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He M, Zhou X, Wang X. Glycosylation: mechanisms, biological functions and clinical implications. Signal Transduct Target Ther 2024; 9:194. [PMID: 39098853 PMCID: PMC11298558 DOI: 10.1038/s41392-024-01886-1] [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: 10/21/2023] [Revised: 05/25/2024] [Accepted: 06/07/2024] [Indexed: 08/06/2024] Open
Abstract
Protein post-translational modification (PTM) is a covalent process that occurs in proteins during or after translation through the addition or removal of one or more functional groups, and has a profound effect on protein function. Glycosylation is one of the most common PTMs, in which polysaccharides are transferred to specific amino acid residues in proteins by glycosyltransferases. A growing body of evidence suggests that glycosylation is essential for the unfolding of various functional activities in organisms, such as playing a key role in the regulation of protein function, cell adhesion and immune escape. Aberrant glycosylation is also closely associated with the development of various diseases. Abnormal glycosylation patterns are closely linked to the emergence of various health conditions, including cancer, inflammation, autoimmune disorders, and several other diseases. However, the underlying composition and structure of the glycosylated residues have not been determined. It is imperative to fully understand the internal structure and differential expression of glycosylation, and to incorporate advanced detection technologies to keep the knowledge advancing. Investigations on the clinical applications of glycosylation focused on sensitive and promising biomarkers, development of more effective small molecule targeted drugs and emerging vaccines. These studies provide a new area for novel therapeutic strategies based on glycosylation.
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Affiliation(s)
- Mengyuan He
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Xiangxiang Zhou
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
- Taishan Scholars Program of Shandong Province, Jinan, Shandong, 250021, China.
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, Shandong, 250021, China.
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2
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Duda HC, von Toerne C, Korbonits L, Didier A, Scholz AM, Märtlbauer E, Hauck SM, Deeg CA. Cathepsin S Is More Abundant in Serum of Mycobacterium avium subsp. paratuberculosis-Infected Dairy Cows. Metabolites 2024; 14:215. [PMID: 38668343 PMCID: PMC11051907 DOI: 10.3390/metabo14040215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of bovine paratuberculosis, a chronic granulomatous enteritis leading to economic losses and posing a risk to human health due to its zoonotic potential. The pathogen cannot reliably be detected by standard methods, and immunological procedures during the infection are not well understood. Therefore, the aim of our study was to explore host-pathogen interactions in MAP-infected dairy cows and to improve diagnostic tests. Serum proteomics analysis using quantitative label-free LC-MS/MS revealed 60 differentially abundant proteins in MAP-infected dairy cows compared to healthy controls from the same infected herd and 90 differentially abundant proteins in comparison to another control group from an uninfected herd. Pathway enrichment analysis provided new insights into the immune response to MAP and susceptibility to the infection. Furthermore, we found a higher abundance of Cathepsin S (CTSS) in the serum of MAP-infected dairy cows, which is involved in multiple enriched pathways associated with the immune system. Confirmed with Western blotting, we identified CTSS as a potential biomarker for bovine paratuberculosis. This study enabled a better understanding of procedures in the host-pathogen response to MAP and improved detection of paratuberculosis-diseased cattle.
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Affiliation(s)
- Heidi C. Duda
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
| | - Christine von Toerne
- Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health, D-85763 Neuherberg, Germany (S.M.H.)
| | - Lucia Korbonits
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
| | - Andrea Didier
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany; (A.D.)
| | - Armin M. Scholz
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany;
| | - Erwin Märtlbauer
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany; (A.D.)
| | - Stefanie M. Hauck
- Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health, D-85763 Neuherberg, Germany (S.M.H.)
| | - Cornelia A. Deeg
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
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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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Fang Z, Huang T, Chai X, Zhan J, Zhu Q, Sun P, Zeng D, Liu C, Jiang B, He L, Zhou X, Liu M, Zhang X. Protein methylation characterization using NMR without isotopic labeling. Talanta 2024; 268:125289. [PMID: 37862753 DOI: 10.1016/j.talanta.2023.125289] [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] [Received: 06/19/2023] [Revised: 09/15/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023]
Abstract
Protein methylation is crucial in epigenetics, and targeting the involved methyltransferases shows great potential for therapeutic intervention with several inhibitors in clinical trials for oncology indications. Therefore, characterization of protein methylation is essential for understanding the methyltransferase function and discovering chemical inhibitors and antagonists. While NMR has been used to measure methylation rates, isotopic labeling of protein or methyl donors can be costly and cannot characterize demethylation of proteins extracted from natural sources. Our method employs a four-quantum filter 1H-13C experiment that selectively detects methyl groups, providing a simple way to characterize methylation and demethylation features of methyltransferases and demethylases, respectively, without requiring isotopic labeling. In our experiments, we successfully observed the methylation of H3 under lysate from various cells and tissues of mice with cancerous growth. The results revealed that H3 undergoes both mono- and dimethylation in all the tested lysates, but at varying rates and degrees. Significantly lower H3 methylation rates and levels were observed in both cervical tumor and breast tumor lysates compared with the corresponding cancerous cells and healthy cells lysates. These findings highlight the variability of histone H3 methylation patterns among healthy cells, cancerous cells, tumor tissues, and different tumor types, and suggest that this method has great potential in facilitating the development of effective interventions against these diseases. By characterizing the methylation features of suspected tumors or areas of concern, it provides valuable insights into the underlying mechanisms of cancer development and aids in identifying potential targets for therapeutic interventions.
