scholarly journals Chondroitin Sulfate/Dermatan Sulfate-Protein Interactions and Their Biological Functions in Human Diseases: Implications and Analytical Tools

2021 ◽  
Vol 9 ◽  
Author(s):  
Bin Zhang ◽  
Lianli Chi
Keyword(s):  
Cell Surface ◽  
Chondroitin Sulfate ◽  
Protein Interactions ◽  
Dermatan Sulfate ◽  
Interaction Analysis ◽  
Structural Complexity ◽  
Protein Characterization ◽  
Biological Functions ◽  
Gag Protein ◽  
Core Proteins

Chondroitin sulfate (CS) and dermatan sulfate (DS) are linear anionic polysaccharides that are widely present on the cell surface and in the cell matrix and connective tissue. CS and DS chains are usually attached to core proteins and are present in the form of proteoglycans (PGs). They not only are important structural substances but also bind to a variety of cytokines, growth factors, cell surface receptors, adhesion molecules, enzymes and fibrillary glycoproteins to execute series of important biological functions. CS and DS exhibit variable sulfation patterns and different sequence arrangements, and their molecular weights also vary within a large range, increasing the structural complexity and diversity of CS/DS. The structure-function relationship of CS/DS PGs directly and indirectly involves them in a variety of physiological and pathological processes. Accumulating evidence suggests that CS/DS serves as an important cofactor for many cell behaviors. Understanding the molecular basis of these interactions helps to elucidate the occurrence and development of various diseases and the development of new therapeutic approaches. The present article reviews the physiological and pathological processes in which CS and DS participate through their interactions with different proteins. Moreover, classic and emerging glycosaminoglycan (GAG)-protein interaction analysis tools and their applications in CS/DS-protein characterization are also discussed.

Sequencing of chondroitin sulfate oligosaccharides using a novel exolyase from a marine bacterium that degrades hyaluronan and chondroitin sulfate/dermatan sulfate

2017 ◽  
Vol 474 (22) ◽  
pp. 3831-3848 ◽  
Author(s):  
Wenshuang Wang ◽  
Xiaojuan Cai ◽  
Naihan Han ◽  
Wenjun Han ◽  
Kazuyuki Sugahara ◽  
...  
Keyword(s):  
Chondroitin Sulfate ◽  
Marine Bacterium ◽  
Dermatan Sulfate ◽  
Specific Activity ◽  
Structural Complexity ◽  
Complex Structures ◽  
Biological Functions ◽  
Chemical Structures ◽  
Lyase Activity ◽  
Sugar Chains

Glycosaminoglycans (GAGs) are a family of chemically heterogeneous polysaccharides that play important roles in physiological and pathological processes. Owing to the structural complexity of GAGs, their sophisticated chemical structures and biological functions have not been extensively studied. Lyases that cleave GAGs are important tools for structural analysis. Although various GAG lyases have been identified, exolytic lyases with unique enzymatic property are urgently needed for GAG sequencing. In the present study, a putative exolytic GAG lyase from a marine bacterium was recombinantly expressed and characterized in detail. Since it showed exolytic lyase activity toward hyaluronan (HA), chondroitin sulfate (CS), and dermatan sulfate (DS), it was designated as HCDLase. This novel exolyase exhibited the highest activity in Tris–HCl buffer (pH 7.0) at 30°C. Especially, it showed a specific activity that released 2-aminobenzamide (2-AB)-labeled disaccharides from the reducing end of 2-AB-labeled CS oligosaccharides, which suggest that HCDLase is not only a novel exolytic lyase that can split disaccharide residues from the reducing termini of sugar chains but also a useful tool for the sequencing of CS chains. Notably, HCDLase could not digest 2-AB-labeled oligosaccharides from HA, DS, or unsulfated chondroitin, which indicated that sulfates and bond types affect the catalytic activity of HCDLase. Finally, this enzyme combined with CSase ABC was successfully applied for the sequencing of several CS hexa- and octasaccharides with complex structures. The identification of HCDLase provides a useful tool for CS-related research and applications.

scholarly journals Predicting glycosaminoglycan surface protein interactions and implications for studying axonal growth

