Cells leave "footprints" of substrate adhesion sites during movement by a very similar process.) SAM contains 1-2% of the cell's total protein and phospholipid content and 5-10% of its glucosamine-radiolabeled polysaccharide, most of which is glycosaminoglycan (GAG). By one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis, there is considerable enrichment in SAM for specific GAGs; for the glycoprotein fibronectin; and for the cytoskeletal proteins actin, myosin, and the subunit protein of the 10 nm-diameter filaments. Fibrillar fibronectin of cellular origin and substratum-bound fibronectin of serum origin (cold-insoluble globulin, CIg) have been visualized by immunofluorescence microscopy. The GAG composition in SAM has been examined under different cellular growth and attachment conditions. Heparan sulfate content correlates with glycopeptide content (derived from glycoprotein). Newly attaching cells deposit SAM with principally heparan sulfate and fibronectin and little of the other GAGs. Hyaluronate and chrondroitin proteoglycans are coordinately deposited in SAM as cells begin spreading and movement over the substrate. Cells attaching to serum-coated or CIg-coated substrates deposited SAM with identical compositions. The proteoglycan nature of the GAGs in SAM has been examined, as well as the ability of proteoglycans to form two classes of reversibly dissociable "supramolecular complexes" - one class with heparan sulfate and glycopeptide-containing material and the second with hyaluronate-chondroitin complexes. Enzymatic digestion of "intact" SAM with trypsin or testicular hyaluronidase indicates that (1) only a small portion of long-term radiolabeled fibronectin and cyto-skeletal protein is bound to the substrate via hyaluronate or chondroitin classes of GAG; (2) most of the fibronectin, cytoskeletal protein and heparan sulfate coordinately resist solubilization; and (3) newly synthesized fibronectin, which is metabolically labile in SAM, is linked to SAM by hyaluronate- and/or chondroitin-dependent binding. All of our studies indicate that heparan sulfate is a direct mediator of adhesion of cells to the substrate, possibly by binding to both cell-surface fibronectin and substrate-bound CIg in the serum coating; hyaluronate-chondroitin complexes in SAM appear to be most important in motility of cells by binding and labilizing fibronectin at the periphery of footpad adhesions, with subsequent cytoskeletal disorganization.     

Influence of charge state and sodium cationization on the electron detachment dissociation and infrared multiphoton dissociation of glycosaminoglycan oligosaccharides

Electron detachment dissociation (EDD) Fourier transform mass spectrometry has recently been shown to be a useful method for tandem mass spectrometry analysis of sulfated glycosaminoglycans (GAGs). EDD produces abundant glycosidic and cross-ring fragmentations that are useful for localizing sites of sulfation in GAG oligosaccharides. Although EDD fragmentation can be used to characterize GAGs in a single tandem mass spectrometry experiment, SO3 loss accompanies many peaks and complicates the resulting mass spectra. In this work we demonstrate the ability to significantly decrease SO3 loss by selection of the proper ionized state of GAG precursor ions. When the degree of ionization is greater than the number of sulfate groups in an oligosaccharide, a significant reduction in SO3 loss is observed in the EDD mass spectra. These data suggested that SO3 loss is reduced when an electron is detached from carboxylate groups instead of sulfate. Electron detachment occurs preferentially from carboxylate versus sulfate for thermodynamic reasons, provided that carboxylate is in its ionized state. Ionization of the carboxylate group is achieved by selecting the appropriate precursor ion charge state, or by the replacement of protons with sodium cations. Increasing the ionization state by sodium cation addition decreases, but does not eliminate, SO3 loss from infrared multiphoton dissociation of the same GAG precursor ions.     

Chemistry and biology of glycosaminoglycans in blood coagulation

Glycosaminoglycans (GAGs) are widely distributed in animal tissues where they are usually associated with proteins. Six types are commonly recognized: heparin (Hep), heparan sulfate (HS), dermatan sulfate (DS), chondroitin sulfate (Ch-S), keratan sulfate (KS) and hyaluronic acid (Hyal). They are structurally related with a carbohydrate backbone consisting of alternating hexuronic acid (L-iduronic acid and/or D-glucuronic acid) or galactose units and hexosamine (D-glucosamine or D-galactosamine) residues. All GAGs, except Hyal, show sulfate groups along their chains. Certain sulfate glycoaminoglycans have the ability to interfere with blood coagulation, as demonstrated by the extensive clinical use of Hep as an anticoagulant agent. HS and DS show a good anticoagulant activity, although weaker than that of Hep. In contrast, Ch-S has a low ability to inhibit plasma serine proteases, and KS and Hyal are devoid of any effect on coagulation cascade. The interaction between blood coagulation serine proteases and GAGs can be found to have two principle mechanisms: the specific “lock and key” binding and the nonspecific cooperative electrostatic association. This different ability of GAGs to interact with coagulation cascade proteins depends on the molecular weight, the ratio of iduronic/glucoronic acid and the sulfation degree. Many attempts have been made to improve or induce anticoagulant activity of natural GAGs-by chemical modification. Increasing sulfation degree of DS and Ch-S is followed by their biological activity increasing. Hyal, which is devoid of any anticoagulant effect, acquires a good ability to inactivate plasma serine proteases, i.e. thrombin and Factor Xa, when it is sulfated. This ability increases by increasing the number of sulfate groups per disaccharide unit, although the mechanism of action is different from that of Hep, but seems to be independent of its molecular weight.     

Glycosaminoglycan-Based Cryogels as Scaffolds for Cell Cultivation and Tissue Regeneration

Cryogels are a class of macroporous, interconnective hydrogels polymerized at sub-zero temperatures forming mechanically robust, elastic networks. In this review, latest advances of cryogels containing mainly glycosaminoglycans (GAGs) or composites of GAGs and other natural or synthetic polymers are presented. Cryogels produced in this way correspond to the native extracellular matrix (ECM) in terms of both composition and molecular structure. Due to their specific structural feature and in addition to an excellent biocompatibility, GAG-based cryogels have several advantages over traditional GAG-hydrogels. This includes macroporous, interconnective pore structure, robust, elastic, and shape-memory-like mechanical behavior, as well as injectability for many GAG-based cryogels. After addressing the cryogelation process, the fabrication of GAG-based cryogels and known principles of GAG monomer crosslinking are discussed. Finally, an overview of specific GAG-based cryogels in biomedicine, mainly as polymeric scaffold material in tissue regeneration and tissue engineering-related controlled release of bioactive molecules and cells, is provided.