scholarly journals Analysis of the Glycosaminoglycan Chains of Proteoglycans

2020 ◽  
pp. 002215542093715 ◽  
Author(s):  
Yuefan Song ◽  
Fuming Zhang ◽  
Robert J. Linhardt
Keyword(s):  
Dermatan Sulfate ◽  
Structural Information ◽  
Keratan Sulfate ◽  
Hyphenated Techniques ◽  
Protein Ligands ◽  
Spectrum Interpretation ◽  
Bioinformatics Software ◽  
Ligand Interactions ◽  
Charged Macromolecules ◽  
Pathway Regulation

Glycosaminoglycans (GAGs) are heterogeneous, negatively charged, macromolecules that are found in animal tissues. Based on the form of component sugar, GAGs have been categorized into four different families: heparin/heparan sulfate, chondroitin/dermatan sulfate, keratan sulfate, and hyaluronan. GAGs engage in biological pathway regulation through their interaction with protein ligands. Detailed structural information on GAG chains is required to further understanding of GAG–ligand interactions. However, polysaccharide sequencing has lagged behind protein and DNA sequencing due to the non-template-driven biosynthesis of glycans. In this review, we summarize recent progress in the analysis of GAG chains, specifically focusing on techniques related to mass spectroscopy (MS), including separation techniques coupled to MS, tandem MS, and bioinformatics software for MS spectrum interpretation. Progress in the use of other structural analysis tools, such as nuclear magnetic resonance (NMR) and hyphenated techniques, is included to provide a comprehensive perspective.

Combiphore (Structure and Ligand Based Pharmacophore) - Approach for the Design of GPR40 Modulators in the Management of Diabetes

2020 ◽  
Vol 17 (2) ◽  
pp. 233-247
Author(s):  
Krishna A. Gajjar ◽  
Anuradha K. Gajjar
Keyword(s):  
Molecular Docking ◽  
Structural Information ◽  
Docking Studies ◽  
Structural Motif ◽  
Roc Curve Analysis ◽  
Ligand Complex ◽  
Discovery Studio ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Pharmacophore Models

Background: Pharmacophore mapping and molecular docking can be synergistically integrated to improve the drug design and discovery process. A rational strategy, combiphore approach, derived from the combined study of Structure and Ligand based pharmacophore has been described to identify novel GPR40 modulators. Methods: DISCOtech module from Discovery studio was used for the generation of the Structure and Ligand based pharmacophore models which gave hydrophobic aromatic, ring aromatic and negative ionizable as essential pharmacophoric features. The generated models were validated by screening active and inactive datasets, GH scoring and ROC curve analysis. The best model was exposed as a 3D query to screen the hits from databases like GLASS (GPCR-Ligand Association), GPCR SARfari and Mini-Maybridge. Various filters were applied to retrieve the hit molecules having good drug-like properties. A known protein structure of hGPR40 (pdb: 4PHU) having TAK-875 as ligand complex was used to perform the molecular docking studies; using SYBYL-X 1.2 software. Results and Conclusion: Clustering both the models gave RMSD of 0.89. Therefore, the present approach explored the maximum features by combining both ligand and structure based pharmacophore models. A common structural motif as identified in combiphore for GPR40 modulation consists of the para-substituted phenyl propionic acid scaffold. Therefore, the combiphore approach, whereby maximum structural information (from both ligand and biological protein) is explored, gives maximum insights into the plausible protein-ligand interactions and provides potential lead candidates as exemplified in this study.

scholarly journals Glycans and glycosaminoglycans in neurobiology: key regulators of neuronal cell function and fate

2018 ◽  
Vol 475 (15) ◽  
pp. 2511-2545 ◽  
Author(s):  
Anthony J. Hayes ◽  
James Melrose
Keyword(s):  
Cell Fate ◽  
Information Transfer ◽  
Cell Function ◽  
Dermatan Sulfate ◽  
Neuronal Cell ◽  
Keratan Sulfate ◽  
Neural Function ◽  
Cellular Survival ◽  
Downstream Signaling ◽  
Blood Group Substances