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Affiliation(s)
- Zhongpei Fang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Huang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xin Chai
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhua Zhan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Qinjun Zhu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Peng Sun
- Philips Healthcare, Wuhan, 430071, China
| | - Danyun Zeng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caixiang Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; Optics Valley Laboratory, Wuhan, 430074, China
| | - Lichun He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; Optics Valley Laboratory, Wuhan, 430074, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; Optics Valley Laboratory, Wuhan, 430074, China.
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; Optics Valley Laboratory, Wuhan, 430074, China.
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5
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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: 4] [Impact Index Per Article: 4.0] [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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6
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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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7
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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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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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Ma J, Pathirana C, Liu DQ, Miller SA. NMR spectroscopy as a characterization tool enabling biologics formulation development. J Pharm Biomed Anal 2023; 223:115110. [DOI: 10.1016/j.jpba.2022.115110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022]
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10
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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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11
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Vogl DP, Conibear AC, Becker CFW. Segmental and site-specific isotope labelling strategies for structural analysis of posttranslationally modified proteins. RSC Chem Biol 2021; 2:1441-1461. [PMID: 34704048 PMCID: PMC8496066 DOI: 10.1039/d1cb00045d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
Posttranslational modifications can alter protein structures, functions and locations, and are important cellular regulatory and signalling mechanisms. Spectroscopic techniques such as nuclear magnetic resonance, infrared and Raman spectroscopy, as well as small-angle scattering, can provide insights into the structural and dynamic effects of protein posttranslational modifications and their impact on interactions with binding partners. However, heterogeneity of modified proteins from natural sources and spectral complexity often hinder analyses, especially for large proteins and macromolecular assemblies. Selective labelling of proteins with stable isotopes can greatly simplify spectra, as one can focus on labelled residues or segments of interest. Employing chemical biology tools for modifying and isotopically labelling proteins with atomic precision provides access to unique protein samples for structural biology and spectroscopy. Here, we review site-specific and segmental isotope labelling methods that are employed in combination with chemical and enzymatic tools to access posttranslationally modified proteins. We discuss illustrative examples in which these methods have been used to facilitate spectroscopic studies of posttranslationally modified proteins, providing new insights into biology.
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Affiliation(s)
- Dominik P Vogl
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
| | - Anne C Conibear
- The University of Queensland, School of Biomedical Sciences St Lucia Brisbane 4072 QLD Australia
| | - Christian F W Becker
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
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12
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Balli OI, Uversky VN, Durdagi S, Coskuner-Weber O. Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective. Proteins 2021; 90:322-339. [PMID: 34549826 DOI: 10.1002/prot.26242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 11/08/2022]
Abstract
Experimenters face challenges and limitations while analyzing glycoproteins due to their high flexibility, stereochemistry, anisotropic effects, and hydration phenomena. Computational studies complement experiments and have been used in characterization of the structural properties of glycoproteins. However, recent investigations revealed that computational studies face significant challenges as well. Here, we introduce and discuss some of these challenges and weaknesses in the investigations of glycoproteins. We also present requirements of future developments in computational biochemistry and computational biology areas that could be necessary for providing more accurate structural property analyses of glycoproteins using computational tools. Further theoretical strategies that need to be and can be developed are discussed herein.
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Affiliation(s)
- Oyku Irem Balli
- Molecular Biotechnology, Turkish-German University, Istanbul, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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13
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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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14
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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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15
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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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/13/2021] [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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16
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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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17
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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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18
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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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19
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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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20
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Andjelković U, Gudelj I, Klarić T, Hinneburg H, Vinković M, Wittine K, Dovezenski N, Vikić-Topić D, Lauc G, Vujčić Z, Josić D. Increased yield of enzymatic synthesis by chromatographic selection of different N-glycoforms of yeast invertase. Electrophoresis 2020; 42:2626-2636. [PMID: 33026663 DOI: 10.1002/elps.202000092] [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] [Received: 04/20/2020] [Revised: 09/20/2020] [Accepted: 09/28/2020] [Indexed: 11/10/2022]
Abstract
Invertases are glycosidases applied for synthesis of alkyl glycosides that are important and effective surfactants. Stability of invertases in the environment with increased content of organic solvent is crucial for increase of productivity of glycosidases. Their stability is significantly influenced by N-glycosylation. However, yeast N-glycosylation pathways may synthesize plethora of N-glycan structures. A total natural crude mixture of invertase glycoforms (EINV) extracted from Saccharomyces cerevisiae was subfractionated by anion-exchange chromatography on industrial monolithic supports to obtain different glycoforms (EINV1-EINV3). Separated glycoforms exhibited different stabilities in water-alcohol solutions that are in direct correlation with the amount of phosphate bound to N-glycans. Observed differences in stability of different invertase glycoforms were used to improve productivity of methyl β-d-fructofuranoside (MF) synthesis. The efficiency and yield of MF synthesis were improved more than 50% when the most stabile glycoform bearing the lowest amount of phosphorylated N-glycans is selected and utilized. These data underline the importance of analysis of glycan structures attached to glycoproteins, demonstrate different impact of N-glycans on the surface charge and enzyme stability in regard to particular reaction environment, and provide a platform for improvement of yield of industrial enzymatic synthesis by chromatographic selection of glycoforms on monolithic supports.
