1
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Yom A, Chiang A, Lewis NE. Boltzmann Model Predicts Glycan Structures from Lectin Binding. Anal Chem 2024; 96:8332-8341. [PMID: 38720429 PMCID: PMC11162346 DOI: 10.1021/acs.analchem.3c04992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Glycans are complex oligosaccharides that are involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese hamster ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego, California 92093, United States
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Immunology Center of Georgia, Augusta University, Augusta, Georgia 30912, United States
- Department of Medicine, Augusta University, Augusta, Georgia 30912, United States
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Department of Bioengineering, University of California, San Diego, California 92093, United States
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2
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den Bakker E, Smith DEC, Finken MJJ, Wamelink MMC, Salomons GS, van de Kamp JM, Bökenkamp A. Sulfate: a neglected (but potentially highly relevant) anion. Essays Biochem 2024:EBC20230097. [PMID: 38639060 DOI: 10.1042/ebc20230097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/20/2024]
Abstract
Sulfate is an important anion as sulfonation is essential in modulation of several compounds, such as exogens, polysaccharide chains of proteoglycans, cholesterol or cholesterol derivatives and tyrosine residues of several proteins. Sulfonation requires the presence of both the sulfate donor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) and a sulfotransferase. Genetic disorders affecting sulfonation, associated with skeletal abnormalities, impaired neurological development and endocrinopathies, demonstrate the importance of sulfate. Yet sulfate is not measured in clinical practice. This review addresses sulfate metabolism and consequences of sulfonation defects, how to measure sulfate and why we should measure sulfate more often.
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Affiliation(s)
- Emil den Bakker
- Department of Pediatric Nephrology, Emma Childrens Hospital, Amsterdam UMC, Amsterdam, the Netherlands
| | - Desiree E C Smith
- Department of Metabolic Diseases, Amsterdam UMC, Amsterdam, the Netherlands
| | - Martijn J J Finken
- Department of Pediatric Endocrinology, Emma Childrens Hospital, Amsterdam UMC, Amsterdam, the Netherlands
| | | | - Gajja S Salomons
- Department of Metabolic Diseases, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
| | - Jiddeke M van de Kamp
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Reproduction and Development, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Human Genetics, Amsterdam UMC, Amsterdam, the Netherlands
| | - Arend Bökenkamp
- Department of Pediatric Nephrology, Emma Childrens Hospital, Amsterdam UMC, Amsterdam, the Netherlands
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3
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Joshi A, Chopra P, Venot A, Boons GJ. Chemical Synthesis of Δ-4,5 Unsaturated Heparan Sulfate Oligosaccharides for Biomarker Discovery. Org Lett 2024; 26:2462-2466. [PMID: 38498917 PMCID: PMC10985652 DOI: 10.1021/acs.orglett.4c00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
A methodology is described that can provide heparan sulfate oligosaccharides having a Δ4,5-double bond, which are needed as analytical standards and biomarkers for mucopolysaccharidoses. It is based on chemical oligosaccharide synthesis followed by modification of the C-4 hydroxyl of the terminal uronic acid moiety as methanesulfonate. This leaving group is stable under conditions used to remove temporary protecting groups, O-sulfation, and hydrogenolysis. Treatment with NaOH results in elimination of the methanesulfonate and formation of a Δ4,5-double bond.
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Affiliation(s)
- Apoorva Joshi
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Pradeep Chopra
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Andre Venot
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Geert-Jan Boons
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg
99, 3584 CG Utrecht, The Netherlands
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4
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Yom A, Chiang A, Lewis NE. A Boltzmann model predicts glycan structures from lectin binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.03.543532. [PMID: 37333412 PMCID: PMC10274649 DOI: 10.1101/2023.06.03.543532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Glycans are complex oligosaccharides involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese Hamster Ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego. CA 92093, USA
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
- Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Medicine, Augusta University, Augusta, GA 30912, USA
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego. CA 92093, USA
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
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5
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Downs M, Zaia J, Sethi MK. Mass spectrometry methods for analysis of extracellular matrix components in neurological diseases. MASS SPECTROMETRY REVIEWS 2023; 42:1848-1875. [PMID: 35719114 PMCID: PMC9763553 DOI: 10.1002/mas.21792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/12/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The brain extracellular matrix (ECM) is a highly glycosylated environment and plays important roles in many processes including cell communication, growth factor binding, and scaffolding. The formation of structures such as perineuronal nets (PNNs) is critical in neuroprotection and neural plasticity, and the formation of molecular networks is dependent in part on glycans. The ECM is also implicated in the neuropathophysiology of disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and Schizophrenia (SZ). As such, it is of interest to understand both the proteomic and glycomic makeup of healthy and diseased brain ECM. Further, there is a growing need for site-specific glycoproteomic information. Over the past decade, sample preparation, mass spectrometry, and bioinformatic methods have been developed and refined to provide comprehensive information about the glycoproteome. Core ECM molecules including versican, hyaluronan and proteoglycan link proteins, and tenascin are dysregulated in AD, PD, and SZ. Glycomic changes such as differential sialylation, sulfation, and branching are also associated with neurodegeneration. A more thorough understanding of the ECM and its proteomic, glycomic, and glycoproteomic changes in brain diseases may provide pathways to new therapeutic options.
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Affiliation(s)
- Margaret Downs
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Manveen K Sethi
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
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6
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Nguan HS, Tsai ST, Liew CY, Reddy NS, Hung SC, Ni CK. The collision-induced dissociation mechanism of sodiated Hex-HexNAc disaccharides. Phys Chem Chem Phys 2023; 25:22179-22194. [PMID: 37565323 DOI: 10.1039/d3cp02530f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Determining carbohydrate structures, such as their compositions, linkage positions, and in particular the anomers and stereoisomers, is a great challenge. Isomers of different anomers or stereoisomers have the same sequences of chemical bonds, but have different orientations of some chemical bonds which are difficult to be distinguished by mass spectrometry. Collision-induced dissociation (CID) tandem mass spectroscopy (MS/MS) is a widely used technique for characterizing carbohydrate structures. Understanding the carbohydrate dissociation mechanism is important for obtaining the structural information from MS/MS. In this work, we studied the CID mechanism of galactose-N-acetylgalactosamine (Gal-GalNAc) and glucose-N-acetylglucosamine (Glc-GlcNAc) disaccharides with 1→3 and 1→4 linkages. For Gal-GalNAc disaccharides, the CID mass spectra of sodium ion adducts show significant difference between the α- and β-anomers of GalNAc at the reducing end, while no difference in the CID mass spectra between two anomers of Glc-GlcNAc disaccharides was found. Quantum chemistry calculations show that for Gal-GalNAc disaccharides, the difference of the dissociation barriers between dehydration and glycosidic bond cleavage is significantly small in the β-anomer compared to that in the α-anomer; while these differences are similar between the α- and β-anomers of Glc-GlcNAc disaccharides. These differences can be attributed to the different orientations of hydroxyl and N-acetyl groups located at GalNAc and GlcNAc. The calculation results are consistent with the CID spectra of isotope labelled disaccharides. Our study provides an insight into the CID of 1→3 and 1→4 linked Gal-GalNAc and Glc-GlcNAc disaccharides. This information is useful for determining the anomeric configurations of GalNAc in oligosaccharides.
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Affiliation(s)
- Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan.
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan.
| | - Chia Yen Liew
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan.
- International Graduate Program of Molecular Science and Technology, National Taiwan University (NTU-MST), Taipei 10617, Taiwan
- Molecular Science and Technology (MST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 10617, Taiwan
| | | | | | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan.
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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7
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Al Mahbuba D, Masuko S, Wang S, Syangtan D, Kang JS, Song Y, Shin TW, Xia K, Zhang F, Linhardt RJ, Boyden ES, Kiessling LL. Dynamic Changes in Heparan Sulfate Nanostructure in Human Pluripotent Stem Cell Differentiation. ACS NANO 2023; 17:7207-7218. [PMID: 37042659 DOI: 10.1021/acsnano.2c10072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Heparan sulfate (HS) is a heterogeneous, cell-surface polysaccharide critical for transducing signals essential for mammalian development. Imaging of signaling proteins has revealed how their localization influences their information transfer. In contrast, the contribution of the spatial distribution and nanostructure of information-rich, signaling polysaccharides like HS is not known. Using expansion microscopy (ExM), we found striking changes in HS nanostructure occur as human pluripotent stem (hPS) cells differentiate, and these changes correlate with growth factor signaling. Our imaging studies show that undifferentiated hPS cells are densely coated with HS displayed as hair-like protrusions. This ultrastructure can recruit fibroblast growth factor for signaling. When the hPS cells differentiate into the ectoderm lineage, HS is localized into dispersed puncta. This striking change in HS distribution coincides with a decrease in fibroblast growth factor binding to neural cells. While developmental variations in HS sequence were thought to be the primary driver of alterations in HS-mediated growth factor signaling, our high-resolution images indicate a role for the HS nanostructure. Our study highlights the utility of high-resolution glycan imaging using ExM. In the case of HS, we found that changes in how the polysaccharide is displayed link to profound differences in growth factor binding.
