1
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Bechtella L, Chunsheng J, Fentker K, Ertürk GR, Safferthal M, Polewski Ł, Götze M, Graeber SY, Vos GM, Struwe WB, Mall MA, Mertins P, Karlsson NG, Pagel K. Ion mobility-tandem mass spectrometry of mucin-type O-glycans. Nat Commun 2024; 15:2611. [PMID: 38521783 PMCID: PMC10960840 DOI: 10.1038/s41467-024-46825-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
The dense O-glycosylation of mucins plays an important role in the defensive properties of the mucus hydrogel. Aberrant glycosylation is often correlated with inflammation and pathology such as COPD, cancer, and Crohn's disease. The inherent complexity of glycans and the diversity in the O-core structure constitute fundamental challenges for the analysis of mucin-type O-glycans. Due to coexistence of multiple isomers, multidimensional workflows such as LC-MS are required. To separate the highly polar carbohydrates, porous graphitized carbon is often used as a stationary phase. However, LC-MS workflows are time-consuming and lack reproducibility. Here we present a rapid alternative for separating and identifying O-glycans released from mucins based on trapped ion mobility mass spectrometry. Compared to established LC-MS, the acquisition time is reduced from an hour to two minutes. To test the validity, the developed workflow was applied to sputum samples from cystic fibrosis patients to map O-glycosylation features associated with disease.
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Affiliation(s)
- Leïla Bechtella
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Jin Chunsheng
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kerstin Fentker
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Güney R Ertürk
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
| | - Marc Safferthal
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Łukasz Polewski
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Michael Götze
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Simon Y Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), associated partner site, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gaël M Vos
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Weston B Struwe
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Marcus A Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), associated partner site, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Berlin Institute of Health, 10178, Berlin, Germany
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany.
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2
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Claasen M, Kofinova Z, Contino M, Struwe WB. Analysis of Protein Complex Formation at Micromolar Concentrations by Coupling Microfluidics with Mass Photometry. J Vis Exp 2024. [PMID: 38345236 DOI: 10.3791/65772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Abstract
Mass photometry is a versatile mass measurement technology that enables the study of biomolecular interactions and complex formation in solution without labels. Mass photometry is generally suited to analyzing samples in the 100 pM-100 nM concentration range. However, in many biological systems, it is necessary to measure more concentrated samples to study low-affinity or transient interactions. Here, we demonstrate a method that effectively expands the range of sample concentrations that can be analyzed by mass photometry from nanomolar to tens of micromolar. In this protocol, mass photometry is combined with a novel microfluidics system to investigate the formation of protein complexes in solution in the micromolar concentration range. With the microfluidics system, users can maintain a sample at a desired higher concentration followed by dilution to the nanomolar range - several milliseconds prior to the mass photometry measurement. Due to the speed of the dilution, data is obtained before the equilibrium of the sample has shifted (i.e., dissociation of the complex). The technique is applied to measure interactions between an immunoglobulin G (IgG) antibody and the neonatal Fc receptor, showing the formation of high-order complexes that were not quantifiable with static mass photometry measurements. In conclusion, the combination of mass photometry and microfluidics makes it possible to characterize samples in the micromolar concentration range and is proficient in measuring biomolecular interactions with weaker affinities. These capabilities can be applied in a range of contexts - including the development and design of biotherapeutics - enabling thorough characterization of diverse protein-protein interactions.
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Affiliation(s)
| | | | | | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford; The Kavli Institute for Nanoscience Discovery, University of Oxford
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3
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Kofinova Z, Karunanithy G, Ferreira AS, Struwe WB. Measuring Protein-Protein Interactions and Quantifying Their Dissociation Constants with Mass Photometry. Curr Protoc 2024; 4:e962. [PMID: 38224147 DOI: 10.1002/cpz1.962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Protein-protein interactions underlie most biological processes, and determining the affinity and abundance of binding partners for each interaction is often a challenging task because these interactions often involve multiple ligands and binding sites. Standard methods for determining the affinity of protein interactions often require a large amount of starting material in addition to potentially disruptive labeling or immobilization of the binding partners. Mass photometry is a bioanalytical technique that measures the mass of single biomolecules in solution, quickly and with minimal sample requirements. This article describes how mass photometry can be used to determine the mass distribution of binding partners, the complexes they form, the relative abundance of each species, and, accordingly, the dissociation constant (KD ) of their interactions. © 2024 Refeyn Ltd. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Using mass photometry to measure protein-protein binding and quantify the KD of this interaction.
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Affiliation(s)
| | | | | | - Weston B Struwe
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
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El-Baba TJ, Lutomski CA, Burnap SA, Bolla JR, Baker LA, Baldwin AJ, Struwe WB, Robinson CV. Uncovering the Role of N-Glycan Occupancy on the Cooperative Assembly of Spike and Angiotensin Converting Enzyme 2 Complexes: Insights from Glycoengineering and Native Mass Spectrometry. J Am Chem Soc 2023; 145:8021-8032. [PMID: 37000485 PMCID: PMC10103161 DOI: 10.1021/jacs.3c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Interactions between the SARS-CoV-2 Spike protein and ACE2 are one of the most scrutinized reactions of our time. Yet, questions remain as to the impact of glycans on mediating ACE2 dimerization and downstream interactions with Spike. Here, we address these unanswered questions by combining a glycoengineering strategy with high-resolution native mass spectrometry (MS) to investigate the impact of N-glycan occupancy on the assembly of multiple Spike-ACE2 complexes. We confirmed that intact Spike trimers have all 66 N-linked sites occupied. For monomeric ACE2, all seven N-linked glycan sites are occupied to various degrees; six sites have >90% occupancy, while the seventh site (Asn690) is only partially occupied (∼30%). By resolving the glycoforms on ACE2, we deciphered the influence of each N-glycan on ACE2 dimerization. Unexpectedly, we found that Asn432 plays a role in mediating dimerization, a result confirmed by site-directed mutagenesis. We also found that glycosylated dimeric ACE2 and Spike trimers form complexes with multiple stoichiometries (Spike-ACE2 and Spike2-ACE2) with dissociation constants (Kds) of ∼500 and <100 nM, respectively. Comparing these values indicates that positive cooperativity may drive ACE2 dimers to complex with multiple Spike trimers. Overall, our results show that occupancy has a key regulatory role in mediating interactions between ACE2 dimers and Spike trimers. More generally, since soluble ACE2 (sACE2) retains an intact SARS-CoV-2 interaction site, the importance of glycosylation in ACE2 dimerization and the propensity for Spike and ACE2 to assemble into higher oligomers are molecular details important for developing strategies for neutralizing the virus.
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Affiliation(s)
- Tarick J El-Baba
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Corinne A Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Sean A Burnap
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Jani R Bolla
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Lindsay A Baker
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, U.K
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
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5
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Younas T, Liu C, Struwe WB, Kukura P, He L. Engineer RNA-Protein Nanowires as Light-Responsive Biomaterials. Small 2023; 19:e2206513. [PMID: 36642821 DOI: 10.1002/smll.202206513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/15/2022] [Indexed: 06/17/2023]
Abstract
RNA molecules have emerged as increasingly attractive biomaterials with important applications such as RNA interference (RNAi) for cancer treatment and mRNA vaccines against infectious diseases. However, it remains challenging to engineer RNA biomaterials with sophisticated functions such as non-covalent light-switching ability. Herein, light-responsive RNA-protein nanowires are engineered to have such functions. It first demonstrates that the high affinity of RNA aptamer enables the formation of long RNA-protein nanowires through designing a dimeric RNA aptamer and an engineered green fluorescence protein (GFP) that contains two TAT-derived peptides at N- and C- termini. GFP is then replaced with an optogenetic protein pair system, LOV2 (light-oxygen-voltage) protein and its binding partner ZDK (Z subunit of protein A), to confer blue light-controlled photo-switching ability. The light-responsive nanowires are long (>500 nm) in the dark, but small (20-30 nm) when exposed to light. Importantly, the co-assembly of this RNA-protein hybrid biomaterial does not rely on the photochemistry commonly used for light-responsive biomaterials, such as bond formation, cleavage, and isomerization, and is thus reversible. These RNA-protein structures can serve as a new class of light-controlled biocompatible frameworks for incorporating versatile elements such as RNA, DNA, and enzymes.
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Affiliation(s)
- Tayyaba Younas
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, 3800, Australia
| | - Chang Liu
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, 3800, Australia
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Lizhong He
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, 3800, Australia
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6
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Burnap SA, Struwe WB. Mass photometry reveals SARS-CoV-2 spike stabilisation to impede ACE2 binding through altered conformational dynamics. Chem Commun (Camb) 2022; 58:12939-12942. [PMID: 36317551 PMCID: PMC9680610 DOI: 10.1039/d2cc04711j] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2023]
Abstract
Here we show using mass photometry how proline substitutions, commonly used for SARS-CoV-2 spike stabilisation in vaccine design, directly affects ACE2 receptor interactions via dynamics of open and closed states. Conformational changes and ACE2 binding were influenced by spike variant and temperature, but independent of site-specific N-glycosylation.
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Affiliation(s)
- Sean A Burnap
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3TA, UK.
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, UK
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3TA, UK.
