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Gass DT, Quintero AV, Hatvany JB, Gallagher ES. Metal adduction in mass spectrometric analyses of carbohydrates and glycoconjugates. MASS SPECTROMETRY REVIEWS 2024; 43:615-659. [PMID: 36005212 DOI: 10.1002/mas.21801] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Glycans, carbohydrates, and glycoconjugates are involved in many crucial biological processes, such as disease development, immune responses, and cell-cell recognition. Glycans and carbohydrates are known for the large number of isomeric features associated with their structures, making analysis challenging compared with other biomolecules. Mass spectrometry has become the primary method of structural characterization for carbohydrates, glycans, and glycoconjugates. Metal adduction is especially important for the mass spectrometric analysis of carbohydrates and glycans. Metal-ion adduction to carbohydrates and glycoconjugates affects ion formation and the three-dimensional, gas-phase structures. Herein, we discuss how metal-ion adduction impacts ionization, ion mobility, ion activation and dissociation, and hydrogen/deuterium exchange for carbohydrates and glycoconjugates. We also compare the use of different metals for these various techniques and highlight the value in using metals as charge carriers for these analyses. Finally, we provide recommendations for selecting a metal for analysis of carbohydrate adducts and describe areas for continued research.
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Affiliation(s)
- Darren T Gass
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Ana V Quintero
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Jacob B Hatvany
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
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2
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Watermann S, Bode MC, Hackl T. Identification of metabolites from complex mixtures by 3D correlation of 1H NMR, MS and LC data using the SCORE-metabolite-ID approach. Sci Rep 2023; 13:15834. [PMID: 37740032 PMCID: PMC10516956 DOI: 10.1038/s41598-023-43056-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023] Open
Abstract
Not only in metabolomics studies, but also in natural product chemistry, reliable identification of metabolites usually requires laborious steps of isolation and purification and remains a bottleneck in many studies. Direct metabolite identification from a complex mixture without individual isolation is therefore a preferred approach, but due to the large number of metabolites present in natural products, this approach is often hampered by signal overlap in the respective 1H NMR spectra. This paper presents a method for the three-dimensional mathematical correlation of NMR with MS data over the third dimension of the time course of a chromatographic fractionation. The MATLAB application SCORE-metabolite-ID (Semi-automatic COrrelation analysis for REliable metabolite IDentification) provides semi-automatic detection of correlated NMR and MS data, allowing NMR signals to be related to associated mass-to-charge ratios from ESI mass spectra. This approach enables fast and reliable dereplication of known metabolites and facilitates the dynamic analysis for the identification of unknown compounds in any complex mixture. The strategy was validated using an artificial mixture and further tested on a polar extract of a pine nut sample. Straightforward identification of 40 metabolites could be shown, including the identification of β-D-glucopyranosyl-1-N-indole-3-acetyl-N-L-aspartic acid (1) and Nα-(2-hydroxy-2-carboxymethylsuccinyl)-L-arginine (2), the latter being identified in a food sample for the first time.
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Affiliation(s)
- Stephanie Watermann
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Marie-Christin Bode
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Thomas Hackl
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany.
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3
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Ye G, Zhang J, Xu X, Zeng C, Ye Q, Wang Z. Comparative Analysis of Water-Soluble Polysaccharides from Dendrobium Second Love 'Tokimeki' and Dendrobium nobile in Structure, Antioxidant, and Anti-Tumor Activity In Vitro. Int J Mol Sci 2023; 24:10361. [PMID: 37373508 DOI: 10.3390/ijms241210361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
With potential anti-tumor and antioxidant properties, the polysaccharide content of D. nobile is relatively lower than that of the other medicinal Dendrobium. To find high-content polysaccharide resources, the polysaccharide (DHPP-Ⅰs) was prepared from D. Second Love 'Tokimeki' (a D. nobile hybrid) and compared with DNPP-Ⅰs from D. nobile. DHPP-Is (Mn 31.09 kDa) and DNPP-Is (Mn 46.65 kDa) were found to be O-acetylated glucomannans (-Glcp-(1,4) and O-acetylated-D-Manp-(1,4) backbones), analogous to other Dendrobium polysaccharides. DHPP-Ⅰs had higher glucose content (31.1%) and a lower degree (0.16) of acetylation than DNPP-Ⅰs (15.8%, 0.28). Meanwhile, DHPP-Ⅰs and DNPP-Ⅰs had the same ability in the radical scavenging assay, which was milder than the control of Vc. Both DHPP-Is and DNPP-Is inhibited SPC-A-1 cell proliferation in vitro, with obvious differences in dose concentrations (0.5-2.0 mg/mL) and treatment times (24-72 h). Therefore, the antioxidant activity of DHPP-Ⅰs and DNPP-Ⅰs is not associated with distinction in anti-proliferative activity. As a glucomannan derived from non-medicinal Dendrobium, DHPP-Ⅰs has similar bioactivity to other medicinal Dendrobium, and this could serve as a starting point for studying the conformational-bioactivity relationship of Dendrobium polysaccharides.
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Affiliation(s)
- Guangying Ye
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jinhui Zhang
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaoli Xu
- Instrumental Analysis and Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Canbiao Zeng
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qingsheng Ye
- Guangdong Province Key Lab for Biotechnology of Plant Development, College of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zaihua Wang
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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4
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Experimental and computational characterization of dynamic biomolecular interaction systems involving glycolipid glycans. Glycoconj J 2022; 39:219-228. [PMID: 35298725 DOI: 10.1007/s10719-022-10056-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/31/2022] [Accepted: 03/09/2022] [Indexed: 02/03/2023]
Abstract
On cell surfaces, carbohydrate chains that modify proteins and lipids mediate various biological functions, which are exerted not only through carbohydrate-protein interactions but also through carbohydrate-carbohydrate interactions. These glycans exhibit considerable degrees of conformational variability and often form clusters providing multiple binding sites. The integration of nuclear magnetic resonance spectroscopy and molecular dynamics simulation has made it possible to delineate the dynamical structures of carbohydrate chains. This approach has facilitated the remodeling of oligosaccharide conformational space in the prebound state to improve protein-binding affinity and has been applied to visualize dynamic carbohydrate-carbohydrate interactions that control glycoprotein-glycoprotein complex formation. Functional glycoclusters have been characterized by experimental and computational approaches applied to various model membranes and artificial self-assembling systems. This line of investigation has provided dynamic views of molecular assembling on glycoclusters, giving mechanistic insights into physiological and pathological molecular events on cell surfaces as well as clues for the design and creation of molecular systems exerting improved glycofunctions. Further development and accumulation of such studies will allow detailed understanding and artificial control of the "glycosynapse" foreseen by Dr. Sen-itiroh Hakomori.