2017 ◽  
Vol 114 (52) ◽  
pp. 13697-13702 ◽  
Author(s):  
Adam R. Griffith ◽  
Claude J. Rogers ◽  
Gregory M. Miller ◽  
Ravinder Abrol ◽  
Linda C. Hsieh-Wilson ◽  
...  
Keyword(s):  
Cell Surface ◽  
Chondroitin Sulfate ◽  
Protein Interactions ◽  
Neural Development ◽  
Structural Information ◽  
Protein Structures ◽  
Computational Method ◽  
Cns Injury ◽  
Gag Protein ◽  
Cord Injury

Cell-surface carbohydrates play important roles in numerous biological processes through their interactions with various protein-binding partners. These interactions are made possible by the vast structural diversity of carbohydrates and the diverse array of carbohydrate presentations on the cell surface. Among the most complex and important carbohydrates are glycosaminoglycans (GAGs), which display varied stereochemistry, chain lengths, and patterns of sulfation. GAG–protein interactions participate in neuronal development, angiogenesis, spinal cord injury, viral invasion, and immune response. Unfortunately, little structural information is available for these complexes; indeed, for the highly sulfated chondroitin sulfate motifs, CS-E and CS-D, there are no structural data. We describe here the development and validation of the GAG-Dock computational method to predict accurately the binding poses of protein-bound GAGs. We validate that GAG-Dock reproduces accurately (<1-Å rmsd) the crystal structure poses for four known heparin–protein structures. Further, we predict the pose of heparin and chondroitin sulfate derivatives bound to the axon guidance proteins, protein tyrosine phosphatase σ (RPTPσ), and Nogo receptors 1–3 (NgR1-3). Such predictions should be useful in understanding and interpreting the role of GAGs in neural development and axonal regeneration after CNS injury.

scholarly journals Glycosaminoglycan–Protein Interactions: The First Draft of the Glycosaminoglycan Interactome

2020 ◽  
pp. 002215542094640 ◽  
Author(s):  
Sylvain D. Vallet ◽  
Olivier Clerc ◽  
Sylvie Ricard-Blum
Keyword(s):  
Extracellular Matrix ◽  
Protein Interactions ◽  
Dermatan Sulfate ◽  
Protein Complexes ◽  
Keratan Sulfate ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Matrix Proteins ◽  
Matrix Assembly ◽  
Gag Protein

The six mammalian glycosaminoglycans (GAGs), chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate, are linear polysaccharides. Except for hyaluronan, they are sulfated to various extent, and covalently attached to proteins to form proteoglycans. GAGs interact with growth factors, morphogens, chemokines, extracellular matrix proteins and their bioactive fragments, receptors, lipoproteins, and pathogens. These interactions mediate their functions, from embryonic development to extracellular matrix assembly and regulation of cell signaling in various physiological and pathological contexts such as angiogenesis, cancer, neurodegenerative diseases, and infections. We give an overview of GAG–protein interactions (i.e., specificity and chemical features of GAG- and protein-binding sequences), and review the available GAG–protein interaction networks. We also provide the first comprehensive draft of the GAG interactome composed of 832 biomolecules (827 proteins and five GAGs) and 932 protein–GAG interactions. This network is a scaffold, which in the future should integrate structures of GAG–protein complexes, quantitative data of the abundance of GAGs in tissues to build tissue-specific interactomes, and GAG interactions with metal ions such as calcium, which plays a major role in the assembly of the extracellular matrix and its interactions with cells. This contextualized interactome will be useful to identify druggable GAG–protein interactions for therapeutic purpose:

scholarly journals Module organizational principles and dynamics in biological networks

2014 ◽  
Author(s):  
Chun-Yu Lin ◽  
Tsai-ling Lee ◽  
Yi-Wei Lin ◽  
Yu-Shu Lo ◽  
Chih-Ta Lin ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Biological Networks ◽  
Biological Functions ◽  
Time And Space ◽  
Interface Evolution ◽  
The Core ◽  
Core Proteins ◽  
Core Components ◽  
Highly Correlated ◽  
Organizational Principles

AbstractA module is a group of closely related proteins that act in concert to perform specific biological functions through protein–protein interactions (PPIs) that occur in time and space. However, the underlying organizational principles of a module remain unclear. In this study, we collected CORUM module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores (PPIES) and interface evolution scores (IES) to infer module elements, including core and ring components. Functions of core components were highly correlated (Pearson’s r = 0.98) with those of 11,384 essential genes. In comparison with ring components, core proteins and PPIs were conserved in multiple species. Subsequently, protein dynamics and module dynamics of biological networks and functional diversities confirmed that core components form dynamic biological network hubs and play key roles in various biological functions. PPIES and IES can reflect module organization principles and protein/module dynamics in biological networks. On the basis of the analyses of gene essentiality, module dynamics, network topology, and gene co-expression, the module organizational principles can be described as follows: 1) a module consists of core and ring components; 2) the core components play major roles in biological functions and collaborate with ring components to perform certain functions in some cases; 3) the core components are conserved and essential in module dynamics in time and space.

scholarly journals Expanding the Chondroitin Sulfate Glycoproteome — But How Far?

