1
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Jia Y, Liu Y, Wang Y, Li J, Li G. Sialylation-induced stabilization of dynamic glycoprotein conformations unveiled by time-aligned parallel unfolding and glycan release mass spectrometry. Chem Sci 2024:d4sc03672g. [PMID: 39165727 PMCID: PMC11331314 DOI: 10.1039/d4sc03672g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 08/09/2024] [Indexed: 08/22/2024] Open
Abstract
Sialylation, a critical post-translational modification, regulates glycoprotein structure and function by tuning their molecular heterogeneity. However, characterizing its subtle and dynamic conformational effects at the intact glycoprotein level remains challenging. We introduce a glycoform-resolved unfolding approach based on a high-throughput ion mobility-mass spectrometry (IM-MS) platform. This method integrates high-throughput unfolding with parallel fragmentation, enabling simultaneous analysis of sialylation patterns, stoichiometries, and their impact on conformational stability. Applying this approach to fetuin, we identified distinct sialylation patterns and their differential influence on protein conformation, namely sialylation-induced stabilization during early unfolding and increased flexibility in later unfolding stages. IM-MS-guided molecular dynamics simulations revealed that increased sialylation enhances the initial conformational stability, likely through enhanced electrostatic interactions and hydrogen bonding. These findings highlight the complex interplay between sialylation and protein dynamics and establish glycoform-resolved unfolding IM-MS as a powerful tool for characterizing glycoprotein conformational landscapes.
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Affiliation(s)
- Yifei Jia
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
| | - Yichang Liu
- School of Pharmacy, Nantong University Nantong 226001 Jiangsu China
| | - Yamei Wang
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
| | - Jinyu Li
- College of Chemistry, Fuzhou University Fuzhou 350108 Fujian China
| | - Gongyu Li
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
- Haihe Laboratory of Sustainable Chemical Transformations Tianjin 300192 China
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2
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Nguan HS, Chen JL, Ni CK. Collision-Induced Dissociation of Fucose and Identification of Anomericity. J Phys Chem A 2024; 128:3812-3820. [PMID: 38690855 PMCID: PMC11103703 DOI: 10.1021/acs.jpca.4c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Structural determination of carbohydrates using mass spectrometry remains challenging, particularly, the differentiation of anomeric configurations. In this work, we studied the collision-induced dissociation (CID) mechanisms of sodiated α- and β-l-fucose using an experimental method and quantum chemistry calculations. The calculations show that α-l-fucose is more likely to undergo dehydration due to the fact that O1 and O2 are on the same side of the sugar ring. In contrast, β-l-fucose is more prone to the ring-opening reaction because more OH groups are on the same side of the sugar ring as O1. These differences suggest a higher preference for the dehydration reaction in sodiated α-l-fucose but a lower preference for ring-opening compared to that of β-l-fucose. The calculation results, which are used to assign the CID mass spectra of α- and β-l-fucose separated by high-performance liquid chromatography, are supported by the fucose produced from the CID of disaccharides Fuc-β-(1 → 3)-GlcNAc and Fuc-α-(1 → 4)-GlcNAc. This study demonstrates that the correlation of cis- and trans-configurations of O1 and O2 to the relative branching ratios of dehydration and cross-ring dissociation in CID, observed in aldohexose and ketohexose in the pyranose form, can be extended to deoxyhexoses for anomericity determination.
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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
| | - Jien-Lian Chen
- Institute
of Atomic and Molecular Sciences, Academia
Sinica, P.O. Box 23-166, 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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3
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Wojtkiewicz M, Subramanian SP, Gundry RL. Multinozzle Emitter for Improved Negative Mode Analysis of Reduced Native N-Glycans by Microflow Porous Graphitized Carbon Liquid Chromatography Mass Spectrometry. Anal Chem 2024; 96:5746-5751. [PMID: 38556995 PMCID: PMC11024887 DOI: 10.1021/acs.analchem.3c03649] [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: 08/15/2023] [Revised: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Microflow porous graphitized carbon liquid chromatography (PGC-LC) combined with negative mode ionization mass spectrometry (MS) provides high resolution separation and identification of reduced native N-glycan structural isomers. However, insufficient spray quality and low ionization efficiency of N-glycans present challenges for negative mode electrospray. Here, we evaluated the performance of a recently developed multinozzle electrospray source (MnESI) and accompanying M3 emitter for microflow PGC-LC-MS analysis of N-glycans in negative mode. In comparison to a standard electrospray ionization source, the MnESI with an M3 emitter improves signal intensity, identification, quantification, and resolution of structural isomers to accommodate low-input samples.
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Affiliation(s)
- Melinda Wojtkiewicz
- CardiOmics
Program, Center for Heart and Vascular Research, and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Sabarinath Peruvemba Subramanian
- CardiOmics
Program, Center for Heart and Vascular Research, and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L. Gundry
- CardiOmics
Program, Center for Heart and Vascular Research, and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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4
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Bechtella L, Chunsheng J, Fentker K, Ertürk GR, Safferthal M, Polewski Ł, Götze M, Graeber SY, Vos GM, Struwe WB, Mall MA, Mertins P, Karlsson NG, Pagel K. Ion mobility-tandem mass spectrometry of mucin-type O-glycans. Nat Commun 2024; 15:2611. [PMID: 38521783 PMCID: PMC10960840 DOI: 10.1038/s41467-024-46825-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
The dense O-glycosylation of mucins plays an important role in the defensive properties of the mucus hydrogel. Aberrant glycosylation is often correlated with inflammation and pathology such as COPD, cancer, and Crohn's disease. The inherent complexity of glycans and the diversity in the O-core structure constitute fundamental challenges for the analysis of mucin-type O-glycans. Due to coexistence of multiple isomers, multidimensional workflows such as LC-MS are required. To separate the highly polar carbohydrates, porous graphitized carbon is often used as a stationary phase. However, LC-MS workflows are time-consuming and lack reproducibility. Here we present a rapid alternative for separating and identifying O-glycans released from mucins based on trapped ion mobility mass spectrometry. Compared to established LC-MS, the acquisition time is reduced from an hour to two minutes. To test the validity, the developed workflow was applied to sputum samples from cystic fibrosis patients to map O-glycosylation features associated with disease.
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Affiliation(s)
- Leïla Bechtella
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Jin Chunsheng
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kerstin Fentker
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Güney R Ertürk
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
| | - Marc Safferthal
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Łukasz Polewski
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Michael Götze
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Simon Y Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), associated partner site, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gaël M Vos
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Weston B Struwe
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Marcus A Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), associated partner site, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Berlin Institute of Health, 10178, Berlin, Germany
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany.
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5
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Liew CY, Chen JL, Lin YT, Luo HS, Hung AT, Magoling BJA, Nguan HS, Lai CPK, Ni CK. Chromatograms and Mass Spectra of High-Mannose and Paucimannose N-Glycans for Rapid Isomeric Identifications. J Proteome Res 2024; 23:939-955. [PMID: 38364797 PMCID: PMC10913092 DOI: 10.1021/acs.jproteome.3c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/18/2024]
Abstract
N-Linked glycosylation is one of the most essential post-translational modifications of proteins. However, N-glycan structural determination remains challenging because of the small differences in structures between isomers. In this study, we constructed a database containing collision-induced dissociation MSn mass spectra and chromatograms of high-performance liquid chromatography for the rapid identification of high-mannose and paucimannose N-glycan isomers. These N-glycans include isomers by breaking of arbitrary numbers of glycosidic bonds at arbitrary positions of canonical Man9GlcNAc2 N-glycans. In addition, some GlcMannGlcNAc2 N-glycan isomers were included in the database. This database is particularly useful for the identification of the N-glycans not in conventional N-glycan standards. This study demonstrated the application of the database to structural assignment for high-mannose N-glycans extracted from bovine whey proteins, soybean proteins, human mammary epithelial cells, and human breast carcinoma cells. We found many N-glycans that are not expected to be generated by conventional biosynthetic pathways of multicellular eukaryotes.
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Affiliation(s)
- Chia Yen Liew
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- International
Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei 106216, Taiwan
- Molecular
Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 106216, Taiwan
| | - Jien-Lian Chen
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Yen-Ting Lin
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Hong-Sheng Luo
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Taiwan Normal University, Taipei 116059, Taiwan
| | - An-Ti Hung
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Bryan John Abel Magoling
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Institute
of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106216, Taiwan
- Chemical
Biology and Molecular Biophysics Program, Taiwan International Graduate
Program, Academia Sinica, Taipei 115201, Taiwan
| | - Hock-Seng Nguan
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Charles Pin-Kuang Lai
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Chemical
Biology and Molecular Biophysics Program, Taiwan International Graduate
Program, Academia Sinica, Taipei 115201, Taiwan
- Genome
and Systems Biology Degree Program, National
Taiwan University and Academia Sinica, Taipei 106216, Taiwan
| | - Chi-Kung Ni
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Molecular
Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
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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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Marie AL, Ray S, Ivanov AR. Highly-sensitive label-free deep profiling of N-glycans released from biomedically-relevant samples. Nat Commun 2023; 14:1618. [PMID: 36959283 PMCID: PMC10036494 DOI: 10.1038/s41467-023-37365-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 03/13/2023] [Indexed: 03/25/2023] Open
Abstract
Alterations of protein glycosylation can serve as sensitive and specific disease biomarkers. Labeling procedures for improved separation and detectability of oligosaccharides have several drawbacks, including incomplete derivatization, side-products, noticeable desialylation/defucosylation, sample loss, and interference with downstream analyses. Here, we develop a label-free workflow based on high sensitivity capillary zone electrophoresis-mass spectrometry (CZE-MS) for profiling of native underivatized released N-glycans. Our workflow provides a >45-fold increase in signal intensity compared to the conventional CZE-MS approaches used for N-glycan analysis. Qualitative and quantitative N-glycan profiling of purified human serum IgG, bovine serum fetuin, bovine pancreas ribonuclease B, blood-derived extracellular vesicle isolates, and total plasma results in the detection of >250, >400, >150, >310, and >520 N-glycans, respectively, using injected amounts equivalent to <25 ng of model protein and nL-levels of plasma-derived samples. Compared to reported results for biological samples of similar amounts and complexity, the number of identified N-glycans is increased up to ~15-fold, enabling highly sensitive analysis of sample amounts as low as sub-0.2 nL of plasma volume equivalents. Furthermore, highly sialylated N-glycans are identified and structurally characterized, and untreated sialic acid-linkage isomers are resolved in a single CZE-MS analysis.