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Bansal P, Ben Faleh A, Warnke S, Rizzo TR. Identification of N-glycan positional isomers by combining IMS and vibrational fingerprinting of structurally determinant CID fragments. Analyst 2022; 147:704-711. [PMID: 35079754 PMCID: PMC8842669 DOI: 10.1039/d1an01861b] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
While glycans are present on the surface of cells in all living organisms and play key roles in most biological processes, their isomeric complexity makes their structural characterization challenging. Of particular importance are positional isomers, for which analytical standards are difficult to obtain. We combine ultrahigh-resolution ion-mobility spectrometry with collision-induced dissociation and cryogenic infrared spectroscopy to determine the structure of N-glycan positional isomers. This approach is based on first separating the parent molecules by SLIM-based IMS, producing diagnostic fragments specific to each positional isomer, separating the fragments by IMS, and identifying them by comparing their IR fingerprints to a previously recorded spectral database. We demonstrate this strategy using a bottom-up scheme to identify the positional isomers of the N-linked glycan G0-N, in which a terminal N-acetylglucosamine (GlcNAc) is attached to either the α-3 or α-6 branch of the common N-glycan pentasaccharide core. We then use IR fingerprints of these newly identified isomers to identify the positional isomers of G1 and G1F, which are biantennary complex-type N-glycans with a terminal galactose attached to either the α-3 or α-6 branch, and in the case of G1F a fucose attached to the reducing-end GlcNAc. Starting with just a few analytical standards, this fragment-based spectroscopy method allows us to develop a database which we can use to identify positional isomers. The generalization of this approach would greatly facilitate glycan analysis. We combine high-resolution IMS-IMS with cryogenic vibrational spectroscopy for the indentification of N-glycan positional isomers.![]()
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Affiliation(s)
- Priyanka Bansal
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
| | - Ahmed Ben Faleh
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
| | - Stephan Warnke
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
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6
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Elwakiel M, Bakx EJ, Szeto IM, Li Y, Hettinga KA, Schols HA. Serum Protein N-Glycans in Colostrum and Mature Milk of Chinese Mothers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6873-6883. [PMID: 32496058 PMCID: PMC7317985 DOI: 10.1021/acs.jafc.0c02161] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
To study the Chinese human milk N-glycome over lactation, N-glycans were released and separated from serum proteins, purified by solid-phase extraction, and analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In total, 66 different putative N-glycans were found in the colostrum (week 1) and mature milk (week 4) of seven Chinese mothers. A clear difference was observed between milk of five secretor and two nonsecretor mothers, based on the type and relative amounts of the individual N-glycans. The relative levels of the total neutral nonfucosylated and the fucosylated N-glycans in milk of five secretor mothers increased and decreased over lactation, respectively. This pattern could not be observed for the milk from the two nonsecretor mothers. Overall, this was the first study that provided detailed information on individual N-glycans in milk among mothers and over time as well as that fucosylation of N-glycans in milk was associated with the mother's secretor status.
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Affiliation(s)
- Mohèb Elwakiel
- Laboratory
of Food Chemistry, Wageningen University
& Research, 6708 WG Wageningen, The Netherlands
- Food
Quality and Design, Wageningen University
& Research, 6708 WG Wageningen, The Netherlands
| | - Edwin J. Bakx
- Laboratory
of Food Chemistry, Wageningen University
& Research, 6708 WG Wageningen, The Netherlands
| | - Ignatius M. Szeto
- Inner
Mongolia Yili Industrial Group Co., Ltd., Jinshan Road 8, 010110 Hohhot, China
| | - Yitong Li
- Inner
Mongolia Yili Industrial Group Co., Ltd., Jinshan Road 8, 010110 Hohhot, China
| | - Kasper A. Hettinga
- Food
Quality and Design, Wageningen University
& Research, 6708 WG Wageningen, The Netherlands
| | - Henk A. Schols
- Laboratory
of Food Chemistry, Wageningen University
& Research, 6708 WG Wageningen, The Netherlands
- . Tel: +31 317 482239
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7
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Modak P, Hammond W, Jaffe M, Nadig M, Russo R. Reproducible, biocompatible medical materials from biologically derived polysaccharides: Processing and Characterization. J Appl Polym Sci 2020. [DOI: 10.1002/app.48454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Krylov VB, Argunov DA, Solovev AS, Petruk MI, Gerbst AG, Dmitrenok AS, Shashkov AS, Latgé JP, Nifantiev NE. Synthesis of oligosaccharides related to galactomannans from Aspergillus fumigatus and their NMR spectral data. Org Biomol Chem 2019; 16:1188-1199. [PMID: 29376539 DOI: 10.1039/c7ob02734f] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of model oligosaccharides related to antigenic galactomannans of the dangerous fungal pathogen Aspergillus fumigatus has been performed employing pyranoside-into-furanoside (PIF) rearrangement and controlled O(5) → O(6) benzoyl migration as key synthetic methods. The prepared compounds along with some previously synthesized oligosaccharides were studied by NMR spectroscopy with the full assignment of 1H and 13C signals and the determination of 13C NMR glycosylation effects. The obtained NMR database on 13C NMR chemical shifts for oligosaccharides representing galactomannan fragments forms the basis for further structural analysis of galactomannan related polysaccharides by a non-destructive approach based on the calculation of the 13C NMR spectra of polysaccharides by additive schemes.
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Affiliation(s)
- V B Krylov
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia.
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9
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Khanal N, Masellis C, Kamrath MZ, Clemmer DE, Rizzo TR. Cryogenic IR spectroscopy combined with ion mobility spectrometry for the analysis of human milk oligosaccharides. Analyst 2019. [PMID: 29541730 DOI: 10.1039/c8an00230d] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report here our combination of cryogenic, messenger-tagging, infrared (IR) spectroscopy with ion mobility spectrometry (IMS) and mass spectrometry (MS) as a way to identify and analyze a set of human milk oligosaccharides (HMOs) ranging from trisaccharides to hexasaccharides. The added dimension of IR spectroscopy provides a diagnostic fingerprint in the OH and NH stretching region, which is crucial to identify these oligosaccharides, which are difficult to distinguish by IMS alone. These results extend our previous work in demonstrating the generality of this combined approach for distinguishing subtly different structural and regioisomers of glycans of biologically relevant size.
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Affiliation(s)
- Neelam Khanal
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, USA
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10
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Abstract
Sialic acids are cytoprotectors, mainly localized on the surface of cell membranes with multiple and outstanding cell biological functions. The history of their structural analysis, occurrence, and functions is fascinating and described in this review. Reports from different researchers on apparently similar substances from a variety of biological materials led to the identification of a 9-carbon monosaccharide, which in 1957 was designated "sialic acid." The most frequently occurring member of the sialic acid family is N-acetylneuraminic acid, followed by N-glycolylneuraminic acid and O-acetylated derivatives, and up to now over about 80 neuraminic acid derivatives have been described. They appeared first in the animal kingdom, ranging from echinoderms up to higher animals, in many microorganisms, and are also expressed in insects, but are absent in higher plants. Sialic acids are masks and ligands and play as such dual roles in biology. Their involvement in immunology and tumor biology, as well as in hereditary diseases, cannot be underestimated. N-Glycolylneuraminic acid is very special, as this sugar cannot be expressed by humans, but is a xenoantigen with pathogenetic potential. Sialidases (neuraminidases), which liberate sialic acids from cellular compounds, had been known from very early on from studies with influenza viruses. Sialyltransferases, which are responsible for the sialylation of glycans and elongation of polysialic acids, are studied because of their significance in development and, for instance, in cancer. As more information about the functions in health and disease is acquired, the use of sialic acids in the treatment of diseases is also envisaged.
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Affiliation(s)
- Roland Schauer
- Biochemisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Johannis P Kamerling
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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11
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Kumbhar ST, Patil SP, Une HD. Phytochemical analysis of Canna indica L. roots and rhizomes extract. Biochem Biophys Rep 2018; 16:50-55. [PMID: 30302404 PMCID: PMC6174820 DOI: 10.1016/j.bbrep.2018.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 08/04/2018] [Accepted: 09/05/2018] [Indexed: 01/05/2023] Open
Abstract
Canna indica L. (Cannaceae) roots and rhizomes were reported to possess various biological properties like antimicrobial, anthelmintic potential and HIV-1 reverse transcriptase inhibition. In our previous studies, they showed antidiabetic activity on normal rats and rats co-addicted with caffeine and nicotine. In the pursuit of the phytochemical/s responsible for these biological activities, present study was aimed at phytochemical evaluation of hydroalcoholic extract (HAE) of C. indica L. roots and rhizomes; including preliminary screening, thin layer chromatography, H1-NMR and HR-LC/MS-MS analysis. After preliminary detection of flavonoids, tannins and sterols, HAE was tested for presence of β-sitosterol using TLC. H1-NMR spectrum of HAE revealed the presence of around 761 deshielded protons corresponding to different polar compounds. HR-LC/MS-MS analysis carried out at both positive and negative ion mode, indicated the presence of more than 90 compounds including short fragment of peptide. As per METLIN database, predicted major phytochemicals were 3′-hydroxytrimethoprim, 3,7-epoxycaryophyllan-6-one, swietenine, typhasterol, hexacosanedioic acid and 3β, 6α,7α-trihydroxy-5β-cholan-24-oic acid few of which, are biologically active. Hydroalcoholic extract (HAE) of ornamental plant Canna indica L. roots and rhizomes was prepared. HAE was checked for phytochemical composition present in it by TLC, H1-NMR analysis and HR-LC/MS analysis. As per METLIN database, important phytochemicals detected were 3′-Hydroxytrimethoprim, 3,7-Epoxycaryophyllan-6-one, Swietenine, Typhasterol, Hexacosanedioic acid and 3β, 6α,7α-Trihydroxy-5β-cholan-24-oic acid. Swietinine and Typhasterol were already proved to have pharmacological activity of decreasing blood glucose levels, supporting the previously antidiabetic activity of C. indica L. roots and rhizomes.