2021 ◽  
Vol 9 ◽  
Author(s):  
Fredrik Noborn ◽  
Mahnaz Nikpour ◽  
Andrea Persson ◽  
Jonas Nilsson ◽  
Göran Larson
Keyword(s):  
Animal Models ◽  
Chondroitin Sulfate ◽  
Structural Complexity ◽  
The Novel ◽  
Connective Tissues ◽  
Cellular Physiology ◽  
Core Proteins ◽  
Attachment Sites ◽  
Improved Methods

Chondroitin sulfate proteoglycans (CSPGs) are found at cell surfaces and in connective tissues, where they interact with a multitude of proteins involved in various pathophysiological processes. From a methodological perspective, the identification of CSPGs is challenging, as the identification requires the combined sequencing of specific core proteins, together with the characterization of the CS polysaccharide modification(s). According to the current notion of CSPGs, they are often considered in relation to a functional role in which a given proteoglycan regulates a specific function in cellular physiology. Recent advances in glycoproteomic methods have, however, enabled the identification of numerous novel chondroitin sulfate core proteins, and their glycosaminoglycan attachment sites, in humans and in various animal models. In addition, these methods have revealed unexpected structural complexity even in the linkage regions. These findings indicate that the number and structural complexity of CSPGs are much greater than previously perceived. In light of these findings, the prospect of finding additional CSPGs, using improved methods for structural and functional characterizations, and studying novel sample matrices in humans and in animal models is discussed. Further, as many of the novel CSPGs are found in low abundance and with not yet assigned functions, these findings may challenge the traditional notion of defining proteoglycans. Therefore, the concept of proteoglycans is considered, discussing whether “a proteoglycan” should be defined mainly on the basis of an assigned function or on the structural evidence of its existence.

scholarly journals Novel Insight Into Glycosaminoglycan Biosynthesis Based on Gene Expression Profiles

2021 ◽  
Vol 9 ◽  
Author(s):  
Yi-Fan Huang ◽  
Shuji Mizumoto ◽  
Morihisa Fujita
Keyword(s):  
Gene Expression ◽  
Chondroitin Sulfate ◽  
Dermatan Sulfate ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Sulfate Proteoglycan ◽  
Expression Levels ◽  
Core Proteins ◽  
Dermatan Sulfate Proteoglycan ◽  
Insight Into

Glycosaminoglycans (GAGs) including chondroitin sulfate, dermatan sulfate, heparan sulfate, and keratan sulfate, except for hyaluronan that is a free polysaccharide, are covalently attached to core proteins to form proteoglycans. More than 50 gene products are involved in the biosynthesis of GAGs. We recently developed a comprehensive glycosylation mapping tool, GlycoMaple, for visualization and estimation of glycan structures based on gene expression profiles. Using this tool, the expression levels of GAG biosynthetic genes were analyzed in various human tissues as well as tumor tissues. In brain and pancreatic tumors, the pathways for biosynthesis of chondroitin and dermatan sulfate were predicted to be upregulated. In breast cancerous tissues, the pathways for biosynthesis of chondroitin and dermatan sulfate were predicted to be up- and down-regulated, respectively, which are consistent with biochemical findings published in the literature. In addition, the expression levels of the chondroitin sulfate-proteoglycan versican and the dermatan sulfate-proteoglycan decorin were up- and down-regulated, respectively. These findings may provide new insight into GAG profiles in various human diseases including cancerous tumors as well as neurodegenerative disease using GlycoMaple analysis.

scholarly journals Transforming growth factor (type beta) promotes the addition of chondroitin sulfate chains to the cell surface proteoglycan (syndecan) of mouse mammary epithelia.