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Affiliation(s)
- Uroš Andjelković
- University of Belgrade-Institute of Chemistry, Technology and Metallurgy-National Institute of the Republic of Serbia, Belgrade, Serbia.,Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Ivan Gudelj
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Thomas Klarić
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Hannes Hinneburg
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | | | - Karlo Wittine
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Nebojša Dovezenski
- Institute for Medical Research, University of Belgrade, Belgrade, Serbia
| | - Dražen Vikić-Topić
- NMR Centre, Ruđer Bošković Institute, Zagreb, Croatia.,Department of Natural and Health Sciences, Juraj Dobrila University of Pula, Pula, Croatia
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Zoran Vujčić
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
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21
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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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22
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Majewska NI, Tejada ML, Betenbaugh MJ, Agarwal N. N-Glycosylation of IgG and IgG-Like Recombinant Therapeutic Proteins: Why Is It Important and How Can We Control It? Annu Rev Chem Biomol Eng 2020; 11:311-338. [DOI: 10.1146/annurev-chembioeng-102419-010001] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Regulatory bodies worldwide consider N-glycosylation to be a critical quality attribute for immunoglobulin G (IgG) and IgG-like therapeutics. This consideration is due to the importance of posttranslational modifications in determining the efficacy, safety, and pharmacokinetic properties of biologics. Given its critical role in protein therapeutic production, we review N-glycosylation beginning with an overview of the myriad interactions of N-glycans with other biological factors. We examine the mechanism and drivers for N-glycosylation during biotherapeutic production and the several competing factors that impact glycan formation, including the abundance of precursor nucleotide sugars, transporters, glycosidases, glycosyltransferases, and process conditions. We explore the role of these factors with a focus on the analytical approaches used to characterize glycosylation and associated processes, followed by the current state of advanced glycosylation modeling techniques. This combination of disciplines allows for a deeper understanding of N-glycosylation and will lead to more rational glycan control.
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Affiliation(s)
- Natalia I. Majewska
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;,
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland 20878, USA
| | - Max L. Tejada
- Bioassay, Impurities and Quality, AstraZeneca, Gaithersburg, Maryland 20878, USA
| | - Michael J. Betenbaugh
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;,
| | - Nitin Agarwal
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland 20878, USA
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23
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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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24
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Hinterholzer A, Stanojlovic V, Cabrele C, Schubert M. Unambiguous Identification of Pyroglutamate in Full-Length Biopharmaceutical Monoclonal Antibodies by NMR Spectroscopy. Anal Chem 2019; 91:14299-14305. [PMID: 31589410 DOI: 10.1021/acs.analchem.9b02513] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Biotherapeutic proteins are an indispensable class of pharmaceuticals that present a high degree of structural complexity and are prone to chemical modifications during production, processing, and storage, which have to be tightly controlled. Pyroglutamate (pGlu), a cyclization product of N-terminal Gln or Glu residues, is a widespread post-translational modification in proteins, including monoclonal antibodies (mAbs). The unambiguous identification and quantification of this modification in proteins is challenging, since the mass difference of -17 Da or -18 Da, when formed from Gln or Glu, respectively, is not unique. Moreover, deamidation and dehydration occur not only during cyclization to pGlu, but also during other reactions leading to different types of modifications, like succinimide or isopeptide bond moieties due to cross-linking between Asn or Gln and Lys side chains. Here we report the unambiguous identification and quantification of pGlu in intact mAbs with natural isotope distribution by NMR spectroscopy. The assignment of all 1H, 13C and 15N random coil chemical shifts of pGlu in short reference peptides led to the identification of unique chemical shift pairs that are distinct from the random coil chemical shifts of the natural amino-acid residues. These characteristic correlations are suited for the detection of pGlu in denatured proteins. We achieved complete denaturation of mAbs using a straightforward protocol, and could detect and quantify pGlu, in agreement with available mass spectrometric data. The application to the mAbs rituximab and adalimumab illustrates the potential of our approach for the characterization of biotherapeutics containing isotopes at natural abundance.