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Affiliation(s)
- Deena Al Mahbuba
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sayaka Masuko
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shiwei Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- McGovern Institute for Brain Research, MIT, Cambridge, Massachusetts 02139, United States
| | - Deepsing Syangtan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeong Seuk Kang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02139, United States
| | - Yuefan Song
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Tay Won Shin
- Media Arts and Sciences, MIT, Cambridge, Massachusetts 02139, United States
| | - Ke Xia
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Fuming Zhang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Edward S Boyden
- McGovern Institute for Brain Research, MIT, Cambridge, Massachusetts 02139, United States
- Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts 02139, United States
- Media Arts and Sciences, MIT, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, United States
- Koch Institute, MIT, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02139, United States
- Centers for Neurobiological Engineering and Extreme Bionics, MIT, Cambridge, Massachusetts 02139, United States
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Koch Institute, MIT, Cambridge, Massachusetts 02139, United States
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8
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Yang X, Yang X, Yu H, Na L, Ghosh T, McArthur JB, Chou TF, Dickson P, Chen X. A GH89 human α-N-acetylglucosaminidase (hNAGLU) homologue from gut microbe Bacteroides thetaiotaomicron capable of hydrolyzing heparosan oligosaccharides. AMB Express 2021; 11:94. [PMID: 34165649 PMCID: PMC8225759 DOI: 10.1186/s13568-021-01253-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 11/10/2022] Open
Abstract
Carbohydrate-Active enZYme (CAZY) GH89 family enzymes catalyze the cleavage of terminal α-N-acetylglucosamine from glycans and glycoconjugates. Although structurally and mechanistically similar to the human lysosomal α-N-acetylglucosaminidase (hNAGLU) in GH89 which is involved in the degradation of heparan sulfate in the lysosome, the reported bacterial GH89 enzymes characterized so far have no or low activity toward α-N-acetylglucosamine-terminated heparosan oligosaccharides, the preferred substrates of hNAGLU. We cloned and expressed several soluble and active recombinant bacterial GH89 enzymes in Escherichia coli. Among these enzymes, a truncated recombinant α-N-acetylglucosaminidase from gut symbiotic bacterium Bacteroides thetaiotaomicron ∆22Bt3590 was found to catalyze the cleavage of the terminal α1-4-linked N-acetylglucosamine (GlcNAc) from a heparosan disaccharide with high efficiency. Heparosan oligosaccharides with lengths up to decasaccharide were also suitable substrates. This bacterial α-N-acetylglucosaminidase could be a useful catalyst for heparan sulfate analysis.
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Affiliation(s)
- Xiaohong Yang
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Xiaoxiao Yang
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Hai Yu
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Lan Na
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Rosalind Franklin Institute and University of Oxford, Harwell Campus, Didcot, OX11 0FA, UK
| | - Tamashree Ghosh
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - John B McArthur
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Integrated Micro-Chromatography Systems, Inc, Irmo, SC, 20963, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Patricia Dickson
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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9
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Zhang Q, Cao HY, Wei L, Lu D, Du M, Yuan M, Shi D, Chen X, Wang P, Chen XL, Chi L, Zhang YZ, Li F. Discovery of exolytic heparinases and their catalytic mechanism and potential application. Nat Commun 2021; 12:1263. [PMID: 33627653 PMCID: PMC7904915 DOI: 10.1038/s41467-021-21441-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Heparinases (Hepases) are critical tools for the studies of highly heterogeneous heparin (HP)/heparan sulfate (HS). However, exolytic heparinases urgently needed for the sequencing of HP/HS chains remain undiscovered. Herein, a type of exolytic heparinases (exoHepases) is identified from the genomes of different bacteria. These exoHepases share almost no homology with known Hepases and prefer to digest HP rather than HS chains by sequentially releasing unsaturated disaccharides from their reducing ends. The structural study of an exoHepase (BIexoHep) shows that an N-terminal conserved DUF4962 superfamily domain is essential to the enzyme activities of these exoHepases, which is involved in the formation of a unique L-shaped catalytic cavity controlling the sequential digestion of substrates through electrostatic interactions. Further, several HP octasaccharides have been preliminarily sequenced by using BIexoHep. Overall, this study fills the research gap of exoHepases and provides urgently needed tools for the structural and functional studies of HP/HS chains.
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Affiliation(s)
- Qingdong Zhang
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Hai-Yan Cao
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China ,grid.4422.00000 0001 2152 3263College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China ,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Lin Wei
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Danrong Lu
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Min Du
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Min Yuan
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Deling Shi
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | | | - Peng Wang
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China ,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xiu-Lan Chen
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China ,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Lianli Chi
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China ,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Fuchuan Li
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
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10
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Miller RL, Guimond SE, Schwörer R, Zubkova OV, Tyler PC, Xu Y, Liu J, Chopra P, Boons GJ, Grabarics M, Manz C, Hofmann J, Karlsson NG, Turnbull JE, Struwe WB, Pagel K. Shotgun ion mobility mass spectrometry sequencing of heparan sulfate saccharides. Nat Commun 2020; 11:1481. [PMID: 32198425 PMCID: PMC7083916 DOI: 10.1038/s41467-020-15284-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/27/2020] [Indexed: 01/23/2023] Open
Abstract
Despite evident regulatory roles of heparan sulfate (HS) saccharides in numerous biological processes, definitive information on the bioactive sequences of these polymers is lacking, with only a handful of natural structures sequenced to date. Here, we develop a “Shotgun” Ion Mobility Mass Spectrometry Sequencing (SIMMS2) method in which intact HS saccharides are dissociated in an ion mobility mass spectrometer and collision cross section values of fragments measured. Matching of data for intact and fragment ions against known values for 36 fully defined HS saccharide structures (from di- to decasaccharides) permits unambiguous sequence determination of validated standards and unknown natural saccharides, notably including variants with 3O-sulfate groups. SIMMS2 analysis of two fibroblast growth factor-inhibiting hexasaccharides identified from a HS oligosaccharide library screen demonstrates that the approach allows elucidation of structure-activity relationships. SIMMS2 thus overcomes the bottleneck for decoding the informational content of functional HS motifs which is crucial for their future biomedical exploitation. Heparan sulfates (HS) contain functionally relevant structural motifs, but determining their monosaccharide sequence remains challenging. Here, the authors develop an ion mobility mass spectrometry-based method that allows unambiguous characterization of HS sequences and structure-activity relationships.
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Affiliation(s)
- Rebecca L Miller
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, N 2200, Denmark. .,Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK. .,Laboratory of Cancer Biology, Department of Oncology, Medical Sciences Division, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7DQ, UK.
| | - Scott E Guimond
- Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.,Institute for Science and Technology in Medicine, School of Medicine, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Ralf Schwörer
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt, 5010, New Zealand
| | - Olga V Zubkova
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt, 5010, New Zealand
| | - Peter C Tyler
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt, 5010, New Zealand
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Pradeep Chopra
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.,Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Márkó Grabarics
- Freie Universitaet Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195, Berlin, Germany.,Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Christian Manz
- Freie Universitaet Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195, Berlin, Germany.,Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Johanna Hofmann
- Freie Universitaet Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195, Berlin, Germany.,Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jeremy E Turnbull
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, N 2200, Denmark.,Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Weston B Struwe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
| | - Kevin Pagel
- Freie Universitaet Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195, Berlin, Germany.,Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
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11
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12
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Heparanase as an Additional Tool for Detecting Structural Peculiarities of Heparin Oligosaccharides. Molecules 2019; 24:molecules24234403. [PMID: 31810297 PMCID: PMC6930493 DOI: 10.3390/molecules24234403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 12/03/2022] Open
Abstract
Due to the biological properties of heparin and low-molecular-weight heparin (LMWH), continuous advances in elucidation of their microheterogeneous structure and discovery of novel structural peculiarities are crucial. Effective strategies for monitoring manufacturing processes and assessment of more restrictive specifications, as imposed by the current regulatory agencies, need to be developed. Hereby, we apply an efficient heparanase-based strategy to assert the structure of two major isomeric octasaccharides of dalteparin and investigate the tetrasaccharides arising from antithrombin binding region (ATBR) of bovine mucosal heparin. Heparanase, especially when combined with other sample preparation methods (e.g., size exclusion, affinity chromatography, heparinase depolymerization), was shown to be a powerful tool providing relevant information about heparin structural peculiarities. The applied approach provided direct evidence that oligomers bearing glucuronic acid–glucosamine-3-O-sulfate at their nonreducing end represent an important structural signature of dalteparin. When extended to ATBR-related tetramers of bovine heparin, the heparanase-based approach allowed for elucidation of the structure of minor sequences that have not been reported yet. The obtained results are of high importance in the view of the growing interest of regulatory agencies and manufacturers in the development of low-molecular-weight heparin generics as well as bovine heparin as alternative source.
