1
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Liu C, Otsuka K, Kawai T. Recent advances in microscale separation techniques for glycome analysis. J Sep Sci 2024; 47:e2400170. [PMID: 38863084 DOI: 10.1002/jssc.202400170] [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: 03/04/2024] [Revised: 05/12/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024]
Abstract
The glycomic analysis holds significant appeal due to the diverse roles that glycans and glycoconjugates play, acting as modulators and mediators in cellular interactions, cell/organism structure, drugs, energy sources, glyconanomaterials, and more. The glycomic analysis relies on liquid-phase separation technologies for molecular purification, separation, and identification. As a miniaturized form of liquid-phase separation technology, microscale separation technologies offer various advantages such as environmental friendliness, high resolution, sensitivity, fast speed, and integration capabilities. For glycan analysis, microscale separation technologies are continuously evolving to address the increasing challenges in their unique manners. This review discusses the fundamentals and applications of microscale separation technologies for glycomic analysis. It covers liquid-phase separation technologies operating at scales generally less than 100 µm, including capillary electrophoresis, nanoflow liquid chromatography, and microchip electrophoresis. We will provide a brief overview of glycomic analysis and describe new strategies in microscale separation and their applications in glycan analysis from 2014 to 2023.
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Affiliation(s)
- Chenchen Liu
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Research Administration Center, Osaka Metropolitan University, Osaka, Japan
| | - Takayuki Kawai
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan
- RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
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2
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Quintana JI, Delgado S, Rábano M, Azkargorta M, Florencio-Zabaleta M, Unione L, Vivanco MDM, Elortza F, Jiménez-Barbero J, Ardá A. The impact of glycosylation on the structure, function, and interactions of CD14. Glycobiology 2024; 34:cwae002. [PMID: 38227775 PMCID: PMC10987292 DOI: 10.1093/glycob/cwae002] [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: 10/02/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/18/2024] Open
Abstract
CD14 is an innate immune receptor that senses pathogen-associated molecular patterns, such as lipopolysaccharide, to activate the innate immune response. Although CD14 is known to be glycosylated, detailed understanding about the structural and functional significance of this modification is still missing. Herein, an NMR and MS-based study, assisted by MD simulations, has provided a 3D-structural model of glycosylated CD14. Our results reveal the existence of a key N-glycosylation site at Asn282 that exclusively contains unprocessed oligomannnose N-glycans that perfectly fit the concave cavity of the bent-solenoid shaped protein. This site is not accessible to glycosidases and is fundamental for protein folding and secretion. A second N-site at Asn151 displays mostly complex N-glycans, with the typical terminal epitopes of the host cell-line expression system (i.e. βGal, α2,3 and α2,6 sialylated βGal, here), but also particularities, such as the lack of core fucosylation. The glycan at this site points outside the protein surface, resulting in N-glycoforms fully exposed and available for interactions with lectins. In fact, NMR experiments show that galectin-4, proposed as a binder of CD14 on monocytes to induce their differentiation into macrophages-like cells, interacts in vitro with CD14 through the recognition of the terminal glycoepitopes on Asn151. This work provides key information about CD14 glycosylation, which helps to better understand its functional roles and significance. Although protein glycosylation is known to be dynamic and influenced by many factors, some of the features found herein (presence of unprocessed N-glycans and lack of core Fuc) are likely to be protein specific.
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Affiliation(s)
- Jon Imanol Quintana
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Sandra Delgado
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Miriam Rábano
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Mirane Florencio-Zabaleta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Luca Unione
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
| | - Maria dM Vivanco
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Félix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Jesús Jiménez-Barbero
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa, Bizkaia 48940, Spain
- Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, Carlos III Health Institute, C. de Melchor Fernández Almagro, 3, Fuencarral-El Pardo, Madrid 28029, Spain
| | - Ana Ardá
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
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3
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Defant P, Regl C, Huber CG, Schubert M. The NMR signature of maltose-based glycation in full-length proteins. JOURNAL OF BIOMOLECULAR NMR 2024; 78:61-72. [PMID: 38114873 PMCID: PMC10981599 DOI: 10.1007/s10858-023-00432-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023]
Abstract
Reducing sugars can spontaneously react with free amines in protein side chains leading to posttranslational modifications (PTMs) called glycation. In contrast to glycosylation, glycation is a non-enzymatic modification with consequences on the overall charge, solubility, aggregation susceptibility and functionality of a protein. Glycation is a critical quality attribute of therapeutic monoclonal antibodies. In addition to glucose, also disaccharides like maltose can form glycation products. We present here a detailed NMR analysis of the Amadori product formed between proteins and maltose. For better comparison, data collection was done under denaturing conditions using 7 M urea-d4 in D2O. The here presented correlation patterns serve as a signature and can be used to identify maltose-based glycation in any protein that can be denatured. In addition to the model protein BSA, which can be readily glycated, we present data of the biotherapeutic abatacept containing maltose in its formulation buffer. With this contribution, we demonstrate that NMR spectroscopy is an independent method for detecting maltose-based glycation, that is suited for cross-validation with other methods.
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Affiliation(s)
- Pauline Defant
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Christof Regl
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Christian G Huber
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria.
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany.