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Affiliation(s)
- Arthur Hinterholzer
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Hellbrunnerstrasse 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
| | - Chiara Cabrele
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Hellbrunnerstrasse 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 , Hellbrunnerstrasse 34 , 5020 Salzburg , Austria.,Department of Biosciences , University of Salzburg , Billrothstrasse 11 , 5020 Salzburg , Austria
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25
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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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26
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Conibear AC, Rosengren KJ, Becker CFW, Kaehlig H. Random coil shifts of posttranslationally modified amino acids. JOURNAL OF BIOMOLECULAR NMR 2019; 73:587-599. [PMID: 31317299 PMCID: PMC6859290 DOI: 10.1007/s10858-019-00270-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/09/2019] [Indexed: 05/14/2023]
Abstract
Most eukaryotic proteins are modified during and/or after translation, regulating their structure, function and localisation. The role of posttranslational modifications (PTMs) in both normal cellular processes and in diseases is already well recognised and methods for detection of PTMs and generation of specifically modified proteins have developed rapidly over the last decade. However, structural consequences of PTMs and their specific effects on protein dynamics and function are not well understood. Furthermore, while random coil NMR chemical shifts of the 20 standard amino acids are available and widely used for residue assignment, dihedral angle predictions and identification of structural elements or propensity, they are not available for most posttranslationally modified amino acids. Here, we synthesised a set of random coil peptides containing common naturally occurring PTMs and determined their random coil NMR chemical shifts under standardised conditions. We highlight unique NMR signatures of posttranslationally modified residues and their effects on neighbouring residues. This comprehensive dataset complements established random coil shift datasets of the 20 standard amino acids and will facilitate identification and assignment of posttranslationally modified residues. The random coil shifts will also aid in determination of secondary structure elements and prediction of structural parameters of proteins and peptides containing PTMs.
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Affiliation(s)
- Anne C Conibear
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria.
- School of Biomedical Sciences, The University of Queensland, QLD, 4072, Brisbane, Australia.
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, QLD, 4072, Brisbane, Australia
| | - Christian F W Becker
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria
| | - Hanspeter Kaehlig
- Faculty of Chemistry, Institute of Organic Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria
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27
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Unione L, Lenza M, Ardá A, Urquiza P, Laín A, Falcón-Pérez JM, Jiménez-Barbero J, Millet O. Glycoprofile Analysis of an Intact Glycoprotein As Inferred by NMR Spectroscopy. ACS CENTRAL SCIENCE 2019; 5:1554-1561. [PMID: 31572782 PMCID: PMC6764210 DOI: 10.1021/acscentsci.9b00540] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Indexed: 05/10/2023]
Abstract
Protein N-glycosylation stands out for its intrinsic and functionally related heterogeneity. Despite its biomedical interest, Glycoprofile analysis still remains a major scientific challenge. Here, we present an NMR-based strategy to delineate the N-glycan composition in intact glycoproteins and under physiological conditions. The employed methodology allowed dissecting the glycan pattern of the IgE high-affinity receptor (FcεRIα) expressed in human HEK 293 cells, identifying the presence and relative abundance of specific glycan epitopes. Chemical shifts and differences in the signal line-broadening between the native and the unfolded states were integrated to build a structural model of FcεRIα that was able to identify intramolecular interactions between high-mannose N-glycans and the protein surface. In turn, complex type N-glycans reflect a large solvent accessibility, suggesting a functional role as interaction sites for receptors. The interaction between intact FcεRIα and the lectin hGal3, also studied here, confirms this hypothesis and opens new avenues for the detection of specific N-glycan epitopes and for the studies of glycoprotein-receptor interactions mediated by N-glycans.
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Affiliation(s)
- Luca Unione
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- E-mail:
| | - Maria
Pia Lenza
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Ana Ardá
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Pedro Urquiza
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Ana Laín
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Juan Manuel Falcón-Pérez
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- Basque
Foundation for Science IKERBASQUE, 48009 Bilbao, Spain
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- Basque
Foundation for Science IKERBASQUE, 48009 Bilbao, Spain
- Dept.
Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Spain
- E-mail:
| | - Oscar Millet
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- E-mail:
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28
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Research and Application of Glycoprotein Sensors Based on Glycosyl Recognition. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61185-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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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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30
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Ståhle J, Fontana C, Weintraub A, Widmalm G. Elucidation of the O-antigen structure of Escherichia coli O63. Glycobiology 2019; 29:179-187. [PMID: 30346540 DOI: 10.1093/glycob/cwy098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 10/18/2018] [Indexed: 11/14/2022] Open
Abstract
The structure of the O-antigen polysaccharide (PS) from the Shiga-toxin producing Escherichia coli O63 has been elucidated using a combination of bioinformatics, component analyses and NMR spectroscopy. The O-antigen is comprised of tetrasaccharide repeating units with the following structure: →2)-β-d-Quip3N(d-allo-ThrAc)-(1→2)-β-d-Ribf-(1→4)-β-d-Galp-(1→3)-α-d-GlcpNAc-(1→ in which the N-acetylated d-allo-threonine is amide-linked to position 3 of the 3-amino-3-deoxy-d-Quip sugar residue. The presence of a predicted flippase and polymerase encoded in the O63 gene cluster is consistent with the Wzx/Wzy biosynthetic pathway and consequently the biological repeating unit has likely an N-acetyl-d-glucosamine residue at its reducing end. A bioinformatics approach based on predictive glycosyltransferase function present in ECODAB (E. coli O-antigen database) suggested the structural element β-d-Galp-(1→3)-d-GlcpNAc in the O-antigen. Notably, multiple gene sequence alignment of fdtA and qdtA from E. coli to that in E. coli O63 resulted in discrimination between the two, confirmation of the latter in E. coli O63, and consequently, together with qdtB, biosynthesis of dTDP-d-Quip3N. The E. coli O63 O-antigen polysaccharide differs in two aspects from that of E. coli O114 where the latter carries instead an l-serine residue, and the glycosidic linkage positions to and from the Quip3N residue are both changed. The structural characterization of the O63 antigen repeat supports the predicted functional assignment of the O-antigen cluster genes.
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Affiliation(s)
- Jonas Ståhle
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Carolina Fontana
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Andrej Weintraub
- Karolinska Institute, Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
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31
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Schweida D, Barraud P, Regl C, Loughlin FE, Huber CG, Cabrele C, Schubert M. The NMR signature of gluconoylation: a frequent N-terminal modification of isotope-labeled proteins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:71-79. [PMID: 30737614 PMCID: PMC6441400 DOI: 10.1007/s10858-019-00228-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 01/24/2019] [Indexed: 05/05/2023]
Abstract
N-terminal gluconoylation is a moderately widespread modification in recombinant proteins expressed in Escherichia coli, in particular in proteins bearing an N-terminal histidine-tag. This post-translational modification has been investigated mainly by mass spectrometry. Although its NMR signals must have been observed earlier in spectra of 13C/15N labeled proteins, their chemical shifts were not yet reported. Here we present the complete 1H and 13C chemical shift assignment of the N-terminal gluconoyl post-translational modification, based on a selection of His-tagged protein constructs (CCL2, hnRNP A1 and Lin28) starting with Met-Gly-...-(His)6. In addition, we show that the modification can hydrolyze over time, resulting in a free N-terminus and gluconate. This leads to the disappearance of the gluconoyl signals and the appearance of gluconate signals during the NMR measurements. The chemical shifts presented here can now be used as a reference for the identification of gluconoylation in recombinant proteins, in particular when isotopically labeled.
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Affiliation(s)
- David Schweida
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria
| | - Pierre Barraud
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland
- Institut de Biologie Physico-Chimique (IBPC), UMR 8261 CNRS, Université Paris Diderot, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Christof Regl
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Fionna E Loughlin
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland
- Department of Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Christian G Huber
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Mario Schubert
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria.
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland.
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria.
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32
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Peng J, Patil SM, Keire DA, Chen K. Chemical Structure and Composition of Major Glycans Covalently Linked to Therapeutic Monoclonal Antibodies by Middle-Down Nuclear Magnetic Resonance. Anal Chem 2018; 90:11016-11024. [PMID: 30102512 PMCID: PMC7040853 DOI: 10.1021/acs.analchem.8b02637] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycosylation of monoclonal antibodies (mAbs) is a critical quality attribute that can impact mAb drug efficacy and safety. The mAb glycans are inherently heterogeneous in chemical structure and composition of monosaccharides. The established fluorescence or mass-spectrometry (MS) detection methods for glycosylation evaluation may require multiple steps of glycan cleavage or extensive digestion of the mAb, chemical labeling of the glycans, column separation and report the chemical identity of glycans indirectly through retention time and molecular weight values. In demonstrating chemical structure similarity and comparability among mAb drugs, orthogonal analytical methods for measuring glycan chemistry are needed to ensure the quality of drug products. Here, a "middle-down" NMR method is developed as a proof-of-concept approach to measure the domain-specific glycosylation of marketed mAb drugs without cleavage of the glycan moieties. Complete glycan 1H/13C chemical shift assignments were obtained at 13C natural abundance from commercial standard glycans that allowed unambiguous determination of the chemical structure, glycosidic linkage position, and anomeric configuration of each monosaccharide in the major N-glycan scaffolds found in mAb molecules. The analysis of glycan anomeric peaks in two-dimensional (2D) 1H-13C NMR spectra yielded metrics for clinically important mAb quality attributes (i.e., galactosylation (Gal%) and fucosylation (Fuc%)), consistent with literature results using a standard glycan-mapping method. Therefore, the middle-down NMR method provided a facile orthogonal measurement for mAb glycosylation characterization with improved chemical information content on glycan structure determination and quantification, compared to standard approaches.