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13
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Zhang C, Tang F, Zhang J, Cao J, Li H, Liu C. Uncovering the detailed mode of cleavage of heparinase I toward structurally defined heparin oligosaccharides. Int J Biol Macromol 2019; 141:756-764. [PMID: 31479666 DOI: 10.1016/j.ijbiomac.2019.08.260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 10/26/2022]
Abstract
For a more insightful investigation into the specificity of bacterial heparinase I, a series of structurally well-defined heparin oligosaccharides was synthesized using a highly efficient chemoenzymatic strategy. Apart from the primary cleavage site, five glycosidic linkages of oligosaccharides with varying modifications to obtain secondary cleavage sites were degraded by a high concentration of heparinase I. The reactivity of linkages toward heparinase I was not entirely dependent on the 2-O-sulfated iduronic acid being cleaved or the neighboring 6-O-sulfated glucosamine residues, but it was dependent on higher degrees of sulfation of oligosaccharides and indispensable N-substituted glucosamine adjacent to the cleavable linkage. Moreover, the enzyme demonstrated less preferential cleavage toward glycosidic linkages containing glucuronic acid than those containing iduronic acid of the counterpart oligosaccharides. Biolayer interferometry revealed differences in reactivity that are not completely consistent with different affinities of substrates to enzyme. Our study presented accurate information on the cleavage promiscuity of heparinase I that is crucial for heparin depolymerization.
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Affiliation(s)
- Chengying Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong, PR China
| | - Fengyan Tang
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong, PR China
| | - Jingjing Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong, PR China
| | - Jichao Cao
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong, PR China
| | - Huijuan Li
- Department of Bioengineering, College of Chemical and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, Shandong, PR China
| | - Chunhui Liu
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong, PR China; National Glycoengineering Research Center, Shandong University, Jinan 250012, Shandong, PR China.
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14
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Liu H, Joshi A, Chopra P, Liu L, Boons GJ, Sharp JS. Salt-free fractionation of complex isomeric mixtures of glycosaminoglycan oligosaccharides compatible with ESI-MS and microarray analysis. Sci Rep 2019; 9:16566. [PMID: 31719635 PMCID: PMC6851191 DOI: 10.1038/s41598-019-53070-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/26/2019] [Indexed: 11/18/2022] Open
Abstract
Heparin and heparan sulfate (Hp/HS) are linear complex glycosaminoglycans which are involved in diverse biological processes. The structural complexity brings difficulties in separation, making the study of structure-function relationships challenging. Here we present a separation method for Hp/HS oligosaccharide fractionation with cross-compatible solvent and conditions, combining size exclusion chromatography (SEC), ion-pair reversed phase chromatography (IPRP), and hydrophilic interaction chromatography (HILIC) as three orthogonal separation methods that do not require desalting or extensive sample handling. With this method, the final eluent is suitable for structure-function relationship studies, including tandem mass spectrometry and microarray printing. Our data indicate that high resolution is achieved on both IPRP and HILIC for Hp/HS isomers. In addition, the fractions co-eluted in IPRP could be further separated by HILIC, with both separation dimensions capable of resolving some isomeric oligosaccharides. We demonstrate this method using both unpurified reaction products from isomeric synthetic hexasaccharides and an octasaccharide fraction from enoxaparin, identifying isomers resolved by this multi-dimensional separation method. We demonstrate both structural analysis by MS, as well as functional analysis by microarray printing and screening using a prototypical Hp/HS binding protein: basic-fibroblast growth factor (FGF2). Collectively, this method provides a strategy for efficient Hp/HS structure-function characterization.
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Affiliation(s)
- Hao Liu
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, 38677, USA
| | - Apoorva Joshi
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.,Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Pradeep Chopra
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Geert-Jan Boons
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.,Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.,Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, 38677, USA.
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15
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Devlin A, Mycroft-West C, Procter P, Cooper L, Guimond S, Lima M, Yates E, Skidmore M. Tools for the Quality Control of Pharmaceutical Heparin. MEDICINA (KAUNAS, LITHUANIA) 2019; 55:E636. [PMID: 31557911 PMCID: PMC6843833 DOI: 10.3390/medicina55100636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 11/25/2022]
Abstract
Heparin is a vital pharmaceutical anticoagulant drug and remains one of the few naturally sourced pharmaceutical agents used clinically. Heparin possesses a structural order with up to four levels of complexity. These levels are subject to change based on the animal or even tissue sources that they are extracted from, while higher levels are believed to be entirely dynamic and a product of their surrounding environments, including bound proteins and associated cations. In 2008, heparin sources were subject to a major contamination with a deadly compound-an over-sulphated chondroitin sulphate polysaccharide-that resulted in excess of 100 deaths within North America alone. In consideration of this, an arsenal of methods to screen for heparin contamination have been applied, based primarily on the detection of over-sulphated chondroitin sulphate. The targeted nature of these screening methods, for this specific contaminant, may leave contamination by other entities poorly protected against, but novel approaches, including library-based chemometric analysis in concert with a variety of spectroscopic methods, could be of great importance in combating future, potential threats.
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Affiliation(s)
- Anthony Devlin
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
| | - Courtney Mycroft-West
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
| | - Patricia Procter
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
| | - Lynsay Cooper
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
| | - Scott Guimond
- Institute for Science and Technology in Medicine, Keele University, Keele, Staffordshire ST5 5BG, UK.
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
| | - Marcelo Lima
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
| | - Edwin Yates
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
| | - Mark Skidmore
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
- Institute for Science and Technology in Medicine, Keele University, Keele, Staffordshire ST5 5BG, UK.
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
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16
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Im J, Lindsay S, Wang X, Zhang P. Single Molecule Identification and Quantification of Glycosaminoglycans Using Solid-State Nanopores. ACS NANO 2019; 13:6308-6318. [PMID: 31121093 DOI: 10.1021/acsnano.9b00618] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Glycosaminoglycans (GAGs) are a class of polysaccharides with potent biological activities. Due to their complex and heterogeneous composition, varied charge, polydispersity, and presence of isobaric stereoisomers, the analysis of GAG samples poses considerable challenges to current analytical techniques. In the present study, we combined solid-state nanopores-a single molecule sensor with a support vector machine (SVM)-a machine learning algorithm for the analysis of GAGs. Our results indicate that the nanopore/SVM technique could distinguish between monodisperse fragments of heparin and chondroitin sulfate with high accuracy (>90%), allowing as low as 0.8% (w/w) of chondroitin sulfate impurities in a heparin sample to be detected. In addition, the nanopore/SVM technique distinguished between unfractionated heparin (UFH) and enoxaparin (low molecular weight heparin) with an accuracy of ∼94% on average. With a reference sample for calibration, a nanopore could achieve nanomolar sensitivity and a 5-Log dynamic range. We were able to quantify heparin with reasonable accuracy using multiple nanopores. Our studies demonstrate the potential of the nanopore/SVM technique to quantify and identify GAGs.
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17
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van Kuppevelt TH, Oosterhof A, Versteeg EMM, Podhumljak E, van de Westerlo EMA, Daamen WF. Sequencing of glycosaminoglycans with potential to interrogate sequence-specific interactions. Sci Rep 2017; 7:14785. [PMID: 29093576 PMCID: PMC5665995 DOI: 10.1038/s41598-017-15009-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/19/2017] [Indexed: 11/23/2022] Open
Abstract
Technologies to sequence nucleic acids/proteins are widely available, but straightforward methodologies to sequence complex polysaccharides are lacking. We here put forward a strategy to sequence glycosaminoglycans, long linear polysaccharides involved in many biochemical processes. The method is based on the covalent immobilization and (immuno)chemical characterization of only those size-separated saccharides that harbor the original reducing end of the full-length chain. Using this methodology, the saccharide sequence of the chondroitin sulfate chain of the proteoglycan bikunin was determined. The method can be performed in any standard biochemical lab and opens studies to the interaction of complex saccharide sequences with other biomolecules.
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Affiliation(s)
- Toin H van Kuppevelt
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Arie Oosterhof
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Elly M M Versteeg
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Emina Podhumljak
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Els M A van de Westerlo
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Willeke F Daamen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
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18
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Identification of Heparin Modifications and Polysaccharide Inhibitors of Plasmodium falciparum Merozoite Invasion That Have Potential for Novel Drug Development. Antimicrob Agents Chemother 2017; 61:AAC.00709-17. [PMID: 28893781 DOI: 10.1128/aac.00709-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/03/2017] [Indexed: 11/20/2022] Open
Abstract
Despite recent successful control efforts, malaria remains a leading global health burden. Alarmingly, resistance to current antimalarials is increasing and the development of new drug families is needed to maintain malaria control. Current antimalarials target the intraerythrocytic developmental stage of the Plasmodium falciparum life cycle. However, the invasive extracellular parasite form, the merozoite, is also an attractive target for drug development. We have previously demonstrated that heparin-like molecules, including those with low molecular weights and low anticoagulant activities, are potent and specific inhibitors of merozoite invasion and blood-stage replication. Here we tested a large panel of heparin-like molecules and sulfated polysaccharides together with various modified chemical forms for their inhibitory activity against P. falciparum merozoite invasion. We identified chemical modifications that improve inhibitory activity and identified several additional sulfated polysaccharides with strong inhibitory activity. These studies have important implications for the further development of heparin-like molecules as antimalarial drugs and for understanding merozoite invasion.