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Affiliation(s)
- Subhash T Kumbhar
- Department of Pharmacology, SCES's Indira College of Pharmacy, Pune 411038, India
| | - Shriniwas P Patil
- Department of Pharmacognosy, SCES's Indira College of Pharmacy, Pune 411038, India
| | - Hemant D Une
- Department of Pharmacology, MAES's Y.B. Chavan College of Pharmacy, Aurangabad, India
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12
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Peng J, Patil SM, Keire DA, Chen K. Chemical Structure and Composition of Major Glycans Covalently Linked to Therapeutic Monoclonal Antibodies by Middle-Down Nuclear Magnetic Resonance. Anal Chem 2018; 90:11016-11024. [PMID: 30102512 PMCID: PMC7040853 DOI: 10.1021/acs.analchem.8b02637] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycosylation of monoclonal antibodies (mAbs) is a critical quality attribute that can impact mAb drug efficacy and safety. The mAb glycans are inherently heterogeneous in chemical structure and composition of monosaccharides. The established fluorescence or mass-spectrometry (MS) detection methods for glycosylation evaluation may require multiple steps of glycan cleavage or extensive digestion of the mAb, chemical labeling of the glycans, column separation and report the chemical identity of glycans indirectly through retention time and molecular weight values. In demonstrating chemical structure similarity and comparability among mAb drugs, orthogonal analytical methods for measuring glycan chemistry are needed to ensure the quality of drug products. Here, a "middle-down" NMR method is developed as a proof-of-concept approach to measure the domain-specific glycosylation of marketed mAb drugs without cleavage of the glycan moieties. Complete glycan 1H/13C chemical shift assignments were obtained at 13C natural abundance from commercial standard glycans that allowed unambiguous determination of the chemical structure, glycosidic linkage position, and anomeric configuration of each monosaccharide in the major N-glycan scaffolds found in mAb molecules. The analysis of glycan anomeric peaks in two-dimensional (2D) 1H-13C NMR spectra yielded metrics for clinically important mAb quality attributes (i.e., galactosylation (Gal%) and fucosylation (Fuc%)), consistent with literature results using a standard glycan-mapping method. Therefore, the middle-down NMR method provided a facile orthogonal measurement for mAb glycosylation characterization with improved chemical information content on glycan structure determination and quantification, compared to standard approaches.
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Affiliation(s)
- Jiangnan Peng
- Division of Pharmaceutical Analysis, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Sharadrao M. Patil
- Division of Pharmaceutical Analysis, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - David A. Keire
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Kang Chen
- Division of Pharmaceutical Analysis, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
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Urakami H, Saeki M, Watanabe Y, Kawamura R, Nishizawa S, Suzuki Y, Watanabe A, Ajisaka K. Isolation and assessment of acidic and neutral oligosaccharides from goat milk and bovine colostrum for use as ingredients of infant formulae. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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In vitro ovicidal and larvicidal activities of some saponins and flavonoids against parasitic nematodes of goats. Parasitology 2018; 145:1884-1889. [PMID: 29781423 DOI: 10.1017/s0031182018000689] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This study assessed the anthelmintic activity of plant-derived compounds against gastrointestinal nematodes of goats using the egg hatch and larval motility assays. The compounds tested were saponins (digitonin and aescin) and their respective sapogenins (aglycones), hecogenin acetate and flavonoids (catechin, hesperidin, isocordoin and a mixture of isocordoin and cordoin). Additionally, cytotoxicity of active substances was analysed on Vero cell through 3-4,5-dimethylthiazol-2-yl,2,5diphenyltetrazolium bromide (MTT) and propidium iodide (PI) tests. Significant reduction on the egg hatching (P 90%). Nevertheless, higher cytotoxicity was observed in the MTT assay, with IC50 of 0.20 mg mL-1 (aescin) and 0.0074 mg mL-1 (digitonin). Aescin and digitonin have a pronounced in vitro anthelmintic effect and the glycone portion of these saponins plays an important role in this activity.
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15
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Satoh T, Kato K. Structural Aspects of ER Glycoprotein Quality-Control System Mediated by Glucose Tagging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1104:149-169. [PMID: 30484248 DOI: 10.1007/978-981-13-2158-0_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
N-linked oligosaccharides attached to proteins act as tags for glycoprotein quality control, ensuring their appropriate folding and trafficking in cells. Interactions with a variety of intracellular lectins determine glycoprotein fates. Monoglucosylated glycoforms are the hallmarks of incompletely folded glycoproteins in the protein quality-control system, in which glucosidase II and UDP-glucose/glycoprotein glucosyltransferase are, respectively, responsible for glucose trimming and attachment. In this review, we summarize a recently emerging view of the structural basis of the functional mechanisms of these key enzymes as well as substrate N-linked oligosaccharides exhibiting flexible structures, as revealed by applying a series of biophysical techniques including small-angle X-ray scattering, X-ray crystallography, high-speed atomic force microscopy , electron microscopy , and computational simulation in conjunction with NMR spectroscopy.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan. .,Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
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16
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VLIEGENTHART JFG. The complexity of glycoprotein-derived glycans. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:64-86. [PMID: 28190870 PMCID: PMC5422628 DOI: 10.2183/pjab.93.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 12/09/2016] [Indexed: 05/31/2023]
Abstract
A brief review is presented of our studies on the structure of glycoprotein-derived glycans. The emphasis is on the introduction of high-resolution 1H-NMR spectroscopy for the unambiguous determination of primary structures. For this purpose, we developed the structural reporter group concept. Structural reporters are defined as unique markers of structural elements in the NMR spectra. Application of this concept led to the discovery of numerous new structures. Furthermore, a number of structures presented in the literature could be corrected. The results are relevant for insight in the various steps in glycan metabolism in health and disease, for the function and mode of action of glycans in vivo and for the interpretation of structural information obtained through other techniques. The strength of the approach is further shown for several highly complex glycoproteins, carrying very heterogeneous and complicated glycans.
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18
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Le NPL, Bowden TA, Struwe WB, Crispin M. Immune recruitment or suppression by glycan engineering of endogenous and therapeutic antibodies. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1860:1655-68. [PMID: 27105835 PMCID: PMC4922387 DOI: 10.1016/j.bbagen.2016.04.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/15/2016] [Accepted: 04/16/2016] [Indexed: 12/20/2022]
Abstract
Human serum IgG contains multiple glycoforms which exhibit a range of binding properties to effector molecules such as cellular Fc receptors. Emerging knowledge of how the Fc glycans contribute to the antibody structure and effector functions has opened new avenues for the exploitation of defined antibody glycoforms in the treatment of diseases. Here, we review the structure and activity of antibody glycoforms and highlight developments in antibody glycoengineering by both the manipulation of the cellular glycosylation machinery and by chemoenzymatic synthesis. We discuss wide ranging applications of antibody glycoengineering in the treatment of cancer, autoimmunity and inflammation. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.