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4
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Mallagaray A, Rudolph L, Lindloge M, Mölbitz J, Thomsen H, Schmelter F, Alhabash MW, Abdullah MR, Saraei R, Ehlers M, Graf T, Sina C, Petersmann A, Nauck M, Günther UL. Towards a Precise NMR Quantification of Acute Phase Inflammation Proteins from Human Serum. Angew Chem Int Ed Engl 2023; 62:e202306154. [PMID: 37341676 DOI: 10.1002/anie.202306154] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 06/22/2023]
Abstract
Nuclear Magnetic Resonance (NMR) spectra of human serum and plasma show, besides metabolites and lipoproteins, two characteristic signals termed GlycA and B arising from the acetyl groups of glycoprotein glycans from acute phase proteins, which constitute good markers for inflammatory processes. Here, we report a comprehensive assignment of glycoprotein glycan NMR signals observed in human serum, showing that GlycA and GlycB signals originate from Neu5Ac and GlcNAc moieties from N-glycans, respectively. Diffusion-edited NMR experiments demonstrate that signal components can be associated with specific acute phase proteins. Conventionally determined concentrations of acute phase glycoproteins correlate well with distinct features in NMR spectra (R2 up to 0.9422, p-value <0.001), allowing the simultaneous quantification of several acute phase inflammation proteins. Overall, a proteo-metabolomics NMR signature of significant diagnostic potential is obtained within 10-20 min acquisition time. This is exemplified in serum samples from COVID-19 and cardiogenic shock patients showing significant changes in several acute phase proteins compared to healthy controls.
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Affiliation(s)
- Alvaro Mallagaray
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Lorena Rudolph
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Melissa Lindloge
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Jarne Mölbitz
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Henrik Thomsen
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Franziska Schmelter
- Institute of Nutritional Medicine, University of Lübeck and Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Mohamad Ward Alhabash
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Mohammed R Abdullah
- Institute of Clinical Chemistry and Laboratory Medicine, Greifswald University Hospital, Fleischmannstraße 8, 17475, Greifswald, Germany
| | - Roza Saraei
- Department of Cardiology, Angiology and Intensive Care Medicine, University Heart Center Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- German Centre for Cardiogenic Vascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany
| | - Marc Ehlers
- Institute of Nutritional Medicine, University of Lübeck and Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Tobias Graf
- Department of Cardiology, Angiology and Intensive Care Medicine, University Heart Center Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- German Centre for Cardiogenic Vascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany
| | - Christian Sina
- Institute of Nutritional Medicine, University of Lübeck and Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering (IMTE), Mönkhofer Weg 239 a, 23538, Lübeck, Germany
| | - Astrid Petersmann
- Institute of Clinical Chemistry and Laboratory Medicine, Greifswald University Hospital, Fleischmannstraße 8, 17475, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, Carl von Ossietzky University, Ammerländer Heerstraße 114-118, 26129, Oldenburg, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, Greifswald University Hospital, Fleischmannstraße 8, 17475, Greifswald, Germany
- German Centre for Cardiogenic Vascular Research (DZHK), Partner Site Greifswald, University Medicine, Greifswald, Germany
| | - Ulrich L Günther
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
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5
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Moises JE, Regl C, Hinterholzer A, Huber CG, Schubert M. Unambiguous Identification of Glucose-Induced Glycation in mAbs and other Proteins by NMR Spectroscopy. Pharm Res 2023; 40:1341-1353. [PMID: 36510116 PMCID: PMC10338404 DOI: 10.1007/s11095-022-03454-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Glycation is a non-enzymatic and spontaneous post-translational modification (PTM) generated by the reaction between reducing sugars and primary amine groups within proteins. Because glycation can alter the properties of proteins, it is a critical quality attribute of therapeutic monoclonal antibodies (mAbs) and should therefore be carefully monitored. The most abundant product of glycation is formed by glucose and lysine side chains resulting in fructoselysine after Amadori rearrangement. In proteomics, which routinely uses a combination of chromatography and mass spectrometry to analyze PTMs, there is no straight-forward way to distinguish between glycation products of a reducing monosaccharide and an additional hexose within a glycan, since both lead to a mass difference of 162 Da. METHODS To verify that the observed mass change is indeed a glycation product, we developed an approach based on 2D NMR spectroscopy spectroscopy and full-length protein samples denatured using high concentrations of deuterated urea. RESULTS The dominating β-pyranose form of the Amadori product shows a characteristic chemical shift correlation pattern in 1H-13C HSQC spectra suited to identify glucose-induced glycation. The same pattern was observed in spectra of a variety of artificially glycated proteins, including two mAbs, as well as natural proteins. CONCLUSION Based on this unique correlation pattern, 2D NMR spectroscopy can be used to unambiguously identify glucose-induced glycation in any protein of interest. We provide a robust method that is orthogonal to MS-based methods and can also be used for cross-validation.
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Affiliation(s)
- Jennifer E Moises
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Christof Regl
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Arthur Hinterholzer
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Christian G Huber
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.
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6
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Trastoy B, Du JJ, Cifuente JO, Rudolph L, García-Alija M, Klontz EH, Deredge D, Sultana N, Huynh CG, Flowers MW, Li C, Sastre DE, Wang LX, Corzana F, Mallagaray A, Sundberg EJ, Guerin ME. Mechanism of antibody-specific deglycosylation and immune evasion by Streptococcal IgG-specific endoglycosidases. Nat Commun 2023; 14:1705. [PMID: 36973249 PMCID: PMC10042849 DOI: 10.1038/s41467-023-37215-3] [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: 06/19/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
Bacterial pathogens have evolved intricate mechanisms to evade the human immune system, including the production of immunomodulatory enzymes. Streptococcus pyogenes serotypes secrete two multi-modular endo-β-N-acetylglucosaminidases, EndoS and EndoS2, that specifically deglycosylate the conserved N-glycan at Asn297 on IgG Fc, disabling antibody-mediated effector functions. Amongst thousands of known carbohydrate-active enzymes, EndoS and EndoS2 represent just a handful of enzymes that are specific to the protein portion of the glycoprotein substrate, not just the glycan component. Here, we present the cryoEM structure of EndoS in complex with the IgG1 Fc fragment. In combination with small-angle X-ray scattering, alanine scanning mutagenesis, hydrolytic activity measurements, enzyme kinetics, nuclear magnetic resonance and molecular dynamics analyses, we establish the mechanisms of recognition and specific deglycosylation of IgG antibodies by EndoS and EndoS2. Our results provide a rational basis from which to engineer novel enzymes with antibody and glycan selectivity for clinical and biotechnological applications.