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19
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Szajek AY, Chess E, Johansen K, Gratzl G, Gray E, Keire D, Linhardt RJ, Liu J, Morris T, Mulloy B, Nasr M, Shriver Z, Torralba P, Viskov C, Williams R, Woodcock J, Workman W, Al-Hakim A. The US regulatory and pharmacopeia response to the global heparin contamination crisis. Nat Biotechnol 2017; 34:625-30. [PMID: 27281424 DOI: 10.1038/nbt.3606] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The contamination of the widely used lifesaving anticoagulant drug heparin in 2007 has drawn renewed attention to the challenges that are associated with the characterization, quality control and standardization of complex biological medicines from natural sources. Heparin is a linear, highly sulfated polysaccharide consisting of alternating glucosamine and uronic acid monosaccharide residues. Heparin has been used successfully as an injectable antithrombotic medicine since the 1930s, and its isolation from animal sources (primarily porcine intestine) as well as its manufacturing processes have not changed substantially since its introduction. The 2007 heparin contamination crisis resulted in several deaths in the United States and hundreds of adverse reactions worldwide, revealing the vulnerability of a complex global supply chain to sophisticated adulteration. This Perspective discusses how the US Food and Drug Administration (FDA), the United States Pharmacopeial Convention (USP) and international stakeholders collaborated to redefine quality expectations for heparin, thus making an important natural product better controlled and less susceptible to economically motivated adulteration.
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Affiliation(s)
- Anita Y Szajek
- Biologics and Biotechnology Department, US Pharmacopeia, Rockville, Maryland, USA
| | - Edward Chess
- Structure Elucidation/Technology Resources, Baxter Healthcare Corporation, Round Lake, Illinois, USA
| | | | - Gyöngyi Gratzl
- Boehringer Ingelheim, Ben Venue Laboratories, Inc., Bedford, Ohio, USA
| | - Elaine Gray
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, UK
| | - David Keire
- US Food and Drug Administration/Division of Pharmaceutical Analysis, St. Louis, Missouri, USA
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Jian Liu
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Tina Morris
- Biologics and Biotechnology Department, US Pharmacopeia, Rockville, Maryland, USA
| | - Barbara Mulloy
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, UK.,Institute of Pharmaceutical Science King's College London, Franklin Wilkins Building, Waterloo Campus, London, UK
| | - Moheb Nasr
- R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Zachary Shriver
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences &Technology, Koch institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Pearle Torralba
- Product Development - Analytical Innovation and Development, Fresenius Kabi USA, Skokie, Illinois, USA
| | | | | | - Janet Woodcock
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Wesley Workman
- Pfizer Quality Operations Biotech, Chesterfield, Missouri, USA
| | - Ali Al-Hakim
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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20
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Mulloy B, Hogwood J, Gray E, Lever R, Page CP. Pharmacology of Heparin and Related Drugs. Pharmacol Rev 2016; 68:76-141. [PMID: 26672027 DOI: 10.1124/pr.115.011247] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Heparin has been recognized as a valuable anticoagulant and antithrombotic for several decades and is still widely used in clinical practice for a variety of indications. The anticoagulant activity of heparin is mainly attributable to the action of a specific pentasaccharide sequence that acts in concert with antithrombin, a plasma coagulation factor inhibitor. This observation has led to the development of synthetic heparin mimetics for clinical use. However, it is increasingly recognized that heparin has many other pharmacological properties, including but not limited to antiviral, anti-inflammatory, and antimetastatic actions. Many of these activities are independent of its anticoagulant activity, although the mechanisms of these other activities are currently less well defined. Nonetheless, heparin is being exploited for clinical uses beyond anticoagulation and developed for a wide range of clinical disorders. This article provides a "state of the art" review of our current understanding of the pharmacology of heparin and related drugs and an overview of the status of development of such drugs.
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Affiliation(s)
- Barbara Mulloy
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - John Hogwood
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Elaine Gray
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Rebecca Lever
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
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21
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Purification, expression and characterization of a novel α-l-fucosidase from a marine bacteria Wenyingzhuangia fucanilytica. Protein Expr Purif 2016; 129:9-17. [PMID: 27576198 DOI: 10.1016/j.pep.2016.08.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 11/22/2022]
Abstract
α-l-Fucosyl residues are frequently found in oligosaccharides, polysaccharides and glycoconjugates which play fundamental roles in various biological processes. α-l-Fucosidases, glycoside hydrolases for catalyzing the removal of α-l-fucose, can serve as desirable tools in the study and the modification of fucose-containing biomolecules. In this study, an α-l-fucosidase named as Alf1_Wf was purified from a marine bacterium Wenyingzhuangia fucanilytica by using a combination of chromatographic procedures. The sequence of Alf1_Wf was identified via proteomics analysis against the predicted proteome of the bacterium. Recombinant Alf1_Wf with 6×His tag was expressed in E. coli and showed α-l-fucosidase activity. Sequence annotation revealed that Alf1_Wf contained a combination of GH29 catalytic domain and CBM35 accessory domain. Alf1_Wf was confirmed as a member of GH29-A subfamily based on the phylogenetic analysis. Furthermore, biochemical properties and kinetic characteristics of the enzyme were also determined. Substrate specificity determination showed that Alf1_Wf was capable in hydrolyzing α1,4-fucosidic linkage and synthetic substrate pNP-fucose. Besides, Alf1_Wf could act on partially degraded fucoidan. This study successfully purified, identified, cloned, expressed and characterized a novel α-l-fucosidase, and meanwhile revealed a new multidomain structure of glycoside hydrolase. The knowledge gained from this study should facilitate the further research and application of α-l-fucosidases.
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22
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Baumann H. Biological Effects of Heparan Sulfates and Regioselectively Modified Heparin-Heparan Mimetics. J BIOACT COMPAT POL 2016. [DOI: 10.1177/0883911503018001006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The heparan sulfates (HS) are structurally the most complex but information rich biopolymers known. They are composed of polysaccharides containing regioselectively distributed carboxyl, sulfate ester, acetyl, amino, and N-sulfonyl groups with sequence- and domain-like arrangements. HS are found ubiquitously on cell surfaces and in extracellular matrices where they are covalently anchored via restricted protein cores. They modulate numerous development cell processes and the pathology of living organisms. HS concentration is extremely low on endothelial cell surfaces (1 pmol/cm2), therefore, they are difficult to isolate and evaluate. Furthermore, their sequence variability is extremely high and the sequence analysis is in its infancy. HS acts as a low affinity receptor which plays a central role in the reception and modulation of a wide range of effector proteins such as growth factors, morphogens, chemokines, enzymes, protease inhibitors. Water soluble fragments of HS and heparin (HE) enzymatically released or synthetic sequences, analogs of heparinoids and heparanoids (HH) mimetics regioselectively modified oligo- and polysaccharides with HE/HS like functional groups, and nonsaccharide containing structures can modulate effector proteins and influence some of the development and pathological processes. Modulation effects are described for anticoagulant antiproliferative properties, for reducing platelet and plasma protein adhesion as well as inhibition or activating growth factors by the influence of HH mimetics. The advantage of defined high molecular weight substrates are discussed and compared to the low molecular weight mimetics. The potential of HH mimetics opens new approaches and strategies for therapeutic treatment.
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Affiliation(s)
- H. Baumann
- Institute for Technical and Macromolecular Chemistry Hemocompatible and Biocompatible Biomaterials RWTH Aachen, Worringer Weg 1, D-52074 Aachen, Germany
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23
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Leary JA, Miller RL, Wei W, Schwörer R, Zubkova OV, Tyler PC, Turnbull JE. Composition, sequencing and ion mobility mass spectrometry of heparan sulfate-like octasaccharide isomers differing in glucuronic and iduronic acid content. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:245-254. [PMID: 26307704 DOI: 10.1255/ejms.1337] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Here we report ion mobility mass spectrometry (IMMS) separation and tandem mass spectrometry (MS(2)) sequencing methods used to analyze and differentiate six synthetically produced heparin/heparan sulfate (HS)-like octasaccharide (dp8) isomeric structures. These structures are isomeric with regard to either glucuronic acid (GlcA) or iduronic acid (IdoA) residues at various positions. IMMS analysis showed that a fully GlcA structure exhibited a more compact conformation, whereas the fully IdoA structure was more extended. Interestingly, the change from IdoA to GlcA in specific locations resulted in strong conformational distortions. MS(2) of the six isomers showed very different spectra with unique sets of diagnostic product ions. Analysis of MS(2) product ion spectra suggests that the GlcA group correlated with the formation of a glycosidic product ion under lower energy conditions. This resulted in an earlier product ion formation and more intense product ions. Importantly, this knowledge enabled a complete sequencing of the positions of GlcA and IdoA in each of the four positions located in each unique dp8 structure.