1989 ◽  
Vol 109 (5) ◽  
pp. 2509-2518 ◽  
Author(s):  
A Rapraeger
Keyword(s):  
Growth Factor ◽  
Cell Surface ◽  
Heparan Sulfate ◽  
Chondroitin Sulfate ◽  
Transforming Growth Factor ◽  
Core Protein ◽  
Protein Characterization ◽  
Tgf Beta ◽  
The Core ◽  
Cell Surface Proteoglycan

Cultured monolayers of NMuMG mouse mammary epithelial cells have augmented amounts of cell surface chondroitin sulfate glycosaminoglycan (GAG) when cultured in transforming growth factor-beta (TGF-beta), presumably because of increased synthesis on their cell surface proteoglycan (named syndecan), previously shown to contain chondroitin sulfate and heparan sulfate GAG. This increase occurs throughout the monolayer as shown using soluble thrombospondin as a binding probe. However, comparison of staining intensity of the GAG chains and syndecan core protein suggests variability among cells in the attachment of GAG chains to the core protein. Characterization of purified syndecan confirms the enhanced addition of chondroitin sulfate in TGF-beta: (a) radiosulfate incorporation into chondroitin sulfate is increased 6.2-fold in this proteoglycan fraction and heparan sulfate is increased 1.8-fold, despite no apparent increase in amount of core protein per cell, and (b) the size and density of the proteoglycan are increased, but reduced by removal of chondroitin sulfate. This is shown in part by treatment of the cells with 0.5 mM xyloside that blocks the chondroitin sulfate addition without affecting heparan sulfate. Higher xyloside concentrations block heparan sulfate as well and syndecan appears at the cell surface as core protein without GAG chains. The enhanced amount of GAG on syndecan is partly attributed to an increase in chain length. Whereas this accounts for the additional heparan sulfate synthesis, it is insufficient to explain the total increase in chondroitin sulfate; an approximately threefold increase in chondroitin sulfate chain addition occurs as well, confirmed by assessing chondroitin sulfate ABC lyase (ABCase)-generated chondroitin sulfate linkage stubs on the core protein. One of the effects of TGF-beta during embryonic tissue interactions is likely to be the enhanced synthesis of chondroitin sulfate chains on this cell surface proteoglycan.

scholarly journals An Overview of in vivo Functions of Chondroitin Sulfate and Dermatan Sulfate Revealed by Their Deficient Mice

2021 ◽  
Vol 9 ◽  
Author(s):  
Shuji Mizumoto ◽  
Shuhei Yamada
Keyword(s):  
Chondroitin Sulfate ◽  
Dermatan Sulfate ◽  
Biological Activities ◽  
Skeletal Development ◽  
Genetic Disorders ◽  
Collagen Fibrils ◽  
Comprehensive Overview ◽  
Core Proteins ◽  
Deficient Mice

Chondroitin sulfate (CS), dermatan sulfate (DS) and heparan sulfate (HS) are covalently attached to specific core proteins to form proteoglycans in their biosynthetic pathways. They are constructed through the stepwise addition of respective monosaccharides by various glycosyltransferases and maturated by epimerases as well as sulfotransferases. Structural diversities of CS/DS and HS are essential for their various biological activities including cell signaling, cell proliferation, tissue morphogenesis, and interactions with a variety of growth factors as well as cytokines. Studies using mice deficient in enzymes responsible for the biosynthesis of the CS/DS and HS chains of proteoglycans have demonstrated their essential functions. Chondroitin synthase 1-deficient mice are viable, but exhibit chondrodysplasia, progression of the bifurcation of digits, delayed endochondral ossification, and reduced bone density. DS-epimerase 1-deficient mice show thicker collagen fibrils in the dermis and hypodermis, and spina bifida. These observations suggest that CS/DS are essential for skeletal development as well as the assembly of collagen fibrils in the skin, and that their respective knockout mice can be utilized as models for human genetic disorders with mutations in chondroitin synthase 1 and DS-epimerase 1. This review provides a comprehensive overview of mice deficient in CS/DS biosyntheses.

scholarly journals Thrombin adhesive properties: induction by plasmin and heparan sulfate.