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, UK
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7
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Zappe A, Miller RL, Struwe WB, Pagel K. State-of-the-art glycosaminoglycan characterization. Mass Spectrom Rev 2022; 41:1040-1071. [PMID: 34608657 DOI: 10.1002/mas.21737] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/02/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Glycosaminoglycans (GAGs) are heterogeneous acidic polysaccharides involved in a range of biological functions. They have a significant influence on the regulation of cellular processes and the development of various diseases and infections. To fully understand the functional roles that GAGs play in mammalian systems, including disease processes, it is essential to understand their structural features. Despite having a linear structure and a repetitive disaccharide backbone, their structural analysis is challenging and requires elaborate preparative and analytical techniques. In particular, the extent to which GAGs are sulfated, as well as variation in sulfate position across the entire oligosaccharide or on individual monosaccharides, represents a major obstacle. Here, we summarize the current state-of-the-art methodologies used for GAG sample preparation and analysis, discussing in detail liquid chromatograpy and mass spectrometry-based approaches, including advanced ion activation methods, ion mobility separations and infrared action spectroscopy of mass-selected species.
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Affiliation(s)
- Andreas Zappe
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Rebecca L Miller
- Department of Cellular and Molecular Medicine, Copenhagen Centre for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Kevin Pagel
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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8
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Meng Y, Sanlidag S, Jensen SA, Burnap SA, Struwe WB, Larsen AH, Feng X, Mittal S, Sansom MSP, Sahlgren C, Handford PA. An N-glycan on the C2 domain of JAGGED1 is important for Notch activation. Sci Signal 2022; 15:eabo3507. [PMID: 36219682 DOI: 10.1126/scisignal.abo3507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The canonical members of the Jagged/Serrate and Delta families of transmembrane ligands have an extracellular, amino-terminal C2 domain that binds to phospholipids and is required for optimal activation of the Notch receptor. Somatic mutations that cause amino substitutions in the C2 domain in human JAGGED1 (JAG1) have been identified in tumors. We found in reporter cell assays that mutations affecting an N-glycosylation site reduced the ligand's ability to activate Notch. This N-glycosylation site located in the C2 domain is conserved in the Jagged/Serrate family but is lacking in the Delta family. Site-specific glycan analysis of the JAG1 amino terminus demonstrated that occupancy of this site by either a complex-type or high-mannose N-glycan was required for full Notch activation in reporter cell assays. Similarly to JAG1 variants with defects in Notch binding, N-glycan removal, either by mutagenesis of the glycosylation site or by endoglycosidase treatment, reduced receptor activation. The N-glycan variants also reduced receptor activation in a Notch signaling-dependent vascular smooth muscle cell differentiation assay. Loss of the C2 N-glycan reduced JAG1 binding to liposomes to a similar extent as the loss of the entire C2 domain. Molecular dynamics simulations suggested that the presence of the N-glycan limits the orientation of JAG1 relative to the membrane, thus facilitating Notch binding. These data are consistent with a critical role for the N-glycan in promoting a lipid-binding conformation that is required to orient Jagged at the cell membrane for full Notch activation.
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Affiliation(s)
- Yao Meng
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Sami Sanlidag
- Faculty for Science and Engineering, Biosciences, Åbo Akademi University, Turku, Finland.,Turku Bioscience Centre, Åbo Akademi University and University of Turku, Turku, Finland
| | - Sacha A Jensen
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Sean A Burnap
- Kavli Institute for NanoScience Discovery and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Weston B Struwe
- Kavli Institute for NanoScience Discovery and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andreas H Larsen
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Xinyi Feng
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Shruti Mittal
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Cecilia Sahlgren
- Faculty for Science and Engineering, Biosciences, Åbo Akademi University, Turku, Finland.,Turku Bioscience Centre, Åbo Akademi University and University of Turku, Turku, Finland.,Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Penny A Handford
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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Hundt N, Cole D, Hantke MF, Miller JJ, Struwe WB, Kukura P. Direct observation of the molecular mechanism underlying protein polymerization. Sci Adv 2022; 8:eabm7935. [PMID: 36044567 PMCID: PMC9432825 DOI: 10.1126/sciadv.abm7935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Protein assembly is a main route to generating complexity in living systems. Revealing the relevant molecular details is challenging because of the intrinsic heterogeneity of species ranging from few to hundreds of molecules. Here, we use mass photometry to quantify and monitor the full range of actin oligomers during polymerization with single-molecule sensitivity. We find that traditional nucleation-based models cannot account for the observed distributions of actin oligomers. Instead, the key step of filament formation is a slow transition between distinct states of an actin filament mediated by cation exchange or ATP hydrolysis. The resulting model reproduces important aspects of actin polymerization, such as the critical concentration for filament formation and bulk growth behavior. Our results revise the mechanism of actin nucleation, shed light on the role and function of actin-associated proteins, and introduce a general and quantitative means to studying protein assembly at the molecular level.
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Affiliation(s)
- Nikolas Hundt
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Daniel Cole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Max F. Hantke
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Jack J. Miller
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PT, UK
- The PET Research Centre and The MR Research Centre, Aarhus University, Aarhus, Denmark
| | - Weston B. Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
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10
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Asor R, Olerinyova A, Kushwah MS, Soltermann F, Powell Rudden L, Vasiljevic S, Brun J, Hensen M, Hill M, Degiacomi M, Zitzmann N, Struwe WB, Kukura P. The spike-ACE2 interaction underlying SARS-CoV-2 infection and inhibition is enhanced by intermolecular cross linking. Biophys J 2022. [PMCID: PMC8833051 DOI: 10.1016/j.bpj.2021.11.1120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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11
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Harvey DJ, Struwe WB, Behrens AJ, Vasiljevic S, Crispin M. Formation and fragmentation of doubly and triply charged ions in the negative ion spectra of neutral N-glycans from viral and other glycoproteins. Anal Bioanal Chem 2021; 413:7277-7294. [PMID: 34342671 PMCID: PMC8329908 DOI: 10.1007/s00216-021-03480-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/28/2021] [Accepted: 06/15/2021] [Indexed: 11/05/2022]
Abstract
Structural determination of N-glycans by mass spectrometry is ideally performed by negative ion collision-induced dissociation because the spectra are dominated by cross-ring fragments leading to ions that reveal structural details not available by many other methods. Most glycans form [M - H]- or [M + adduct]- ions but larger ones (above approx. m/z 2000) typically form doubly charged ions. Differences have been reported between the fragmentation of singly and doubly charged ions but a detailed comparison does not appear to have been reported. In addition to [M + adduct]- ions (this paper uses phosphate as the adduct) other doubly, triply, and quadruply charged ions of composition [Mn + (H2PO4)n]n- have been observed in mixtures of N-glycans released from viral and other glycoproteins. This paper explores the formation and fragmentation of these different types of multiply charged ions with particular reference to the presence of diagnostic fragments in the CID spectra and comments on how these ions can be used to characterize these glycans.
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Affiliation(s)
- David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
| | - Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- GlycoEra AG, Grabenstrasse 3, 8952, Schlieren, Switzerland
| | - Snezana Vasiljevic
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
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12
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Harvey DJ, Behrens AJ, Crispin M, Struwe WB. Identification of N-glycans with GalNAc-containing antennae from recombinant HIV trimers by ion mobility and negative ion fragmentation. Anal Bioanal Chem 2021; 413:7229-7240. [PMID: 34327564 PMCID: PMC8321768 DOI: 10.1007/s00216-021-03477-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Negative ion collision-induced dissociation (CID) of underivatized N-glycans has proved to be a simple, yet powerful method for their structural determination. Recently, we have identified a series of such structures with GalNAc rather than the more common galactose capping the antennae of hybrid and complex glycans. As part of a series of publications describing the negative ion fragmentation of different types of N-glycan, this paper describes their CID spectra and estimated nitrogen cross sections recorded by travelling wave ion mobility mass spectrometry (TWIMS). Most of the glycans were derived from the recombinant glycoproteins gp120 and gp41 from the human immunodeficiency virus (HIV), recombinantly derived from human embryonic kidney (HEK 293T) cells. Twenty-six GalNAc-capped hybrid and complex N-glycans were identified by a combination of TWIMS, negative ion CID, and exoglycosidase digestions. They were present as the neutral glycans and their sulfated and α2→3-linked sialylated analogues. Overall, negative ion fragmentation of glycans generates fingerprints that reveal their structural identity.
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Affiliation(s)
- David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- GlycoEra AG, Grabenstrasse 3, 8952, Schlieren, Switzerland
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
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13
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Soltermann F, Struwe WB, Kukura P. Label-free methods for optical in vitro characterization of protein-protein interactions. Phys Chem Chem Phys 2021; 23:16488-16500. [PMID: 34342317 PMCID: PMC8359934 DOI: 10.1039/d1cp01072g] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions are involved in the regulation and function of the majority of cellular processes. As a result, much effort has been aimed at the development of methodologies capable of quantifying protein-protein interactions, with label-free methods being of particular interest due to the associated simplified workflows and minimisation of label-induced perturbations. Here, we review recent advances in optical technologies providing label-free in vitro measurements of affinities and kinetics. We provide an overview and comparison of existing techniques and their principles, discussing advantages, limitations, and recent applications.