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Affiliation(s)
- Julie A Leary
- De partments of Molecular and Cellular Biology and Chemistry, University of California, USA..
| | - Rebecca L Miller
- Departments of Molecular and Cellular Biology and Chemistry, University of California. Centre for Glycobiology, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
| | - Wei Wei
- Departments of Molecular and Cellular Biology and Chemistry, University of California, USA..
| | - Ralf Schwörer
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand.
| | - Olga V Zubkova
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand.
| | - Peter C Tyler
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand.
| | - Jeremy E Turnbull
- Centre for Glycobiology, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
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24
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Casu B, Naggi A, Torri G. Re-visiting the structure of heparin. Carbohydr Res 2014; 403:60-8. [PMID: 25088334 DOI: 10.1016/j.carres.2014.06.023] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 06/22/2014] [Indexed: 01/12/2023]
Abstract
The sulfated polysaccharide heparin has been used as a life-saving anticoagulant in clinics well before its detailed structure was known. This mini-review is a survey of the evolution in the discovery of the primary and secondary structure of heparin. Highlights in this history include elucidation and synthesis of the specific sequence that binds to antithrombin, the development of low-molecular-weight heparins currently used as antithrombotic drugs, and the most promising start of chemo-enzymatic synthesis. Special emphasis is given to peculiar conformational properties contributing to interaction with proteins that modulate different biological properties.
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Affiliation(s)
- Benito Casu
- G. Ronzoni Institute for Chemical and Biochemical Research, via G. Colombo, 81 20133 Milan, Italy.
| | - Annamaria Naggi
- G. Ronzoni Institute for Chemical and Biochemical Research, via G. Colombo, 81 20133 Milan, Italy
| | - Giangiacomo Torri
- G. Ronzoni Institute for Chemical and Biochemical Research, via G. Colombo, 81 20133 Milan, Italy
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25
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Scientific considerations in the review and approval of generic enoxaparin in the United States. Nat Biotechnol 2013; 31:220-6. [DOI: 10.1038/nbt.2528] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 02/08/2013] [Indexed: 12/16/2022]
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26
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Furukawa JI, Fujitani N, Shinohara Y. Recent advances in cellular glycomic analyses. Biomolecules 2013; 3:198-225. [PMID: 24970165 PMCID: PMC4030886 DOI: 10.3390/biom3010198] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/28/2013] [Accepted: 02/14/2013] [Indexed: 12/21/2022] Open
Abstract
A large variety of glycans is intricately located on the cell surface, and the overall profile (the glycome, given the entire repertoire of glycoconjugate-associated sugars in cells and tissues) is believed to be crucial for the diverse roles of glycans, which are mediated by specific interactions that control cell-cell adhesion, immune response, microbial pathogenesis and other cellular events. The glycomic profile also reflects cellular alterations, such as development, differentiation and cancerous change. A glycoconjugate-based approach would therefore be expected to streamline discovery of novel cellular biomarkers. Development of such an approach has proven challenging, due to the technical difficulties associated with the analysis of various types of cellular glycomes; however, recent progress in the development of analytical methodologies and strategies has begun to clarify the cellular glycomics of various classes of glycoconjugates. This review focuses on recent advances in the technical aspects of cellular glycomic analyses of major classes of glycoconjugates, including N- and O-linked glycans, derived from glycoproteins, proteoglycans and glycosphingolipids. Articles that unveil the glycomics of various biologically important cells, including embryonic and somatic stem cells, induced pluripotent stem (iPS) cells and cancer cells, are discussed.
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Affiliation(s)
- Jun-Ichi Furukawa
- Laboratory of Medical and Functional Glycomics, Graduate School of Advanced Life Science and Frontier Research Center for Post-Genome Science and Technology, Hokkaido University, Sapporo 001-0021, Japan
| | - Naoki Fujitani
- Laboratory of Medical and Functional Glycomics, Graduate School of Advanced Life Science and Frontier Research Center for Post-Genome Science and Technology, Hokkaido University, Sapporo 001-0021, Japan
| | - Yasuro Shinohara
- Laboratory of Medical and Functional Glycomics, Graduate School of Advanced Life Science and Frontier Research Center for Post-Genome Science and Technology, Hokkaido University, Sapporo 001-0021, Japan.
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Puvirajesinghe TM, Turnbull JE. Glycomics approaches for the bioassay and structural analysis of heparin/heparan sulphates. Metabolites 2012; 2:1060-89. [PMID: 24957775 PMCID: PMC3901230 DOI: 10.3390/metabo2041060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 11/13/2012] [Accepted: 11/15/2012] [Indexed: 01/16/2023] Open
Abstract
The glycosaminoglycan heparan sulphate (HS) has a heterogeneous structure; evidence shows that specific structures may be responsible for specific functions in biological processes such as blood coagulation and regulation of growth factor signalling. This review summarises the different experimental tools and methods developed to provide more rapid methods for studying the structure and functions of HS. Rapid and sensitive methods for the facile purification of HS, from tissue and cell sources are reviewed. Data sets for the structural analysis are often complex and include multiple sample sets, therefore different software and tools have been developed for the analysis of different HS data sets. These can be readily applied to chromatographic data sets for the simplification of data (e.g., charge separation using strong anion exchange chromatography and from size separation using gel filtration techniques. Finally, following the sequencing of the human genome, research has rapidly advanced with the introduction of high throughput technologies to carry out simultaneous analyses of many samples. Microarrays to study macromolecular interactions (including glycan arrays) have paved the way for bioassay technologies which utilize cell arrays to study the effects of multiple macromolecules on cells. Glycan bioassay technologies are described in which immobilisation techniques for saccharides are exploited to develop a platform to probe cell responses such as signalling pathway activation. This review aims at reviewing available techniques and tools for the purification, analysis and bioassay of HS saccharides in biological systems using "glycomics" approaches.
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Affiliation(s)
- Tania M Puvirajesinghe
- Centre de Recherche en Cancérologie de Marseille, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, 10039 Marseille, France.
| | - Jeremy E Turnbull
- Centre for Glycobiology, Department of Biochemistry and Cell Biology, Institute of Integrative Biology, The University of Liverpool, Liverpool, L69 7ZB, UK.
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Kreuger J, Kjellén L. Heparan sulfate biosynthesis: regulation and variability. J Histochem Cytochem 2012; 60:898-907. [PMID: 23042481 DOI: 10.1369/0022155412464972] [Citation(s) in RCA: 206] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nearly all vertebrate cells have been shown to express heparan sulfate proteoglycans (HSPGs) at the cell surface. The HSPGs bind to many secreted signaling proteins, including numerous growth factors, cytokines, and morphogens, to affect their tissue distribution and signaling. The heparan sulfate (HS) chains may have variable length and may differ with regard to both degree and pattern of sulfation. As the sulfation pattern of HS chains in most cases will determine if an interaction with a potential ligand will take place, as well as the affinity of the interaction, a key to understanding the function of HSPGs is to clarify how HS biosynthesis is regulated in different biological contexts. This review provides an introduction to the current understanding of HS biosynthesis and its regulation, and identifies research areas where more knowledge is needed to better understand how the HS biosynthetic machinery works.
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Affiliation(s)
- Johan Kreuger
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Abstract
Proteoglycans (PGs) are among the most structurally complex biomacromolecules in nature. They are present in all animal cells and frequently exert their critical biological functions through interactions with protein ligands and receptors. PGs are comprised of a core protein to which one or multiple, heterogeneous, and polydisperse glycosaminoglycan (GAG) chains are attached. Proteins, including the protein core of PGs, are now routinely sequenced either directly using proteomics or indirectly using molecular biology through their encoding DNA. The sequencing of the GAG component of PGs poses a considerably more difficult challenge because of the relatively underdeveloped state of glycomics and because the control of their biosynthesis in the endoplasmic reticulum and the Golgi is poorly understood and not believed to be template driven. Recently, the GAG chain of the simplest PG has been suggested to have a defined sequence based on its top-down Fourier transform mass spectral sequencing. This review examines the advances made over the past decade in the sequencing of GAG chains and the challenges the field face in sequencing complex PGs having critical biological functions in developmental biology and pathogenesis.
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Affiliation(s)
- Lingyun Li
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA; Fax: +1 518-276-3405; Tel: +1 518-276-3404
| | - Mellisa Ly
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA; Fax: +1 518-276-3405; Tel: +1 518-276-3404
| | - Robert J. Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA; Fax: +1 518-276-3405; Tel: +1 518-276-3404
- Department of Biology, Chemical and Biological Engineering and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA
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Abstract
Heparan sulphate (HS), discovered in 1948 in heparin by-products, only emerged slowly from the shadow of heparin. Its inauspicious beginning was followed by the gradual realisation that HS was a separate entity with distinctive features. Both HS and heparin follow a common biosynthetic route but while heparin reaches full maturity, HS holds on to some of its youthful traits. The novel design and complex patterning of sulphation in HS enable it fulfil key roles in many, diverse biological processes.
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Abstract
Proteoglycans are complex glycoconjugates that regulate critical biological pathways in all higher organisms. Bikunin, the simplest proteoglycan having a single glycosaminoglycan chain, is a serine protease inhibitor used to treat acute pancreatitis. Unlike the template driven synthesis of nucleic acids and proteins, Golgi synthesized glycosaminoglycans are not believed to have predictable or deterministic sequence. Bikunin peptidoglycosaminoglycans were prepared and fractionated to obtain a collection of size similar and charge similar chains. Fourier transform mass spectral analysis identified a small number of parent molecular-ions corresponding to mono-compositional peptidoglycosaminoglycans. Fragmentation using collision induced dissociation surprisingly afforded a single sequence for each mono-compositional parent-ion, unequivocally demonstrating the presence of a defined sequence. The common biosynthetic pathway for all proteoglycans suggests that even more structurally complex proteoglycans, such as heparan sulfate, may have defined sequences, requiring a readjustment of our understanding of information storage in complex glycans.