The aim of the present study was to examine the roles of l-fucose and the glycosaminoglycans (GAGs) keratan sulfate (KS) and chondroitin sulfate/dermatan sulfate (CS/DS) with selected functional molecules in neural tissues. Cell surface glycans and GAGs have evolved over millions of years to become cellular mediators which regulate fundamental aspects of cellular survival. The glycocalyx, which surrounds all cells, actuates responses to growth factors, cytokines and morphogens at the cellular boundary, silencing or activating downstream signaling pathways and gene expression. In this review, we have focused on interactions mediated by l-fucose, KS and CS/DS in the central and peripheral nervous systems. Fucose makes critical contributions in the area of molecular recognition and information transfer in the blood group substances, cytotoxic immunoglobulins, cell fate-mediated Notch-1 interactions, regulation of selectin-mediated neutrophil extravasation in innate immunity and CD-34-mediated new blood vessel development, and the targeting of neuroprogenitor cells to damaged neural tissue. Fucosylated glycoproteins regulate delivery of synaptic neurotransmitters and neural function. Neural KS proteoglycans (PGs) were examined in terms of cellular regulation and their interactive properties with neuroregulatory molecules. The paradoxical properties of CS/DS isomers decorating matrix and transmembrane PGs and the positive and negative regulatory cues they provide to neurons are also discussed.

scholarly journals Conformational states of vitronectin: preferential expression of an antigenic epitope when vitronectin is covalently and noncovalently complexed with thrombin-antithrombin III or treated with urea

Blood ◽  
1988 ◽  
Vol 72 (3) ◽  
pp. 903-912 ◽  
Author(s):  
BR Tomasini ◽  
DF Mosher
Keyword(s):  
Monoclonal Antibody ◽  
Antithrombin Iii ◽  
Dermatan Sulfate ◽  
Factor Xa ◽  
Keratan Sulfate ◽  
Urea Treatment ◽  
Preferential Expression ◽  
Covalently Linked ◽  
Thrombin Antithrombin Iii Complex ◽  
Protein Serum

Abstract A difference in recognition of the adhesive glycoprotein vitronectin (also called S-protein, serum spreading factor, and epibolin) by monoclonal antibody 8E6 (Hayman EG, et al, Proc Natl Acad Sci USA 80:4003, 1983) was investigated using a competitive enzyme- immunosorbent assay and immunoaffinity chromatography. Recognition of vitronectin in serum was approximately 50-fold greater than recognition of vitronectin in plasma. Recognition of vitronectin incubated with heparin, thrombin-antithrombin III complex, or heparin and thrombin- antithrombin III complex together was 2.5-, 7-, or 32-fold greater, respectively, than recognition of vitronectin alone. Thrombin or antithrombin III by itself did not induce the antigenic change. Factor Xa-antithrombin III was less effective than thrombin-antithrombin III in induction of the change. Dextran sulfate and fucoidan were more potent than heparin in induction of the antigenic change, whereas dermatan sulfate, hyaluronic acid, heparan sulfate, chondroitin sulfate, or keratan sulfate were less effective. Immunoblotting analysis of serum and of vitronectin incubated with thrombin and antithrombin III demonstrated the presence of complexes composed of vitronectin and thrombin-antithrombin III that could only be dissociated with reducing agent. N-ethylmaleimide completely blocked the formation of the presumably disulfide-bonded complexes and partially blocked the antigenic change. Both non-disulfide-bonded and disulfide-bonded vitronectin bound to antibody-Sepharose from a mixture of vitronectin and thrombin-antithrombin III. Treatment of vitronectin with 8 mol/L urea resulted in enhanced recognition by the monoclonal antibody. Thus, the 8E6 antibody reacts with an epitope that is preferentially expressed by noncovalently and covalently linked vitronectin/thrombin-antithrombin III complexes and by urea-treated vitronectin. The change in vitronectin induced by thrombin-antithrombin III, therefore, is a physiological correlate of urea treatment and of adsorption of vitronectin onto tissue culture plastic (as is done in cell adhesion assays). The change may be important for expression of vitronectin activity.