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Affiliation(s)
- Anne-Lise Marie
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Somak Ray
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA.
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8
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McDowell CT, Lu X, Mehta AS, Angel PM, Drake RR. Applications and continued evolution of glycan imaging mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:674-705. [PMID: 34392557 PMCID: PMC8946722 DOI: 10.1002/mas.21725] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/16/2021] [Accepted: 08/03/2021] [Indexed: 05/03/2023]
Abstract
Glycosylation is an important posttranslational modifier of proteins and lipid conjugates critical for the stability and function of these macromolecules. Particularly important are N-linked glycans attached to asparagine residues in proteins. N-glycans have well-defined roles in protein folding, cellular trafficking and signal transduction, and alterations to them are implicated in a variety of diseases. However, the non-template driven biosynthesis of these N-glycans leads to significant structural diversity, making it challenging to identify the most biologically and clinically relevant species using conventional analyses. Advances in mass spectrometry instrumentation and data acquisition, as well as in enzymatic and chemical sample preparation strategies, have positioned mass spectrometry approaches as powerful analytical tools for the characterization of glycosylation in health and disease. Imaging mass spectrometry expands upon these strategies by capturing the spatial component of a glycan's distribution in-situ, lending additional insight into the organization and function of these molecules. Herein we review the ongoing evolution of glycan imaging mass spectrometry beginning with widely adopted tissue imaging approaches and expanding to other matrices and sample types with potential research and clinical implications. Adaptations of these techniques, along with their applications to various states of disease, are discussed. Collectively, glycan imaging mass spectrometry analyses broaden our understanding of the biological and clinical relevance of N-glycosylation to human disease.
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Affiliation(s)
- Colin T. McDowell
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Xiaowei Lu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
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9
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Phan HT, Tsou PK, Hsu PJ, Kuo JL. A first-principles exploration of the conformational space of sodiated pyranose assisted by neural network potentials. Phys Chem Chem Phys 2023; 25:5817-5826. [PMID: 36745400 DOI: 10.1039/d2cp04411k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Sampling the conformational space of monosaccharides using the first-principles methods is important and as a database of local minima provides a solid base for interpreting experimental measurements such as infrared photo-dissociation (IRPD) spectroscopy or collision-induced dissociation (CID). IRPD emphasizes low-energy conformers and CID can distinguish conformers with distinct reaction pathways. A typical computational approach is to engage empirical or semi-empirical methods to sample the conformational space first, and only selected minima are reoptimized at first-principles levels. In this work, we propose a computational scheme to explore the configurational space of 12 types of sodiated pyranoses with the assistance of a neural network potential (NNP). We demonstrated that it is possible to train an NNP based on the density functional calculations extracted from a previous study on sodiated glucose (Glc), galactose (Gal), and mannose (Man). This NNP yields a better description of the other five types of aldohexoses than the four types of ketohexoses. We further show that such a discrepancy in the accuracy of NNP can be resolved by an active learning scheme where the NNP model is engaged in generating the data and has itself updated. Through this iterative process, we can locate more than 17 000 distinct local minima at the B3LYP/6-311+G(d,p) level and an NNP with an accuracy of 1 kJ mol-1 was created, which can be used for further studies.
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Affiliation(s)
- Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Pei-Kang Tsou
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.,International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
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10
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Nguan HS, Ni CK. Collision-Induced Dissociation of α-Isomaltose and α-Maltose. J Phys Chem A 2022; 126:8799-8808. [DOI: 10.1021/acs.jpca.2c04278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, 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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11
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Peng W, Kobeissy F, Mondello S, Barsa C, Mechref Y. MS-based glycomics: An analytical tool to assess nervous system diseases. Front Neurosci 2022; 16:1000179. [PMID: 36408389 PMCID: PMC9671362 DOI: 10.3389/fnins.2022.1000179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/05/2022] [Indexed: 08/27/2023] Open
Abstract
Neurological diseases affect millions of peopleochemistryorldwide and are continuously increasing due to the globe's aging population. Such diseases affect the nervous system and are characterized by a progressive decline in brain function and progressive cognitive impairment, decreasing the quality of life for those with the disease as well as for their families and loved ones. The increased burden of nervous system diseases demands a deeper insight into the biomolecular mechanisms at work during disease development in order to improve clinical diagnosis and drug design. Recently, evidence has related glycosylation to nervous system diseases. Glycosylation is a vital post-translational modification that mediates many biological functions, and aberrant glycosylation has been associated with a variety of diseases. Thus, the investigation of glycosylation in neurological diseases could provide novel biomarkers and information for disease pathology. During the last decades, many techniques have been developed for facilitation of reliable and efficient glycomic analysis. Among these, mass spectrometry (MS) is considered the most powerful tool for glycan analysis due to its high resolution, high sensitivity, and the ability to acquire adequate structural information for glycan identification. Along with MS, a variety of approaches and strategies are employed to enhance the MS-based identification and quantitation of glycans in neurological samples. Here, we review the advanced glycomic tools used in nervous system disease studies, including separation techniques prior to MS, fragmentation techniques in MS, and corresponding strategies. The glycan markers in common clinical nervous system diseases discovered by utilizing such MS-based glycomic tools are also summarized and discussed.
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Affiliation(s)
- Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Chloe Barsa
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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12
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Liew CY, Hsu HC, Nguan HS, Huang YC, Zhong YQ, Hung SC, Ni CK. The Good, the Bad, and the Ugly Memories of Carbohydrate Fragments in Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1891-1903. [PMID: 36111786 DOI: 10.1021/jasms.2c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Collision-induced dissociation (CID) tandem mass spectrometry is commonly used for carbohydrate structural determinations. In the CID tandem mass spectrometry approach, carbohydrates are dissociated into fragments, and this is followed by the structural identification of fragments through subsequent CID. The success of the structural analysis depends on the structural correlation of fragments before and after dissociation, that is, structural memory of fragments. Fragments that completely lose the memory of their original structures cannot be used for structural analysis. By contrast, fragments with extremely strong correlations between the structures before and after fragmentation retain the information on their original structures as well as have memories of their precursors' entire structures. The CID spectra of these fragments depend on their own structures and on the remaining parts of the precursor structures, making structural analysis impractical. For effective structural analysis, the fragments produced from a precursor must have good structural memory, meaning that the structures of these fragments retain their original structure, and they must not be strongly affected by the remaining parts of the precursors. In this study, we found that most of the carbohydrate fragments produced by low-energy CID have good memory in terms of linkage position and anomericity. Fragments with ugly memory, where fragment structures change with the remaining parts of the precursors, can be attributed to C ion formation in a linear form. Fragments with ugly memory can be changed to have good memory by preventing linear C ion generation by using an alternative CID sequence, or the fragments of ugly memory can become useful in structural analysis when the contribution of linear C ions in fragmentation patterns is understood.
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Affiliation(s)
- Chia Yen Liew
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- International Graduate Program of Molecular Science and Technology, National Taiwan University (NTU-MST), Taipei 10617, Taiwan
- Taiwan International Graduate Program (TIGP) of Molecular Science and Technology (MST), Academia Sinica, Taipei 10617, Taiwan
| | - Hsu Chen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Yu-Chao Huang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yong-Qing Zhong
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | | | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Taiwan International Graduate Program (TIGP) of Molecular Science and Technology (MST), Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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13
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Zhou X, Song W, Novotny MV, Jacobson SC. Fractionation and characterization of sialyl linkage isomers of serum N-glycans by CE-MS. J Sep Sci 2022; 45:3348-3361. [PMID: 35819141 PMCID: PMC9473921 DOI: 10.1002/jssc.202200223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/12/2022] [Accepted: 07/07/2022] [Indexed: 11/07/2022]
Abstract
Structural isomers of sialylated N-glycans contribute to the diversity of the N-glycome and to a range of biological functions. Sialyl linkage isomers can be readily distinguished by mass spectrometry with mass differences between α2,3- and α2,6-linkages generated by a two-step sialic acid linkage-specific alkylamidation. To improve the identification of N-glycans from complex mixtures, we added a delactonization step after the first alkylamidation step, which regenerates negatively charged carboxylic acids on α2,3-sialic acids. N-glycan isomers with α2,3-sialic acids are then fractionated by ion-exchange chromatography prior to the second alkylamidation step. With this modified alkylamidation method, sialylated N-glycans were enriched and stabilized for structural characterization by capillary electrophoresis-mass spectrometry and tandem mass spectrometry. We identified 52 sialylated N-glycan structures, including 107 linkage isomers, in human serum and confirmed the presence of positional isomers of specific sialyl linkage isomers. Due to the reduced sample complexity after ion-exchange fractionation and CE separation, substructural features of N-glycans were rapidly evaluated and included core- and antenna-fucosylation and poly-lactosamine.