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Xiao Z, Tappen BR, Ly M, Zhao W, Canova LP, Guan H, Linhardt RJ. Heparin mapping using heparin lyases and the generation of a novel low molecular weight heparin. J Med Chem 2011; 54:603-10. [PMID: 21166465 PMCID: PMC3024469 DOI: 10.1021/jm101381k] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Seven pharmaceutical heparins were investigated by oligosaccharide mapping by digestion with heparin lyase 1, 2, or 3, followed by high performance liquid chromatography analysis. The structure of one of the prepared mapping standards, ΔUA-Gal-Gal-Xyl-O-CH(2)CONHCH(2)COOH (where ΔUA is 4-deoxy-α-l-threo-hex-4-eno-pyranosyluronic acid, Gal is β-d-galactpyranose, and Xyl is β-d-xylopyranose) released from the linkage region using either heparin lyase 2 or heparin lyase 3 digestion, is reported for the first time. A size-dependent susceptibility of site cleaved by heparin lyase 3 was also observed. Heparin lyase 3 acts on the undersulfated domains of the heparin chain and does not cleave the linkages within heparin's antithrombin III binding site. Thus, a novel low molecular weight heparin (LMWH) is afforded on heparin lyase 3 digestion of heparin due to this unique substrate specificity, which has anticoagulant activity comparable to that of currently available LMWH.
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Affiliation(s)
- Zhongping Xiao
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Institute of Marine Drug and Food, Ocean University of China, Qingdao, 266003, China
- Departments of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Britney R. Tappen
- Department of Biochemistry and Biophysics, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Mellisa Ly
- Departments of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Wenjing Zhao
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Lauren P. Canova
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Huashi Guan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Institute of Marine Drug and Food, Ocean University of China, Qingdao, 266003, China
| | - Robert J. Linhardt
- Departments of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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Abstract
HSs (heparan sulfates) are a complex family of cell-surface and matrix polysaccharides that have diverse biological functions, underpinned by structurally diverse patterns of backbone chain modification, especially by sulfate groups. These variant structures represent a molecular code, the 'heparanome', that confers the ability to interact selectively with a wide interactome of proteins, the 'heparactome', and thereby influence a network of cellular events. It is becoming increasingly apparent that understanding the structure-activity relationships of these enigmatic molecules requires the development of a holistic systems biology view of their structure and interactions. In the present paper, I describe some of the new tools available to realize this strategy, and discuss the future potential for the combined application of glycomics and other '-omics' approaches to define the molecular code of the heparanome.
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Malavaki CJ, Theocharis AD, Lamari FN, Kanakis I, Tsegenidis T, Tzanakakis GN, Karamanos NK. Heparan sulfate: biological significance, tools for biochemical analysis and structural characterization. Biomed Chromatogr 2010; 25:11-20. [DOI: 10.1002/bmc.1536] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Disaccharide compositional analysis of heparan sulfate and heparin polysaccharides using UV or high-sensitivity fluorescence (BODIPY) detection. Nat Protoc 2010; 5:1983-92. [DOI: 10.1038/nprot.2010.145] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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36
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Smits NC, Kurup S, Rops AL, ten Dam GB, Massuger LF, Hafmans T, Turnbull JE, Spillmann D, Li JP, Kennel SJ, Wall JS, Shworak NW, Dekhuijzen PNR, van der Vlag J, van Kuppevelt TH. The heparan sulfate motif (GlcNS6S-IdoA2S)3, common in heparin, has a strict topography and is involved in cell behavior and disease. J Biol Chem 2010; 285:41143-51. [PMID: 20837479 DOI: 10.1074/jbc.m110.153791] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heparan sulfate (HS) is a structurally complex polysaccharide that interacts with a broad spectrum of extracellular effector ligands and thereby is thought to regulate a diverse array of biologic processes. The specificity of HS-ligand interactions is determined by the arrangement of sulfate groups on HS, which creates distinct binding motifs. Biologically important HS motifs are expected to exhibit regulated expression, yet there is a profound lack of tools to identify such motifs; consequently, little is known of their structures and functions. We have identified a novel phage display-derived antibody (NS4F5) that recognizes a highly regulated HS motif (HS(NS4F5)), which we have rigorously identified as (GlcNS6S-IdoA2S)(3). HS(NS4F5) exhibits a restricted expression in healthy adult tissues. Blocking HS(NS4F5) on cells in culture resulted in reduced proliferation and enhanced sensitivity to apoptosis. HS(NS4F5) is up-regulated in tumor endothelial cells, consistent with a role in endothelial cell activation. Indeed, TNF-α stimulated endothelial expression of HS(NS4F5), which contributed to leukocyte adhesion. In a mouse model of severe systemic amyloid protein A amyloidosis, HS(NS4F5) was expressed within amyloid deposits, which were successfully detected by microSPECT imaging using NS4F5 as a molecularly targeted probe. Combined, our results demonstrate that NS4F5 is a powerful tool for elucidating the biological function of HS(NS4F5) and can be exploited as a probe to detect novel polysaccharide biomarkers of disease processes.
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Affiliation(s)
- Nicole C Smits
- Department of Biochemistry, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands
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37
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Smits NC, Shworak NW, Dekhuijzen PR, van Kuppevelt TH. Heparan Sulfates in the Lung: Structure, Diversity, and Role in Pulmonary Emphysema. Anat Rec (Hoboken) 2010; 293:955-67. [DOI: 10.1002/ar.20895] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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38
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Spencer JL, Bernanke JA, Buczek-Thomas JA, Nugent MA. A computational approach for deciphering the organization of glycosaminoglycans. PLoS One 2010; 5:e9389. [PMID: 20186334 PMCID: PMC2826411 DOI: 10.1371/journal.pone.0009389] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 02/01/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Increasing evidence has revealed important roles for complex glycans as mediators of normal and pathological processes. Glycosaminoglycans are a class of glycans that bind and regulate the function of a wide array of proteins at the cell-extracellular matrix interface. The specific sequence and chemical organization of these polymers likely define function; however, identification of the structure-function relationships of glycosaminoglycans has been met with challenges associated with the unique level of complexity and the nontemplate-driven biosynthesis of these biopolymers. METHODOLOGY/PRINCIPAL FINDINGS To address these challenges, we have devised a computational approach to predict fine structure and patterns of domain organization of the specific glycosaminoglycan, heparan sulfate (HS). Using chemical composition data obtained after complete and partial digestion of mixtures of HS chains with specific degradative enzymes, the computational analysis produces populations of theoretical HS chains with structures that meet both biosynthesis and enzyme degradation rules. The model performs these operations through a modular format consisting of input/output sections and three routines called chainmaker, chainbreaker, and chainsorter. We applied this methodology to analyze HS preparations isolated from pulmonary fibroblasts and epithelial cells. Significant differences in the general organization of these two HS preparations were observed, with HS from epithelial cells having a greater frequency of highly sulfated domains. Epithelial HS also showed a higher density of specific HS domains that have been associated with inhibition of neutrophil elastase. Experimental analysis of elastase inhibition was consistent with the model predictions and demonstrated that HS from epithelial cells had greater inhibitory activity than HS from fibroblasts. CONCLUSIONS/SIGNIFICANCE This model establishes the conceptual framework for a new class of computational tools to use to assess patterns of domain organization within glycosaminoglycans. These tools will provide a means to consider high-level chain organization in deciphering the structure-function relationships of polysaccharides in biology.
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Affiliation(s)
- Jean L Spencer
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, United States of America.
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Bruinsma IB, te Riet L, Gevers T, ten Dam GB, van Kuppevelt TH, David G, Küsters B, de Waal RMW, Verbeek MM. Sulfation of heparan sulfate associated with amyloid-beta plaques in patients with Alzheimer's disease. Acta Neuropathol 2010; 119:211-20. [PMID: 19636575 DOI: 10.1007/s00401-009-0577-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 07/02/2009] [Accepted: 07/16/2009] [Indexed: 12/23/2022]
Abstract
Alzheimer's disease (AD) is characterized by pathological lesions such as amyloid-beta (Abeta) plaques and cerebral amyloid angiopathy. Both these lesions consist mainly of aggregated Abeta protein and this aggregation is affected by macromolecules such as heparan sulfate (HS) proteoglycans. Previous studies demonstrated that HS enhances fibrillogenesis of Abeta and that this enhancement is dependent on the degree of sulfation of HS. In addition, it has been reported that these sulfation epitopes do not occur randomly but have a defined tissue distribution. Until now, the distribution of sulfation epitopes of HS has not yet been studied in human brain. We investigated whether a specific HS epitope is associated with Abeta plaques by performing immunohistochemistry on occipital neocortical and hippocampal tissue sections from AD patients using five HS epitope-specific phage display antibodies. Antibodies recognizing highly N-sulfated HS demonstrated the highest level of staining in both fibrillar Abeta plaques and non-fibrillar Abeta plaques, whereas antibodies recognizing HS regions with a lower degree of N-sulfate modifications were only immunoreactive with fibrillar Abeta plaques. Thus, our results suggest that a larger variety of HS epitopes is associated with fibrillar Abeta plaques, but the HS epitopes associated with non-fibrillar Abeta plaques seem to be more restricted, selectively consisting of highly N-sulfated epitopes.