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Affiliation(s)
- Ngoc Phuong Lan Le
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Thomas A Bowden
- Division of Structural Biology, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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19
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Yamamoto S, Kinoshita M, Suzuki S. Current landscape of protein glycosylation analysis and recent progress toward a novel paradigm of glycoscience research. J Pharm Biomed Anal 2016; 130:273-300. [PMID: 27461579 DOI: 10.1016/j.jpba.2016.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 07/09/2016] [Accepted: 07/09/2016] [Indexed: 12/25/2022]
Abstract
This review covers the basics and some applications of methodologies for the analysis of glycoprotein glycans. Analytical techniques used for glycoprotein glycans, including liquid chromatography (LC), capillary electrophoresis (CE), mass spectrometry (MS), and high-throughput analytical methods based on microfluidics, were described to supply the essentials about biopharmaceutical and biomarker glycoproteins. We will also describe the MS analysis of glycoproteins and glycopeptides as well as the chemical and enzymatic releasing methods of glycans from glycoproteins and the chemical reactions used for the derivatization of glycans. We hope the techniques have accommodated most of the requests from glycoproteomics researchers.
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Affiliation(s)
- Sachio Yamamoto
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1, Kowakae, Higashi-osaka, Osaka, 577-8502, Japan.
| | - Mitsuhiro Kinoshita
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1, Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
| | - Shigeo Suzuki
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1, Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
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20
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Ribeiro JP, Diercks T, Jiménez-Barbero J, André S, Gabius HJ, Cañada FJ. Fluorinated Carbohydrates as Lectin Ligands: (19)F-Based Direct STD Monitoring for Detection of Anomeric Selectivity. Biomolecules 2015; 5:3177-92. [PMID: 26580665 PMCID: PMC4693274 DOI: 10.3390/biom5043177] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 12/29/2022] Open
Abstract
The characterization of the binding of reducing carbohydrates present as mixtures of anomers in solution to a sugar recepor (lectin) poses severe difficulties. In this situation, NMR spectroscopy enables the observation of signals for each anomer in the mixture by applying approaches based on ligand observation. Saturation transfer difference (STD) NMR allows fast and efficient screening of compound mixtures for reactivity to a receptor. Owing to the exceptionally favorable properties of 19F in NMR spectroscopy and the often complex 1H spectra of carbohydrates, 19F-containing sugars have the potential to be turned into versatile sensors for recognition. Extending the recently established 1H → 1H STDre19F-NMR technique, we here demonstrate its applicability to measure anomeric selectivity of binding in a model system using the plant lectin concanavalin A (ConA) and 2-deoxy-2-fluoro-d-mannose. Indeed, it is also possible to account for the mutual inhibition between the anomers on binding to the lectin by means of a kinetic model. The monitoring of 19F-NMR signal perturbation disclosed the relative activities of the anomers in solution and thus enabled the calculation of their binding affinity towards ConA. The obtained data show a preference for the α anomer that increases with temperature. This experimental approach can be extended to others systems of biomedical interest by testing human lectins with suitably tailored glycan derivatives.
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Affiliation(s)
- João P Ribeiro
- Centre de Recherches sur les Macromolécules Végétales, UPR5301, CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France.
| | - Tammo Diercks
- CIC bioGUNE, Bizkaia Technological Park, Building 800, 48160 Derio, Spain.
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technological Park, Building 800, 48160 Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
| | - Sabine André
- Institut für Physiologische Chemie, Tierärztliche Fakultät der Ludwig-Maximilians-Universität, Veterinärstr. 13, 80539 München, Germany.
| | - Hans-Joachim Gabius
- Institut für Physiologische Chemie, Tierärztliche Fakultät der Ludwig-Maximilians-Universität, Veterinärstr. 13, 80539 München, Germany.
| | - Francisco Javier Cañada
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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21
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Kong L, Torrents de la Peña A, Deller MC, Garces F, Sliepen K, Hua Y, Stanfield RL, Sanders RW, Wilson IA. Complete epitopes for vaccine design derived from a crystal structure of the broadly neutralizing antibodies PGT128 and 8ANC195 in complex with an HIV-1 Env trimer. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2099-108. [PMID: 26457433 PMCID: PMC4601371 DOI: 10.1107/s1399004715013917] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/22/2015] [Indexed: 03/31/2023]
Abstract
The HIV-1 envelope gp160 glycoprotein (Env) is a trimer of gp120 and gp41 heterodimers that mediates cell entry and is the primary target of the humoral immune response. Broadly neutralizing antibodies (bNAbs) to HIV-1 have revealed multiple epitopes or sites of vulnerability, but mapping of most of these sites is incomplete owing to a paucity of structural information on the full epitope in the context of the Env trimer. Here, a crystal structure of the soluble BG505 SOSIP gp140 trimer at 4.6 Å resolution with the bNAbs 8ANC195 and PGT128 reveals additional interactions in comparison to previous antibody-gp120 structures. For 8ANC195, in addition to previously documented interactions with gp120, a substantial interface with gp41 is now elucidated that includes extensive interactions with the N637 glycan. Surprisingly, removal of the N637 glycan did not impact 8ANC195 affinity, suggesting that the antibody has evolved to accommodate this glycan without loss of binding energy. PGT128 indirectly affects the N262 glycan by a domino effect, in which PGT128 binds to the N301 glycan, which in turn interacts with and repositions the N262 glycan, thereby illustrating the important role of neighboring glycans on epitope conformation and stability. Comparisons with other Env trimer and gp120 structures support an induced conformation for glycan N262, suggesting that the glycan shield is allosterically modified upon PGT128 binding. These complete epitopes of two broadly neutralizing antibodies on the Env trimer can now be exploited for HIV-1 vaccine design.
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Affiliation(s)
- Leopold Kong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery
- International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery
| | - Alba Torrents de la Peña
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Marc C. Deller
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Fernando Garces
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery
- International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery
| | - Kwinten Sliepen
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Yuanzi Hua
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery
- International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery
| | - Rogier W. Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery
- International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery
- Joint Center for Structural Genomics, http://www.jcsg.org
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
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22
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Emerging structural insights into glycoprotein quality control coupled with N-glycan processing in the endoplasmic reticulum. Molecules 2015; 20:2475-91. [PMID: 25647580 PMCID: PMC6272264 DOI: 10.3390/molecules20022475] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/04/2015] [Accepted: 01/22/2015] [Indexed: 01/22/2023] Open
Abstract
In the endoplasmic reticulum (ER), the sugar chain is initially introduced onto newly synthesized proteins as a triantennary tetradecasaccharide (Glc3Man9GlcNAc2). The attached oligosaccharide chain is subjected to stepwise trimming by the actions of specific glucosidases and mannosidases. In these processes, the transiently expressed N-glycans, as processing intermediates, function as signals for the determination of glycoprotein fates, i.e., folding, transport, or degradation through interactions of a series of intracellular lectins. The monoglucosylated glycoforms are hallmarks of incompletely folded states of glycoproteins in this system, whereas the outer mannose trimming leads to ER-associated glycoprotein degradation. This review outlines the recently emerging evidence regarding the molecular and structural basis of this glycoprotein quality control system, which is regulated through dynamic interplay among intracellular lectins, glycosidases, and glycosyltransferase. Structural snapshots of carbohydrate-lectin interactions have been provided at the atomic level using X-ray crystallographic analyses. Conformational ensembles of uncomplexed triantennary high-mannose-type oligosaccharides have been characterized in a quantitative manner using molecular dynamics simulation in conjunction with nuclear magnetic resonance spectroscopy. These complementary views provide new insights into glycoprotein recognition in quality control coupled with N-glycan processing.