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Affiliation(s)
- Jiangnan Peng
- Division of Pharmaceutical Analysis, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Sharadrao M. Patil
- Division of Pharmaceutical Analysis, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - David A. Keire
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Kang Chen
- Division of Pharmaceutical Analysis, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
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33
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Klukowski P, Schubert M. Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics. Bioinformatics 2018; 35:293-300. [DOI: 10.1093/bioinformatics/bty465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/10/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Piotr Klukowski
- Department of Computer Science, Faculty of Computer Science and Management, Wrocław University of Science and Technology, 50-370 Wrocław, Poland
| | - Mario Schubert
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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34
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Grassi L, Regl C, Wildner S, Gadermaier G, Huber CG, Cabrele C, Schubert M. Complete NMR Assignment of Succinimide and Its Detection and Quantification in Peptides and Intact Proteins. Anal Chem 2017; 89:11962-11970. [PMID: 29058416 DOI: 10.1021/acs.analchem.7b01645] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Detecting and quantifying post-translational modifications (PTMs) in full-length proteins is a challenge, especially in the case of spontaneously occurring, nonenzymatic PTMs. Such a PTM is the formation of succinimide (Snn) in a protein that occurs spontaneously in prone primary sequences and leads typically to an equilibrium between Snn and its hydrolysis products isoaspartate (isoAsp) and aspartate. In order to detect these modifications in proteins by NMR spectroscopy, chemical shift assignments of reference compounds are required. We used peptide synthesis and 2D NMR spectroscopy to assign all 1H and 13C chemical shifts of Snn and isoAsp and found characteristic chemical shift correlations. To provide chemical shift reference data suitable for comparison with data of denatured proteins, we repeated the assignment in 7 M urea (pH 2.3) and in DMSO. Most characteristic of Snn are the two downfield shifted carbonyl chemical shifts, the chemical shift correlations of Cβ-Hβ of Snn and Cα-Hα of the succeeding residue which are clearly distinct from random coil chemical shift correlations. The characteristic 2D NMR fingerprints of Snn were used to detect and quantify this PTM in the model protein lysozyme, the biotherapeutic filgrastim, and the Fc part of immunoglobulin G1. Mass spectrometry (MS) was applied as an additional independent method. The orthogonality of the NMR and MS techniques allows cross-validation, which is especially important to search for subtle PTMs in proteins. Studying PTMs by NMR spectroscopy is a promising method to analyze proteins and peptides from natural sources, recombinant expression, or chemical synthesis.
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Affiliation(s)
- Luigi Grassi
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, 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 Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Sabrina Wildner
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Gabriele Gadermaier
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 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 Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 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 Molecular Biology, 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 Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
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35
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Diniz A, Dias JS, Jiménez-Barbero J, Marcelo F, Cabrita EJ. Protein-Glycan Quinary Interactions in Crowding Environment Unveiled by NMR Spectroscopy. Chemistry 2017. [PMID: 28649731 DOI: 10.1002/chem.201702800] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein-glycan interactions as modulators for quinary structures in crowding environments were explored. The interaction between human galectin 3 (Gal-3) and distinct macromolecular crowders, such as bovine and human serum albumin (BSA and HSA), Ficoll 70 and PEG3350, was scrutinized. The molecular recognition event of the specific ligand, lactose, by Gal-3 in crowding conditions was evaluated. Gal-3 interactions were monitored by NMR analysing chemical shift perturbation (CSP) and line broadening of 1 H15 N-HSQC signals. The intensity of the Gal-3 1 H15 N-HSQC signals decreased in the presence of all crowders, due to the increase in the solution viscosity and to the formation of large protein complexes. When glycosylated containing samples of BSA and HSA were used, signal broadening was more severe than that observed in the presence of the more viscous solutions of PEG3350 and Ficoll 70. However, for the samples containing glycoproteins, the signal intensity of 1 H15 N-HSQC recovered upon addition of lactose. We show that serum proteins interact with Gal-3, through their α2,3-linked sialylgalactose moieties exposed at their surfaces, competing with lactose for the same binding site. The quinary interaction between Gal-3 and serum glycoproteins, could help to co-localize Gal-3 at the cell surface, and may play a role in adhesion and signalling functions of this protein.