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Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
| | - Weston B. Struwe
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
| | - Philipp Kukura
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
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14
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Chen S, Wu D, Robinson CV, Struwe WB. Native Mass Spectrometry Meets Glycomics: Resolving Structural Detail and Occupancy of Glycans on Intact Glycoproteins. Anal Chem 2021; 93:10435-10443. [PMID: 34279906 DOI: 10.1021/acs.analchem.1c01460] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glycoproteins are inherently heterogeneous and therefore resolving structures in their entirety remains a major challenge in structural biology. Native mass spectrometry has transformed our ability to study glycoproteins, and despite advances in high-resolution instrumentation, there are comparatively a few studies demonstrating its potential with data largely limited to an overall measure of monosaccharide composition for all glycans across glycosylation sites for a given protein. Clearly, these readouts lack glycan topology information, namely, monosaccharide linkage and glycan branching. To address this deficiency, we developed a new approach that joins native mass spectrometry with glycan exoglycosidase sequencing, the combination of which provides remarkable glycoprotein structural details. We show how N-glycan branching, terminal fucosylation, LacNAc extensions, and N- and O-glycan occupancy (i.e., total number of glycans) can be directly characterized on intact glycoproteins with minimal sample preparation. Taken together, native exoglycosidase sequencing mass spectrometry (NES-MS) notably improves our ability to characterize protein glycosylation, addressing a significant need in structural biology that will enable new routes to understand glycoprotein function.
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Affiliation(s)
- Siyun Chen
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Di Wu
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Carol V Robinson
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Weston B Struwe
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
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15
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Brun J, Vasiljevic S, Gangadharan B, Hensen M, V. Chandran A, Hill ML, Kiappes J, Dwek RA, Alonzi DS, Struwe WB, Zitzmann N. Assessing Antigen Structural Integrity through Glycosylation Analysis of the SARS-CoV-2 Viral Spike. ACS Cent Sci 2021; 7:586-593. [PMID: 34056088 PMCID: PMC8029450 DOI: 10.1021/acscentsci.1c00058] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 is the causative pathogen of the COVID-19 pandemic which as of March 29, 2021, has claimed 2 776 175 lives worldwide. Vaccine development efforts focus on the viral trimeric spike glycoprotein as the main target of the humoral immune response. Viral spikes carry glycans that facilitate immune evasion by shielding specific protein epitopes from antibody neutralization, and antigen efficacy is influenced by spike glycoprotein production in vivo. Therefore, immunogen integrity is important for glycoprotein-based vaccine candidates. Here, we show how site-specific glycosylation differs between virus-derived spikes, wild-type, non-stabilized spikes expressed from a plasmid with a CMV promoter and tPA signal sequence, and commonly used recombinant, engineered spike glycoproteins. Furthermore, we show that their distinctive cellular secretion pathways result in different protein glycosylation and secretion patterns, including shedding of spike monomeric subunits for the non-stabilized wild-type spike tested, which may have implications for the resulting immune response and vaccine design.
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Affiliation(s)
- Juliane Brun
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Snežana Vasiljevic
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Bevin Gangadharan
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Mario Hensen
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anu V. Chandran
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Michelle L. Hill
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - J.L. Kiappes
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Raymond A. Dwek
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Dominic S. Alonzi
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Weston B. Struwe
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Nicole Zitzmann
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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16
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Olerinyova A, Sonn-Segev A, Gault J, Eichmann C, Schimpf J, Kopf AH, Rudden LSP, Ashkinadze D, Bomba R, Frey L, Greenwald J, Degiacomi MT, Steinhilper R, Killian JA, Friedrich T, Riek R, Struwe WB, Kukura P. Mass Photometry of Membrane Proteins. Chem 2021; 7:224-236. [PMID: 33511302 PMCID: PMC7815066 DOI: 10.1016/j.chempr.2020.11.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/20/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023]
Abstract
Integral membrane proteins (IMPs) are biologically highly significant but challenging to study because they require maintaining a cellular lipid-like environment. Here, we explore the application of mass photometry (MP) to IMPs and membrane-mimetic systems at the single-particle level. We apply MP to amphipathic vehicles, such as detergents and amphipols, as well as to lipid and native nanodiscs, characterizing the particle size, sample purity, and heterogeneity. Using methods established for cryogenic electron microscopy, we eliminate detergent background, enabling high-resolution studies of membrane-protein structure and interactions. We find evidence that, when extracted from native membranes using native styrene-maleic acid nanodiscs, the potassium channel KcsA is present as a dimer of tetramers—in contrast to results obtained using detergent purification. Finally, using lipid nanodiscs, we show that MP can help distinguish between functional and non-functional nanodisc assemblies, as well as determine the critical factors for lipid nanodisc formation. We introduce a label-free, single molecule approach for membrane-protein characterization Mass photometry quantifies membrane proteins in different membrane-mimetic systems MP reveals carrier and protein heterogeneity It helps distinguish different functional states of membrane proteins
Membrane proteins are some of the most important biological molecules, carrying out vital functions and being frequent drug targets. Yet, preferring lipid environments and so requiring solubilization, they are challenging to study. Here, we show that mass photometry can characterize the heterogeneity of membrane proteins and the carriers in which they are solubilized. It can also distinguish different functional states of membrane proteins. Our approach thus opens the door to more comprehensive studies of function, structure, and interaction of these critical proteins in their native membrane environment at the single-molecule level.
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Affiliation(s)
- Anna Olerinyova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Adar Sonn-Segev
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität, Alberstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Adrian H Kopf
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Lucas S P Rudden
- Department of Physics, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Dzmitry Ashkinadze
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Radoslaw Bomba
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Matteo T Degiacomi
- Department of Physics, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Ralf Steinhilper
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität, Alberstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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17
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Tjondro HC, Ugonotti J, Kawahara R, Chatterjee S, Loke I, Chen S, Soltermann F, Hinneburg H, Parker BL, Venkatakrishnan V, Dieckmann R, Grant OC, Bylund J, Rodger A, Woods RJ, Karlsson-Bengtsson A, Struwe WB, Thaysen-Andersen M. Hyper-truncated Asn355- and Asn391-glycans modulate the activity of neutrophil granule myeloperoxidase. J Biol Chem 2021; 296:100144. [PMID: 33273015 PMCID: PMC7857493 DOI: 10.1074/jbc.ra120.016342] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022] Open
Abstract
Myeloperoxidase (MPO) plays essential roles in neutrophil-mediated immunity via the generation of reactive oxidation products. Complex carbohydrates decorate MPO at discrete sites, but their functional relevance remains elusive. To this end, we have characterised the structure-biosynthesis-activity relationship of neutrophil MPO (nMPO). Mass spectrometry demonstrated that nMPO carries both characteristic under-processed and hyper-truncated glycans. Occlusion of the Asn355/Asn391-glycosylation sites and the Asn323-/Asn483-glycans, located in the MPO dimerisation zone, was found to affect the local glycan processing, thereby providing a molecular basis of the site-specific nMPO glycosylation. Native mass spectrometry, mass photometry and glycopeptide profiling revealed significant molecular complexity of diprotomeric nMPO arising from heterogeneous glycosylation, oxidation, chlorination and polypeptide truncation variants and a previously unreported low-abundance monoprotomer. Longitudinal profiling of maturing, mature, granule-separated and pathogen-stimulated neutrophils demonstrated that nMPO is dynamically expressed during granulopoiesis, unevenly distributed across granules and degranulated upon activation. We also show that proMPO-to-MPO maturation occurs during early/mid-stage granulopoiesis. While similar global MPO glycosylation was observed across conditions, the conserved Asn355-/Asn391-sites displayed elevated glycan hyper-truncation, which correlated with higher enzyme activities of MPO in distinct granule populations. Enzymatic trimming of the Asn355-/Asn391-glycans recapitulated the activity gain and showed that nMPO carrying hyper-truncated glycans at these positions exhibits increased thermal stability, polypeptide accessibility and ceruloplasmin-mediated inhibition potential relative to native nMPO. Finally, molecular modelling revealed that hyper-truncated Asn355-glycans positioned in the MPO-ceruloplasmin interface are critical for uninterrupted inhibition. Here, through an innovative and comprehensive approach, we report novel functional roles of MPO glycans, providing new insight into neutrophil-mediated immunity.
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Affiliation(s)
- Harry C Tjondro
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Julian Ugonotti
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Sayantani Chatterjee
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Ian Loke
- Cordlife Group Limited, Singapore, Singapore
| | - Siyun Chen
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Fabian Soltermann
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Hannes Hinneburg
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Benjamin L Parker
- Department of Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Vignesh Venkatakrishnan
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Regis Dieckmann
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Johan Bylund
- Department of Oral Microbiology and Immunology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alison Rodger
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Anna Karlsson-Bengtsson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Weston B Struwe
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia.