1993 ◽  
Vol 123 (5) ◽  
pp. 1279-1287 ◽  
Author(s):  
R Bar-Shavit ◽  
Y Eskohjido ◽  
J W Fenton ◽  
J D Esko ◽  
I Vlodavsky
Keyword(s):  
Cell Surface ◽  
Heparan Sulfate ◽  
Chondroitin Sulfate ◽  
Dermatan Sulfate ◽  
Basement Membranes ◽  
Dependent Manner ◽  
Heparin Binding ◽  
Adhesive Properties ◽  
Adhesive Protein ◽  
Adhesive Molecule

We have previously demonstrated that chemically modified thrombin preparations induce endothelial cell (EC) adhesion, spreading and cytoskeletal reorganization via an Arg-Gly-Asp (RGD) sequence and the alpha v beta 3 integrin. Native thrombin, however, did not exhibit adhesive properties, consistent with crystal structure analysis, showing that Gly-Asp residues of the RGD epitope are buried within the molecule. We have now identified a possible physiological mean of converting thrombin to an adhesive protein. Plasmin, the major end product of the fibrinolytic system, converted thrombin to an adhesive protein for EC in a time and dose-dependent manner. EC adhesion and spreading was also induced by a low molecular weight (approximately 3,000 D) cleavage fragment generated upon incubation of thrombin with plasmin. Cell adhesion mediated by this fragment was completely inhibited by the synthetic peptide GRGDSP. Conversion of thrombin to an adhesive molecule was significantly enhanced in the presence of heparin or heparan sulfate, while other glycosaminoglycans (GAGs) (e.g., dermatan sulfate, keratan sulfate, chondroitin sulfate) had no effect. The role of cell surface heparan sulfate in thrombin conversion to EC adhesive protein was investigated using CHO cell mutants defective in various aspects of GAG synthesis. Incubation of both thrombin and a suboptimal amount of plasmin on the surface of formaldehyde fixed wild-type CHO-KI cells resulted in an efficient conversion of thrombin to an adhesive molecule, as indicated by subsequent induction of EC attachment. In contrast, there was no effect to incubation of thrombin and plasmin with fixed CHO mutant cells lacking both heparan sulfate and chondroitin sulfate, or with cells expressing no heparan sulfate and a three-fold increase in chondroitin sulfate. A similar gain of adhesive properties was obtained upon incubation of thrombin and plasmin in contact with native, but not heparinase-treated extracellular matrix (ECM) produced by cultured ECs. It appears that cell surface and ECM-associated heparan sulfate modulate thrombin adhesive properties through its heparin binding site in a manner that enables suboptimal amounts of plasmin to expose the RGD domain. Our results demonstrate, for the first time, a significant modulation of thrombin molecule by heparin, resulting in its conversion to a potent adhesive protein for ECs. This conversion is most effective in contact with cell surfaces, basement membranes and ECM.

NMR and molecular modeling reveal specificity of the interactions between CXCL14 and glycosaminoglycans

Glycobiology ◽  
2019 ◽  
Vol 29 (10) ◽  
pp. 715-725 ◽  
Author(s):  
Anja Penk ◽  
Lars Baumann ◽  
Daniel Huster ◽  
Sergey A Samsonov
Keyword(s):  
Protein Interactions ◽  
Electrostatic Interactions ◽  
Dermatan Sulfate ◽  
Driving Forces ◽  
Immune Surveillance ◽  
Receptor Activation ◽  
Free Energy Calculations ◽  
Resonance Spectroscopy ◽  
Binding Modes ◽  
Gag Protein

Abstract CXCL14, chemokine (C-X-C motif) ligand 14, is a novel highly conserved chemokine with unique features. Despite exhibiting the typical chemokine fold, it has a very short N-terminus of just two amino acid residues responsible for chemokine receptor activation. CXCL14 actively participates in homeostatic immune surveillance of skin and mucosae, is linked to metabolic disorders and fibrotic lung diseases and possesses strong anti-angiogenic properties in early tumor development. In this work, we investigated the interaction of CXCL14 with various glycosaminoglycans (GAGs) by nuclear magnetic resonance spectroscopy, microscale thermophoresis, analytical heparin (HE) affinity chromatography and in silico approaches to understand the molecular basis of GAG-binding. We observed different GAG-binding modes specific for the GAG type used in the study. In particular, the CXCL14 epitope for HE suggests a binding pose distinguishable from the ones of the other GAGs investigated (hyaluronic acid, chondroitin sulfate-A/C, −D, dermatan sulfate). This observation is also supported by computational methods that included molecular docking, molecular dynamics and free energy calculations. Based on our results, we suggest that distinct GAG sulfation patterns confer specificity beyond simple electrostatic interactions usually considered to represent the driving forces in protein–GAG interactions. The CXCL14–GAG system represents a promising approach to investigate the specificity of GAG–protein interactions, which represents an important topic for developing the rational approaches to novel strategies in regenerative medicine.

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