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Affiliation(s)
- Ana Diniz
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Jorge S Dias
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Jesús Jiménez-Barbero
- CIC-bioGUNE Bizkaia, 48160, Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48005, Bilbao, Spain.,Departament Organic Chemistry II, EHU-UPV, 48040, Leioa, Spain
| | - Filipa Marcelo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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36
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Grünwald-Gruber C, Thader A, Maresch D, Dalik T, Altmann F. Determination of true ratios of different N-glycan structures in electrospray ionization mass spectrometry. Anal Bioanal Chem 2017; 409:2519-2530. [PMID: 28271226 PMCID: PMC5359385 DOI: 10.1007/s00216-017-0235-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/27/2017] [Indexed: 12/25/2022]
Abstract
An ideal method for the analysis of N-glycans would both identify the isomeric structure and deliver a true picture of the relative, if not absolute, amounts of the various structures in one sample. Porous graphitic carbon chromatography coupled with electrospray ionization mass spectrometry (ESI-MS) detection has emerged as a method with a particularly high potential of resolving isomeric oligosaccharides, but little attention has so far been paid to quantitation of the results obtained. In this work, we isolated a range of structures from Man5 to complex type N-glycans with zero to four sialic acids and blended them into an equimolar "glyco tune mix". When subjected to liquid chromatography-ESI-MS in positive and negative modes, the glyco tune mix clearly demonstrated the futility of quantitation of N-glycans of different overall composition, different number of sialic acids, and strongly differing size without compensation for their very different molar responses. Relative quantitation of human plasma N-glycans was performed with correction factors deduced from this external glyco tune mix. Addition of just one isotope-coded internal standard with enzymatically added 13C-galactose led to absolute quantification in the same experiment. Graphical Abstract Discrepancy between desirable (grey bars) and real (green bars) relative ion abundance of equimolar amounts of glycans in positive mode ESI-MS.
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Affiliation(s)
- Clemens Grünwald-Gruber
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Andreas Thader
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Thomas Dalik
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
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Mackay JP, Landsberg MJ, Whitten AE, Bond CS. Whaddaya Know: A Guide to Uncertainty and Subjectivity in Structural Biology. Trends Biochem Sci 2017; 42:155-167. [PMID: 28089412 DOI: 10.1016/j.tibs.2016.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 10/20/2016] [Accepted: 11/01/2016] [Indexed: 12/28/2022]
Abstract
The methods of structural biology, while powerful, are technically complex. Although the Protein Data Bank (PDB) provides a repository that allows anyone to download any structure, many users would not appreciate the caveats that should be considered when examining a structure. Here, we describe several key uncertainties associated with the application of X-ray crystallography, NMR spectroscopy, single-particle electron microscopy (SPEM), and small-angle scattering (SAS) to biological macromolecules. The take-home message is that structures are not absolute truths - they are models that fit the experimental data and therefore have uncertainty and subjectivity associated with them. These uncertainties must be appreciated - careful reading of the associated paper, and any validation report provided by the structure database, is highly recommended.
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Affiliation(s)
- Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia
| | - Andrew E Whitten
- Australian Centre for Neutron Science, ANSTO, Lucas Heights, NSW, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6014, Australia
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Xiao H, Wu R. Quantitative investigation of human cell surface N-glycoprotein dynamics. Chem Sci 2017; 8:268-277. [PMID: 28616130 PMCID: PMC5458730 DOI: 10.1039/c6sc01814a] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/13/2016] [Indexed: 12/21/2022] Open
Abstract
Surface glycoproteins regulate nearly every extracellular event and they are dynamic for cells to adapt to the ever-changing extracellular environment. These glycoproteins contain a wealth of information on cellular development and disease states, and have significant biomedical implications. Systematic investigation of surface glycoproteins will result in a better understanding of surface protein functions, cellular activities and the molecular mechanisms of disease. However, it is extraordinarily challenging to specifically and globally analyze surface glycoproteins. Here we designed the first method to systematically analyze surface glycoprotein dynamics and measure their half-lives by integrating pulse-chase labeling, selective enrichment of surface glycoproteins, and multiplexed proteomics. The current results clearly demonstrated that surface glycoproteins with catalytic activities were more stable than those with binding and receptor activities. Glycosylation sites located outside of any domain had a notably longer median half-life than those within domains, which strongly suggests that glycans within domains regulate protein interactions with other molecules while those outside of domains mainly play a role in protecting the protein from degradation. This method can be extensively applied to biological and biomedical research.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry , The Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , USA . ; ; Tel: +1-404-385-1515
| | - Ronghu Wu
- School of Chemistry and Biochemistry , The Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , USA . ; ; Tel: +1-404-385-1515
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39
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Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases. Int J Mol Sci 2016; 17:ijms17121969. [PMID: 27898009 PMCID: PMC5187769 DOI: 10.3390/ijms17121969] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 02/06/2023] Open
Abstract
Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications.
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40
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Marchetti R, Perez S, Arda A, Imberty A, Jimenez‐Barbero J, Silipo A, Molinaro A. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling. ChemistryOpen 2016; 5:274-96. [PMID: 27547635 PMCID: PMC4981046 DOI: 10.1002/open.201600024] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.