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18
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Abstract
Mass photometry is a recently developed methodology capable of measuring the mass of individual proteins under solution conditions. Here, we show that this approach is equally applicable to nucleic acids, enabling their facile, rapid and accurate detection and quantification using sub-picomoles of sample. The ability to count individual molecules directly measures relative concentrations in complex mixtures without need for separation. Using a dsDNA ladder, we find a linear relationship between the number of bases per molecule and the associated imaging contrast for up to 1200 bp, enabling us to quantify dsDNA length with up to 2 bp accuracy. These results introduce mass photometry as an accurate, rapid and label-free single molecule method complementary to existing DNA characterization techniques.
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Affiliation(s)
- Yiwen Li
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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19
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Yen H, Liko I, Gault J, Wu D, Struwe WB, Robinson CV. Correlating Glycoforms of DC-SIGN with Stability Using a Combination of Enzymatic Digestion and Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2020; 59:15560-15564. [PMID: 33462887 PMCID: PMC7496578 DOI: 10.1002/anie.202005727] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/05/2020] [Indexed: 01/03/2023]
Abstract
The immune scavenger protein DC-SIGN interacts with glycosylated proteins and has a putative role in facilitating viral infection. How these recognition events take place with different viruses is not clear and the effects of glycosylation on the folding and stability of DC-SIGN have not been reported. Herein, we report the development and application of a mass-spectrometry-based approach to both uncover and characterise the effects of O-glycans on the stability of DC-SIGN. We first quantify the Core 1 and 2 O-glycan structures on the carbohydrate recognition and extracellular domains of the protein using sequential exoglycosidase sequencing. Using ion mobility mass spectrometry, we show how specific O-glycans, and/or single monosaccharide substitutions, alter both the overall collision cross section and the gas-phase stability of the DC-SIGN isoforms. We find that rather than the mass or length of glycoprotein modifications, the stability of DC-SIGN is better correlated with the number of glycosylation sites.
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Affiliation(s)
- Hsin‐Yung Yen
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
- Present address: OMass TherapeuticsThe Schrodinger Building, Oxford Science ParkOxfordOX4 4GEUK
| | - Idlir Liko
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
- Present address: OMass TherapeuticsThe Schrodinger Building, Oxford Science ParkOxfordOX4 4GEUK
| | - Joseph Gault
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Di Wu
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Carol V. Robinson
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
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20
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Yen H, Liko I, Gault J, Wu D, Struwe WB, Robinson CV. Correlating Glycoforms of DC‐SIGN with Stability Using a Combination of Enzymatic Digestion and Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hsin‐Yung Yen
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
- Present address: OMass Therapeutics The Schrodinger Building, Oxford Science Park Oxford OX4 4GE UK
| | - Idlir Liko
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
- Present address: OMass Therapeutics The Schrodinger Building, Oxford Science Park Oxford OX4 4GE UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
| | - Di Wu
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
| | - Weston B. Struwe
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Department of Chemistry University of Oxford South Parks Road Oxford OX1 3TA UK
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21
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Soltermann F, Foley EDB, Pagnoni V, Galpin M, Benesch JLP, Kukura P, Struwe WB. Quantifying Protein–Protein Interactions by Molecular Counting with Mass Photometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Eric D. B. Foley
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Veronica Pagnoni
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Martin Galpin
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Justin L. P. Benesch
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Philipp Kukura
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
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22
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Soltermann F, Foley EDB, Pagnoni V, Galpin M, Benesch JLP, Kukura P, Struwe WB. Frontispiz: Quantifying Protein–Protein Interactions by Molecular Counting with Mass Photometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202082761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Eric D. B. Foley
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Veronica Pagnoni
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Martin Galpin
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Justin L. P. Benesch
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Philipp Kukura
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
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23
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Soltermann F, Foley EDB, Pagnoni V, Galpin M, Benesch JLP, Kukura P, Struwe WB. Quantifying Protein-Protein Interactions by Molecular Counting with Mass Photometry. Angew Chem Int Ed Engl 2020; 59:10774-10779. [PMID: 32167227 PMCID: PMC7318626 DOI: 10.1002/anie.202001578] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/11/2020] [Indexed: 12/12/2022]
Abstract
Interactions between biomolecules control the processes of life in health and their malfunction in disease, making their characterization and quantification essential. Immobilization- and label-free analytical techniques are desirable because of their simplicity and minimal invasiveness, but they struggle with quantifying tight interactions. Here, we show that mass photometry can accurately count, distinguish by molecular mass, and thereby reveal the relative abundances of different unlabelled biomolecules and their complexes in mixtures at the single-molecule level. These measurements determine binding affinities over four orders of magnitude at equilibrium for both simple and complex stoichiometries within minutes, as well as the associated kinetics. These results introduce mass photometry as a rapid, simple and label-free method for studying sub-micromolar binding affinities, with potential for extension towards a universal approach for characterizing complex biomolecular interactions.
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Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Eric D. B. Foley
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Veronica Pagnoni
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Martin Galpin
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Justin L. P. Benesch
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Philipp Kukura
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
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24
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Soltermann F, Foley EDB, Pagnoni V, Galpin M, Benesch JLP, Kukura P, Struwe WB. Frontispiece: Quantifying Protein–Protein Interactions by Molecular Counting with Mass Photometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.202082761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Eric D. B. Foley
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Veronica Pagnoni
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Martin Galpin
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Justin L. P. Benesch
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Philipp Kukura
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
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25
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Miller RL, Guimond SE, Schwörer R, Zubkova OV, Tyler PC, Xu Y, Liu J, Chopra P, Boons GJ, Grabarics M, Manz C, Hofmann J, Karlsson NG, Turnbull JE, Struwe WB, Pagel K. Shotgun ion mobility mass spectrometry sequencing of heparan sulfate saccharides. Nat Commun 2020; 11:1481. [PMID: 32198425 PMCID: PMC7083916 DOI: 10.1038/s41467-020-15284-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/27/2020] [Indexed: 01/23/2023] Open
Abstract
Despite evident regulatory roles of heparan sulfate (HS) saccharides in numerous biological processes, definitive information on the bioactive sequences of these polymers is lacking, with only a handful of natural structures sequenced to date. Here, we develop a “Shotgun” Ion Mobility Mass Spectrometry Sequencing (SIMMS2) method in which intact HS saccharides are dissociated in an ion mobility mass spectrometer and collision cross section values of fragments measured. Matching of data for intact and fragment ions against known values for 36 fully defined HS saccharide structures (from di- to decasaccharides) permits unambiguous sequence determination of validated standards and unknown natural saccharides, notably including variants with 3O-sulfate groups. SIMMS2 analysis of two fibroblast growth factor-inhibiting hexasaccharides identified from a HS oligosaccharide library screen demonstrates that the approach allows elucidation of structure-activity relationships. SIMMS2 thus overcomes the bottleneck for decoding the informational content of functional HS motifs which is crucial for their future biomedical exploitation. Heparan sulfates (HS) contain functionally relevant structural motifs, but determining their monosaccharide sequence remains challenging. Here, the authors develop an ion mobility mass spectrometry-based method that allows unambiguous characterization of HS sequences and structure-activity relationships.
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Affiliation(s)
- Rebecca L Miller
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, N 2200, Denmark. .,Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK. .,Laboratory of Cancer Biology, Department of Oncology, Medical Sciences Division, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7DQ, UK.
| | - Scott E Guimond
- Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.,Institute for Science and Technology in Medicine, School of Medicine, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Ralf Schwörer
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt, 5010, New Zealand
| | - Olga V Zubkova
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt, 5010, New Zealand
| | - Peter C Tyler
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt, 5010, New Zealand
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Pradeep Chopra
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.,Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Márkó Grabarics
- Freie Universitaet Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195, Berlin, Germany.,Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Christian Manz
- Freie Universitaet Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195, Berlin, Germany.,Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Johanna Hofmann
- Freie Universitaet Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195, Berlin, Germany.,Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jeremy E Turnbull
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, N 2200, Denmark.,Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Weston B Struwe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
| | - Kevin Pagel
- Freie Universitaet Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195, Berlin, Germany.,Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
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26
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Soltermann F, Pagnoni V, Foley E, Galpin M, Benesch JL, Struwe WB, Kukura P. Quantifying Binding Affinities, Kinetics and Stoichiometry of Biomolecular Complexes with Mass Photometry. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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27
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Li Y, Struwe WB, Häußermann K, Kukura P. Label-Free Single-Molecule Quantification of DNA by Mass Photometry. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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28
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Campbell MP, Abrahams JL, Rapp E, Struwe WB, Costello CE, Novotny M, Ranzinger R, York WS, Kolarich D, Rudd PM, Kettner C. The minimum information required for a glycomics experiment (MIRAGE) project: LC guidelines. Glycobiology 2019; 29:349-354. [PMID: 30778580 DOI: 10.1093/glycob/cwz009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 11/13/2022] Open
Abstract
The Minimum Information Required for a Glycomics Experiment (MIRAGE) is an initiative created by experts in the fields of glycobiology, glycoanalytics and glycoinformatics to design guidelines that improve the reporting and reproducibility of glycoanalytical methods. Previously, the MIRAGE Commission has published guidelines for describing sample preparation methods and the reporting of glycan array and mass spectrometry techniques and data collections. Here, we present the first version of guidelines that aim to improve the quality of the reporting of liquid chromatography (LC) glycan data in the scientific literature. These guidelines cover all aspects of instrument setup and modality of data handling and manipulation and is cross-linked with other MIRAGE recommendations. The most recent version of the MIRAGE-LC guidelines is freely available at the MIRAGE project website doi:10.3762/mirage.4.