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Affiliation(s)
- Beatriz Trastoy
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Javier O Cifuente
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Lorena Rudolph
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Mikel García-Alija
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Erik H Klontz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Nazneen Sultana
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chau G Huynh
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Maria W Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Diego E Sastre
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Francisco Corzana
- Departamento Química and Centro de Investigación en Síntesis Quı́mica, Universidad de La Rioja, 26006, Rioja, Spain
| | - Alvaro Mallagaray
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, Ratzeburger Allee 160, 23562, Lübeck, Germany.
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
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7
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Lenza M, Atxabal U, Nycholat C, Oyenarte I, Franconetti A, Quintana JI, Delgado S, Núñez-Franco R, Garnica Marroquín CT, Coelho H, Unione L, Jiménez-Oses G, Marcelo F, Schubert M, Paulson JC, Jiménez-Barbero J, Ereño-Orbea J. Structures of the Inhibitory Receptor Siglec-8 in Complex with a High-Affinity Sialoside Analogue and a Therapeutic Antibody. JACS AU 2023; 3:204-215. [PMID: 36711084 PMCID: PMC9875244 DOI: 10.1021/jacsau.2c00592] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/18/2023]
Abstract
Human sialic acid binding immunoglobulin-like lectin-8 (Siglec-8) is an inhibitory receptor that triggers eosinophil apoptosis and can inhibit mast cell degranulation when engaged by specific monoclonal antibodies (mAbs) or sialylated ligands. Thus, Siglec-8 has emerged as a critical negative regulator of inflammatory responses in diverse diseases, such as allergic airway inflammation. Herein, we have deciphered the molecular recognition features of the interaction of Siglec-8 with the mAb lirentelimab (2C4, under clinical development) and with a sialoside mimetic with the potential to suppress mast cell degranulation. The three-dimensional structure of Siglec-8 and the fragment antigen binding (Fab) portion of the anti-Siglec-8 mAb 2C4, solved by X-ray crystallography, reveal that 2C4 binds close to the carbohydrate recognition domain (V-type Ig domain) on Siglec-8. We have also deduced the binding mode of a high-affinity analogue of its sialic acid ligand (9-N-napthylsufonimide-Neu5Ac, NSANeuAc) using a combination of NMR spectroscopy and X-ray crystallography. Our results show that the sialoside ring of NSANeuAc binds to the canonical sialyl binding pocket of the Siglec receptor family and that the high affinity arises from the accommodation of the NSA aromatic group in a nearby hydrophobic patch formed by the N-terminal tail and the unique G-G' loop. The results reveal the basis for the observed high affinity of this ligand and provide clues for the rational design of the next generation of Siglec-8 inhibitors. Additionally, the specific interactions between Siglec-8 and the N-linked glycans present on the high-affinity receptor FcεRIα have also been explored by NMR.
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Affiliation(s)
- Maria
Pia Lenza
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
| | - Unai Atxabal
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
| | - Corwin Nycholat
- Department
of Molecular Medicine and Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California92037, United States
| | - Iker Oyenarte
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
| | - Antonio Franconetti
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
| | - Jon Imanol Quintana
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
| | - Sandra Delgado
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
| | - Reyes Núñez-Franco
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
| | | | - Helena Coelho
- UCIBIO,
REQUIMTE, Departamento de Química, Faculdade de Ciências
e Tecnologia, Universidade de Nova de Lisboa, Caparica2829-516, Portugal
| | - Luca Unione
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
| | - Gonzalo Jiménez-Oses
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
- IKERBASQUE, Basque
Foundation for Science and Technology, Euskadi Plaza 5, Bilbao48009, Spain
| | - Filipa Marcelo
- UCIBIO,
REQUIMTE, Departamento de Química, Faculdade de Ciências
e Tecnologia, Universidade de Nova de Lisboa, Caparica2829-516, Portugal
| | - Mario Schubert
- Department
of Biosciences, University of Salzburg, Hellbrunnel Str. 34, Salzburg5020, Austria
| | - James C. Paulson
- Department
of Molecular Medicine and Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California92037, United States
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
- Department
of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, Leioa48940, Spain
- IKERBASQUE, Basque
Foundation for Science and Technology, Euskadi Plaza 5, Bilbao48009, Spain
- Centro
de Investigacion Biomedica En Red de Enfermedades Respiratorias, Madrid28029, Spain
| | - June Ereño-Orbea
- CIC
bioGUNE, Bizkaia Technology Park, Building 800, Derio-Bizkaia48160, Spain
- IKERBASQUE, Basque
Foundation for Science and Technology, Euskadi Plaza 5, Bilbao48009, Spain
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8
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Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
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Affiliation(s)
- Carolina Fontana
- Departamento
de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden,
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9
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Mao L, Schneider JW, Robinson AS. Progress toward rapid, at-line N-glycosylation detection and control for recombinant protein expression. Curr Opin Biotechnol 2022; 78:102788. [PMID: 36126382 DOI: 10.1016/j.copbio.2022.102788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/06/2022] [Accepted: 08/07/2022] [Indexed: 12/14/2022]
Abstract
Proteins continue to represent a large fraction of the therapeutics market, reaching over a hundred billion dollars in market size globally. One key feature of protein modification that can affect both structure and function is the addition of glycosylation following protein folding, leading to regulatory requirements for the accurate assessment of protein attributes, including glycan structures. The non-template-driven, innately heterogeneous N-glycosylation process thus requires accurate detection to robustly generate protein therapies. A challenge exists in the timely detection of protein glycosylation without labor-intensive manipulation. In this article, we discuss progress toward N-glycoprotein control, focusing on novel control strategies and the advancement of rapid, high-throughput analysis methods.