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23
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Development of a 1 H NMR structural-reporter-group concept for the analysis of prebiotic galacto-oligosaccharides of the [β- d -Gal p -(1→ x )] n - d -Glc p type. Carbohydr Res 2014; 400:54-58. [DOI: 10.1016/j.carres.2014.08.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/11/2014] [Accepted: 08/13/2014] [Indexed: 11/15/2022]
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24
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Petersen BO, Lok F, Meier S. Probing the structural details of xylan degradation by real-time NMR spectroscopy. Carbohydr Polym 2014; 112:587-94. [DOI: 10.1016/j.carbpol.2014.06.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/10/2014] [Accepted: 06/13/2014] [Indexed: 10/25/2022]
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25
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Wiegandt A, Meyer B. Unambiguous Characterization of N-Glycans of Monoclonal Antibody Cetuximab by Integration of LC-MS/MS and 1H NMR Spectroscopy. Anal Chem 2014; 86:4807-14. [DOI: 10.1021/ac404043g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Alena Wiegandt
- Organic Chemistry, Department
of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Bernd Meyer
- Organic Chemistry, Department
of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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26
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van Leeuwen SS, Schoemaker RJW, Gerwig GJ, van Leusen-van Kan EJM, Dijkhuizen L, Kamerling JP. Rapid milk group classification by 1H NMR analysis of Le and H epitopes in human milk oligosaccharide donor samples. Glycobiology 2014; 24:728-39. [DOI: 10.1093/glycob/cwu036] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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27
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Aguiar TQ, Maaheimo H, Heiskanen A, Wiebe MG, Penttilä M, Domingues L. Characterization of the Ashbya gossypii secreted N-glycome and genomic insights into its N-glycosylation pathway. Carbohydr Res 2013; 381:19-27. [DOI: 10.1016/j.carres.2013.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/04/2013] [Accepted: 08/14/2013] [Indexed: 10/26/2022]
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28
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Likhosherstov LM, Novikova OS, Yamskov IA, Piskarev VE. Synthesis of N-glycyl-β-glycopyranosylamines, human milk fucooligosaccharide derivatives. Russ Chem Bull 2013. [DOI: 10.1007/s11172-012-0250-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Fellenberg M, Behnken HN, Nagel T, Wiegandt A, Baerenfaenger M, Meyer B. Glycan analysis: scope and limitations of different techniques--a case for integrated use of LC-MS(/MS) and NMR techniques. Anal Bioanal Chem 2013; 405:7291-305. [PMID: 23852147 DOI: 10.1007/s00216-013-7164-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 06/13/2013] [Accepted: 06/19/2013] [Indexed: 01/16/2023]
Abstract
The structure of glycans from glycoproteins is highly relevant for their function. We tightly integrate liquid chromatography-mass spectrometry (LC-MS), MS/MS, and nuclear magnetic resonance (NMR) data to achieve a complete characterization of even isobaric glycans differing in only one linkage position or in the substitution in one branch. As example, we analyzed ten desialylated underivatized glycans from bovine fibrinogen. The molecules were separated on a PGC column, and LC-MS data allowed an assignment of the compositions of the glycans. MS/MS data of the same glycans allowed elucidation of sequence and to some extent of branching and linkage. All MS/MS fragmentation methods led to multiple dissociations, resulting in several cases in ambiguous data. The MS/MS data were interpreted both by scientists and automatically by software, and the differential results are compared. Additional data from a tight integration of LC-MS and NMR data resulted in a complete structural characterization of the glycans. The acquisition of simple 1D (1)H NMR data led--in combination with LC-MS and MS/MS data--to an unambiguous assignment of the isobaric glycans. Compounds that were not separated in the chromatography could easily be assigned structurally by applying the 3D cross-correlation (3DCC) technology to arrive at NMR spectra of the pure components-without actually separating them. By applying LC-MS, MS/MS, 1D (1)H NMR, and 3DCC together, one can assign glycan structures from glycoconjugates with high confidence affording only 200 pmol of glycan material.
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Affiliation(s)
- Meike Fellenberg
- Organic Chemistry, Department of Chemistry, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
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30
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Yu X, Baruah K, Harvey D, Vasiljevic S, Alonzi DS, Song BD, Higgins M, Bowden TA, Scanlan CN, Crispin M. Engineering hydrophobic protein-carbohydrate interactions to fine-tune monoclonal antibodies. J Am Chem Soc 2013; 135:9723-32. [PMID: 23745692 PMCID: PMC3788586 DOI: 10.1021/ja4014375] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Indexed: 12/20/2022]
Abstract
Biologically active conformations of the IgG1 Fc homodimer are maintained by multiple hydrophobic interactions between the protein surface and the N-glycan. The Fc glycan modulates biological effector functions, including antibody-dependent cellular cytotoxicity (ADCC) which is mediated in part through the activatory Fc receptor, FcγRIIIA. Consistent with previous reports, we found that site-directed mutations disrupting the protein-carbohydrate interface (F241A, F243A, V262E, and V264E) increased galactosylation and sialylation of the Fc and, concomitantly, reduced the affinity for FcγRIIIA. We rationalized this effect by crystallographic analysis of the IgG1 Fc F241A mutant, determined here to a resolution of 1.9 Å, which revealed localized destabilization of this glycan-protein interface. Given that sialylation of Fc glycans decreases ADCC, one explanation for the effect of these mutants on FcγRIIIA binding is their increased sialylation. However, a glycan-engineered IgG1 with hypergalactosylated and hypersialylated glycans exhibited unchanged binding affinity to FcγRIIIA. Moreover, when we expressed these mutants as a chemically uniform (Man5GlcNAc2) glycoform, the individual effect of each mutation on FcγRIIIA affinity was preserved. This effect was broadly recapitulated for other Fc receptors (FcγRI, FcγRIIA, FcγRIIB, and FcγRIIIB). These data indicate that destabilization of the glycan-protein interactions, rather than increased galactosylation and sialylation, modifies the Fc conformation(s) relevant for FcγR binding. Engineering of the protein-carbohydrate interface thus provides an independent parameter in the engineering of Fc effector functions and a route to the synthesis of new classes of Fc domain with novel combinations of affinities for activatory and inhibitory Fc receptors.
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Affiliation(s)
- Xiaojie Yu
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1
3QU, United Kingdom
| | - Kavitha Baruah
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1
3QU, United Kingdom
| | - David
J. Harvey
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1
3QU, United Kingdom
| | - Snezana Vasiljevic
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1
3QU, United Kingdom
| | - Dominic S. Alonzi
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1
3QU, United Kingdom
| | - Byeong-Doo Song
- Scripps Korea Antibody
Institute, 192-1 Hyoja-dong, Chuncheon, Gangwon 200-701,
Korea
| | - Matthew
K. Higgins
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1
3QU, United Kingdom
| | - Thomas A. Bowden
- Division of Structural
Biology, University of Oxford, Wellcome
Trust Centre for Human
Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Christopher N. Scanlan
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1
3QU, United Kingdom
| | - Max Crispin
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1
3QU, United Kingdom
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31
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Johansen KT, Wubshet SG, Nyberg NT. HPLC-NMR revisited: using time-slice high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance with database-assisted dereplication. Anal Chem 2013; 85:3183-9. [PMID: 23432092 DOI: 10.1021/ac303455j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Time-based trapping of chromatographically separated compounds onto solid-phase extraction (SPE) cartridges and subsequent elution to NMR tubes was done to emulate the function of HPLC-NMR for dereplication purposes. Sufficient mass sensitivity was obtained by use of a state-of-the-art HPLC-SPE-NMR system with a cryogenically cooled probe head, designed for 1.7 mm NMR tubes. The resulting (1)H NMR spectra (600 MHz) were evaluated against a database of previously acquired and prepared spectra. The in-house-developed matching algorithm, based on partitioning of the spectra and allowing for changes in the chemical shifts, is described. Two mixtures of natural products were used to test the approach: an extract of Carthamus oxyacantha (wild safflower), containing an array of spiro compounds, and an extract of the endophytic fungus Penicillum namyslowski, containing griseofulvin and analogues. The database matching of the resulting spectra positively identified expected compounds, while the number of false positives was few and easily recognized.