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Affiliation(s)
- Matthew P Campbell
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Jodie L Abrahams
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, Magdeburg, Germany
| | - Weston B Struwe
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, UK
| | - Catherine E Costello
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA, USA
| | - Milos Novotny
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, USA
| | - Rene Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, USA
| | - William S York
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, USA
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia.,ARC Centre for Nanoscale BioPhotonics, Griffith University, Gold Coast, Queensland, Australia
| | - Pauline M Rudd
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros, Singapore
| | - Carsten Kettner
- Beilstein-Institut, Trakehner Str. 7-9, Frankfurt am Main, Germany
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29
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Struwe WB, Harvey DJ. Ion Mobility-Mass Spectrometry of Glycoconjugates. Methods Mol Biol 2019; 2084:203-219. [PMID: 31729663 DOI: 10.1007/978-1-0716-0030-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Glycoconjugates are diverse biomolecules that are dynamically assembled to regulate and fine-tune numerous cellular processes. Their biosynthesis is nontemplate-driven, achieved stepwise in discrete locations within the cell, giving rise to a range of complex branched structures that pose a significant challenge in structural biology. Mass spectrometry is the leading method for analysis of glycoconjugates, and the addition of ion mobility has proven valuable for improving structural assignments of individual glycans in complex biological mixtures. In this chapter, we briefly discuss recent applications of IM for glycomics and describe how to acquire, interpret, and analyze IM-MS data for the analysis of glycans.
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Affiliation(s)
- Weston B Struwe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, UK.
| | - David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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30
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Rojas-Macias MA, Mariethoz J, Andersson P, Jin C, Venkatakrishnan V, Aoki NP, Shinmachi D, Ashwood C, Madunic K, Zhang T, Miller RL, Horlacher O, Struwe WB, Watanabe Y, Okuda S, Levander F, Kolarich D, Rudd PM, Wuhrer M, Kettner C, Packer NH, Aoki-Kinoshita KF, Lisacek F, Karlsson NG. Towards a standardized bioinformatics infrastructure for N- and O-glycomics. Nat Commun 2019; 10:3275. [PMID: 31332201 PMCID: PMC6796180 DOI: 10.1038/s41467-019-11131-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/24/2019] [Indexed: 12/21/2022] Open
Abstract
The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.
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Affiliation(s)
- Miguel A Rojas-Macias
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
- Computer Science Department, University of Geneva, Geneva, 1227, Switzerland
| | - Peter Andersson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Vignesh Venkatakrishnan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Nobuyuki P Aoki
- Soka University, Hachioji, 192-8577, Tokyo, Japan
- SparqLite LLC., Hachioji, 192-0032, Tokyo, Japan
| | - Daisuke Shinmachi
- Soka University, Hachioji, 192-8577, Tokyo, Japan
- SparqLite LLC., Hachioji, 192-0032, Tokyo, Japan
| | - Christopher Ashwood
- Department of Molecular Sciences, Macquarie University, Sydney, 2109, Australia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | | | - Tao Zhang
- Leiden University Medical Center, Leiden, 2333ZA, Netherlands
| | - Rebecca L Miller
- Copenhagen Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, København, DK-2200, Denmark
| | - Oliver Horlacher
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
| | - Weston B Struwe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Yu Watanabe
- Graduate School of Medical and Dental Sciences, Niigata University, 950-2181, Niigata, Japan
| | - Shujiro Okuda
- Graduate School of Medical and Dental Sciences, Niigata University, 950-2181, Niigata, Japan
| | - Fredrik Levander
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Immunotechnology, Lund University, Lund, 22387, Sweden
| | - Daniel Kolarich
- Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, QLD, QLD 4222, Australia
- ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, North Ryde and Gold Coast, NSW and QLD, NSW 2109 and QLD 4222, Australia
| | - Pauline M Rudd
- Bioprocessing Technology Institute, AStar, Singapore, 138668, Singapore
| | - Manfred Wuhrer
- Leiden University Medical Center, Leiden, 2333ZA, Netherlands
| | | | - Nicolle H Packer
- Department of Molecular Sciences, Macquarie University, Sydney, 2109, Australia
- Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, QLD, QLD 4222, Australia
- ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, North Ryde and Gold Coast, NSW and QLD, NSW 2109 and QLD 4222, Australia
| | | | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
- Computer Science Department, University of Geneva, Geneva, 1227, Switzerland
- Section of Biology, University of Geneva, Geneva, 1211, Switzerland
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden.
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31
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Jin C, Harvey DJ, Struwe WB, Karlsson NG. Separation of Isomeric O-Glycans by Ion Mobility and Liquid Chromatography–Mass Spectrometry. Anal Chem 2019; 91:10604-10613. [DOI: 10.1021/acs.analchem.9b01772] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - David J. Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Weston B. Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Chemistry Research laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Niclas G. Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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32
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Wu D, Li J, Struwe WB, Robinson CV. Probing N-glycoprotein microheterogeneity by lectin affinity purification-mass spectrometry analysis. Chem Sci 2019; 10:5146-5155. [PMID: 31183067 PMCID: PMC6524569 DOI: 10.1039/c9sc00360f] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/16/2019] [Indexed: 12/18/2022] Open
Abstract
A lectin affinity purification-mass spectrometry approach to characterize lectin-reactive glycoproteoforms and elucidate lectin specificities at the intact protein level.
Lectins are carbohydrate binding proteins that recognize specific epitopes present on target glycoproteins. Changes in lectin-reactive carbohydrate repertoires are related to many biological signaling pathways and recognized as hallmarks of several pathological processes. Consequently, lectins are valuable probes, commonly used for examining glycoprotein structural and functional microheterogeneity. However, the molecular interactions between a given lectin and its preferred glycoproteoforms are largely unknown due to the inherent complexity and limitations of methods used to investigate intact glycoproteins. Here, we apply a lectin-affinity purification procedure coupled with native mass spectrometry to characterize lectin-reactive glycoproteoforms at the intact protein level. We investigate the interactions between the highly fucosylated and highly branched glycoproteoforms of haptoglobin and α1-acid glycoprotein using two different lectins Aleuria aurantia lectin (AAL) and Phaseolus vulgaris leucoagglutinin (PHA-L), respectively. Firstly we show a co-occurrence of fucosylation and N-glycan branching on haptoglobin, particularly among highly fucosylated glycoproteoforms. Secondly, we analyze the global heterogeneity of highly branched glycoproteoforms of haptoglobin and α1-acid glycoprotein and reveal that while multi-fucosylation attenuates the lectin PHA-L binding to haptoglobin, it has no impact on AGP. Taken together, our lectin affinity purification native MS approach elucidates lectin specificities between intact glycoproteins, not achievable by other methods. Moreover, since aberrant glycosylation of Hp and AGP are potential markers for many diseases, including pancreatic, hepatic and ovarian cancers, understanding their interactions with lectins will help the development of carbohydrate-centric monitoring methods to understand their pathophysiological implications.
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Affiliation(s)
- Di Wu
- Department of Chemistry , University of Oxford , South Parks Road , OX1 3QZ , Oxford , UK .
| | - Jingwen Li
- Department of Chemistry , University of Oxford , South Parks Road , OX1 3QZ , Oxford , UK .
| | - Weston B Struwe
- Department of Chemistry , University of Oxford , South Parks Road , OX1 3QZ , Oxford , UK .
| | - Carol V Robinson
- Department of Chemistry , University of Oxford , South Parks Road , OX1 3QZ , Oxford , UK .
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33
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Mucha E, Stuckmann A, Marianski M, Struwe WB, Meijer G, Pagel K. In-depth structural analysis of glycans in the gas phase. Chem Sci 2019; 10:1272-1284. [PMID: 30809341 PMCID: PMC6357860 DOI: 10.1039/c8sc05426f] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/04/2019] [Indexed: 12/26/2022] Open
Abstract
Although there have been substantial improvements in glycan analysis over the past decade, the lack of both high-resolution and high-throughput methods hampers progress in glycomics. This perspective article highlights the current developments of liquid chromatography, mass spectrometry, ion-mobility spectrometry and cryogenic IR spectroscopy for glycan analysis and gives a critical insight to their individual strengths and limitations. Moreover, we discuss a novel concept in which ion mobility-mass spectrometry and cryogenic IR spectroscopy is combined in a single instrument such that datasets consisting of m/z, collision cross sections and IR fingerprints can be obtained. This multidimensional data will then be compared to a comprehensive reference library of intact glycans and their fragments to accurately identify unknown glycans on a high-throughput scale with minimal sample requirements. Due to the complementarity of the obtained information, this novel approach is highly diagnostic and also suitable for the identification of larger glycans; however, the workflow and instrumentation is straightforward enough to be implemented into a user-friendly setup.