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Affiliation(s)
- Roberta Marchetti
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Serge Perez
- Department Molecular Pharmacochemistry UMR 5063CNRS and University of GrenobleAlpes, BP 5338041 Grenoble cedex 9France
| | - Ana Arda
- Bizkaia Technological ParkCIC bioGUNEBuilding 801A-148160Derio-BizkaiaSpain
| | - Anne Imberty
- Centre de Recherche sur les CNRSand University of Grenoble Macromolécules Végétales, UPR 5301Alpes, BP 5338041Grenoble cedex 9France
| | | | - Alba Silipo
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Antonio Molinaro
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
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41
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Garay PG, Martin OA, Scheraga HA, Vila JA. Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study. PeerJ 2016; 4:e2253. [PMID: 27547559 PMCID: PMC4963218 DOI: 10.7717/peerj.2253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/23/2016] [Indexed: 11/20/2022] Open
Abstract
Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using (13)C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the (13)C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used (13)C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the (13)Cε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable (13)C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.
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Affiliation(s)
- Pablo G. Garay
- IMASL-CONICET, Universidad Nacional de San Luis, San Luis, Argentina
| | - Osvaldo A. Martin
- IMASL-CONICET, Universidad Nacional de San Luis, San Luis, Argentina
| | | | - Jorge A. Vila
- IMASL-CONICET, Universidad Nacional de San Luis, San Luis, Argentina
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Abstract
There is an ongoing race between bacterial evolution and medical advances. Pathogens have the advantages of short generation times and horizontal gene transfer that enable rapid adaptation to new host environments and therapeutics that currently outpaces clinical research. Antibiotic resistance, the growing impact of nosocomial infections, cancer-causing bacteria, the risk of zoonosis, and the possibility of biowarfare all emphasize the increasingly urgent need for medical research focussed on bacterial pathogens. Bacterial glycoproteins are promising targets for alternative therapeutic intervention since they are often surface exposed, involved in host-pathogen interactions, required for virulence, and contain distinctive glycan structures. The potential exists to exploit these unique structures to improve clinical prevention, diagnosis, and treatment strategies. Translation of the potential in this field to actual clinical impact is an exciting prospect for fighting infectious diseases.
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Affiliation(s)
- Kelly M Fulton
- a Human Health Therapeutics Portfolio , National Research Council Canada , Ottawa , Canada
| | - Jeffrey C Smith
- b Department of Chemistry and Institute of Biochemistry , Carleton University , Ottawa , Canada
| | - Susan M Twine
- a Human Health Therapeutics Portfolio , National Research Council Canada , Ottawa , Canada
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43
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MALDI-TOF mass spectrometry and reversed-phase HPLC-ELSD chromatography for structural and quantitative studies of major steroid saponins in commercial extracts of Yucca schidigera Roezl. J Pharm Biomed Anal 2016; 120:270-82. [DOI: 10.1016/j.jpba.2015.12.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 11/23/2022]
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44
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Clerc F, Reiding KR, Jansen BC, Kammeijer GSM, Bondt A, Wuhrer M. Human plasma protein N-glycosylation. Glycoconj J 2015; 33:309-43. [PMID: 26555091 PMCID: PMC4891372 DOI: 10.1007/s10719-015-9626-2] [Citation(s) in RCA: 293] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 09/30/2015] [Accepted: 10/05/2015] [Indexed: 01/09/2023]
Abstract
Glycosylation is the most abundant and complex protein modification, and can have a profound structural and functional effect on the conjugate. The oligosaccharide fraction is recognized to be involved in multiple biological processes, and to affect proteins physical properties, and has consequentially been labeled a critical quality attribute of biopharmaceuticals. Additionally, due to recent advances in analytical methods and analysis software, glycosylation is targeted in the search for disease biomarkers for early diagnosis and patient stratification. Biofluids such as saliva, serum or plasma are of great use in this regard, as they are easily accessible and can provide relevant glycosylation information. Thus, as the assessment of protein glycosylation is becoming a major element in clinical and biopharmaceutical research, this review aims to convey the current state of knowledge on the N-glycosylation of the major plasma glycoproteins alpha-1-acid glycoprotein, alpha-1-antitrypsin, alpha-1B-glycoprotein, alpha-2-HS-glycoprotein, alpha-2-macroglobulin, antithrombin-III, apolipoprotein B-100, apolipoprotein D, apolipoprotein F, beta-2-glycoprotein 1, ceruloplasmin, fibrinogen, immunoglobulin (Ig) A, IgG, IgM, haptoglobin, hemopexin, histidine-rich glycoprotein, kininogen-1, serotransferrin, vitronectin, and zinc-alpha-2-glycoprotein. In addition, the less abundant immunoglobulins D and E are included because of their major relevance in immunology and biopharmaceutical research. Where available, the glycosylation is described in a site-specific manner. In the discussion, we put the glycosylation of individual proteins into perspective and speculate how the individual proteins may contribute to a total plasma N-glycosylation profile determined at the released glycan level.
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Affiliation(s)
- Florent Clerc
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Karli R Reiding
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Bas C Jansen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Guinevere S M Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Albert Bondt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.,Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands. .,Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands.
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