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Affiliation(s)
- Kenneth T Johansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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32
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Nadanaka S, Zhou S, Kagiyama S, Shoji N, Sugahara K, Sugihara K, Asano M, Kitagawa H. EXTL2, a member of the EXT family of tumor suppressors, controls glycosaminoglycan biosynthesis in a xylose kinase-dependent manner. J Biol Chem 2013; 288:9321-33. [PMID: 23395820 DOI: 10.1074/jbc.m112.416909] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutant alleles of EXT1 or EXT2, two members of the EXT gene family, are causative agents in hereditary multiple exostoses, and their gene products function together as a polymerase in the biosynthesis of heparan sulfate. EXTL2, one of three EXT-like genes in the human genome that are homologous to EXT1 and EXT2, encodes a transferase that adds not only GlcNAc but also N-acetylgalactosamine to the glycosaminoglycan (GAG)-protein linkage region via an α1,4-linkage. However, both the role of EXTL2 in the biosynthesis of GAGs and the biological significance of EXTL2 remain unclear. Here we show that EXTL2 transfers a GlcNAc residue to the tetrasaccharide linkage region that is phosphorylated by a xylose kinase 1 (FAM20B) and thereby terminates chain elongation. We isolated an oligosaccharide from the mouse liver, which was not detected in EXTL2 knock-out mice. Based on structural analysis by a combination of glycosidase digestion and 500-MHz (1)H NMR spectroscopy, the oligosaccharide was found to be GlcNAcα1-4GlcUAβ1-3Galβ1-3Galβ1-4Xyl(2-O-phosphate), which was considered to be a biosynthetic intermediate of an immature GAG chain. Indeed, EXTL2 specifically transferred a GlcNAc residue to a phosphorylated linkage tetrasaccharide, GlcUAβ1-3Galβ1-3Galβ1-4Xyl(2-O-phosphate). Remarkably, the phosphorylated linkage pentasaccharide generated by EXTL2 was not used as an acceptor for heparan sulfate or chondroitin sulfate polymerases. Moreover, production of GAGs was significantly higher in EXTL2 knock-out mice than in wild-type mice. These results indicate that EXTL2 functions to suppress GAG biosynthesis that is enhanced by a xylose kinase and that the EXTL2-dependent mechanism that regulates GAG biosynthesis might be a "quality control system" for proteoglycans.
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Affiliation(s)
- Satomi Nadanaka
- Department of Biochemistry, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan
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33
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Kamiya Y, Yanagi K, Kitajima T, Yamaguchi T, Chiba Y, Kato K. Application of Metabolic 13C Labeling in Conjunction with High-Field Nuclear Magnetic Resonance Spectroscopy for Comparative Conformational Analysis of High Mannose-Type Oligosaccharides. Biomolecules 2013; 3:108-23. [PMID: 24970159 PMCID: PMC4030882 DOI: 10.3390/biom3010108] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/10/2013] [Accepted: 01/15/2013] [Indexed: 11/30/2022] Open
Abstract
High mannose-type oligosaccharides are enzymatically trimmed in the endoplasmic reticulum, resulting in various processing intermediates with exposed glycotopes that are recognized by a series of lectins involved in glycoprotein fate determination in cells. Although recent crystallographic data have provided the structural basis for the carbohydrate recognition of intracellular lectins, atomic information of dynamic oligosaccharide conformations is essential for a quantitative understanding of the energetics of carbohydrate–lectin interactions. Carbohydrate NMR spectroscopy is useful for characterizing such conformational dynamics, but often hampered by poor spectral resolution and lack of recombinant techniques required to produce homogeneous glycoforms. To overcome these difficulties, we have recently developed a methodology for the preparation of a homogeneous high mannose-type oligosaccharide with 13C labeling using a genetically engineered yeast strain. We herein successfully extended this method to result in the overexpression of 13C-labeled Man9GlcNAc2 (M9) with a newly engineered yeast strain with the deletion of four genes involved in N-glycan processing. This enabled high-field NMR analyses of 13C-labeled M9 in comparison with its processing product lacking the terminal mannose residue ManD2. Long-range NOE data indicated that the outer branches interact with the core in both glycoforms, and such foldback conformations are enhanced upon the removal of ManD2. The observed conformational variabilities might be significantly associated with lectins and glycan-trimming enzymes.
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Affiliation(s)
- Yukiko Kamiya
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaiji, Okazaki 444-8787, Japan.
| | - Kotaro Yanagi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaiji, Okazaki 444-8787, Japan.
| | - Toshihiko Kitajima
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaiji, Okazaki 444-8787, Japan.
| | - Yasunori Chiba
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaiji, Okazaki 444-8787, Japan.
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van Leeuwen SS, Schoemaker RJW, Timmer CJAM, Kamerling JP, Dijkhuizen L. N- and o-glycosylation of a commercial bovine whey protein product. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:12553-12564. [PMID: 23194161 DOI: 10.1021/jf304000b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bovine whey protein products are used as a base ingredient in infant formulas to optimize the amino acid pattern to a more human-like composition. Although the protein composition of bovine milk has been studied in detail, glycosylation details of commercial whey protein products are missing. To this end, both the N- and O-glycans of such a protein concentrate were sequentially released, the N-glycans enzymatically and the O-glycans chemically (reducing and nonreducing conditions). For the structural analysis of the N- and O-glycans a combination of MALDI-TOF-MS, one-dimensional (1)H NMR spectroscopy, Wisteria floribunda agglutinin affinity chromatography, HPAEC-PAD profiling, and HPLC-FD profiling (2-aminobenzamide derivatives), together with exoglycosidase treatments, were used. A mixture of over 60 N-glycans and 10 O-glycans was characterized, giving a detailed insight into the glycosylation of a bovine whey protein product, Deminal 90, which is applied as an ingredient for infant formulas.
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Affiliation(s)
- Sander S van Leeuwen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen , Nijenborgh 7, NL-9747 AG Groningen, The Netherlands
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35
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Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
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36
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Bowden TA, Baruah K, Coles CH, Harvey DJ, Yu X, Song BD, Stuart DI, Aricescu AR, Scanlan CN, Jones EY, Crispin M. Chemical and structural analysis of an antibody folding intermediate trapped during glycan biosynthesis. J Am Chem Soc 2012; 134:17554-63. [PMID: 23025485 PMCID: PMC3593610 DOI: 10.1021/ja306068g] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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Human IgG Fc glycosylation modulates immunological effector
functions
such as antibody-dependent cellular cytotoxicity and phagocytosis.
Engineering of Fc glycans therefore enables fine-tuning of the therapeutic
properties of monoclonal antibodies. The N-linked glycans of Fc are
typically complex-type, forming a network of noncovalent interactions
along the protein surface of the Cγ2 domain. Here, we manipulate
the mammalian glycan-processing pathway to trap IgG1 Fc at sequential
stages of maturation, from oligomannose- to hybrid- to complex-type
glycans, and show that the Fc is structurally stabilized following
the transition of glycans from their hybrid- to complex-type state.
X-ray crystallographic analysis of this hybrid-type intermediate reveals
that N-linked glycans undergo conformational changes upon maturation,
including a flip within the trimannosyl core. Our crystal structure
of this intermediate reveals a molecular basis for antibody biogenesis
and provides a template for the structure-guided engineering of the
protein–glycan interface of therapeutic antibodies.
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Affiliation(s)
- Thomas A Bowden
- Division of Structural Biology, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.