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Affiliation(s)
- Xiaomei Zhou
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401-7102, U.S.A
| | - Woran Song
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401-7102, U.S.A
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401-7102, U.S.A
| | - Stephen C. Jacobson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401-7102, U.S.A
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14
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Poorasadollah D, Bagheri Lotfabad T, Heydarinasab A, Yaghmaei S, Mohseni FA. Biological activated carbon process for biotransformation of azo dye Carmoisine by Klebsiella spp. ENVIRONMENTAL TECHNOLOGY 2022; 43:2713-2729. [PMID: 33641622 DOI: 10.1080/09593330.2021.1897167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The feasibility of employing the biological activated carbon (BAC) process to debilitate azo dye Carmoisine by Klebsiella spp. was investigated. Plate assay revealed the capability of Klebsiella spp. for removal of Carmoisine via degradation. Kinetic parameters were measured for Carmoisine debilitation by Klebsiella spp. using the suspended anaerobic process. Two types of granular and rod-shaped activated carbon were used to form the biological beds in order to study the Carmoisine debilitation in batch processes. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) were used to indicate the colonization and biofilm formation of bacteria grown on activated carbon particles (ACPs). Thin-layer chromatography (TLC), liquid chromatography-mass spectrometry (LC-MS), high-pressure liquid chromatography (HPLC) and biosorption studies demonstrated biotransformation of Carmoisine into its constituent aromatic amines during the Carmoisine debilitation in suspended anaerobic and BAC processes. The porosity of activated carbons, inoculation size and age of biological beds were the important factors affecting the viability of bacterial cells grown on ACPs and, consequently, the rate and efficiency of the Carmoisine debilitation process determined through spectrophotometry. The reusability of biological beds was demonstrated by conducting sequential batch experiments. In conclusion, the BAC process proved to be an efficient method for anaerobic dye degradation.
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Affiliation(s)
- Delaram Poorasadollah
- Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Tayebe Bagheri Lotfabad
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Amir Heydarinasab
- Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Soheila Yaghmaei
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Farzaneh Aziz Mohseni
- Persian Type Culture Collection, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
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15
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Gao Z, He Y, He Q, Wei W, Luo Y, Ma Z, Chen W, Chu F, Zhang S, Liu Y, Pan Y. Multidimensional identification of disaccharide isomers based on non-covalent complexes and tandem mass spectrometry. Talanta 2022; 249:123674. [PMID: 35717753 DOI: 10.1016/j.talanta.2022.123674] [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: 03/07/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/26/2022]
Abstract
Glycans are the most abundant organic polymers in nature. They are essential to living organisms and regulate a wide range of biological functions. However, mass spectrometry-based identification of glycan isomers remains challenging due to the complexity of their structures including their complex compositions, linkages, and anomeric configurations. In this study, two novel complex ions, the mononuclear copper-bound dimeric ions [(Cu2+)(A)(L-His)-H]+ and the mononuclear copper-bound quaternary ions [(Cu2+)(A)(L-Ser)3-H]+ (where A denotes a disaccharide, and L-Ser/His denotes l-serine/histidine), were designed for the collision-induced dissociation-based identification and relative quantification of 14 disaccharide isomers. When the unique fragmentation patterns of the above two types of complex ions were mapped into a three-dimensional vector, all the isomers were completely distinguished. Of note, the established method is able to identify mixtures of linkage isomers only using tandem mass spectrometry based on linkage-specific fragment ions of histidine-based complex ions. Finally, the method was successfully applied to the identification and relative quantification of two disaccharide isomers (lactose and sucrose) in dairy beverages. In conclusion, the established method is sensitive to subtle structural differences in disaccharide isomers and has the potential to be used for the differentiation of various glycans.
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Affiliation(s)
- Zhan Gao
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yuwen He
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Quan He
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Wei Wei
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yuanqing Luo
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Zihan Ma
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Weiwei Chen
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Fengjian Chu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, 310027, PR China
| | - Shuheng Zhang
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yaqin Liu
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China.
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16
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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17
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Nguan HS, Tsai ST, Ni CK. Collision-Induced Dissociation of Cellobiose and Maltose. J Phys Chem A 2022; 126:1486-1495. [PMID: 35212541 DOI: 10.1021/acs.jpca.1c10046] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure determination is a longstanding bottleneck of carbohydrate research. Tandem mass spectrometry (MS/MS) is one of the most widely used methods for carbohydrate structure determination. However, the effectiveness of MS/MS depends on how the precursor structures are derived from the observed fragments. Understanding the dissociation mechanisms is crucial for MS/MS-based structure determination. Herein, we investigate the collision-induced dissociation mechanism of β-cellobiose and β-maltose sodium adducts using quantum chemical calculations and experimental measurements. Four dissociation channels are studied. Dehydration mainly occurs through the transfer of an H atom to O1 of the sugar at the reducing end, followed by a C1-O1 bond cleavage; cross-ring dissociation starts with a ring-opening reaction, which occurs through the transfer of an H atom from O1 to O5 of the sugar at the reducing end. These two dissociation channels are analogous to that of glucose monosaccharide. The third channel, generation of B1 and Y1 ions, occurs through the transfer of an H atom from O3 (cellobiose) or O2 (maltose) to O1 of the sugar at the nonreducing end, followed by a glycosidic bond cleavage. The fourth channel, C1-Z1 fragmentation, has two mechanisms: (1) the transfer of an H atom from O3 or O2 to O4 of the sugar at the reducing end to generate C ions in the ring form and (2) the transfer of an H atom from O3 of the sugar at the reducing end to O5 of the sugar at the nonreducing end to produce C ions in the linear form. The results of calculations are supported by experimental collision-induced dissociation spectral measurements.
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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
| | - 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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18
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Tsai YH, Tsai CW, Tipple CA. A Validated Method for the Analysis of Sugars and Sugar Alcohols Related to Explosives Via Liquid Chromatography Mass Spectrometry (LC-MS) With Post-Column Addition. Forensic Chem 2022. [DOI: 10.1016/j.forc.2022.100404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Butnev VY, May JV, Brown AR, Sharma T, Butnev VY, White WK, Harvey DJ, Bousfield GR. Human FSH Glycoform α-Subunit Asparagine 52 Glycans: Major Glycan Structural Consistency, Minor Glycan Variation in Abundance. Front Endocrinol (Lausanne) 2022; 13:767661. [PMID: 36329887 PMCID: PMC9623679 DOI: 10.3389/fendo.2022.767661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Follicle-stimulating hormone (FSH), an α/β heterodimeric glycoprotein hormone, consists of functionally significant variants resulting from the presence or absence of either one of two FSHβ subunit N-glycans. The two most abundant variants are fully-glycosylated FSH24 (based on 24 kDa FSHβ band in Western blots) and hypo-glycosylated FSH21 (21 kDa band, lacks βAsn24 glycans). Due to its ability to bind more rapidly to the FSH receptor and occupy more FSH binding sites than FSH24, hypo-glycosylated FSH21 exhibits greater biological activity. Endoglycosidase F1-deglycosylated FSH bound to the complete extracellular domain of the FSH receptor crystallized as a trimeric complex. It was noted that a single biantennary glycan attached to FSHα Asn52 might preemptively fill the central pocket in this complex and prevent the other two FSH ligands from binding the remaining ligand-binding sites. As the most active FSH21 preparations possessed more rapidly migrating α-subunit bands in Western blots, we hypothesized that Asn52 glycans in these preparations were small enough to enable greater FSH21 receptor occupancy in the putative FSHR trimer model. Highly purified hFSH oligosaccharides derived from each FSH subunit, were characterized by electrospray ionization-ion mobility-collision-induced dissociation (ESI-IM-CID) mass spectrometry. FSHβ glycans typically possessed core-linked fucose and were roughly one third bi-antennary, one third tri-antennary and one third tetra-antennary. FSHα oligosaccharides largely lacked core fucose and were bi- or tri-antennary. Those αAsn52 glycans exhibiting tetra-antennary glycan m/z values were found to be tri-antennary, with lactosamine repeats accounting for the additional mass. Selective αAsn52 deglycosylation of representative pituitary hFSH glycoform Superdex 75 gel filtration fractions followed by ESI-IM-CID mass spectrometry revealed tri-antennary glycans predominated even in the lowest molecular weight FSH glycoforms. Accordingly, the differences in binding capacity of the same receptor preparation to different FSH glycoforms are likely the organization of the FSH receptor in cell membranes, rather than the αAsn52 oligosaccharide.
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Affiliation(s)
- Viktor Y Butnev
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
| | - Jeffrey V May
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
| | - Alan R Brown
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
| | - Tarak Sharma
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
| | - Vladimir Y Butnev
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
| | - William K White
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
| | - David J Harvey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - George R Bousfield
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
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20
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Harvey DJ, Struwe WB, Behrens AJ, Vasiljevic S, Crispin M. Formation and fragmentation of doubly and triply charged ions in the negative ion spectra of neutral N-glycans from viral and other glycoproteins. Anal Bioanal Chem 2021; 413:7277-7294. [PMID: 34342671 PMCID: PMC8329908 DOI: 10.1007/s00216-021-03480-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/28/2021] [Accepted: 06/15/2021] [Indexed: 11/05/2022]
Abstract
Structural determination of N-glycans by mass spectrometry is ideally performed by negative ion collision-induced dissociation because the spectra are dominated by cross-ring fragments leading to ions that reveal structural details not available by many other methods. Most glycans form [M - H]- or [M + adduct]- ions but larger ones (above approx. m/z 2000) typically form doubly charged ions. Differences have been reported between the fragmentation of singly and doubly charged ions but a detailed comparison does not appear to have been reported. In addition to [M + adduct]- ions (this paper uses phosphate as the adduct) other doubly, triply, and quadruply charged ions of composition [Mn + (H2PO4)n]n- have been observed in mixtures of N-glycans released from viral and other glycoproteins. This paper explores the formation and fragmentation of these different types of multiply charged ions with particular reference to the presence of diagnostic fragments in the CID spectra and comments on how these ions can be used to characterize these glycans.
