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Yang Y, Du Y, Ivanov D, Niu C, Clare R, Smith JW, Nazy I, Kaltashov IA. Molecular architecture and platelet-activating properties of small immune complexes assembled on heparin and platelet factor 4. Commun Biol 2024; 7:308. [PMID: 38467823 PMCID: PMC10928113 DOI: 10.1038/s42003-024-05982-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Heparin-induced thrombocytopenia (HIT) is an adverse reaction to heparin leading to a reduction in circulating platelets with an increased risk of thrombosis. It is precipitated by polymerized immune complexes consisting of pathogenic antibodies that recognize a small chemokine platelet factor 4 (PF4) bound to heparin. Characterization of these immune complexes is extremely challenging due to the enormous structural heterogeneity of such macromolecular assemblies and their constituents. Native mass spectrometry demonstrates that up to three PF4 tetramers can be assembled on a heparin chain, consistent with the molecular modeling studies showing facile polyanion wrapping along the polycationic belt on the PF4 surface. Although these assemblies can accommodate a maximum of only two antibodies, the resulting immune complexes are capable of platelet activation despite their modest size. Taken together, these studies provide further insight into molecular mechanisms of HIT and other immune disorders where anti-PF4 antibodies play a central role.
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Affiliation(s)
- Yang Yang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Yi Du
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Daniil Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Chendi Niu
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Rumi Clare
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - James W Smith
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ishac Nazy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA.
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Jeanroy F, Comby-Zerbino C, Demesmay C, Dugas V. Miniaturized affinity chromatography: A powerful technique for the isolation of high affinity GAGs sequences prior to their identification by MALDI-TOF MS. Anal Chim Acta 2023; 1277:341656. [PMID: 37604620 DOI: 10.1016/j.aca.2023.341656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023]
Abstract
Glycosaminoglycans (GAGS) are involved in many biological processes through interactions with a variety of proteins, including proteases, growth factors, cytokines, chemokines and adhesion molecules. Identifying druggable GAG-protein interactions for therapeutic purposes is a challenge for the analytical community. In this context, this work investigates the use of a new miniaturized monolithic affinity column (poly(GMA-co-MBA) grafted with antithrombin III (AT III)) to specifically capture and elute high affinity sequences contained in low molecular weight heparin (enoxaparin) for further on-line characterization. This miniaturized, high binding capacity affinity column allows the specific capture of high-affinity oligosaccharide chains from Enoxaparin, even at low concentrations and with a minimal consumption of AT III. In addition to purification, this elution process enables preconcentration for direct analysis by capillary zone electrophoresis. It was found that many of oligosaccharide chains in enoxaparin were eliminated and that certain chain sequences were retained and enriched. Direct coupling with MALDI-TOF MS was successfully used to further characterize the specifically retained oligosaccharides where nano-ESI-TOF MS failed. After optimization of the sample preparation and ionization parameters, direct on-line analysis was performed by applying the elution volume released from the miniaturized affinity column (≤1 μL) directly to the MALDI plate. Finally, this original miniaturized analytical workflow coupling miniaturized AT III-affinity chromatography to MALDI-TOF MS detection is able to select, enrich and detect and identify high affinity sequences (mainly DP4 in size length with a high degree of sulfation) from low molecular weight heparin samples. A more specific selection of GAG sequences can be achieved by increasing the ionic strength during the washing step of affinity chromatography. This is consistent with the known binding pattern between heparin and AT III.
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Affiliation(s)
- Frédéric Jeanroy
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR, 5280, 5 Rue de la Doua, F-69100, Villeurbanne, France
| | - Clothilde Comby-Zerbino
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut Lumière Matière, UMR 5306, F-69100, Villeurbanne, France
| | - Claire Demesmay
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR, 5280, 5 Rue de la Doua, F-69100, Villeurbanne, France
| | - Vincent Dugas
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR, 5280, 5 Rue de la Doua, F-69100, Villeurbanne, France.
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Muneeruddin K, Kaltashov IA, Wang G. Characterizing Soluble Protein Aggregates Using Native Mass Spectrometry Coupled with Temperature-Controlled Electrospray Ionization and Size-Excl usion Chromatography. Methods Mol Biol 2022; 2406:455-468. [PMID: 35089574 DOI: 10.1007/978-1-0716-1859-2_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Characterization of soluble protein aggregates provides valuable information for revealing mechanisms of protein aggregation process and assessing the activity and safety of protein therapeutics. However, the noncovalent interaction, the transient nature and higher degree of structural heterogeneity of the soluble aggregation system hinders precise characterization at the molecular level. Here, we describe methods using native mass spectrometry coupled with temperature-control electrospray ionization and size-exclusion chromatography to monitor the aggregation process and profile the aggregates in detail.