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Affiliation(s)
- Leran Mao
- Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA
| | - James W Schneider
- Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA
| | - Anne S Robinson
- Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA.
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10
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Li H, Chiang AWT, Lewis NE. Artificial intelligence in the analysis of glycosylation data. Biotechnol Adv 2022; 60:108008. [PMID: 35738510 PMCID: PMC11157671 DOI: 10.1016/j.biotechadv.2022.108008] [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: 01/08/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022]
Abstract
Glycans are complex, yet ubiquitous across biological systems. They are involved in diverse essential organismal functions. Aberrant glycosylation may lead to disease development, such as cancer, autoimmune diseases, and inflammatory diseases. Glycans, both normal and aberrant, are synthesized using extensive glycosylation machinery, and understanding this machinery can provide invaluable insights for diagnosis, prognosis, and treatment of various diseases. Increasing amounts of glycomics data are being generated thanks to advances in glycoanalytics technologies, but to maximize the value of such data, innovations are needed for analyzing and interpreting large-scale glycomics data. Artificial intelligence (AI) provides a powerful analysis toolbox in many scientific fields, and here we review state-of-the-art AI approaches on glycosylation analysis. We further discuss how models can be analyzed to gain mechanistic insights into glycosylation machinery and how the machinery shapes glycans under different scenarios. Finally, we propose how to leverage the gained knowledge for developing predictive AI-based models of glycosylation. Thus, guiding future research of AI-based glycosylation model development will provide valuable insights into glycosylation and glycan machinery.
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Affiliation(s)
- Haining Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Austin W T Chiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
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11
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Proceedings of workshop: "Neuroglycoproteins in health and disease", INNOGLY cost action. Glycoconj J 2022; 39:579-586. [PMID: 36001187 PMCID: PMC9399589 DOI: 10.1007/s10719-022-10078-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/27/2022]
Abstract
The Cost Action "Innovation with glycans: new frontiers from synthesis to new biological targets" (INNOGLY) hosted the Workshop "Neuroglycoproteins in health and disease", in Alicante, Spain, on March 2022. This event brought together an european group of scientists that presented novel insights into changes in glycosylation in diseases of the central nervous system and cancer, as well as new techniques to study protein glycosylation. Herein we provide the abstracts of all the presentations.
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12
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Hinterholzer A, Moises J, Regl C, Schwap S, Rapp E, Huber CG, Schubert M. Unambiguous identification of α-Gal epitopes in intact monoclonal antibodies by NMR spectroscopy. MAbs 2022; 14:2132977. [PMID: 36239533 PMCID: PMC9578466 DOI: 10.1080/19420862.2022.2132977] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The α-Gal epitope consisting of the terminal trisaccharide Galα1,3Galβ1,4GlcNAc exposed on cell or protein surfaces can cause severe immune reactions, such as hypersensitivity reactions, in humans. This epitope is also called the xenotransplantation epitope because it is one of the main reasons for the rejection of non-human organ transplants by the human innate immune response. Recombinant therapeutic proteins expressed in murine cell lines may contain α-Gal epitopes, and therefore their absence or presence needs to be tightly monitored to minimize any undesired adverse effects. The analytical identification of α-Gal epitopes in glycoproteins using the common standard techniques based on liquid chromatography and mass spectrometry is challenging, mainly due to the isobaricity of hexose stereoisomers. Here, we present a straightforward NMR approach to detect the presence of α-Gal in biotherapeutics based on a quick screen with sensitive 1H-1H TOCSY spectra followed by a confirmation using 1H-13C HSQC spectra.Abbreviations: α-Gal: α1,3-linked galactose; AGC: automatic gain control; CHO: Chinese hamster ovary; CE: capillary electrophoreses coupled to mass spectrometry; COSY: correlation spectroscopy; DSS: 2,2-dimethyl-2-silapentane-5-sulfonate; DTT: dithiothreitol; GlcNAc: N-acetyl glusomamine; HCD: higher-energy collisional dissociation; HMBC: heteronuclear multiple-bond correlation; HPLC: high-performance liquid chromatography; HSQC: heteronuclear single-quantum corre; LacNAc: N-acetyl lactosamine; mAb: monoclonal antibody; MS: mass spectrometry; NMR: nuclear magnetic resonance; NOESY: 2D) nuclear Overhauser spectroscopy; PEG: polyethylenglycol; pH*: observed pH meter reading without correction for isotope effects; PTM: post-translational modification; TCEP: tris(2-carboxyethyl) phosphine hydrochloride; TOCSY: total correlation spectroscopy; xCGE-LIF: multiplex capillary gel electrophoresis with laser-induced fluorescence detection.
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Affiliation(s)
- Arthur Hinterholzer
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria,Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Jennifer Moises
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Christof Regl
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria,Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Sebastian Schwap
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria,Bundesrealgymnasium Salzburg, Salzburg, Austria
| | - Erdmann Rapp
- glyXera GmbH, Brenneckestraße, Magdeburg, Germany,Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Christian G. Huber
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria,Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Mario Schubert
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria,Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria,CONTACT Mario Schubert Department of Biosciences and Medical Biology,University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
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13
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Abstract
Glycosylation, one of the most common post-translational modifications in mammalian cells, impacts many biological processes such as cell adhesion, proliferation and differentiation. As the most abundant glycoprotein in human serum, immunoglobulin G (IgG) plays a vital role in immune response and protection. There is a growing body of evidence suggests that IgG structure and function are modulated by attached glycans, especially N-glycans, and aberrant glycosylation is associated with disease states. In this chapter, we review IgG glycan repertoire and function, strategies for profiling IgG N-glycome and recent studies. Mass spectrometry (MS) based techniques are the most powerful tools for profiling IgG glycome. IgG glycans can be divided into high-mannose, biantennary complex and hybrid types, modified with mannosylation, core-fucosylation, galactosylation, bisecting GlcNAcylation, or sialylation. Glycosylation of IgG affects antibody half-life and their affinity and avidity for antigens, regulates crystallizable fragment (Fc) structure and Fcγ receptor signaling, as well as antibody effector function. Because of their critical roles, IgG N-glycans appear to be promising biomarkers for various disease states. Specific IgG glycosylation can convert a pro-inflammatory response to an anti-inflammatory activity. Accordingly, IgG glycoengineering provides a powerful approach to potentially develop effective drugs and treat disease. Based on the understanding of the functional role of IgG glycans, the development of vaccines with enhanced capacity and long-term protection are possible in the near future.