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Affiliation(s)
- David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
| | - Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- GlycoEra AG, Grabenstrasse 3, 8952, Schlieren, Switzerland
| | - Snezana Vasiljevic
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
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21
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Harvey DJ, Behrens AJ, Crispin M, Struwe WB. Identification of N-glycans with GalNAc-containing antennae from recombinant HIV trimers by ion mobility and negative ion fragmentation. Anal Bioanal Chem 2021; 413:7229-7240. [PMID: 34327564 PMCID: PMC8321768 DOI: 10.1007/s00216-021-03477-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Negative ion collision-induced dissociation (CID) of underivatized N-glycans has proved to be a simple, yet powerful method for their structural determination. Recently, we have identified a series of such structures with GalNAc rather than the more common galactose capping the antennae of hybrid and complex glycans. As part of a series of publications describing the negative ion fragmentation of different types of N-glycan, this paper describes their CID spectra and estimated nitrogen cross sections recorded by travelling wave ion mobility mass spectrometry (TWIMS). Most of the glycans were derived from the recombinant glycoproteins gp120 and gp41 from the human immunodeficiency virus (HIV), recombinantly derived from human embryonic kidney (HEK 293T) cells. Twenty-six GalNAc-capped hybrid and complex N-glycans were identified by a combination of TWIMS, negative ion CID, and exoglycosidase digestions. They were present as the neutral glycans and their sulfated and α2→3-linked sialylated analogues. Overall, negative ion fragmentation of glycans generates fingerprints that reveal their structural identity.
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Affiliation(s)
- David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- GlycoEra AG, Grabenstrasse 3, 8952, Schlieren, Switzerland
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
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22
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Liew CY, Chan CK, Huang SP, Cheng YT, Tsai ST, Hsu HC, Wang CC, Ni CK. De novo structural determination of oligosaccharide isomers in glycosphingolipids using logically derived sequence tandem mass spectrometry. Analyst 2021; 146:7345-7357. [PMID: 34766961 DOI: 10.1039/d1an01448j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite the importance of carbohydrates in biological systems, structural determination of carbohydrates remains difficult because of the large number of isomers. In this study, a new mass spectrometry method, namely logically derived sequence tandem mass spectrometry (LODES/MSn), was developed to characterize oligosaccharide structures. In this approach, sequential collision-induced dissociation (CID) of oligosaccharides is performed in an ion trap mass spectrometer to identify the linkage position, anomeric configuration, and stereoisomers of each monosaccharide in the oligosaccharides. The CID sequences are derived from carbohydrate dissociation mechanisms. LODES/MSn does not require oligosaccharide standards or the prior knowledge of the rules and principles of biosynthetic pathways; thus LODES/MSn is particularly useful for the investigation of undiscovered oligosaccharides. We demonstrated that the structure of core oligosaccharides in glycosphingolipids can be identified from more than 500 000 isomers using LODES/MSn. The same method can be applied for determining the structures of other oligosaccharides, such as N-, and O-glycans, and free oligosaccharides in milk.
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Affiliation(s)
- Chia Yen Liew
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.,International Graduate Program of Molecular Science and Technology, National Taiwan University (NTU-MST), Taipei, 10617, Taiwan.,an International Graduate Program (TIGP) of Molecular Science and Technology (MST), Academia Sinica, Taiw, Taipei, 10617, Taiwan
| | - Chieh-Kai Chan
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shih-Pei Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Yu-Ting Cheng
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Hsu Chen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | | | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
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23
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Valadbeigi Y, Ilbeigi V, Khodabandeh Z. Formation of anionic clusters of triols in the atmospheric pressure chemical ionization source: An ion mobility spectrometry and theoretical study. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Juvonen M, Bakx E, Schols H, Tenkanen M. Separation of isomeric cereal-derived arabinoxylan-oligosaccharides by collision induced dissociation-travelling wave ion mobility spectrometry-tandem mass spectrometry (CID-TWIMS-MS/MS). Food Chem 2021; 366:130544. [PMID: 34314932 DOI: 10.1016/j.foodchem.2021.130544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 06/12/2021] [Accepted: 07/04/2021] [Indexed: 01/08/2023]
Abstract
The potential of travelling wave ion mobility spectroscopy in combination with collision induced dissociation tandem mass spectrometry (CID-TWIMS-MS/MS) to separate cereal-derived isomeric arabinoxylan-oligosaccharides (A)XOS was investigated. Three trisaccharide, four tetrasaccharide, and four pentasaccharide (A)XOS isomers were analyzed by positive and negative ionization TWIMS-MS and CID-TWIMS-MS/MS. The tri- and pentasaccharide isomers were distinguishable by the ATDs of the precursor ions. The CID-TWIMS-MS/MS could separate most of the isomeric fragment ions produced from tetra- and pentasaccharide (A)XOS. Finally, the base peak mobility spectrum is introduced as a practical tool for (A)XOS fingerprinting.
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Affiliation(s)
- Minna Juvonen
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, 00014 University of Helsinki, Finland.
| | - Edwin Bakx
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
| | - Henk Schols
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
| | - Maija Tenkanen
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, 00014 University of Helsinki, Finland
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25
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Gao Z, Li L, Chen W, Ma Z, Li Y, Gao Y, Ding CF, Zhao X, Pan Y. Distinguishment of Glycan Isomers by Trapped Ion Mobility Spectrometry. Anal Chem 2021; 93:9209-9217. [PMID: 34165974 DOI: 10.1021/acs.analchem.1c01461] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The in-depth study of glycan has drawn large research interests since it is one of the main biopolymers on the earth with a variety of biological functions. However, the distinguishment of glycans is still difficult due to the similarity of the monosaccharide building block, the anomer, and the linkage of glycosidic bonds. In this study, four novel and representative copper-bound diastereoisomeric complex ions were simultaneously detected in a single measurement by trapped ion mobility mass spectrometry, including mononuclear copper-bound dimeric ions [(Cu2+)(A)(l-Ser)-H]+ and [(Cu2+)(A)(l-His)-H]+, the mononuclear copper-bound trimeric ion [(Cu2+)(A)(l-Ser)(l-His)-H]+, and the binuclear copper-bound tetrameric ion [(Cu2+)2(A)(l-Ser)2(l-His)-3H]+ (where A denotes an oligosaccharide, and l-Ser and l-His denote l-serine and l-histidine, respectively). By combining the collision cross sections of complex ions, 23 oligosaccharide isomers were successfully distinguished including two pairs of sialylated glycan linkage isomers. In addition, due to the unique dissociation pathways of the trimeric ion, both the relative and absolute quantification of the individual isomer in the mixture could be determined using a mass spectrometry-based kinetic method. Finally, the method established above was successfully applied to the identification and quantification of glycan isomers in dairy beverages and juice. The method in the present study was sensitive to the fine difference of glycan isomers and might have wide applicability in glycoscience.
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Affiliation(s)
- Zhan Gao
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| | - Lei Li
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, Zhejiang, P. R. China
| | - Weiwei Chen
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| | - Zihan Ma
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| | - Yuan Li
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| | - Yuanji Gao
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
| | - Chuan-Fan Ding
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, Zhejiang, P. R. China
| | - Xiaoyong Zhao
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China
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26
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Structural identification of N-glycan isomers using logically derived sequence tandem mass spectrometry. Commun Chem 2021; 4:92. [PMID: 36697781 PMCID: PMC9814355 DOI: 10.1038/s42004-021-00532-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/19/2021] [Indexed: 01/28/2023] Open
Abstract
N-linked glycosylation is one of the most important protein post-translational modifications. Despite the importance of N-glycans, the structural determination of N-glycan isomers remains challenging. Here we develop a mass spectrometry method, logically derived sequence tandem mass spectrometry (LODES/MSn), to determine the structures of N-glycan isomers that cannot be determined using conventional mass spectrometry. In LODES/MSn, the sequences of successive collision-induced dissociation are derived from carbohydrate dissociation mechanisms and apply to N-glycans in an ion trap for structural determination. We validate LODES/MSn using synthesized N-glycans and subsequently applied this method to N-glycans extracted from soybean, ovalbumin, and IgY. Our method does not require permethylation, reduction, and labeling of N-glycans, or the mass spectrum databases of oligosaccharides and N-glycan standards. Moreover, it can be applied to all types of N-glycans (high-mannose, hybrid, and complex), as well as the N-glycans degraded from larger N-glycans by any enzyme or acid hydrolysis.