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Affiliation(s)
- Eike Mucha
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany . .,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Alexandra Stuckmann
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany . .,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Mateusz Marianski
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
| | - Weston B Struwe
- Oxford Glycobiology Institute , Department of Biochemistry , University of Oxford , OX1 3QU Oxford , UK
| | - Gerard Meijer
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany . .,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
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34
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Manz C, Grabarics M, Hoberg F, Pugini M, Stuckmann A, Struwe WB, Pagel K. Separation of isomeric glycans by ion mobility spectrometry – the impact of fluorescent labelling. Analyst 2019; 144:5292-5298. [DOI: 10.1039/c9an00937j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bloodgroup oligosaccharides have been derivatized with labels common in HPLC and evaluated regarding their ion mobility behaviour.
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Affiliation(s)
- Christian Manz
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Fritz Haber Institute of the Max Planck Society
| | - Márkó Grabarics
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Fritz Haber Institute of the Max Planck Society
| | - Friederike Hoberg
- Fritz Haber Institute of the Max Planck Society
- Department of Molecular Physics
- 14195 Berlin
- Germany
| | - Michele Pugini
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Fritz Haber Institute of the Max Planck Society
| | - Alexandra Stuckmann
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Weston B. Struwe
- Oxford Glycobiology Institute
- Department of Biochemistry
- University of Oxford
- Oxford OX1 3QU
- UK
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Fritz Haber Institute of the Max Planck Society
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35
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Hansen K, Lau AM, Giles K, McDonnell JM, Struwe WB, Sutton BJ, Politis A. A Mass-Spectrometry-Based Modelling Workflow for Accurate Prediction of IgG Antibody Conformations in the Gas Phase. Angew Chem Int Ed Engl 2018; 57:17194-17199. [PMID: 30408305 PMCID: PMC6392142 DOI: 10.1002/anie.201812018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Indexed: 11/09/2022]
Abstract
Immunoglobulins are biomolecules involved in defence against foreign substances. Flexibility is key to their functional properties in relation to antigen binding and receptor interactions. We have developed an integrative strategy combining ion mobility mass spectrometry (IM-MS) with molecular modelling to study the conformational dynamics of human IgG antibodies. Predictive models of all four human IgG subclasses were assembled and their dynamics sampled in the transition from extended to collapsed state during IM-MS. Our data imply that this collapse of IgG antibodies is related to their intrinsic structural features, including Fab arm flexibility, collapse towards the Fc region, and the length of their hinge regions. The workflow presented here provides an accurate structural representation in good agreement with the observed collision cross section for these flexible IgG molecules. These results have implications for studying other nonglobular flexible proteins.
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Affiliation(s)
- Kjetil Hansen
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Andy M. Lau
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | | | | | | | - Brian J. Sutton
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonUK
| | - Argyris Politis
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
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36
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Hansen K, Lau AM, Giles K, McDonnell JM, Struwe WB, Sutton BJ, Politis A. A Mass‐Spectrometry‐Based Modelling Workflow for Accurate Prediction of IgG Antibody Conformations in the Gas Phase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kjetil Hansen
- Department of Chemistry King's College London 7 Trinity Street London SE1 1DB UK
| | - Andy M. Lau
- Department of Chemistry King's College London 7 Trinity Street London SE1 1DB UK
| | - Kevin Giles
- Waters Corp. Stamford Road Wilmslow SK9 4AX UK
| | - James M. McDonnell
- Randall Centre for Cell and Molecular Biophysics King's College London UK
| | | | - Brian J. Sutton
- Randall Centre for Cell and Molecular Biophysics King's College London UK
| | - Argyris Politis
- Department of Chemistry King's College London 7 Trinity Street London SE1 1DB UK
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37
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Struwe WB, Chertova E, Allen JD, Seabright GE, Watanabe Y, Harvey DJ, Medina-Ramirez M, Roser JD, Smith R, Westcott D, Keele BF, Bess JW, Sanders RW, Lifson JD, Moore JP, Crispin M. Site-Specific Glycosylation of Virion-Derived HIV-1 Env Is Mimicked by a Soluble Trimeric Immunogen. Cell Rep 2018; 24:1958-1966.e5. [PMID: 30134158 PMCID: PMC6113929 DOI: 10.1016/j.celrep.2018.07.080] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/18/2018] [Accepted: 07/24/2018] [Indexed: 12/29/2022] Open
Abstract
Many broadly neutralizing antibodies (bnAbs) against HIV-1 recognize and/or penetrate the glycan shield on native, virion-associated envelope glycoprotein (Env) spikes. The same bnAbs also bind to recombinant, soluble trimeric immunogens based on the SOSIP design. While SOSIP trimers are close structural and antigenic mimics of virion Env, the extent to which their glycan structures resemble ones on infectious viruses is undefined. Here, we compare the overall glycosylation of gp120 and gp41 subunits from BG505 (clade A) virions produced in a lymphoid cell line with those from recombinant BG505 SOSIP trimers, including CHO-derived clinical grade material. We also performed detailed site-specific analyses of gp120. Glycans relevant to key bnAb epitopes are generally similar on the recombinant SOSIP and virion-derived Env proteins, although the latter do contain hotspots of elevated glycan processing. Knowledge of native versus recombinant Env glycosylation will guide vaccine design and manufacturing programs.
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Affiliation(s)
- Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, UK
| | - Elena Chertova
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joel D Allen
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Gemma E Seabright
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yasunori Watanabe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - David J Harvey
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Max Medina-Ramirez
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - James D Roser
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rodman Smith
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - David Westcott
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Julian W Bess
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rogier W Sanders
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA; Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA.
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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38
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Markolovic S, Zhuang Q, Wilkins SE, Eaton CD, Abboud MI, Katz MJ, McNeil HE, Leśniak RK, Hall C, Struwe WB, Konietzny R, Davis S, Yang M, Ge W, Benesch JLP, Kessler BM, Ratcliffe PJ, Cockman ME, Fischer R, Wappner P, Chowdhury R, Coleman ML, Schofield CJ. The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases. Nat Chem Biol 2018; 14:688-695. [PMID: 29915238 PMCID: PMC6027965 DOI: 10.1038/s41589-018-0071-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/03/2018] [Indexed: 11/14/2022]
Abstract
Biochemical, structural and cellular studies reveal Jumonji-C (JmjC) domain-containing 7 (JMJD7) to be a 2-oxoglutarate (2OG)-dependent oxygenase that catalyzes (3S)-lysyl hydroxylation. Crystallographic analyses reveal JMJD7 to be more closely related to the JmjC hydroxylases than to the JmjC demethylases. Biophysical and mutation studies show that JMJD7 has a unique dimerization mode, with interactions between monomers involving both N- and C-terminal regions and disulfide bond formation. A proteomic approach identifies two related members of the translation factor (TRAFAC) family of GTPases, developmentally regulated GTP-binding proteins 1 and 2 (DRG1/2), as activity-dependent JMJD7 interactors. Mass spectrometric analyses demonstrate that JMJD7 catalyzes Fe(II)- and 2OG-dependent hydroxylation of a highly conserved lysine residue in DRG1/2; amino-acid analyses reveal that JMJD7 catalyzes (3S)-lysyl hydroxylation. The functional assignment of JMJD7 will enable future studies to define the role of DRG hydroxylation in cell growth and disease.
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Affiliation(s)
- Suzana Markolovic
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Qinqin Zhuang
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sarah E Wilkins
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Charlotte D Eaton
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Helen E McNeil
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Robert K Leśniak
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Charlotte Hall
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Weston B Struwe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Simon Davis
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Ming Yang
- Target Discovery Institute, University of Oxford, Oxford, UK
- The Francis Crick Institute, London, UK
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Justin L P Benesch
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Peter J Ratcliffe
- Target Discovery Institute, University of Oxford, Oxford, UK
- The Francis Crick Institute, London, UK
| | - Matthew E Cockman
- Target Discovery Institute, University of Oxford, Oxford, UK
- The Francis Crick Institute, London, UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, UK
| | | | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Clark Center, Stanford, CA, USA.
| | - Mathew L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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39
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Young G, Hundt N, Cole D, Fineberg A, Andrecka J, Tyler A, Olerinyova A, Ansari A, Marklund EG, Collier MP, Chandler SA, Tkachenko O, Allen J, Crispin M, Billington N, Takagi Y, Sellers JR, Eichmann C, Selenko P, Frey L, Riek R, Galpin MR, Struwe WB, Benesch JLP, Kukura P. Quantitative mass imaging of single biological macromolecules. Science 2018; 360:423-427. [PMID: 29700264 DOI: 10.1126/science.aar5839] [Citation(s) in RCA: 305] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 03/26/2018] [Indexed: 12/17/2022]
Abstract
The cellular processes underpinning life are orchestrated by proteins and their interactions. The associated structural and dynamic heterogeneity, despite being key to function, poses a fundamental challenge to existing analytical and structural methodologies. We used interferometric scattering microscopy to quantify the mass of single biomolecules in solution with 2% sequence mass accuracy, up to 19-kilodalton resolution, and 1-kilodalton precision. We resolved oligomeric distributions at high dynamic range, detected small-molecule binding, and mass-imaged proteins with associated lipids and sugars. These capabilities enabled us to characterize the molecular dynamics of processes as diverse as glycoprotein cross-linking, amyloidogenic protein aggregation, and actin polymerization. Interferometric scattering mass spectrometry allows spatiotemporally resolved measurement of a broad range of biomolecular interactions, one molecule at a time.