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14
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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15
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Hargett AA, Marcella AM, Yu H, Li C, Orwenyo J, Battistel MD, Wang LX, Freedberg DI. Glycosylation States on Intact Proteins Determined by NMR Spectroscopy. Molecules 2021; 26:molecules26144308. [PMID: 34299586 PMCID: PMC8303171 DOI: 10.3390/molecules26144308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/23/2022] Open
Abstract
Protein glycosylation is important in many organisms for proper protein folding, signaling, cell adhesion, protein-protein interactions, and immune responses. Thus, effectively determining the extent of glycosylation in glycoprotein therapeutics is crucial. Up to now, characterizing protein glycosylation has been carried out mostly by liquid chromatography mass spectrometry (LC-MS), which requires careful sample processing, e.g., glycan removal or protein digestion and glycopeptide enrichment. Herein, we introduce an NMR-based method to better characterize intact glycoproteins in natural abundance. This non-destructive method relies on exploiting differences in nuclear relaxation to suppress the NMR signals of the protein while maintaining glycan signals. Using RNase B Man5 and RNase B Man9, we establish reference spectra that can be used to determine the different glycoforms present in heterogeneously glycosylated commercial RNase B.
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Affiliation(s)
- Audra A. Hargett
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Aaron M. Marcella
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Huifeng Yu
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Jared Orwenyo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Marcos D. Battistel
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Darón I. Freedberg
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
- Correspondence:
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16
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Cañada FJ, Canales Á, Valverde P, de Toro BF, Martínez-Orts M, Phillips PO, Pereda A. Conformational and Structural characterization of carbohydrates and their interactions studied by NMR. Curr Med Chem 2021; 29:1147-1172. [PMID: 34225601 DOI: 10.2174/0929867328666210705154046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.
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Affiliation(s)
- Francisco Javier Cañada
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Pablo Valverde
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Beatriz Fernández de Toro
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Mónica Martínez-Orts
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Paola Oquist Phillips
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Amaia Pereda
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
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17
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Höfurthner T, Mateos B, Konrat R. On-Cell NMR Contributions to Membrane Receptor Binding Characterization. Chempluschem 2021; 86:938-945. [PMID: 34160899 DOI: 10.1002/cplu.202100134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/28/2021] [Indexed: 12/21/2022]
Abstract
NMR spectroscopy has matured into a powerful tool to characterize interactions between biological molecules at atomic resolution, most importantly even under near to native (physiological) conditions. The field of in-cell NMR aims to study proteins and nucleic acids inside living cells. However, cells interrogate their environment and are continuously modulated by external stimuli. Cell signaling processes are often initialized by membrane receptors on the cell surface; therefore, characterizing their interactions at atomic resolution by NMR, hereafter referred as on-cell NMR, can provide valuable mechanistic information. This review aims to summarize recent on-cell NMR tools that give information about the binding site and the affinity of membrane receptors to their ligands together with potential applications to in vivo drug screening systems.
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Affiliation(s)
- Theresa Höfurthner
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
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18
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Bryan L, Clynes M, Meleady P. The emerging role of cellular post-translational modifications in modulating growth and productivity of recombinant Chinese hamster ovary cells. Biotechnol Adv 2021; 49:107757. [PMID: 33895332 DOI: 10.1016/j.biotechadv.2021.107757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023]
Abstract
Chinese hamster ovary (CHO) cells are one of the most commonly used host cell lines used for the production human therapeutic proteins. Much research over the past two decades has focussed on improving the growth, titre and cell specific productivity of CHO cells and in turn lowering the costs associated with production of recombinant proteins. CHO cell engineering has become of particular interest in recent years following the publication of the CHO cell genome and the availability of data relating to the proteome, transcriptome and metabolome of CHO cells. However, data relating to the cellular post-translational modification (PTMs) which can affect the functionality of CHO cellular proteins has only begun to be presented in recent years. PTMs are important to many cellular processes and can further alter proteins by increasing the complexity of proteins and their interactions. In this review, we describe the research presented from CHO cells to date related on three of the most important PTMs; glycosylation, phosphorylation and ubiquitination.
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Affiliation(s)
- Laura Bryan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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19
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Mateos B, Holzinger J, Conrad-Billroth C, Platzer G, Żerko S, Sealey-Cardona M, Anrather D, Koźmiński W, Konrat R. Hyperphosphorylation of Human Osteopontin and Its Impact on Structural Dynamics and Molecular Recognition. Biochemistry 2021; 60:1347-1355. [PMID: 33876640 PMCID: PMC8154273 DOI: 10.1021/acs.biochem.1c00050] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein phosphorylation is an abundant post-translational modification (PTM) and an essential modulator of protein functionality in living cells. Intrinsically disordered proteins (IDPs) are particular targets of PTM protein kinases due to their involvement in fundamental protein interaction networks. Despite their dynamic nature, IDPs are far from having random-coil conformations but exhibit significant structural heterogeneity. Changes in the molecular environment, most prominently in the form of PTM via phosphorylation, can modulate these structural features. Therefore, how phosphorylation events can alter conformational ensembles of IDPs and their interactions with binding partners is of great interest. Here we study the effects of hyperphosphorylation on the IDP osteopontin (OPN), an extracellular target of the Fam20C kinase. We report a full characterization of the phosphorylation sites of OPN using a combined nuclear magnetic resonance/mass spectrometry approach and provide evidence for an increase in the local flexibility of highly phosphorylated regions and the ensuing overall structural elongation. Our study emphasizes the simultaneous importance of electrostatic and hydrophobic interactions in the formation of compact substates in IDPs and their relevance for molecular recognition events.