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27
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Pallister EG, Choo MSF, Walsh I, Tai JN, Tay SJ, Yang YS, Ng SK, Rudd PM, Flitsch SL, Nguyen-Khuong T. Utility of Ion-Mobility Spectrometry for Deducing Branching of Multiply Charged Glycans and Glycopeptides in a High-Throughput Positive ion LC-FLR-IMS-MS Workflow. Anal Chem 2020; 92:15323-15335. [DOI: 10.1021/acs.analchem.0c01954] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Edward G. Pallister
- Bioprocessing Technology Institute, Agency for Science Technology and Research, 20 Biopolis Way, Biopolis 138668, Singapore
- School of Chemistry & Manchester Institute of Biotechnology (MIB), The University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Matthew S. F. Choo
- Bioprocessing Technology Institute, Agency for Science Technology and Research, 20 Biopolis Way, Biopolis 138668, Singapore
| | - Ian Walsh
- Bioprocessing Technology Institute, Agency for Science Technology and Research, 20 Biopolis Way, Biopolis 138668, Singapore
| | - Jien Nee Tai
- Bioprocessing Technology Institute, Agency for Science Technology and Research, 20 Biopolis Way, Biopolis 138668, Singapore
| | - Shi Jie Tay
- Bioprocessing Technology Institute, Agency for Science Technology and Research, 20 Biopolis Way, Biopolis 138668, Singapore
| | - Yuan Sheng Yang
- Bioprocessing Technology Institute, Agency for Science Technology and Research, 20 Biopolis Way, Biopolis 138668, Singapore
| | - Say Kong Ng
- Bioprocessing Technology Institute, Agency for Science Technology and Research, 20 Biopolis Way, Biopolis 138668, Singapore
| | - Pauline M. Rudd
- Bioprocessing Technology Institute, Agency for Science Technology and Research, 20 Biopolis Way, Biopolis 138668, Singapore
| | - Sabine L. Flitsch
- School of Chemistry & Manchester Institute of Biotechnology (MIB), The University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Terry Nguyen-Khuong
- Bioprocessing Technology Institute, Agency for Science Technology and Research, 20 Biopolis Way, Biopolis 138668, Singapore
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28
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Leiva-Carrasco MJ, Jiménez-Chávez S, Harvey DJ, Parra NC, Tavares KC, Camacho F, González A, Sánchez O, Montesino R, Toledo JR. In vivo modification of the goat mammary gland glycosylation pathway. N Biotechnol 2020; 61:11-21. [PMID: 33157282 DOI: 10.1016/j.nbt.2020.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/25/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
Complex recombinant glycoproteins produced as potential biopharmaceuticals in goat's milk have an aberrant pattern of N-glycosylation due to the lack of multi-antennary structures. Overexpression of glycosyltransferases may increase oligosaccharide branching of the desired glycoproteins. Here, human erythropoietin fused to human IgG Fc (EPO-Fc) was co-expressed with N-acetyl-glucosaminyltransferase-IVa (GnT-IVa) by adenoviral transduction in goat mammary gland to evaluate the in vivo modification of N-glycosylation pattern in this tissue. Adenoviral vectors, containing the EPO-Fc and GnT-IVa sequences were assembled for in vitro and in vivo expression in mammalian cell culture or in goat mammary gland. Protein detection was assessed by gel electrophoresis and western blot, and N-glycans were identified by HPLC and mass spectrometry. GnT-IVa overexpression and its colocalization with EPO-Fc in the Golgi apparatus of SiHa cells were demonstrated. N-glycan analysis of in vitro and in vivo expression of EPO-Fc modified by GnT-IVa (EPO-Fc/GnT-IVa) showed an increase in high molecular weight structures, which corresponded to tri- and tetra-antennary N-glycans in SiHa cells and mostly tri-antennary N-glycans in goat's milk from transformed mammary tissue. The results confirmed that successful modification of the goat mammary gland secretion pathway could be achieved by co-expressing glycoenzymes together with the glycoprotein of interest. This is the first report of modification of the N-glycosylation pattern in the goat mammary gland in vivo, and constitutes a step forward for improving the use of the mammary gland as a bioreactor for the production of complex recombinant proteins.
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Affiliation(s)
- María J Leiva-Carrasco
- Biotechnology and Biopharmaceuticals Laboratory, Pathophysiology Department, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile; Biotechnology and Biomedicine Center SpA, Granada 168, Villumanque, Concepcion, Chile
| | - Silvana Jiménez-Chávez
- Biotechnology and Biopharmaceuticals Laboratory, Pathophysiology Department, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile; Biotechnology and Biomedicine Center SpA, Granada 168, Villumanque, Concepcion, Chile
| | - David J Harvey
- Oxford Glycobiology Institute, Biochemistry Department, South Parks Road, Oxford, OX1 3QU, UK
| | - Natalie C Parra
- Department of Pharmacology, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile
| | - Kaio C Tavares
- Molecular and Developmental Biology Laboratory, Experimental Biology Center (NUBEX), University of Fortaleza (UNIFOR), Fortaleza, CE, Brazil
| | - Frank Camacho
- Department of Pharmacology, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile
| | - Alain González
- Biotechnology and Biopharmaceuticals Laboratory, Pathophysiology Department, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile
| | - Oliberto Sánchez
- Department of Pharmacology, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile
| | - Raquel Montesino
- Biotechnology and Biopharmaceuticals Laboratory, Pathophysiology Department, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile; Biotechnology and Biomedicine Center SpA, Granada 168, Villumanque, Concepcion, Chile.
| | - Jorge R Toledo
- Biotechnology and Biopharmaceuticals Laboratory, Pathophysiology Department, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile; Biotechnology and Biomedicine Center SpA, Granada 168, Villumanque, Concepcion, Chile.
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29
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Harvey DJ. NEGATIVE ION MASS SPECTROMETRY FOR THE ANALYSIS OF N-LINKED GLYCANS. MASS SPECTROMETRY REVIEWS 2020; 39:586-679. [PMID: 32329121 DOI: 10.1002/mas.21622] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/13/2019] [Accepted: 12/22/2019] [Indexed: 05/03/2023]
Abstract
N-glycans from glycoproteins are complex, branched structures whose structural determination presents many analytical problems. Mass spectrometry, usually conducted in positive ion mode, often requires extensive sample manipulation, usually by derivatization such as permethylation, to provide the necessary structure-revealing fragment ions. The newer but, so far, lesser used negative ion techniques, on the contrary, provide a wealth of structural information not present in positive ion spectra that greatly simplify the analysis of these compounds and can usually be conducted without the need for derivatization. This review describes the use of negative ion mass spectrometry for the structural analysis of N-linked glycans and emphasises the many advantages that can be gained by this mode of operation. Biosynthesis and structures of the compounds are described followed by methods for release of the glycans from the protein. Methods for ionization are discussed with emphasis on matrix-assisted laser desorption/ionization (MALDI) and methods for producing negative ions from neutral compounds. Acidic glycans naturally give deprotonated species under most ionization conditions. Fragmentation of negative ions is discussed next with particular reference to those ions that are diagnostic for specific features such as the branching topology of the glycans and substitution positions of moieties such as fucose and sulfate, features that are often difficult to identify easily by conventional techniques such as positive ion fragmentation and exoglycosidase digestions. The advantages of negative over positive ions for this structural work are emphasised with an example of a series of glycans where all other methods failed to produce a structure. Fragmentation of derivatized glycans is discussed next, both with respect to derivatives at the reducing terminus of the molecules, and to methods for neutralization of the acidic groups on sialic acids to both stabilize them for MALDI analysis and to produce the diagnostic fragments seen with the neutral glycans. The use of ion mobility, combined with conventional mass spectrometry is described with emphasis on its use to extract clean glycan spectra both before and after fragmentation, to separate isomers and its use to extract additional information from separated fragment ions. A section on applications follows with examples of the identification of novel structures from lower organisms and tables listing the use of negative ions for structural identification of specific glycoproteins, glycans from viruses and uses in the biopharmaceutical industry and in medicine. The review concludes with a summary of the advantages and disadvantages of the technique. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
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30
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Jjunju FPM, Damon DE, Romero-Perez D, Young IS, Ward RJ, Marshall A, Maher S, Badu-Tawiah AK. Analysis of non-conjugated steroids in water using paper spray mass spectrometry. Sci Rep 2020; 10:10698. [PMID: 32612114 PMCID: PMC7329809 DOI: 10.1038/s41598-020-67484-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 06/01/2020] [Indexed: 11/09/2022] Open
Abstract
A novel strategy for the direct analysis of non-conjugated steroids in water using paper spray mass spectrometry (PS-MS) has been developed. PS-MS was used in the identification and quantification of non-conjugated (free) steroids in fish tank water samples. Data shown herein indicates that individual amounts of free steroids can be detected in aqua as low as; 0.17 ng/µL, 0.039 ng/µL, 0.43 ng/µL, 0.0076 ng/µL for aldosterone, corticosterone, cortisol, and β-estrone, respectively, and with an average relative standard deviation of ca. < 10% in the positive ion mode using PS-MS/MS. Direct detection of free steroids in a raw water mixture, from aquaculture, without prior sample preparation is demonstrated. The presence of free steroids released in fish water samples was confirmed via tandem mass spectrometry using collision-induced dissociation. This approach shows promise for rapid and direct water quality monitoring to provide a holistic assessment of non-conjugated steroids in aqua.
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Affiliation(s)
- Fred P M Jjunju
- Department of Electrical Engineering and Electronics, University of Liverpool, Brownlow Hill, Liverpool, L69 3GJ, UK
| | - Deidre E Damon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - David Romero-Perez
- Department of Electrical Engineering and Electronics, University of Liverpool, Brownlow Hill, Liverpool, L69 3GJ, UK
| | - Iain S Young
- Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Ryan J Ward
- Department of Electrical Engineering and Electronics, University of Liverpool, Brownlow Hill, Liverpool, L69 3GJ, UK
| | - Alan Marshall
- Department of Electrical Engineering and Electronics, University of Liverpool, Brownlow Hill, Liverpool, L69 3GJ, UK
| | - Simon Maher
- Department of Electrical Engineering and Electronics, University of Liverpool, Brownlow Hill, Liverpool, L69 3GJ, UK.
| | - Abraham K Badu-Tawiah
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.