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Kubota Y, Hori H, Sawa R, Seki H, Uzawa J. Structural analyses of mannose pentasaccharide of high mannose type oligosaccharides by 1D and 2D NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:659-664. [PMID: 22930529 DOI: 10.1002/mrc.3859] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 07/09/2012] [Accepted: 07/17/2012] [Indexed: 06/01/2023]
Abstract
NMR spectroscopy is a very important and useful method for the structural analysis of oligosaccharides, despite its low sensitivity. We first applied conventional measuring methods, 2D DQF COSY, (1)H-(13)C HSQC, and (1)H-(13)C HMBC, and also the Double Pulsed Field Gradient Spin Echo (DPFGSE)-TOCSY and DPFGSE-NOESY/ROESY techniques to analyze a branched mannose pentasaccharide as a model of high mannose type N-glycans in natural abundance. The NMR spectra of the model compound are very complex and difficult to analyze owing to overlapping signals. The superior selective irradiation capability of the DPFGSE technique is useful for fine structural and conformational analyses of such complex oligosaccharides. We here introduce a novel technique called DPFGSE-Double-Selective Population Transfer (SPT)-Difference and DPFGSE-NOE/ROE-SPT-Difference spectroscopy. The DPFGSE-Double-SPT-Difference method involves irradiation of two peaks from one proton and the subtraction of higher and lower peaks from each spectrum. The DPFGSE-NOE/ROE-SPT-Difference method involves the transfer of the magnetization polarized by NOE/ROE from the nuclei to the spin-coupled nuclei through scalar spin-spin interaction using the SPT method. Even if the signals in the NMR spectra overlap, each signal can be accurately assigned. In particular, DPFGSE-NOE/ROE-SPT-Difference is very useful for identifying sugar connectivity.
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Affiliation(s)
- Yumiko Kubota
- Institute of Microbial Chemistry, Tokyo, Shinagawa, Tokyo, Japan
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38
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Mizumoto S, Murakoshi S, Kalayanamitra K, Deepa SS, Fukui S, Kongtawelert P, Yamada S, Sugahara K. Highly sulfated hexasaccharide sequences isolated from chondroitin sulfate of shark fin cartilage: insights into the sugar sequences with bioactivities. Glycobiology 2012; 23:155-68. [PMID: 23019154 DOI: 10.1093/glycob/cws137] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Chondroitin sulfate (CS) chains regulate the development of the central nervous system in vertebrates and are linear polysaccharides consisting of variously sulfated repeating disaccharides, [-4GlcUAβ1-3GalNAcβ1-](n), where GlcUA and GalNAc represent D-glucuronic acid and N-acetyl-D-galactosamine, respectively. CS chains containing D-disaccharide units [GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate)] are involved in the development of cerebellar Purkinje cells and neurite outgrowth-promoting activity through interaction with a neurotrophic factor, pleiotrophin, resulting in the regulation of signaling. In this study, to obtain further structural information on the CS chains containing d-disaccharide units involved in brain development, oligosaccharides containing D-units were isolated from a shark fin cartilage. Seven novel hexasaccharide sequences, ΔO-D-D, ΔA-D-D, ΔC-D-D, ΔE-A-D, ΔD-D-C, ΔE-D-D and ΔA-B-D, in addition to three previously reported sequences, ΔC-A-D, ΔC-D-C and ΔA-D-A, were isolated from a CS preparation of shark fin cartilage after exhaustive digestion with chondroitinase AC-I, which cannot act on the galactosaminidic linkages bound to D-units. The symbol Δ stands for a 4,5-unsaturated bond of uronic acids, whereas A, B, C, D, E and O represent [GlcUA-GalNAc(4-O-sulfate)], [GlcUA(2-O-sulfate)-GalNAc(4-O-sulfate)], [GlcUA-GalNAc(6-O-sulfate)], [GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate)], [GlcUA-GalNAc(4-O-, 6-O-sulfate)] and [GlcUA-GalNAc], respectively. In binding studies using an anti-CS monoclonal antibody, MO-225, the epitopes of which are involved in cerebellar development in mammals, novel epitope structures, ΔA-D-A, ΔA-D-D and ΔA-B-D, were revealed. Hexasaccharides containing two consecutive D-units or a B-unit will be useful for the structural and functional analyses of CS chains particularly in the neuroglycobiological fields.
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Affiliation(s)
- Shuji Mizumoto
- Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
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39
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Resolving the problem of chromatographic overlap by 3D cross correlation (3DCC) processing of LC, MS and NMR data for characterization of complex glycan mixtures. Anal Bioanal Chem 2012; 404:1427-37. [DOI: 10.1007/s00216-012-6241-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 06/26/2012] [Accepted: 06/29/2012] [Indexed: 12/18/2022]
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40
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Kamiya Y, Satoh T, Kato K. Molecular and structural basis for N-glycan-dependent determination of glycoprotein fates in cells. Biochim Biophys Acta Gen Subj 2012; 1820:1327-37. [PMID: 22240168 DOI: 10.1016/j.bbagen.2011.12.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 12/27/2011] [Accepted: 12/27/2011] [Indexed: 11/18/2022]
Abstract
BACKGROUND N-linked oligosaccharides operate as tags for protein quality control, consigning glycoproteins to different fates, i.e. folding in the endoplasmic reticulum (ER), vesicular transport between the ER and the Golgi complex, and ER-associated degradation of glycoproteins, by interacting with a panel of intracellular lectins in the early secretory pathway. SCOPE OF REVIEW This review summarizes the current state of knowledge regarding the molecular and structural basis for glycoprotein-fate determination in cells that is achieved through the actions of the intracellular lectins and its partner proteins. MAJOR CONCLUSIONS Cumulative frontal affinity chromatography (FAC) data demonstrated that the intracellular lectins exhibit distinct sugar-binding specificity profiles. The glycotopes recognized by these lectins as fate determinants are embedded in the triantennary structures of the high-mannose-type oligosaccharides and are exposed upon trimming of the outer glucose and mannose residues during the N-glycan processing pathway. Furthermore, recently emerged 3D structural data offer mechanistic insights into functional interplay between an intracellular lectin and its binding partner in the early secretory pathway. GENERAL SIGNIFICANCE Structural biology approaches in conjunction with FAC methods provide atomic pictures of the mechanisms behind the glycoprotein-fate determination in cells. This article is a part of a Special issue entitled: Glycoproteomics.
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Affiliation(s)
- Yukiko Kamiya
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
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41
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Suzuki K, Matsuo I, Isomura M, Ajisaka K. CHEMOENZYMATIC SYNTHESIS OF NeuAcα-(2→3)-Galβ-(1→3)-[NeuAcα-(2→6)]-GalNAcα1- O-(Z)-Serine (N-PROTECTED MUC II OLIGOSACCHARIDE–SERINE). J Carbohydr Chem 2011. [DOI: 10.1081/car-120003741] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Katsuhiko Suzuki
- a Department of Enviromental Science , Faculty of Science and Engineering , Iwaki Meisei University , 5-5-1 Iino, Chuohdai, Iwaki, Fukushima, 970-8551, Japan
| | - Ichiro Matsuo
- b Nutrition Research Institute , Meiji Milk Products Co., Ltd. , 540 Naruda, Odawara, Kanagawa, 250-0862, Japan
| | - Megumi Isomura
- b Nutrition Research Institute , Meiji Milk Products Co., Ltd. , 540 Naruda, Odawara, Kanagawa, 250-0862, Japan
| | - Katsumi Ajisaka
- b Nutrition Research Institute , Meiji Milk Products Co., Ltd. , 540 Naruda, Odawara, Kanagawa, 250-0862, Japan
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42
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Harvey DJ, Merry AH, Royle L, Campbell MP, Rudd PM. Symbol nomenclature for representing glycan structures: Extension to cover different carbohydrate types. Proteomics 2011; 11:4291-5. [PMID: 21954138 DOI: 10.1002/pmic.201100300] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/08/2011] [Accepted: 08/10/2011] [Indexed: 11/10/2022]
Abstract
This Viewpoint article addresses comments made on our original article describing a symbolic system for the depiction of N- and O-linked carbohydrate structures and proposes a method for extending the symbol set to include monosaccharides commonly found in carbohydrates present in bacteria and plants. As before, basic monosaccharides are shown by shape with one or more additions such as solid fill or additions of lines, crosses or dots to represent functional groups. The use of colour to differentiate constituent monosaccharides is avoided, thus enabling the system to be used in a variety of formats. Linkage and anomericity are shown by the angle and type of line connecting the symbols. In this extended version, new symbols are proposed for additional hexoses and it is proposed that pyranose and furanose forms of the monosaccharides could be shown by solid or broken outlines to the symbols. Conventions for depicting the presence of multiple functional groups such as deoxy-(NH(2))(2) are also discussed. It is hoped that these proposals will stimulate discussion so that a consensus can be reached as to how the glycobiology community can best convey complex information in a simple manner.