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Affiliation(s)
- Borja Mateos
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna BioCenter Campus 5, 1030 Vienna, Austria
| | - Julian Holzinger
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna BioCenter Campus 5, 1030 Vienna, Austria
| | - Clara Conrad-Billroth
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna BioCenter Campus 5, 1030 Vienna, Austria
| | - Gerald Platzer
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna BioCenter Campus 5, 1030 Vienna, Austria
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093 Warsaw, Poland
| | | | - Dorothea Anrather
- Mass Spectrometry Facility, Max Perutz Laboratories, Vienna BioCenter Campus 5, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093 Warsaw, Poland
| | - Robert Konrat
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna BioCenter Campus 5, 1030 Vienna, Austria
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20
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Lenza MP, Oyenarte I, Diercks T, Quintana JI, Gimeno A, Coelho H, Diniz A, Peccati F, Delgado S, Bosch A, Valle M, Millet O, Abrescia NGA, Palazón A, Marcelo F, Jiménez‐Osés G, Jiménez‐Barbero J, Ardá A, Ereño‐Orbea J. Structural Characterization of N-Linked Glycans in the Receptor Binding Domain of the SARS-CoV-2 Spike Protein and their Interactions with Human Lectins. Angew Chem Int Ed Engl 2020; 59:23763-23771. [PMID: 32915505 PMCID: PMC7894318 DOI: 10.1002/anie.202011015] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/08/2020] [Indexed: 01/17/2023]
Abstract
The glycan structures of the receptor binding domain of the SARS-CoV2 spike glycoprotein expressed in human HEK293F cells have been studied by using NMR. The different possible interacting epitopes have been deeply analysed and characterized, providing evidence of the presence of glycan structures not found in previous MS-based analyses. The interaction of the RBD 13 C-labelled glycans with different human lectins, which are expressed in different organs and tissues that may be affected during the infection process, has also been evaluated by NMR. In particular, 15 N-labelled galectins (galectins-3, -7 and -8 N-terminal), Siglecs (Siglec-8, Siglec-10), and C-type lectins (DC-SIGN, MGL) have been employed. Complementary experiments from the glycoprotein perspective or from the lectin's point of view have permitted to disentangle the specific interacting epitopes in each case. Based on these findings, 3D models of the interacting complexes have been proposed.
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Affiliation(s)
- Maria Pia Lenza
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Iker Oyenarte
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Tammo Diercks
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Jon Imanol Quintana
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Ana Gimeno
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Helena Coelho
- UCIBIOREQUIMTEDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516CaparicaPortugal
| | - Ana Diniz
- UCIBIOREQUIMTEDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516CaparicaPortugal
| | - Francesca Peccati
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Sandra Delgado
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Alexandre Bosch
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Mikel Valle
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Oscar Millet
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Nicola G. A. Abrescia
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Instituto de Salud Carlos IIIMadridSpain
| | - Asís Palazón
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
| | - Filipa Marcelo
- UCIBIOREQUIMTEDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516CaparicaPortugal
| | - Gonzalo Jiménez‐Osés
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Jesús Jiménez‐Barbero
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
- Department of Organic Chemistry IIUniversity of the Basque CountryUPV/EHU48940LeioaSpain
| | - Ana Ardá
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - June Ereño‐Orbea
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
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21
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Zhuo Y, Keire DA, Chen K. Minor N-Glycan Mapping of Monoclonal Antibody Therapeutics Using Middle-Down NMR Spectroscopy. Mol Pharm 2020; 18:441-450. [PMID: 33305950 DOI: 10.1021/acs.molpharmaceut.0c01083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The N-glycosylation pattern of Asn-297 may have impacts on monoclonal antibody (mAb) drug plasma clearance, antibody-dependent cell mediated cytotoxicity (ADCC), and complement-dependent cytotoxicity (CDC). Notably, the changes in the relative abundance of certain minor glycans, like the afucosylation, high-mannose, or galactosylation are known to change mAb properties and functions. Here, a middle-down NMR spectroscopy based analytical procedure was applied to assess the composition and structure of glycans on adalimumab and trastuzumab without glycan cleavage from the mAbs. The anomeric 2D 1H-13C spectra showed distinct patterns that could be used to profile and differentiate mAb glycan compositions. Specifically, the anomeric C1/H1 resonances from N-acetylglucosamine (GlcNAc2 and -5) and mannose (Man4) were identified as characteristic peaks for key glycan anomeric linkages and branching states. They were also utilized for measuring the relative abundance of minor glycans of total afucosylation (aFuc%), high mannose (HM%), and branch specific galactosylation (Gal1-3% and Gal1-6%). The obtained total aFuc% value of 11-12% was similar between the two mAbs; however, trastuzumab had significantly lower level of high mannose and a higher level of galactosylation than adalimumab. Overall, the 2D-NMR measurements provided functionally relevant mAb glycan composition and structure information. The method was deemed fit-for-purpose for assessment of these mAb quality attributes and involved fewer chemical preparation steps than the classical approaches that cleave glycans prior to making measurements.