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Affiliation(s)
- Ilona B Bruinsma
- Department of Neurology and Alzheimer Centre, Donders Institute for Brain, Cognition and Behaviour, Centre for Neuroscience, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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41
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Abstract
The heparan sulfate (HS) family of glycosaminoglycans are highly complex and structurally diverse polysaccharides with information encoded within the chains that imparts the ability to bind selectively to a wide range of proteins-the "HS interactome"-and to regulate their biological activities. However, there are two key questions which need to be addressed; first, the extent of structural variation of expressed HS structures-the "heparanome"-in specific biological contexts and second, the degree of functional selectivity exerted by these structures in regulating biological processes. There is a clear need to develop more systematic and high throughput approaches in order to address these questions. Here, we describe a cohort of protocols for profiling different aspects of HS structure and activity, focusing particularly on disaccharide building blocks and larger oligosaccharide domains, the latter representing the functional units of HS chains. A range of other complementary methods in the literature are also discussed. Together these provide a new and more comprehensive toolkit to investigate HS structure and activity in a higher throughput manner in selected biological systems. The implementation of such a glycomics strategy will enable development of a systems biology view of HS structure-function relationships and help to resolve the significant puzzle of the extensive interactome of HS, which remains a key question in the glycobiology field. We anticipate that the next decade will see major advances in our understanding of the complex biology of HS.
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42
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Thompson SM, Fernig DG, Jesudason EC, Losty PD, van de Westerlo EMA, van Kuppevelt TH, Turnbull JE. Heparan sulfate phage display antibodies identify distinct epitopes with complex binding characteristics: insights into protein binding specificities. J Biol Chem 2009; 284:35621-31. [PMID: 19837661 PMCID: PMC2790993 DOI: 10.1074/jbc.m109.009712] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 10/02/2009] [Indexed: 01/03/2023] Open
Abstract
Heparan sulfate (HS) binds and modulates the transport and activity of a large repertoire of regulatory proteins. The HS phage display antibodies are powerful tools for the analysis of native HS structure in situ; however, their epitopes are not well defined. Analysis of the binding specificities of a set of HS antibodies by competitive binding assays with well defined chemically modified heparins demonstrates that O-sulfates are essential for binding; however, increasing sulfation does not necessarily correlate with increased antibody reactivity. IC50 values for competition with double modified heparins were not predictable from IC50 values with corresponding singly modified heparins. Binding assays and immunohistochemistry revealed that individual antibodies recognize distinct epitopes and that these are not single linear sequences but families of structurally similar motifs in which subtle variations in sulfation and conformation modify the affinity of interaction. Modeling of the antibodies demonstrates that they possess highly basic CDR3 and surrounding surfaces, presenting a number of possible orientations for HS binding. Unexpectedly, there are significant differences between the existence of epitopes in tissue sections and observed in vitro in dot blotted tissue extracts, demonstrating that in vitro specificity does not necessarily correlate with specificity in situ/vivo. The epitopes are therefore more complex than previously considered. Overall, these data have significance for structure-activity relationships of HS, because the model of one antibody recognizing multiple HS structures and the influence of other in situ HS-binding proteins on epitope availability are likely to reflect the selectivity of many HS-protein interactions in vivo.
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Affiliation(s)
- Sophie M. Thompson
- From the School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - David G. Fernig
- From the School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Edwin C. Jesudason
- the Division of Child Health, School of Reproductive and Developmental Medicine, Royal Liverpool Children's Hospital, Alder Hey, Liverpool L12 2AP, United Kingdom, and
| | - Paul D. Losty
- the Division of Child Health, School of Reproductive and Developmental Medicine, Royal Liverpool Children's Hospital, Alder Hey, Liverpool L12 2AP, United Kingdom, and
| | - Els M. A. van de Westerlo
- the Department of Matrix Biochemistry, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, P. O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Toin H. van Kuppevelt
- the Department of Matrix Biochemistry, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, P. O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Jeremy E. Turnbull
- From the School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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43
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Guimond SE, Puvirajesinghe TM, Skidmore MA, Kalus I, Dierks T, Yates EA, Turnbull JE. Rapid purification and high sensitivity analysis of heparan sulfate from cells and tissues: toward glycomics profiling. J Biol Chem 2009; 284:25714-22. [PMID: 19596853 PMCID: PMC2757973 DOI: 10.1074/jbc.m109.032755] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 07/06/2009] [Indexed: 11/24/2022] Open
Abstract
Studies on glycosaminoglycans and proteoglycans (PGs) have been hampered by difficulties in isolation and analysis by traditional methods that are laborious and lack sensitivity and throughput. Here we demonstrate a simple method for rapid isolation of proteoglycans (RIP) employing phenol/guanidine/chloroform reagent to purify heparan sulfate (HS) PGs quantitatively from various tissues and cells. We further show that this generic purification methodology, when applied in concert with a BODIPY fluorescent label, permits structural analyses on RIP-purified HS at approximately 1,000-fold higher sensitivity than standard UV detection methods and approximately 10-100-fold higher sensitivity than previous fluorescence detection methods. The utility of RIP-BODIPY methodology was demonstrated by rapid profiling of HS structural composition from small tissue samples, multiple mouse organs, and as little as a few thousand cultured cells. It was also used to generate novel insights into in vivo structural changes in HS from Sulf1 knock-out mice for the first time that differed significantly from previous observations limited to tissue culture experiments. RIP was also applied to purify HS for bioassay testing, exemplified by cell assays of fibroblast growth factor signaling activation; this generated data from 2-O-sulfotransferase knock-out mice and revealed an unexpected deficiency in fibroblast growth factor activation by HS from heterozygous mice. These data demonstrate that RIP will underpin emerging efforts to develop glycomics profiling strategies for HS and other glycosaminoglycans to explore their structure-function relationships in complex biological systems.
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Affiliation(s)
- Scott E. Guimond
- From the Centre for Glycobiology, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom and
| | - Tania M. Puvirajesinghe
- From the Centre for Glycobiology, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom and
| | - Mark A. Skidmore
- From the Centre for Glycobiology, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom and
| | - Ina Kalus
- the Department of Chemistry, Biochemistry I, Bielefeld University, 33615 Bielefeld, Germany
| | - Thomas Dierks
- the Department of Chemistry, Biochemistry I, Bielefeld University, 33615 Bielefeld, Germany
| | - Edwin A. Yates
- From the Centre for Glycobiology, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom and
| | - Jeremy E. Turnbull
- From the Centre for Glycobiology, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom and
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44
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Abstract
Glycosylation is the most common form of post-translational modifications by which oligosaccharide side chains are covalently attached to specific residues of the core protein. Especially O-linked glycan structures like the glycosaminoglycans were found to contribute significantly to many (patho-)biological processes like inflammation, coagulation, cancer and viral infections. Glycans exert their function by interacting with proteins thereby changing the structure of the interacting proteins and consequently modulating their function. Given the complex nature of cell-surface and extracellular matrix glycan structures, this therapeutic site has been neglected for a long time, the only exception being the antithrombin III-glycan interaction which has been successfully targeted by unfractionated and low-molecular weight heparins for many decades. Due to the recent breakthrough in the '-ome' sciences, among them proteomics and glycomics, protein-glycan interactions became more amenable for therapeutic approaches so that novel inhibitors of this interaction are currently in preclinical and clinical studies. An overview of current approaches, their advantages and disadvantages, is given and the promising potential of pharmacologically interfering with protein-glycan interactions is highlighted here.
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Affiliation(s)
- A Rek
- ProtAffin Biotechnologie AG, Graz, Austria
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45
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Zaia J. On-line separations combined with MS for analysis of glycosaminoglycans. MASS SPECTROMETRY REVIEWS 2009; 28:254-72. [PMID: 18956477 PMCID: PMC4119066 DOI: 10.1002/mas.20200] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The glycosaminoglycan (GAG) family of polysaccharides includes the unsulfated hyaluronan and the sulfated heparin, heparan sulfate, keratan sulfate, and chondroitin/dermatan sulfate. GAGs are biosynthesized by a series of enzymes, the activities of which are controlled by complex factors. Animal cells alter their responses to different growth conditions by changing the structures of GAGs expressed on their cell surfaces and in extracellular matrices. Because this variation is a means whereby the functions of the limited number of protein gene products in animal genomes is elaborated, the phenotypic and functional assessment of GAG structures expressed spatially and temporally is an important goal in glycomics. On-line mass spectrometric separations are essential for successful determination of expression patterns for the GAG compound classes due to their inherent complexity and heterogeneity. Options include size exclusion, anion exchange, reversed phase, reversed phase ion pairing, hydrophilic interaction, and graphitized carbon chromatographic modes and capillary electrophoresis. This review summarizes the application of these approaches to on-line MS analysis of the GAG classes.