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Affiliation(s)
- David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX, UK.
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43
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Serna S, Yan S, Martin-Lomas M, Wilson IBH, Reichardt NC. Fucosyltransferases as Synthetic Tools: Glycan Array Based Substrate Selection and Core Fucosylation of Synthetic N-Glycans. J Am Chem Soc 2011; 133:16495-502. [DOI: 10.1021/ja205392z] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sonia Serna
- Biofunctional Nanomaterials Unit, CICbiomaGUNE, Paseo Miramon 182, 20009 San Sebastian, Spain
| | - Shi Yan
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, A-1190 Vienna, Austria
| | - Manuel Martin-Lomas
- Biofunctional Nanomaterials Unit, CICbiomaGUNE, Paseo Miramon 182, 20009 San Sebastian, Spain
- CIBER-BBN, Paseo Miramon 182, 20009 San Sebastian, Spain
| | - Iain B. H. Wilson
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, A-1190 Vienna, Austria
| | - Niels-Christian Reichardt
- Biofunctional Nanomaterials Unit, CICbiomaGUNE, Paseo Miramon 182, 20009 San Sebastian, Spain
- CIBER-BBN, Paseo Miramon 182, 20009 San Sebastian, Spain
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44
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Roslund MU, Säwén E, Landström J, Rönnols J, Jonsson KM, Lundborg M, Svensson MV, Widmalm G. Complete 1H and 13C NMR chemical shift assignments of mono-, di-, and trisaccharides as basis for NMR chemical shift predictions of polysaccharides using the computer program casper. Carbohydr Res 2011; 346:1311-9. [DOI: 10.1016/j.carres.2011.04.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 04/14/2011] [Accepted: 04/25/2011] [Indexed: 11/29/2022]
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45
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Bond AE, Row PE, Dudley E. Post-translation modification of proteins; methodologies and applications in plant sciences. PHYTOCHEMISTRY 2011; 72:975-96. [PMID: 21353264 DOI: 10.1016/j.phytochem.2011.01.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 10/21/2010] [Accepted: 01/21/2011] [Indexed: 05/03/2023]
Abstract
Proteins have the potential to undergo a variety of post-translational modifications and the different methods available to study these cellular processes has advanced rapidly with the continuing development of proteomic technologies. In this review we aim to detail five major post-translational modifications (phosphorylation, glycosylaion, lipid modification, ubiquitination and redox-related modifications), elaborate on the techniques that have been developed for their analysis and briefly discuss the study of these modifications in selected areas of plant science.
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Affiliation(s)
- A E Bond
- Biochemistry Group, College of Medicine, Swansea University, Swansea, UK
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46
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Pereira F. Prediction of the anomeric configuration, type of linkage, and residues in disaccharides from 1D 13C NMR data. Carbohydr Res 2011; 346:960-72. [DOI: 10.1016/j.carres.2011.02.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 02/12/2011] [Accepted: 02/16/2011] [Indexed: 11/28/2022]
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47
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Dallas DC, Martin WF, Strum JS, Zivkovic AM, Smilowitz JT, Underwood MA, Affolter M, Lebrilla CB, German JB. N-linked glycan profiling of mature human milk by high-performance microfluidic chip liquid chromatography time-of-flight tandem mass spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:4255-63. [PMID: 21384928 PMCID: PMC4422756 DOI: 10.1021/jf104681p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
N-Linked glycans of skim human milk proteins were determined for three mothers. N-Linked glycans are linked to immune defense, cell growth, and cell-cell adhesion, but their functions in human milk are undetermined. Protein-bound N-linked glycans were released with peptidyl N-glycosidase F (PNGase F), enriched by graphitized carbon chromatography, and analyzed with Chip-TOF MS. To be defined as N-glycans, compounds were required, in all three procedural replicates, to match, within 6 ppm, against a theoretical human N-glycan library and be at least 2-fold higher in abundance in PNGase F-treated than in control samples. Fifty-two N-linked glycan compositions were identified, and 24 were confirmed via tandem mass spectra analysis. Twenty-seven compositions have been found previously in human milk, and 25 are novel compositions. By abundance, 84% of N-glycans were fucosylated and 47% were sialylated. The majority (70%) of total N-glycan abundance was composed of N-glycans found in all three milk samples.
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Affiliation(s)
- David C. Dallas
- Department of Food Science, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - William F. Martin
- Department of Food Science, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - John S. Strum
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Angela M. Zivkovic
- Department of Food Science, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Jennifer T. Smilowitz
- Department of Food Science, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Mark A. Underwood
- Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Department of Pediatrics, University of California Davis, 2315 Stockton Blvd., Sacramento, CA, 95817, USA
| | - Michael Affolter
- Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - J. Bruce German
- Department of Food Science, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
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48
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Irague R, Massou S, Moulis C, Saurel O, Milon A, Monsan P, Remaud-Siméon M, Portais JC, Potocki-Véronèse G. NMR-based structural glycomics for high-throughput screening of carbohydrate-active enzyme specificity. Anal Chem 2011; 83:1202-6. [PMID: 21271685 DOI: 10.1021/ac1032148] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here the development of a straightforward, sensitive, and quantitative NMR-based method for high-throughput characterization of carbohydrate structure and screening of carbohydrate active enzyme (CAZyme) specificity. Automated assays starting from gene library expression to carbohydrate structure determination directly from crude reaction media have been established and successfully used to screen a library of 4032 CAZymes obtained by combinatorial engineering, at a rate of 480 enzyme variants per day. This allowed one to accurately discriminate 303 enzyme variants with altered specificity. The results demonstrate the potential of high-throughput NMR technology in glycomics, to mine artificial and natural enzyme diversity for novel biocatalysts.
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49
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NMR analysis demonstrates immunoglobulin G N-glycans are accessible and dynamic. Nat Chem Biol 2011; 7:147-53. [PMID: 21258329 PMCID: PMC3074608 DOI: 10.1038/nchembio.511] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 08/04/2010] [Indexed: 11/08/2022]
Abstract
The N-glycan at Asn297 of the immunoglobulin G Fc fragment modulates cellular responses of the adaptive immune system. However, the underlying mechanism remains undefined, as existing structural data suggest the glycan does not directly engage cell surface receptors. Here we characterize the dynamics of the glycan termini using solution NMR spectroscopy. Contrary to previous conclusions based on X-ray crystallography and limited NMR data, our spin relaxation studies indicate that the termini of both glycan branches are highly dynamic and experience considerable motion in addition to tumbling of the Fc molecule. Relaxation dispersion and temperature-dependent chemical shift perturbations demonstrate exchange of the α1-6Man-linked branch between a protein-bound and a previously unobserved unbound state, suggesting the glycan samples conformational states that can be accessed by glycan-modifying enzymes and possibly glycan recognition domains. These findings suggest a role for Fc-glycan dynamics in Fc-receptor interactions and enzymatic glycan remodeling.
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50
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Liu C, Richards MR, Lowary TL. Synthesis and NMR spectroscopic analysis of acylated pentasaccharide fragments of mycobacterial arabinogalactan. Org Biomol Chem 2011; 9:165-76. [DOI: 10.1039/c0ob00423e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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