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31
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Kuo CW, Khoo KH. Strategic Applications of Negative-Mode LC-MS/MS Analyses to Expedite Confident Mass Spectrometry-Based Identification of Multiple Glycosylated Peptides. Anal Chem 2020; 92:7612-7620. [PMID: 32384234 DOI: 10.1021/acs.analchem.0c00236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although recent advances in mass spectrometry (MS) have enabled meaningful glycoproteomic undertakings, many technical limitations remain unsolved. Among these, the ability to efficiently sequence the peptide backbone for de novo identification, delineating multiple N- and O-glycosylation sites on single glycopeptides, and deriving more glycan structure information to discriminate isomeric glycoforms are well acknowledged practical problems to be tackled. To address these issues, we explored the use of negative-mode MS2/MS3 fragmentation to supplement current nanoLC-MS2-based sequencing and identification of intact glycopeptides largely performed in positive mode. Consistent with previous reports by others, we found that sulfation and sialylation drastically alter the MS2 fragmentation pattern of glycopeptides in negative mode and the characteristic features identified can be utilized to program the most informative MS3 on the glycan moiety itself. Importantly, direct elimination of one or more O-glycans under negative-mode MS2 affords an easy way to discover additional O-glycosylations on a multiply glycosylated peptide by virtue of enumerating the dehydration scars imprinted on the O-glycosylated sites. Moreover, the characteristic peptide core ion carrying a ring cleavage remnant of the innermost amino sugar residue of an N-glycan can be relied upon to filter out all related N-glycopeptides carrying additional O-glycans defined by specific mass increments. Such enhanced ability to advance from definitive identification of single to multiple site-specific glycosylation on the same peptide backbones is anticipated to have a significant impact on the level of structural and biological insights one can gain in glycoproteomic applications.
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Affiliation(s)
- Chu-Wei Kuo
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
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32
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Zhang T, Madunić K, Holst S, Zhang J, Jin C, Ten Dijke P, Karlsson NG, Stavenhagen K, Wuhrer M. Development of a 96-well plate sample preparation method for integrated N- and O-glycomics using porous graphitized carbon liquid chromatography-mass spectrometry. Mol Omics 2020; 16:355-363. [PMID: 32281997 DOI: 10.1039/c9mo00180h] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Changes in glycosylation signatures of cells have been associated with pathological processes in cancer as well as infectious and autoimmune diseases. The current protocols for comprehensive analysis of N-glycomics and O-glycomics derived from cells and tissues often require a large amount of biological material. They also only allow the processing of very limited numbers of samples at a time. Here we established a workflow for sequential release of N-glycans and O-glycans based on PVDF membrane immobilization in 96-well format from 5 × 105 cells. Released glycans are reduced, desalted, purified, and reconstituted, all in 96-well format plates, without additional staining or derivatization. Glycans are then analyzed with porous graphitized carbon nano-liquid chromatography coupled to tandem mass spectrometry using negative-mode electrospray ionization, enabling the chromatographic resolution and structural elucidation of glycan species including many compositional isomers. The approach was demonstrated using glycoprotein standards and further applied to analyze the glycosylation of the murine mammary gland NMuMG cell line. The developed protocol allows the analysis of N- and O-glycans from relatively large numbers of samples in a less time consuming way with high repeatability. Inter- and intraday repeatability of the fetuin N-glycan analysis showed two median intraday coefficients of variations (CVs) of 7.6% and 8.0%, and a median interday CV of 9.8%. Median CVs of 7.9% and 8.7% for the main peaks of N- and O-glycans released from the NMuMG cell line indicate a very good repeatability. The method is applicable to purified glycoproteins as well as to biofluids and cell- or tissue-based samples.
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Affiliation(s)
- Tao Zhang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
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33
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Huang SP, Hsu HC, Liew CY, Tsai ST, Ni CK. Logically derived sequence tandem mass spectrometry for structural determination of Galactose oligosaccharides. Glycoconj J 2020; 38:177-189. [PMID: 32062823 DOI: 10.1007/s10719-020-09915-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/30/2019] [Accepted: 02/03/2020] [Indexed: 12/30/2022]
Abstract
Mass spectrometry has high sensitivity and is widely used in the identification of molecular structures, however, the structural determination of oligosaccharides through mass spectrometry is still challenging. A novel method, namely the logically derived sequence (LODES) tandem mass spectrometry (MSn), for the structural determination of underivatized oligosaccharides was developed. This method, which is based on the dissociation mechanisms, involves sequential low-energy collision-induced dissociation (CID) of sodium ion adducts, a logical sequence for identifying the structurally decisive product ions for subsequent CID, and a specially prepared disaccharide CID spectrum database. In this work, we reported the assignment of the specially prepared galactose disaccharide CID spectra. We used galactose trisaccharides and tetrasaccharides as examples to demonstrate LODES/MSn is a general method that can be used for the structural determination of hexose oligosaccharides. LODES/MSn has the potential to be extended to oligosaccharides containing other monosaccharides provided the dissociation mechanisms are understood and the corresponding disaccharide database is available.
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Affiliation(s)
- Shih-Pei Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei, 10617, Taiwan
| | - Hsu Chen Hsu
- 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.,Molecular Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei, 10617, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, 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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34
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Chiu CC, Lin CK, Kuo JL. Improved agreement between experimental and computational results for collision-induced dissociation mass spectrometry of cation-tagged hexoses. Phys Chem Chem Phys 2020; 22:6928-6941. [DOI: 10.1039/d0cp00286k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low exact exchange DFT methods underestimate the dehydration barriers as the charge localization in such transition states is challenging to describe.
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Affiliation(s)
- Cheng-chau Chiu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
| | - Chih-Kai Lin
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
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35
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Aldon Y, McKay PF, Allen J, Ozorowski G, Felfödiné Lévai R, Tolazzi M, Rogers P, He L, de Val N, Fábián K, Scarlatti G, Zhu J, Ward AB, Crispin M, Shattock RJ. Rational Design of DNA-Expressed Stabilized Native-Like HIV-1 Envelope Trimers. Cell Rep 2019; 24:3324-3338.e5. [PMID: 30232012 PMCID: PMC6167709 DOI: 10.1016/j.celrep.2018.08.051] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 05/16/2018] [Accepted: 08/17/2018] [Indexed: 11/17/2022] Open
Abstract
The HIV-1-envelope glycoprotein (Env) is the main target of antigen design for antibody-based prophylactic vaccines. The generation of broadly neutralizing antibodies (bNAb) likely requires the appropriate presentation of stabilized trimers preventing exposure of non-neutralizing antibody (nNAb) epitopes. We designed a series of membrane-bound Envs with increased trimer stability through the introduction of key stabilization mutations. We derived a stabilized HIV-1 trimer, ConSOSL.UFO.750, which displays a dramatic reduction in nNAb binding while maintaining high quaternary and MPER-specific bNAb binding. Its soluble counterpart, ConSOSL.UFO.664, displays similar antigenicity, and its native-like Env structure is confirmed by negative stain-EM and glycosylation profiling of the soluble ConSOSL.UFO.664 trimer. A rabbit immunization study demonstrated that the ConSOSL.UFO.664 can induce autologous tier 2 neutralization. We have successfully designed a stabilized native-like Env trimer amenable to nucleic acid or viral vector-based vaccination strategies. DNA-expressed closed pre-fusion native-like Env with preserved MPER exposure Env antigenicity varies across cell types and assays Muscle cells present properly folded and glycosylated membrane-bound Envs Fully glycosylated ConSOSL.UFO.664 induces autologous tier 2 neutralization
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Affiliation(s)
- Yoann Aldon
- Imperial College London, Department of Medicine, Division of Infectious Diseases, Section of Virology, Norfolk Place, London W2 1PG, UK
| | - Paul F McKay
- Imperial College London, Department of Medicine, Division of Infectious Diseases, Section of Virology, Norfolk Place, London W2 1PG, UK
| | - Joel Allen
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Réka Felfödiné Lévai
- Department of Immunology, National Food Chain Safety Office, Directorate of Veterinary Medicinal Products, Budapest, Hungary
| | - Monica Tolazzi
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation, and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | - Paul Rogers
- Imperial College London, Department of Medicine, Division of Infectious Diseases, Section of Virology, Norfolk Place, London W2 1PG, UK
| | - Linling He
- Department of Integrative Structural and Computational Biology, Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Natalia de Val
- Department of Integrative Structural and Computational Biology, Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katalin Fábián
- Department of Immunology, National Food Chain Safety Office, Directorate of Veterinary Medicinal Products, Budapest, Hungary
| | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation, and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robin J Shattock
- Imperial College London, Department of Medicine, Division of Infectious Diseases, Section of Virology, Norfolk Place, London W2 1PG, UK.
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36
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Struwe WB, Harvey DJ. Ion Mobility-Mass Spectrometry of Glycoconjugates. Methods Mol Biol 2019; 2084:203-219. [PMID: 31729663 DOI: 10.1007/978-1-0716-0030-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Glycoconjugates are diverse biomolecules that are dynamically assembled to regulate and fine-tune numerous cellular processes. Their biosynthesis is nontemplate-driven, achieved stepwise in discrete locations within the cell, giving rise to a range of complex branched structures that pose a significant challenge in structural biology. Mass spectrometry is the leading method for analysis of glycoconjugates, and the addition of ion mobility has proven valuable for improving structural assignments of individual glycans in complex biological mixtures. In this chapter, we briefly discuss recent applications of IM for glycomics and describe how to acquire, interpret, and analyze IM-MS data for the analysis of glycans.