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 Prediction of Binding Stability of Pu(IV) and PuO2(VI) by Nitrogen Tridentate Ligands in Aqueous Solution

2020 ◽  
Vol 21 (8) ◽  
pp. 2791 ◽  
Author(s):  
Keunhong Jeong ◽  
Hye Jin Jeong ◽  
Seung Min Woo ◽  
Sungchul Bae
Keyword(s):  
Chemical Sensors ◽  
Nuclear Power ◽  
Power Plants ◽  
Chemical Sensor ◽  
Structural Information ◽  
Population Analysis ◽  
Binding Energies ◽  
Tridentate Ligands ◽  
Ligand Interactions ◽  
Bonding Characteristics

Plutonium has potential applications in energy production in well-controlled nuclear reactors. Since nuclear power plants have great merit as environmentally friendly energy sources with a recyclable system, a recycling system for extracting Pu from spent fuels using suitable extractants has been proposed. Pu leakage is a potential environmental hazard, hence the need for chemical sensor development. Both extractants and chemical sensors involve metal–ligand interactions and to develop efficient extractants and chemical sensors, structural information about Pu ligands must be obtained by quantum calculations. Herein, six representative nitrogen tridentate ligands were introduced, and their binding stabilities were evaluated. The tridentate L6, which contains tri-pyridine chelate with benzene connectors, showed the highest binding energies for Pu(IV) and PuO2(VI) in water. Analysis based on the quantum theory of atoms in molecular analysis, including natural population analysis and electron density studies, provided insight into the bonding characteristics for each structure. We propose that differences in ionic bonding characteristics account for the Pu-ligand stability differences. These results form a basis for designing novel extractants and organic Pu sensors.

scholarly journals Cytotoxic and Anti- Inflammatory Activities of Glycosaminoglycans (GAGs) from Selected Sea Food Waste Extract on Cell Lines

2020 ◽  
Vol 981 ◽  
pp. 258-264
Author(s):  
Nurul Haida Idrus ◽  
Nina Suhaity Azmi ◽  
Che Nur Mazadillina Che Zahari ◽  
Solachuddin Jauhari Arief Ichwan
Keyword(s):  
Dermatan Sulfate ◽  
Biological Activities ◽  
Keratan Sulfate ◽  
Sea Bass ◽  
Raw Material ◽  
No Production ◽  
Dependent Manner ◽  
Alternative Source ◽  
Anti Inflammatory ◽  
Dose Dependent

Glycosaminoglycans (GAGs) are long unbranched polysaccharide that composed of repeating disaccharide units. They are classified into heparan sulfate (HS), heparin, chondroitin sulfate (CS), dermatan sulfate (DS), keratan sulfate (KS) and hyaluronic acid (HA). During the last decade, demand of GAGs were getting increased due to their potential uses. Vertebrate animal, commonly cartilaginous mammalian tissue, were potential producer of GAGs and have the higher number of biological activities extracted from sea bass waste. Sea bass waste from Lates calcarifer was used as the raw material to extract crude GAGs. Different part of sea bass waste such as, gills, viscera and air bladders were used. The higher content of crude GAGs in sea bass waste was used in cytotoxic and inflammatory study. Different concentration of extract GAGs from gills were used ranging between 0.16-20 mg/mL. GAGs from sea bass waste (gills) showed dose-dependent cytotoxic activity towards MCF-7 cell line in lower concentration. Meanwhile, for anti-inflammatory study GAGs from sea bass waste (gills) showed dose-dependent manner and also reduce NO production in LPS-stimulated cells. This research study concluded that, GAGs from sea bass waste are the alternative source that can be used for cancer and inflammation study.

scholarly journals Immunohistochemical localization of glycosaminoglycans and proteoglycans in predentin and dentin of rat incisors.

1990 ◽  
Vol 38 (3) ◽  
pp. 319-324 ◽  
Author(s):  
M Takagi ◽  
H Hishikawa ◽  
Y Hosokawa ◽  
A Kagami ◽  
F Rahemtulla
Keyword(s):  
Dermatan Sulfate ◽  
Core Protein ◽  
Polyclonal Antibodies ◽  
Keratan Sulfate ◽  
Immunohistochemical Localization ◽  
Immunoperoxidase Staining ◽  
Weak Staining ◽  
Dentin Matrix ◽  
Pre Treatment ◽  
Definite Difference