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Affiliation(s)
- You Zhuo
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - David A Keire
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri 63110, United States
| | - Kang Chen
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
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22
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Jonker HRA, Saxena K, Shcherbakova A, Tiemann B, Bakker H, Schwalbe H. NMR Spectroscopic Characterization of the C‐Mannose Conformation in a Thrombospondin Repeat Using a Selective Labeling Approach. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe University Frankfurt Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe University Frankfurt Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Aleksandra Shcherbakova
- Institute of Clinical Biochemistry Hannover Medical School Carl-Neuberg-Strasse 1 30625 Hannover Germany
| | - Birgit Tiemann
- Institute of Clinical Biochemistry Hannover Medical School Carl-Neuberg-Strasse 1 30625 Hannover Germany
| | - Hans Bakker
- Institute of Clinical Biochemistry Hannover Medical School Carl-Neuberg-Strasse 1 30625 Hannover Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe University Frankfurt Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
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23
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Jonker HRA, Saxena K, Shcherbakova A, Tiemann B, Bakker H, Schwalbe H. NMR Spectroscopic Characterization of the C-Mannose Conformation in a Thrombospondin Repeat Using a Selective Labeling Approach. Angew Chem Int Ed Engl 2020; 59:20659-20665. [PMID: 32745319 PMCID: PMC7692951 DOI: 10.1002/anie.202009489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Indexed: 12/24/2022]
Abstract
Despite the great interest in glycoproteins, structural information reporting on conformation and dynamics of the sugar moieties are limited. We present a new biochemical method to express proteins with glycans that are selectively labeled with NMR-active nuclei. We report on the incorporation of 13 C-labeled mannose in the C-mannosylated UNC-5 thrombospondin repeat. The conformational landscape of the C-mannose sugar puckers attached to tryptophan residues of UNC-5 is characterized by interconversion between the canonical 1 C4 state and the B03 / 1 S3 state. This flexibility may be essential for protein folding and stabilization. We foresee that this versatile tool to produce proteins with selectively labeled C-mannose can be applied and adjusted to other systems and modifications and potentially paves a way to advance glycoprotein research by unravelling the dynamical and conformational properties of glycan structures and their interactions.
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Affiliation(s)
- Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Aleksandra Shcherbakova
- Institute of Clinical BiochemistryHannover Medical SchoolCarl-Neuberg-Strasse 130625HannoverGermany
| | - Birgit Tiemann
- Institute of Clinical BiochemistryHannover Medical SchoolCarl-Neuberg-Strasse 130625HannoverGermany
| | - Hans Bakker
- Institute of Clinical BiochemistryHannover Medical SchoolCarl-Neuberg-Strasse 130625HannoverGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
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24
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Unione L, Ardá A, Jiménez-Barbero J, Millet O. NMR of glycoproteins: profiling, structure, conformation and interactions. Curr Opin Struct Biol 2020; 68:9-17. [PMID: 33129067 DOI: 10.1016/j.sbi.2020.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
In glycoproteins, carbohydrates are responsible for the selective interaction and tight regulation of cellular processes, constituting the main information transducer interface in protein-glycoprotein interactions. Increasing experimental and computational evidence suggest that such interactions often induce allosteric changes in the host protein, underlining the importance of studying intact glycoproteins. Technical issues have precluded such studies for years but, nowadays, a promising era is emerging where NMR spectroscopy, among other techniques, allows the characterization of the composition, structure and segmental dynamics of glycoproteins. In this review, we discuss such advances and highlight some selected examples. This novel technology unravels multiple new functional mechanisms, subtly hidden within the sugar code.
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Affiliation(s)
- Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
| | - Oscar Millet
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain.
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25
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Lenza MP, Oyenarte I, Diercks T, Quintana JI, Gimeno A, Coelho H, Diniz A, Peccati F, Delgado S, Bosch A, Valle M, Millet O, Abrescia NGA, Palazón A, Marcelo F, Jiménez‐Osés G, Jiménez‐Barbero J, Ardá A, Ereño‐Orbea J. Structural Characterization of N‐Linked Glycans in the Receptor Binding Domain of the SARS‐CoV‐2 Spike Protein and their Interactions with Human Lectins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Maria Pia Lenza
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Iker Oyenarte
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Tammo Diercks
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Jon Imanol Quintana
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Ana Gimeno
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Helena Coelho
- UCIBIO REQUIMTE Departamento de Química Faculdade de Ciências e Tecnologia Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Ana Diniz
- UCIBIO REQUIMTE Departamento de Química Faculdade de Ciências e Tecnologia Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Francesca Peccati
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Sandra Delgado
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Alexandre Bosch
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Mikel Valle
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Oscar Millet
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Nicola G. A. Abrescia
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) Instituto de Salud Carlos III Madrid Spain
| | - Asís Palazón
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
| | - Filipa Marcelo
- UCIBIO REQUIMTE Departamento de Química Faculdade de Ciências e Tecnologia Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Gonzalo Jiménez‐Osés
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Jesús Jiménez‐Barbero
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
- Department of Organic Chemistry II University of the Basque Country UPV/EHU 48940 Leioa Spain
| | - Ana Ardá
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - June Ereño‐Orbea
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
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26
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Hinterholzer A, Stanojlovic V, Regl C, Huber CG, Cabrele C, Schubert M. Identification and Quantification of Oxidation Products in Full-Length Biotherapeutic Antibodies by NMR Spectroscopy. Anal Chem 2020; 92:9666-9673. [PMID: 32530275 PMCID: PMC7467420 DOI: 10.1021/acs.analchem.0c00965] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Therapeutic
proteins are an indispensable class of drugs and often
therapeutics of last resort. They are sensitive to oxidation, which
is of critical concern, because it can affect drug safety and efficacy.