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Affiliation(s)
- Gavin Young
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Nikolas Hundt
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Daniel Cole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Adam Fineberg
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Joanna Andrecka
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Andrew Tyler
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Anna Olerinyova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Ayla Ansari
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Erik G Marklund
- Department of Chemistry Biomedicinskt Centrum, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Miranda P Collier
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Shane A Chandler
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Olga Tkachenko
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Joel Allen
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Neil Billington
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD 20892, USA
| | - Yasuharu Takagi
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD 20892, USA
| | - James R Sellers
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD 20892, USA
| | - Cédric Eichmann
- In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Rössle Straße 10, 13125 Berlin, Germany
| | - Philipp Selenko
- In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Rössle Straße 10, 13125 Berlin, Germany
| | - Lukas Frey
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.,Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Martin R Galpin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Justin L P Benesch
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
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40
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Watanabe Y, Vasiljevic S, Allen JD, Seabright GE, Duyvesteyn HME, Doores KJ, Crispin M, Struwe WB. Signature of Antibody Domain Exchange by Native Mass Spectrometry and Collision-Induced Unfolding. Anal Chem 2018; 90:7325-7331. [PMID: 29757629 PMCID: PMC6008249 DOI: 10.1021/acs.analchem.8b00573] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of domain-exchanged antibodies offers a route to high-affinity targeting to clustered multivalent epitopes, such as those associated with viral infections and many cancers. One strategy to generate these antibodies is to introduce mutations into target antibodies to drive domain exchange using the only known naturally occurring domain-exchanged anti-HIV (anti-human immunodeficiency virus) IgG1 antibody, 2G12 , as a template. Here, we show that domain exchange can be sensitively monitored by ion-mobility mass spectrometry and gas-phase collision-induced unfolding. Using native 2G12 and a mutated form that disrupts domain exchange such that it has a canonical IgG1 architecture ( 2G12 I19R ), we show that the two forms can be readily distinguished by their unfolding profiles. Importantly, the same signature of domain exchange is observed for both intact antibody and isolated Fab fragments. The development of a mass spectrometric method to detect antibody domain exchange will enable rapid screening and selection of candidate antibodies engineered to exhibit this and other unusual quaternary antibody architectures.
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Affiliation(s)
- Yasunori Watanabe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
- Biological Sciences & the Institute for Life Sciences, University of Southampton, SO17 1BJ, United Kingdom
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Roosevelt Drive, OX3 7BN, United Kingdom
| | - Snezana Vasiljevic
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
| | - Joel D. Allen
- Biological Sciences & the Institute for Life Sciences, University of Southampton, SO17 1BJ, United Kingdom
| | - Gemma E. Seabright
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
- Biological Sciences & the Institute for Life Sciences, University of Southampton, SO17 1BJ, United Kingdom
| | - Helen M. E. Duyvesteyn
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Roosevelt Drive, OX3 7BN, United Kingdom
| | - Katie J. Doores
- Department of Infectious Diseases, King’s College London, SE1 9RT, United Kingdom
| | - Max Crispin
- Biological Sciences & the Institute for Life Sciences, University of Southampton, SO17 1BJ, United Kingdom
| | - Weston B. Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, OX1 3QZ, United Kingdom
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41
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Harvey DJ, Struwe WB. Structural Studies of Fucosylated N-Glycans by Ion Mobility Mass Spectrometry and Collision-Induced Fragmentation of Negative Ions. J Am Soc Mass Spectrom 2018; 29:1179-1193. [PMID: 29790113 PMCID: PMC6003995 DOI: 10.1007/s13361-018-1950-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 05/03/2023]
Abstract
There is considerable potential for the use of ion mobility mass spectrometry in structural glycobiology due in large part to the gas-phase separation attributes not typically observed by orthogonal methods. Here, we evaluate the capability of traveling wave ion mobility combined with negative ion collision-induced dissociation to provide structural information on N-linked glycans containing multiple fucose residues forming the Lewisx and Lewisy epitopes. These epitopes are involved in processes such as cell-cell recognition and are important as cancer biomarkers. Specific information that could be obtained from the intact N-glycans by negative ion CID included the general topology of the glycan such as the presence or absence of a bisecting GlcNAc residue and the branching pattern of the triantennary glycans. Information on the location of the fucose residues was also readily obtainable from ions specific to each antenna. Some isobaric fragment ions produced prior to ion mobility could subsequently be separated and, in some cases, provided additional valuable structural information that was missing from the CID spectra alone. Graphical abstract ᅟ.
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Affiliation(s)
- David J Harvey
- Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Weston B Struwe
- Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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42
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Harvey DJ, Watanabe Y, Allen JD, Rudd P, Pagel K, Crispin M, Struwe WB. Collision Cross Sections and Ion Mobility Separation of Fragment Ions from Complex N-Glycans. J Am Soc Mass Spectrom 2018; 29:1250-1261. [PMID: 29675741 DOI: 10.1007/s13361-018-1930-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/27/2018] [Accepted: 02/27/2018] [Indexed: 05/17/2023]
Abstract
Ion mobility mass spectrometry (IM-MS) holds great potential for structural glycobiology, in particular in its ability to resolve glycan isomers. Generally, IM-MS has largely been applied to intact glycoconjugate ions with reports focusing on the separation of different adduct types. Here, we explore IM separation and report the collision cross section (CCS) of complex type N-glycans and their fragments in negative ion mode following collision-induced dissociation (CID). CCSs of isomeric fragment ions were found, in some cases, to reveal structural details that were not present in CID spectra themselves. Many fragment ions were confirmed as possessing multiple structure, details of which could be obtained by comparing their drift time profiles to different glycans. By using fragmentation both before and after mobility separation, information was gathered on the fragmentation pathways producing some of the ions. These results help demonstrate the utility of IM and will contribute to the growing use of IM-MS for glycomics. Graphical Abstract ᅟ.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Yasunori Watanabe
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Joel D Allen
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Pauline Rudd
- NIBRT GlycoScience Group, The National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
- Institut für Chemie und Biochemie, Freien Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Max Crispin
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK.
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43
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Mucha E, Lettow M, Marianski M, Thomas DA, Struwe WB, Harvey DJ, Meijer G, Seeberger PH, von Helden G, Pagel K. Fucose-Migration in intakten protonierten Glykan-Ionen - ein universelles Phänomen in der Massenspektrometrie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
- Institut für Chemie und Biochemie, der; Freien Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Maike Lettow
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
- Institut für Chemie und Biochemie, der; Freien Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Daniel A. Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Weston B. Struwe
- Oxford Glycobiology Institute; Department of Biochemistry; University of Oxford; Großbritannien
| | - David J. Harvey
- Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Großbritannien
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Peter H. Seeberger
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Potsdam Deutschland
- Institut für Chemie und Biochemie; der Freien Universität Berlin; Deutschland
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
- Institut für Chemie und Biochemie, der; Freien Universität Berlin; Takustraße 3 14195 Berlin Deutschland
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44
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Mucha E, Lettow M, Marianski M, Thomas DA, Struwe WB, Harvey DJ, Meijer G, Seeberger PH, von Helden G, Pagel K. Fucose Migration in Intact Protonated Glycan Ions: A Universal Phenomenon in Mass Spectrometry. Angew Chem Int Ed Engl 2018; 57:7440-7443. [PMID: 29688603 DOI: 10.1002/anie.201801418] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/23/2018] [Indexed: 11/10/2022]
Abstract
Fucose is an essential deoxysugar that is found in a wide range of biologically relevant glycans and glycoconjugates. A recurring problem in mass spectrometric analyses of fucosylated glycans is the intramolecular migration of fucose units, which can lead to erroneous sequence assignments. This migration reaction is typically assigned to activation during collision-induced dissociation (CID) in tandem mass spectrometry (MS). In this work, we utilized cold-ion spectroscopy and show for the first time that fucose migration is not limited to fragments obtained in tandem MS and can also be observed in intact glycan ions. This observation suggests a possible low-energy barrier for this transfer reaction and generalizes fucose migration to an issue that may universally occur in any type of mass spectrometry experiment.