We examined immunocytochemically the type and distribution of glycosaminoglycans and proteoglycans (PG) in predentin and dentin demineralized with EDTA after aldehyde fixation of rat incisors using (a) four monoclonal antibodies (1-B-5,9-A-2,3-B-3, and 5-D-4) which recognize epitopes in unsulfated chondroitin (C0-S), chondroitin 4-sulfate (C4-S), chondroitin 6-sulfate (C6-S), and keratan sulfate (KS) associated with the PG, and (b) monoclonal (5-D-5) and polyclonal antibodies specific for the core protein of large and small dermatan sulfate (DS) PG. Light microscope immunoperoxidase staining after pre-treatment of tissue sections with chondroitinase ABC localized the majority of stainable PG (C4-S, KS, DSPG, C0-S, and C6-S) in predentin and, to a lesser extent (C4-S and small DSPG), in the dentin matrix. The former site demonstrated relatively homogeneous PG distribution, whereas the latter site revealed that strong staining of C4-S and small DSPG was confined mostly to dentinal tubules surrounding odontoblastic processes, with only weak staining in the rest of the dentin matrix. These results indicate that there is not only a definite difference between PG of predentin and dentin but also a selective decrease in the concentration or alteration of these macromolecules during dentinogenesis and mineralization.

Multishell EXAFS Fitting Analysis of a Compositionally Precise Thiolate-Gold Nanocluster

2014 ◽  
Vol 1655 ◽  
Author(s):  
Daniel M. Chevrier ◽  
Amares Chatt ◽  
Peng Zhang ◽  
Chenjie Zeng ◽  
Rongchao Jin
Keyword(s):  
Structural Information ◽  
Gold Nanoclusters ◽  
Gold Nanocluster ◽  
Experimental Conditions ◽  
X Ray ◽  
Metal Metal ◽  
Ligand Interactions ◽  
Novel Applications ◽  
X Ray Absorption ◽  
Metal Ligand

ABSTRACTThiolate-gold nanoclusters exhibit unique optical, magnetic and chiral properties, which are attractive for novel applications in nanotechnology. A fundamental challenge facing these nanomaterials is being able to study and understand their physical properties in various experimental conditions. To overcome this, extended X-ray absorption fine structure (EXAFS) spectroscopy can be employed to probe the Au local structure of thiolate-gold nanoclusters in a variety of conditions, providing valuable structural information from multiple bonding environments (i.e. metal-metal and metal-ligand interactions). This study discusses a methodology for conducting a multishell EXAFS fitting analysis that can be implemented for thiolate-gold nanocluster systems. Specifically, experimental and simulated EXAFS data for Au36(SR)24 nanoclusters are examined with a total of 5 scattering paths fitted to the experimental data.

scholarly journals Biosensors for the Detection of Interaction between Legionella pneumophila Collagen-Like Protein and Glycosaminoglycans

Sensors ◽  
2018 ◽  
Vol 18 (8) ◽  
pp. 2668 ◽  
Author(s):  
Han Su ◽  
Shaopei Li ◽  
Mauricio Terebiznik ◽  
Cyril Guyard ◽  
Kagan Kerman
Keyword(s):  
Legionella Pneumophila ◽  
Dermatan Sulfate ◽  
Electrochemical Impedance ◽  
Host Cells ◽  
High Affinity ◽  
Extracellular Matrix Components ◽  
Biophysical Studies ◽  
Ligand Interactions ◽  
Matrix Components ◽  
Chondroitin Sulfate A

The adhesin Legionella collagen-like (Lcl) protein can bind to extracellular matrix components and mediate the binding of Legionella pneumophila to host cells. In this study, electrochemical impedance spectroscopy (EIS) and surface plasmon resonance (SPR)-based biosensors were employed to characterize these interactions between glycosaminoglycans (GAGs) and the adhesin Lcl protein. Fucoidan displayed a high affinity (KD 18 nM) for Lcl protein. Chondroitin sulfate A and dermatan sulfate differ in the position of a carboxyl group replacing D-glucuronate with D-iduronate. Our results indicated that the presence of D-iduronate in dermatan sulfate strongly hindered its interaction with Lcl. These biophysical studies provided valuable information in our understanding of adhesin-ligand interactions related to Legionella pneumophila infections.

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