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Affiliation(s)
- Weston B Struwe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, UK.
| | - David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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Gray CJ, Migas LG, Barran PE, Pagel K, Seeberger PH, Eyers CE, Boons GJ, Pohl NLB, Compagnon I, Widmalm G, Flitsch SL. Advancing Solutions to the Carbohydrate Sequencing Challenge. J Am Chem Soc 2019; 141:14463-14479. [PMID: 31403778 DOI: 10.1021/jacs.9b06406] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Carbohydrates possess a variety of distinct features with stereochemistry playing a particularly important role in distinguishing their structure and function. Monosaccharide building blocks are defined by a high density of chiral centers. Additionally, the anomericity and regiochemistry of the glycosidic linkages carry important biological information. Any carbohydrate-sequencing method needs to be precise in determining all aspects of this stereodiversity. Recently, several advances have been made in developing fast and precise analytical techniques that have the potential to address the stereochemical complexity of carbohydrates. This perspective seeks to provide an overview of some of these emerging techniques, focusing on those that are based on NMR and MS-hybridized technologies including ion mobility spectrometry and IR spectroscopy.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Lukasz G Migas
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Perdita E Barran
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Kevin Pagel
- Institute for Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Peter H Seeberger
- Biomolecular Systems Department , Max Planck Institute for Colloids and Interfaces , Am Muehlenberg 1 , 14476 Potsdam , Germany
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology , University of Liverpool , Crown Street , Liverpool L69 7ZB , U.K
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Nicola L B Pohl
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Isabelle Compagnon
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS , Université de Lyon , 69622 Villeurbanne Cedex , France.,Institut Universitaire de France IUF , 103 Blvd St Michel , 75005 Paris , France
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , S-106 91 Stockholm , Sweden
| | - Sabine L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
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38
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Tsai S, Liew CY, Hsu C, Huang S, Weng W, Kuo Y, Ni C. Automatic Full Glycan Structural Determination through Logically Derived Sequence Tandem Mass Spectrometry. Chembiochem 2019; 20:2351-2359. [DOI: 10.1002/cbic.201900228] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Shang‐Ting Tsai
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Chia Yen Liew
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
- Molecular Science and Technology International Graduate ProgramAcademia Sinica and National University Taipei 10617 Taiwan
| | - Chen Hsu
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Shih‐Pei Huang
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Wei‐Chien Weng
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Yu‐Hsiang Kuo
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Chi‐Kung Ni
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
- Department of ChemistryNational Tsing Hua University Hsinchu 30013 Taiwan
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39
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Chiu CC, Huynh HT, Tsai ST, Lin HY, Hsu PJ, Phan HT, Karumanthra A, Thompson H, Lee YC, Kuo JL, Ni CK. Toward Closing the Gap between Hexoses and N-Acetlyhexosamines: Experimental and Computational Studies on the Collision-Induced Dissociation of Hexosamines. J Phys Chem A 2019; 123:6683-6700. [DOI: 10.1021/acs.jpca.9b04143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cheng-chau Chiu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Hai Thi Huynh
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Hou-Yu Lin
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Arya Karumanthra
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Undergraduate Programme, Indian Institute of Science, Bangalore, 560012, India
| | - Hayden Thompson
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Yu-Chi Lee
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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40
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Kiayi Z, Lotfabad TB, Heidarinasab A, Shahcheraghi F. Microbial degradation of azo dye carmoisine in aqueous medium using Saccharomyces cerevisiae ATCC 9763. JOURNAL OF HAZARDOUS MATERIALS 2019; 373:608-619. [PMID: 30953978 DOI: 10.1016/j.jhazmat.2019.03.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 03/23/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Carmoisine is an azo dye widely used in many industries, and therefore frequently occurs in the effluent of many factories. To our knowledge, biological degradation of carmoisine has received little attention. The present study investigates the capability of Saccharomyces cerevisiae ATCC 9763 for degradation of carmoisine. Spectrophotometry data indicates that carmoisine (50 mg/l) was eliminated from the aqueous medium after approximately 7 h of incubation with Saccharomyces under anaerobic shaking conditions. Thin layer chromatography (TLC) revealed the removal of carmoisine as well as the appearance of aromatic amines in samples collected from the decolourized medium by S. cerevisiae and this was subsequently confirmed by Fourier transform infrared (FTIR) spectroscopy. Liquid chromatography mass spectrometry (LC/MS) was carried out on fractions from consecutive column chromatography and two-dimensional (2D) chromatography. LC/MS indicated degradation of carmoisine into its constituent aromatic amines. In addition, investigating the effect of environmental conditions on the decolourization process indicated that yeast extract could positively affect decolourization rates; shaking significantly accelerated decolourization and shortened the time required for complete biodecolourization from ≃ 8 days to ≃ 7 h; and Saccharomyces was able to consume sucrose as a carbon source and remove the carmoisine despite the presence of sunset yellow, which remained unaffected.
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Affiliation(s)
- Zahra Kiayi
- Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Tayebe Bagheri Lotfabad
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran-Karaj Highway, P.O. Box: 14965/161, Tehran, Iran.
| | - Amir Heidarinasab
- Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran.
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41
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Shen Y, You Y, Xiao K, Chen Y, Tian Z. Large-Scale Identification and Fragmentation Pathways Analysis of N-Glycans from Mouse Brain. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1254-1261. [PMID: 31098956 DOI: 10.1007/s13361-019-02181-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 02/18/2019] [Accepted: 02/24/2019] [Indexed: 06/09/2023]
Abstract
N-linked glycosylation is one of the most common protein PTMs, and the topological structure (monosaccharide composition and sequence as well as glycosidic linkages) of N-glycans is vital information to understand their biological functions and roles. Tandem mass spectrometry has been widely used for topological structure characterization of N-glycans, where comprehensive understanding of fragmentation pathways and characteristics of product ions are essential to achieve best interpretation of MS/MS data and highest confidence of identification. Here, we report our glycomic study of N-glycome of mouse brain as well as fragmentation pathway analysis of the identified N-glycans. With LC-MS/MS analysis at both the positive and negative ESI modes together with our recently developed N-glycan database search engine GlySeeker, 221 unique N-glycans with putative topological structures were identified with target-decoy searches and number of best hits of 1. Analysis of fragmentation pathways and characteristics of product ions of permethylated N-glycans in the positive mode and native N-glycans in the negative mode were further carried out. The reported N-glycans serve as a basic reference for future glycosylation study of mouse brain; and in general database search of tandem mass spectra of N-glycans, B/Y/Z ions should be preferentially considered for the permethylated form in the positive mode and B/C/Z ions for the native form in the negative mode.
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Affiliation(s)
- Yun Shen
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Yiwen You
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Kaijie Xiao
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China.
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42
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Huang C, Yan J, Zhan L, Zhao M, Zhou J, Gao H, Xie W, Li Y, Chai W. Linkage and sequence analysis of neutral oligosaccharides by negative-ion MALDI tandem mass spectrometry with laser-induced dissociation. Anal Chim Acta 2019; 1071:25-35. [PMID: 31128752 DOI: 10.1016/j.aca.2019.04.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 11/25/2022]
Abstract
Mass spectrometry (MS) has become the primary method for high-sensitivity structural determination of oligosaccharides. Fragmentation in the negative-ion MS can provide a wealth of structural information and these can be used for sequence determination. However, although negative-ion MS of neutral oligosaccharide using the deprotonated molecule [M-H]- as the precursor has been very successful for electrospray ionization (ESI), it has only limited success for matrix-assisted laser desorption/ionization (MALDI). In the present study, the features of negative-ion MALDI primary spectra were investigated in detail and the product-ion spectra using [M-H]- and [M+Cl]- as the precursors were carefully compared. The formation of [M-H]- was the main difficulty for MALDI while [M+Cl]- was proved to be useful as alternative precursor anion for MALDI-MS/MS to produce similar fragmentation for sequencing of neutral oligosaccharides. N-(1-naphthyl)ethylenediamine dihydrochloride was then used as both the matrix and the Cl- dopant to evaluate the extent of structural information that can be obtained by negative-ion fragmentation from [M+Cl]- using laser-induced dissociation (LID)-MS/MS for linkage assignment of gluco-oligosaccharides and for typing of blood-group ABO(H) and Lewis antigens on either type 1 or type 2 backbone-chains.