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Affiliation(s)
- Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Mass Spectrometry Resource, Boston University School of Medicine, Boston, MA 02118, USA.
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46
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Hu P, Fang L, Chess EK. Source-Induced Fragmentation of Heparin, Heparan, and Galactosaminoglycans and Application. Anal Chem 2009; 81:2332-43. [DOI: 10.1021/ac802626e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peifeng Hu
- Technology Resources, Baxter Healthcare Inc., 25212 Illinois Route 120, Round Lake, Illinois 60073
| | - Liqiong Fang
- Technology Resources, Baxter Healthcare Inc., 25212 Illinois Route 120, Round Lake, Illinois 60073
| | - Edward K. Chess
- Technology Resources, Baxter Healthcare Inc., 25212 Illinois Route 120, Round Lake, Illinois 60073
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47
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Puvirajesinghe TM, Guimond SE, Turnbull JE, Guenneau S. Chemometric analysis for comparison of heparan sulphate oligosaccharides. J R Soc Interface 2009; 6:997-1004. [PMID: 19158013 DOI: 10.1098/rsif.2008.0483] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Heparan sulphate (HS) is a glycosaminoglycan present in all metazoan organisms. It is an unbranched chain made up of repeating disaccharide units of uronic acid and glucosamine sugars, and is present in both cells and the extracellular matrix. It is one of the most structurally diverse biological molecules and its biosynthesis involves a variety of enzymic modification steps. Unlike the genome and the transcriptome, HS synthesis is not template driven. Nevertheless, the HS structure and function are highly regulated with modification steps occurring in discrete regions of the polysaccharide chain to give rise to diverse structures interacting with, and regulating, many different proteins. The resulting variation leads to diverse biological roles of HS. To study this structural diversity, rapid isolation and characterization of HS from small amounts of tissues, followed by digestion with bacterially derived enzymes (heparitinases) and chromatography techniques can be used to separate HS oligosaccharides of different size and charge. However, this leads to complex datasets where comparison of just a few samples leads to difficulties in data analysis. Using automatically integrated peak data obtained from chromatographic software, one can apply the effective disc technique to the data points to obtain the centre of mass in each dataset, for example from different murine tissues. This allows facile comparative analysis of different datasets. When the cloud of points displays some preferential direction (anisotropy), it is preferable to compute its effective ellipse. Analysis of the dynamics of the cloud of points for repeated experiments allows the quantification of their reproducibility through evaluation of an average Lyapunov exponent characterizing the area-preserving nature of a sequence of effective ellipses. These basic mathematical approaches allow a more systematic comparison of datasets derived from structural analysis using basic spreadsheet software calculations and contribute to the development of system biology strategies for tackling biocomplexity of HS polysaccharides.
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Affiliation(s)
- T M Puvirajesinghe
- School of Biological Sciences, Department of Mathematical Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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48
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Abstract
There is accumulating evidence of the importance of linear polysaccharides in modulating biological phenomena in both the normal and the diseased states. This layer of regulation results from interactions between polysaccharides and other biomolecules, such as proteins, at the cell-extracellular matrix interface. The specific sequence of chemical modifications within the polymer backbone imparts a potential for interaction with other molecular species, and thus there exists important information within the various sulfation, acetylation, and epimerization states of such complex carbohydrates. A variety of factors have made the deciphering of this chemical code elusive. To this end, this report describes several techniques to elucidate the structural information inherent in glycosaminoglycan species. First, the use of depolymerizing enzymes that cleave polysaccharides at specific sites is described. Then, capillary electrophoretic (CE) techniques are employed to characterize the disaccharide species present in an enzymatically-cleaved polysaccharide sample. Mass spectrometry (MS) procedures can further be used to establish the length of an oligosaccharide chain and the presence of specific functional groups.
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Affiliation(s)
- Vikas Prabhakar
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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49
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Tissot B, Ceroni A, Powell AK, Morris HR, Yates EA, Turnbull JE, Gallagher JT, Dell A, Haslam SM. Software Tool for the Structural Determination of Glycosaminoglycans by Mass Spectrometry. Anal Chem 2008; 80:9204-12. [DOI: 10.1021/ac8013753] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bérangère Tissot
- Division of Molecular Biosciences, Imperial College, London, London, SW7 2AZ, United Kingdom, Molecular Glycobiology Laboratory, School of Biological Sciences, University of Liverpool, L69 7ZB, United Kingdom, Glyco-Oncology Group, School of Cancer and Imaging Sciences, Paterson Institute for Cancer Research, University of Manchester, Christie Hospital, Manchester, M20 4BX, United Kingdom, and M-SCAN Ltd., Wokingham, Berks, RG41 2TZ, United Kingdom
| | - Alessio Ceroni
- Division of Molecular Biosciences, Imperial College, London, London, SW7 2AZ, United Kingdom, Molecular Glycobiology Laboratory, School of Biological Sciences, University of Liverpool, L69 7ZB, United Kingdom, Glyco-Oncology Group, School of Cancer and Imaging Sciences, Paterson Institute for Cancer Research, University of Manchester, Christie Hospital, Manchester, M20 4BX, United Kingdom, and M-SCAN Ltd., Wokingham, Berks, RG41 2TZ, United Kingdom
| | - Andrew K. Powell
- Division of Molecular Biosciences, Imperial College, London, London, SW7 2AZ, United Kingdom, Molecular Glycobiology Laboratory, School of Biological Sciences, University of Liverpool, L69 7ZB, United Kingdom, Glyco-Oncology Group, School of Cancer and Imaging Sciences, Paterson Institute for Cancer Research, University of Manchester, Christie Hospital, Manchester, M20 4BX, United Kingdom, and M-SCAN Ltd., Wokingham, Berks, RG41 2TZ, United Kingdom
| | - Howard R. Morris
- Division of Molecular Biosciences, Imperial College, London, London, SW7 2AZ, United Kingdom, Molecular Glycobiology Laboratory, School of Biological Sciences, University of Liverpool, L69 7ZB, United Kingdom, Glyco-Oncology Group, School of Cancer and Imaging Sciences, Paterson Institute for Cancer Research, University of Manchester, Christie Hospital, Manchester, M20 4BX, United Kingdom, and M-SCAN Ltd., Wokingham, Berks, RG41 2TZ, United Kingdom
| | - Edwin A. Yates
- Division of Molecular Biosciences, Imperial College, London, London, SW7 2AZ, United Kingdom, Molecular Glycobiology Laboratory, School of Biological Sciences, University of Liverpool, L69 7ZB, United Kingdom, Glyco-Oncology Group, School of Cancer and Imaging Sciences, Paterson Institute for Cancer Research, University of Manchester, Christie Hospital, Manchester, M20 4BX, United Kingdom, and M-SCAN Ltd., Wokingham, Berks, RG41 2TZ, United Kingdom
| | - Jeremy E. Turnbull
- Division of Molecular Biosciences, Imperial College, London, London, SW7 2AZ, United Kingdom, Molecular Glycobiology Laboratory, School of Biological Sciences, University of Liverpool, L69 7ZB, United Kingdom, Glyco-Oncology Group, School of Cancer and Imaging Sciences, Paterson Institute for Cancer Research, University of Manchester, Christie Hospital, Manchester, M20 4BX, United Kingdom, and M-SCAN Ltd., Wokingham, Berks, RG41 2TZ, United Kingdom
| | - John T. Gallagher
- Division of Molecular Biosciences, Imperial College, London, London, SW7 2AZ, United Kingdom, Molecular Glycobiology Laboratory, School of Biological Sciences, University of Liverpool, L69 7ZB, United Kingdom, Glyco-Oncology Group, School of Cancer and Imaging Sciences, Paterson Institute for Cancer Research, University of Manchester, Christie Hospital, Manchester, M20 4BX, United Kingdom, and M-SCAN Ltd., Wokingham, Berks, RG41 2TZ, United Kingdom
| | - Anne Dell
- Division of Molecular Biosciences, Imperial College, London, London, SW7 2AZ, United Kingdom, Molecular Glycobiology Laboratory, School of Biological Sciences, University of Liverpool, L69 7ZB, United Kingdom, Glyco-Oncology Group, School of Cancer and Imaging Sciences, Paterson Institute for Cancer Research, University of Manchester, Christie Hospital, Manchester, M20 4BX, United Kingdom, and M-SCAN Ltd., Wokingham, Berks, RG41 2TZ, United Kingdom
| | - Stuart M. Haslam
- Division of Molecular Biosciences, Imperial College, London, London, SW7 2AZ, United Kingdom, Molecular Glycobiology Laboratory, School of Biological Sciences, University of Liverpool, L69 7ZB, United Kingdom, Glyco-Oncology Group, School of Cancer and Imaging Sciences, Paterson Institute for Cancer Research, University of Manchester, Christie Hospital, Manchester, M20 4BX, United Kingdom, and M-SCAN Ltd., Wokingham, Berks, RG41 2TZ, United Kingdom
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50
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Disaccharide structure code for the easy representation of constituent oligosaccharides from glycosaminoglycans. Nat Methods 2008; 5:291-2. [PMID: 18376390 DOI: 10.1038/nmeth0408-291] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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