Protein oxidation, with methionine and tryptophan as the most susceptible
moieties, is mainly monitored by HPLC–MS techniques. However,
since several oxidation products display the same mass difference,
their identification by MS is often ambiguous. Therefore, an alternative
analytical method able to unambiguously identify and, ideally, also
quantify oxidation species in proteins is highly desired. Here, we
present an NMR-based approach to monitor oxidation in full-length
proteins under denaturing conditions, as demonstrated on two biotherapeutic
monoclonal antibodies (mAbs). We show that methionine sulfoxide, methionine
sulfone, N-formylkynurenine, kynurenine, oxindolylalanine,
hydroxypyrroloindole, and 5-hydroxytryptophan result in characteristic
chemical shift correlations suited for their identification and quantification.
We identified the five most abundant oxidation products in forced
degradation studies of two full-length therapeutic mAbs and can also
unambiguously distinguish oxindolylalanine from 5-hydroxytryptophan,
which are undistinguishable by MS due to the same mass shift. Quantification
of the abundant methionine sulfoxide by NMR and MS gave highly comparable
values. These results underline the suitability of NMR spectroscopy
for the identification and quantification of critical quality attributes
of biotherapeutics.
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Affiliation(s)
- Arthur Hinterholzer
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Vesna Stanojlovic
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Christof Regl
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Christian G Huber
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Chiara Cabrele
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Mario Schubert
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
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27
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Gimeno A, Valverde P, Ardá A, Jiménez-Barbero J. Glycan structures and their interactions with proteins. A NMR view. Curr Opin Struct Biol 2019; 62:22-30. [PMID: 31835069 PMCID: PMC7322516 DOI: 10.1016/j.sbi.2019.11.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 12/28/2022]
Abstract
Carbohydrate molecules are essential actors in key biological events, being involved as recognition points for cell-cell and cell-matrix interactions related to health and disease. Despite outstanding advances in cryoEM, X-ray crystallography and NMR still remain the most employed techniques to unravel their conformational features and to describe the structural details of their interactions with biomolecular receptors. Given the intrinsic flexibility of saccharides, NMR methods are of paramount importance to deduce the extent of motion around their glycosidic linkages and to explore their receptor-bound conformations. We herein present our particular view on the latest advances in NMR methodologies that are permitting to magnify their applications for deducing glycan conformation and dynamics and understanding the recognition events in which there are involved.
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Affiliation(s)
- Ana Gimeno
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Pablo Valverde
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Ana Ardá
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain; Department of Organic Chemistry II, University of the Basque Country, UPV/EHU, 48940 Leioa, Bizkaia, Spain
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28
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Li H, Li L, Cheng K, Ning Z, Mayne J, Zhang X, Walker K, Chen R, Twine S, Li J, Figeys D. Chemoenzymatic Method for Glycoproteomic N-Glycan Type Quantitation. Anal Chem 2019; 92:1618-1627. [DOI: 10.1021/acs.analchem.9b04937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Henghui Li
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Leyuan Li
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Kai Cheng
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Zhibin Ning
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Janice Mayne
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Xu Zhang
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Krystal Walker
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Rui Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Susan Twine
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Jianjun Li
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Daniel Figeys
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto M5G 1M1, Canada
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29
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Kumar A, Narayanan V, Sekhar A. Characterizing Post-Translational Modifications and Their Effects on Protein Conformation Using NMR Spectroscopy. Biochemistry 2019; 59:57-73. [PMID: 31682116 DOI: 10.1021/acs.biochem.9b00827] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diversity of the cellular proteome substantially exceeds the number of genes coded by the DNA of an organism because one or more residues in a majority of eukaryotic proteins are post-translationally modified (PTM) by the covalent conjugation of specific chemical groups. We now know that PTMs alter protein conformation and function in ways that are not entirely understood at the molecular level. NMR spectroscopy has been particularly successful as an analytical tool in elucidating the themes underlying the structural role of PTMs. In this Perspective, we focus on the NMR-based characterization of three abundant PTMs: phosphorylation, acetylation, and glycosylation. We detail NMR methods that have found success in detecting these modifications at a site-specific level. We also highlight NMR studies that have mapped the conformational changes ensuing from these PTMs as well as evaluated their relation to function. The NMR toolbox is expanding rapidly with experiments available to probe not only the average structure of biomolecules but also how this structure changes with time on time scales ranging from picoseconds to seconds. The atomic resolution insights into the biomolecular structure, dynamics, and mechanism accessible from NMR spectroscopy ensure that NMR will continue to be at the forefront of research in the structural biology of PTMs.
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Affiliation(s)
- Ajith Kumar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
| | - Vaishali Narayanan
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
| | - Ashok Sekhar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
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30
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Valverde P, Quintana JI, Santos JI, Ardá A, Jiménez-Barbero J. Novel NMR Avenues to Explore the Conformation and Interactions of Glycans. ACS OMEGA 2019; 4:13618-13630. [PMID: 31497679 PMCID: PMC6714940 DOI: 10.1021/acsomega.9b01901] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/02/2019] [Indexed: 05/12/2023]
Abstract
This perspective article is focused on the presentation of the latest advances in NMR methods and applications that are behind the exciting achievements in the understanding of glycan receptors in molecular recognition events. Different NMR-based methodologies are discussed along with their applications to scrutinize the conformation and dynamics of glycans as well as their interactions with protein receptors.
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Affiliation(s)
- Pablo Valverde
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Jon I. Quintana
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Jose I. Santos
- SGIker
UPV/EHU, Centro Joxe Mari Korta, Tolosa Hiribidea 72, 20018 Donostia, Spain
| | - Ana Ardá
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
- E-mail: (A.A.)
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
- Department
Organic Chemistry II, Faculty Science &
Technology, EHU-UPV, 48940 Leioa, Bizkaia, Spain
- E-mail: (J.J.-B.)
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