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Affiliation(s)
- Chuncui Huang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; GuangDong Bio-healtech Advanced, Foshan, 528315, China
| | - Jingyu Yan
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Key Laboratory of Separation Science for Analytical Chemistry, Dalian, 116023, China
| | - Lingpeng Zhan
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China; Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Min Zhao
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Jinyu Zhou
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Huanyu Gao
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Wenchun Xie
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; GuangDong Bio-healtech Advanced, Foshan, 528315, China
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.
| | - Wengang Chai
- Glycosciences Laboratory, Faculty of Medicine, Imperial College London, Hammersmith Campus, London, W12 0NN, UK
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43
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De novo structural determination of mannose oligosaccharides by using a logically derived sequence for tandem mass spectrometry. Anal Bioanal Chem 2019; 411:3241-3255. [DOI: 10.1007/s00216-019-01817-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/04/2019] [Accepted: 03/28/2019] [Indexed: 10/26/2022]
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44
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Juvonen M, Kotiranta M, Jokela J, Tuomainen P, Tenkanen M. Identification and structural analysis of cereal arabinoxylan-derived oligosaccharides by negative ionization HILIC-MS/MS. Food Chem 2019; 275:176-185. [DOI: 10.1016/j.foodchem.2018.09.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 12/30/2022]
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45
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Hinneburg H, Chatterjee S, Schirmeister F, Nguyen-Khuong T, Packer NH, Rapp E, Thaysen-Andersen M. Post-Column Make-Up Flow (PCMF) Enhances the Performance of Capillary-Flow PGC-LC-MS/MS-Based Glycomics. Anal Chem 2019; 91:4559-4567. [DOI: 10.1021/acs.analchem.8b05720] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | | | - Terry Nguyen-Khuong
- Analytics Group, Bioprocessing Technology Institute, A*STAR, Singapore 138668, Singapore
| | | | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
- glyXera GmbH, 39106 Magdeburg, Germany
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46
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Bythell BJ, Rabus JM, Wagoner AR, Abutokaikah MT, Maître P. Sequence Ion Structures and Dissociation Chemistry of Deprotonated Sucrose Anions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2380-2393. [PMID: 30284205 DOI: 10.1007/s13361-018-2065-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
We investigate the tandem mass spectrometry of regiospecifically labeled, deprotonated sucrose analytes. We utilize density functional theory calculations to model the pertinent gas-phase fragmentation chemistry of the prevalent glycosidic bond cleavages (B1-Y1 and C1-Z1 reactions) and compare these predictions to infrared spectroscopy experiments on the resulting B1 and C1 product anions. For the C1 anions, barriers to interconversion of the pyranose [α-glucose-H]-, C1 anions to entropically favorable ring-open aldehyde-terminated forms were modest (41 kJ mol-1) consistent with the observation of a band assigned to a carbonyl stretch at ~ 1680-1720 cm-1. For the B1 anions, our transition structure calculations predict the presence of both deprotonated 1,6-anhydroglucose and carbon 2-ketone ((4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one) anion structures, with the latter predominating. This hypothesis is supported by our spectroscopic data which show diagnostic bands at 1600, 1674, and 1699 cm-1 (deprotonated carbon 2-ketone structures), and at ~ 1541 cm-1 (both types of structure) and RRKM rate calculations. The deprotonated carbon 2-ketone structures are also the lowest energy product B1 anions. Graphical Abstract ᅟ.
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Affiliation(s)
- Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri St. Louis, St. Louis, MO, 63121, USA.
| | - Jordan M Rabus
- Department of Chemistry and Biochemistry, University of Missouri St. Louis, St. Louis, MO, 63121, USA
| | - Ashley R Wagoner
- Department of Chemistry and Biochemistry, University of Missouri St. Louis, St. Louis, MO, 63121, USA
| | - Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri St. Louis, St. Louis, MO, 63121, USA
| | - Philippe Maître
- Laboratoire de Chimie Physique (UMR8000), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
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47
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He L, Kumar S, Allen JD, Huang D, Lin X, Mann CJ, Saye-Francisco KL, Copps J, Sarkar A, Blizard GS, Ozorowski G, Sok D, Crispin M, Ward AB, Nemazee D, Burton DR, Wilson IA, Zhu J. HIV-1 vaccine design through minimizing envelope metastability. SCIENCE ADVANCES 2018; 4:eaau6769. [PMID: 30474059 PMCID: PMC6248932 DOI: 10.1126/sciadv.aau6769] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/19/2018] [Indexed: 05/17/2023]
Abstract
Overcoming envelope metastability is crucial to trimer-based HIV-1 vaccine design. Here, we present a coherent vaccine strategy by minimizing metastability. For 10 strains across five clades, we demonstrate that the gp41 ectodomain (gp41ECTO) is the main source of envelope metastability by replacing wild-type gp41ECTO with BG505 gp41ECTO of the uncleaved prefusion-optimized (UFO) design. These gp41ECTO-swapped trimers can be produced in CHO cells with high yield and high purity. The crystal structure of a gp41ECTO-swapped trimer elucidates how a neutralization-resistant tier 3 virus evades antibody recognition of the V2 apex. UFO trimers of transmitted/founder viruses and UFO trimers containing a consensus-based ancestral gp41ECTO suggest an evolutionary root of metastability. The gp41ECTO-stabilized trimers can be readily displayed on 24- and 60-meric nanoparticles, with incorporation of additional T cell help illustrated for a hyperstable 60-mer, I3-01. In mice and rabbits, these gp140 nanoparticles induced tier 2 neutralizing antibody responses more effectively than soluble trimers.
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Affiliation(s)
- Linling He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joel D. Allen
- Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaohe Lin
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Colin J. Mann
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karen L. Saye-Francisco
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anita Sarkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabrielle S. Blizard
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA 02139-3583, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Corresponding author. (I.A.W.); (J.Z.)
| | - Jiang Zhu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Corresponding author. (I.A.W.); (J.Z.)
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Abstract
Glycosylation is one of the most common and complex posttranslation modifications that significantly influences protein structure and function. However, linking individual glycan structures to protein interactions remains challenging and typically requires multiple techniques. Here, we establish a mass-spectrometric approach to systematically dissect the microheterogeneity of two important serum proteins, α1-acid glycoprotein and haptoglobin, and relate glycan features to drug and protein-binding interaction kinetics. We found that the degree of N-glycan branching and extent of terminal fucosylation can attenuate or enhance these interactions, providing important insight into drug transport in plasma. Our study demonstrates an approach capable of investigating how protein glycosylation fine-tunes protein–drug interactions at the glycan-specific level and will prove universally useful for studying glycoprotein interactions. Altered glycosylation patterns of plasma proteins are associated with autoimmune disorders and pathogenesis of various cancers. Elucidating glycoprotein microheterogeneity and relating subtle changes in the glycan structural repertoire to changes in protein–protein, or protein–small molecule interactions, remains a significant challenge in glycobiology. Here, we apply mass spectrometry-based approaches to elucidate the global and site-specific microheterogeneity of two plasma proteins: α1-acid glycoprotein (AGP) and haptoglobin (Hp). We then determine the dissociation constants of the anticoagulant warfarin to different AGP glycoforms and reveal how subtle N-glycan differences, namely, increased antennae branching and terminal fucosylation, reduce drug-binding affinity. Conversely, similar analysis of the haptoglobin–hemoglobin (Hp–Hb) complex reveals the contrary effects of fucosylation and N-glycan branching on Hp–Hb interactions. Taken together, our results not only elucidate how glycoprotein microheterogeneity regulates protein–drug/protein interactions but also inform the pharmacokinetics of plasma proteins, many of which are drug targets, and whose glycosylation status changes in various disease states.
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Kurogochi M, Mizuno M, Matsuda A. Binding Assessment of Monosaccharide-Boronic Acid Complexes via Tandem Mass Spectrometry. ChemistrySelect 2018. [DOI: 10.1002/slct.201800555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Masaki Kurogochi
- Laboratory of Glyco-Organic Chemistry; The Noguchi Institute, 1-9-7 Kaga, Itabashi-ku; Tokyo JAPAN
| | - Mamoru Mizuno
- Laboratory of Glyco-Organic Chemistry; The Noguchi Institute, 1-9-7 Kaga, Itabashi-ku; Tokyo JAPAN
| | - Akio Matsuda
- Laboratory of Glyco-Organic Chemistry; The Noguchi Institute, 1-9-7 Kaga, Itabashi-ku; Tokyo JAPAN
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Franc V, Zhu J, Heck AJR. Comprehensive Proteoform Characterization of Plasma Complement Component C8αβγ by Hybrid Mass Spectrometry Approaches. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1099-1110. [PMID: 29532326 PMCID: PMC6003997 DOI: 10.1007/s13361-018-1901-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/12/2018] [Accepted: 01/13/2018] [Indexed: 09/27/2023]
Abstract
The human complement hetero-trimeric C8αβγ (C8) protein assembly (~ 150 kDa) is an important component of the membrane attack complex (MAC). C8 initiates membrane penetration and coordinates MAC pore formation. Here, we charted in detail the structural micro-heterogeneity within C8, purified from human plasma, combining high-resolution native mass spectrometry and (glyco)peptide-centric proteomics. The intact C8 proteoform profile revealed at least ~ 20 co-occurring MS signals. Additionally, we employed ion exchange chromatography to separate purified C8 into four distinct fractions. Their native MS analysis revealed even more detailed structural micro-heterogeneity on C8. Subsequent peptide-centric analysis, by proteolytic digestion of C8 and LC-MS/MS, provided site-specific quantitative profiles of different types of C8 glycosylation. Combining all this data provides a detailed specification of co-occurring C8 proteoforms, including experimental evidence on N-glycosylation, C-mannosylation, and O-glycosylation. In addition to the known N-glycosylation sites, two more N-glycosylation sites were detected on C8. Additionally, we elucidated the stoichiometry of all C-mannosylation sites in all the thrombospondin-like (TSP) domains of C8α and C8β. Lastly, our data contain the first experimental evidence of O-linked glycans located on C8γ. Albeit low abundant, these O-glycans are the first PTMs ever detected on this subunit. By placing the observed PTMs in structural models of free C8 and C8 embedded in the MAC, it may be speculated that some of the newly identified modifications may play a role in the MAC formation. Graphical Abstract ᅟ.
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Affiliation(s)
- Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jing Zhu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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