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Affiliation(s)
- Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.,Institut für Chemie und Biochemie, der Freien Universität Berlin, Takustraße 3, 14195, Berlin, Germany
| | - Maike Lettow
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.,Institut für Chemie und Biochemie, der Freien Universität Berlin, Takustraße 3, 14195, Berlin, Germany
| | - Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Peter H Seeberger
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institut für Chemie und Biochemie, der Freien Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.,Institut für Chemie und Biochemie, der Freien Universität Berlin, Takustraße 3, 14195, Berlin, Germany
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45
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Harvey DJ, Seabright GE, Vasiljevic S, Crispin M, Struwe WB. Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments. J Am Soc Mass Spectrom 2018; 29:972-988. [PMID: 29508223 PMCID: PMC5940726 DOI: 10.1007/s13361-018-1890-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 01/02/2018] [Accepted: 01/08/2018] [Indexed: 05/15/2023]
Abstract
Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man8GlcNAc2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. Graphical Abstract ᅟ.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Center for Biological Sciences, Faculty of Natural and Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK.
| | - Gemma E Seabright
- Center for Biological Sciences, Faculty of Natural and Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Snezana Vasiljevic
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Max Crispin
- Center for Biological Sciences, Faculty of Natural and Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Weston B Struwe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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46
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Hochberg GKA, Shepherd DA, Marklund EG, Santhanagoplan I, Degiacomi MT, Laganowsky A, Allison TM, Basha E, Marty MT, Galpin MR, Struwe WB, Baldwin AJ, Vierling E, Benesch JLP. Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions. Science 2018; 359:930-935. [PMID: 29472485 PMCID: PMC6587588 DOI: 10.1126/science.aam7229] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 09/25/2017] [Accepted: 01/08/2018] [Indexed: 12/26/2022]
Abstract
Oligomeric proteins assemble with exceptional selectivity, even in the presence of closely related proteins, to perform their cellular roles. We show that most proteins related by gene duplication of an oligomeric ancestor have evolved to avoid hetero-oligomerization and that this correlates with their acquisition of distinct functions. We report how coassembly is avoided by two oligomeric small heat-shock protein paralogs. A hierarchy of assembly, involving intermediates that are populated only fleetingly at equilibrium, ensures selective oligomerization. Conformational flexibility at noninterfacial regions in the monomers prevents coassembly, allowing interfaces to remain largely conserved. Homomeric oligomers must overcome the entropic benefit of coassembly and, accordingly, homomeric paralogs comprise fewer subunits than homomers that have no paralogs.
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Affiliation(s)
- Georg K A Hochberg
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Dale A Shepherd
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Erik G Marklund
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Indu Santhanagoplan
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Matteo T Degiacomi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Arthur Laganowsky
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Timothy M Allison
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Eman Basha
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael T Marty
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Martin R Galpin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Justin L P Benesch
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK.
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47
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Altamirano A, Naschberger A, Fürnrohr BG, Saldova R, Struwe WB, Jennings PM, Millán Martín S, Malic S, Plangger I, Lechner S, Pisano R, Peretti N, Linke B, Aguiar MM, Fresser F, Ritsch A, Lenac Rovis T, Goode C, Rudd PM, Scheffzek K, Rupp B, Dieplinger H. Expression, Purification, and Biochemical Characterization of Human Afamin. J Proteome Res 2018; 17:1269-1277. [PMID: 29441788 DOI: 10.1021/acs.jproteome.7b00867] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Afamin is an 87 kDa glycoprotein with five predicted N-glycosylation sites. Afamin's glycan abundance contributes to conformational and chemical inhomogeneity presenting great challenges for molecular structure determination. For the purpose of studying the structure of afamin, various forms of recombinantly expressed human afamin (rhAFM) with different glycosylation patterns were thus created. Wild-type rhAFM and various hypoglycosylated forms were expressed in CHO, CHO-Lec1, and HEK293T cells. Fully nonglycosylated rhAFM was obtained by transfection of point-mutated cDNA to delete all N-glycosylation sites of afamin. Wild-type and hypo/nonglycosylated rhAFM were purified from cell culture supernatants by immobilized metal ion affinity and size exclusion chromatography. Glycan analysis of purified proteins demonstrated differences in micro- and macro-heterogeneity of glycosylation enabling the comparison between hypoglycosylated, wild-type rhAFM, and native plasma afamin. Because antibody fragments can work as artificial chaperones by stabilizing the structure of proteins and consequently enhance the chance for successful crystallization, we incubated a Fab fragment of the monoclonal anti-afamin antibody N14 with human afamin and obtained a stoichiometric complex. Subsequent results showed sufficient expression of various partially or nonglycosylated forms of rhAFM in HEK293T and CHO cells and revealed that glycosylation is not necessary for expression and secretion.
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Affiliation(s)
| | | | | | - Radka Saldova
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research & Training , Dublin, Ireland
| | - Weston B Struwe
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research & Training , Dublin, Ireland
| | - Patrick M Jennings
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research & Training , Dublin, Ireland
| | - Silvia Millán Martín
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research & Training , Dublin, Ireland
| | - Suzana Malic
- Center for Proteomics, Faculty of Medicine, University of Rijeka , 51000 Rijeka, Croatia
| | | | | | | | | | | | | | | | | | - Tihana Lenac Rovis
- Center for Proteomics, Faculty of Medicine, University of Rijeka , 51000 Rijeka, Croatia
| | | | - Pauline M Rudd
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research & Training , Dublin, Ireland
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48
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Behrens AJ, Kumar A, Medina-Ramirez M, Cupo A, Marshall K, Cruz Portillo VM, Harvey DJ, Ozorowski G, Zitzmann N, Wilson IA, Ward AB, Struwe WB, Moore JP, Sanders RW, Crispin M. Integrity of Glycosylation Processing of a Glycan-Depleted Trimeric HIV-1 Immunogen Targeting Key B-Cell Lineages. J Proteome Res 2018; 17:987-999. [PMID: 29420040 DOI: 10.1021/acs.jproteome.7b00639] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Broadly neutralizing antibodies (bNAbs) that target the trimeric HIV-1 envelope glycoprotein spike (Env) are tools that can guide the design of recombinant Env proteins intended to engage the predicted human germline precursors of bNAbs (gl-bNAbs). The protein components of gl-bNAb epitopes are often masked by glycans, while mature bNAbs can evolve to accommodate or bypass these shielding glycans. The design of germline-targeting Env immunogens therefore includes the targeted deletion of specific glycan sites. However, the processing of glycans on Env trimers can be influenced by the density with which they are packed together, a highly relevant point given the essential contributions under-processed glycans make to multiple bNAb epitopes. We sought to determine the impact of the removal of 15 potential N-glycan sites (5 per protomer) from the germline-targeting soluble trimer, BG505 SOSIP.v4.1-GT1, using quantitative, site-specific N-glycan mass spectrometry analysis. We find that, compared with SOSIP.664, there was little overall change in the glycan profile but only subtle increases in the extent of processing at sites immediately adjacent to where glycans had been deleted. We conclude that multiple glycans can be deleted from BG505 SOSIP trimers without perturbing the overall integrity of the glycan shield.
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Affiliation(s)
- Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Abhinav Kumar
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Max Medina-Ramirez
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam , 1105 AZ Amsterdam, The Netherlands
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York , New York, New York 10021, United States
| | - Kevin Marshall
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York , New York, New York 10021, United States
| | - Victor M Cruz Portillo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York , New York, New York 10021, United States
| | - David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, IAVI Neutralizing Antibody Center and CAVD, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, IAVI Neutralizing Antibody Center and CAVD, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute , La Jolla, California 92037, United States.,Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, IAVI Neutralizing Antibody Center and CAVD, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York , New York, New York 10021, United States
| | - Rogier W Sanders
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam , 1105 AZ Amsterdam, The Netherlands.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York , New York, New York 10021, United States
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom.,Centre for Biological Sciences and Institute for Life Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
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49
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Struwe WB, Baldauf C, Hofmann J, Rudd PM, Pagel K. Ion mobility separation of deprotonated oligosaccharide isomers - evidence for gas-phase charge migration. Chem Commun (Camb) 2018; 52:12353-12356. [PMID: 27711324 DOI: 10.1039/c6cc06247d] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There has been increasing evidence that certain isomeric glycans can be separated efficiently by ion mobility-mass spectrometry when deprotonated ions are analyzed. To better understand the fundamentals behind these separations, we here investigate the impact of ionisation mode and adduct formation using IM-MS, density-functional theory and ab initio molecular dynamics.
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Affiliation(s)
- W B Struwe
- National Institute of Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Dublin, Ireland.
| | - C Baldauf
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
| | - J Hofmann
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
| | - P M Rudd
- National Institute of Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Dublin, Ireland.
| | - K Pagel
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany. and Institut für Chemie und Biochemie der Freien Universität Berlin, Takustr. 3, 14195 Berlin, Germany.
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50
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Abstract
INTRODUCTION Much of the efforts to develop a vaccine against the human immunodeficiency virus (HIV) have focused on the design of recombinant mimics of the viral attachment glycoprotein (Env). The leading immunogens exhibit native-like antigenic properties and are being investigated for their ability to induce broadly neutralizing antibodies (bNAbs). Understanding the relative abundance of glycans at particular glycosylation sites on these immunogens is important as most bNAbs have evolved to recognize or evade the dense coat of glycans that masks much of the protein surface. Understanding the glycan structures on candidate immunogens enables triaging between native-like conformations and immunogens lacking key structural features as steric constraints limit glycan processing. The sensitivity of the processing state of a particular glycan to its structural environment has led to the need for quantitative glycan profiling and site-specific analysis to probe the structural integrity of immunogens. Areas covered: We review analytical methodologies for HIV immunogen evaluation and discuss how these studies have led to a greater understanding of the structural constraints that control the glycosylation state of the HIV attachment and fusion spike. Expert commentary: Total composition and site-specific glycosylation profiling are emerging as standard methods in the evaluation of Env-based immunogen candidates.
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Affiliation(s)
- Anna-Janina Behrens
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK
| | - Weston B Struwe
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK
| | - Max Crispin
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK.,b Department of Immunology and Microbial Science , The Scripps Research Institute , La Jolla , CA , USA.,c Centre for Biological Sciences and Institute for Life Sciences , University of Southampton , Southampton SO17 1BJ , UK
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