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Affiliation(s)
- Khaja Muneeruddin
- The Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Guanbo Wang
- Biomedical Pioneering Innovation Center, Peking University, Beijing, China.
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China.
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Miniaturized antithrombin III affinity monolithic columns coupled to TOF-MS for the selective capture and release of fondaparinux a high affinity antithrombin III ligand. Talanta 2022; 241:123275. [DOI: 10.1016/j.talanta.2022.123275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/06/2021] [Accepted: 01/14/2022] [Indexed: 11/19/2022]
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Shi D, Sheng A, Chi L. Glycosaminoglycan-Protein Interactions and Their Roles in Human Disease. Front Mol Biosci 2021; 8:639666. [PMID: 33768117 PMCID: PMC7985165 DOI: 10.3389/fmolb.2021.639666] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
Glycosaminoglycans (GAGs) are a family of linear and negatively charged polysaccharides that exist ubiquitously on the human cell surface as well as in the extracellular matrix. GAGs interact with a wide range of proteins, including proteases, growth factors, cytokines, chemokines and adhesion molecules, enabling them to mediate many physiological processes, such as protein function, cellular adhesion and signaling. GAG-protein interactions participate in and intervene in a variety of human diseases, including cardiovascular disease, infectious disease, neurodegenerative diseases and tumors. The breakthrough in analytical tools and approaches during the last two decades has facilitated a greater understanding of the importance of GAG-protein interactions and their roles in human diseases. This review focuses on aspects of the molecular basis and mechanisms of GAG-protein interactions involved in human disease. The most recent advances in analytical tools, especially mass spectrometry-based GAG sequencing and binding motif characterization methods, are introduced. An update of selected families of GAG binding proteins is presented. Perspectives on development of novel therapeutics targeting specific GAG-protein interactions are also covered in this review.
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Affiliation(s)
- Deling Shi
- National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Anran Sheng
- National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Lianli Chi
- National Glycoengineering Research Center, Shandong University, Qingdao, China
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Yang Y, Du Y, Kaltashov IA. The Utility of Native MS for Understanding the Mechanism of Action of Repurposed Therapeutics in COVID-19: Heparin as a Disruptor of the SARS-CoV-2 Interaction with Its Host Cell Receptor. Anal Chem 2020; 92:10930-10934. [PMID: 32678978 PMCID: PMC7384394 DOI: 10.1021/acs.analchem.0c02449] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023]
Abstract
The emergence and rapid proliferation of the novel coronavirus (SARS-CoV-2) resulted in a global pandemic, with over 6,000,000 cases and nearly 400,000 deaths reported worldwide by the end of May 2020. A rush to find a cure prompted re-evaluation of a range of existing therapeutics vis-à-vis their potential role in treating COVID-19, placing a premium on analytical tools capable of supporting such efforts. Native mass spectrometry (MS) has long been a tool of choice in supporting the mechanistic studies of drug/therapeutic target interactions, but its applications remain limited in the cases that involve systems with a high level of structural heterogeneity. Both SARS-CoV-2 spike protein (S-protein), a critical element of the viral entry to the host cell, and ACE2, its docking site on the host cell surface, are extensively glycosylated, making them challenging targets for native MS. However, supplementing native MS with a gas-phase ion manipulation technique (limited charge reduction) allows meaningful information to be obtained on the noncovalent complexes formed by ACE2 and the receptor-binding domain (RBD) of the S-protein. Using this technique in combination with molecular modeling also allows the role of heparin in destabilizing the ACE2/RBD association to be studied, providing critical information for understanding the molecular mechanism of its interference with the virus docking to the host cell receptor. Both short (pentasaccharide) and relatively long (eicosasaccharide) heparin oligomers form 1:1 complexes with RBD, indicating the presence of a single binding site. This association alters the protein conformation (to maximize the contiguous patch of the positive charge on the RBD surface), resulting in a notable decrease in its ability to associate with ACE2. The destabilizing effect of heparin is more pronounced in the case of the longer chains due to the electrostatic repulsion between the low-pI ACE2 and the heparin segments not accommodated on the RBD surface. In addition to providing important mechanistic information on attenuation of the ACE2/RBD association by heparin, the study demonstrates the yet untapped potential of native MS coupled to gas-phase ion chemistry as a means of facilitating rational repurposing of the existing medicines for treating COVID-19.
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Affiliation(s)
- Yang Yang
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, MA 01003
| | - Yi Du
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, MA 01003
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, MA 01003
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Yang Y, Du Y, Kaltashov IA. The utility of native MS for understanding the mechanism of action of repurposed therapeutics in COVID-19: heparin as a disruptor of the SARS-CoV-2 interaction with its host cell receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32577646 DOI: 10.1101/2020.06.09.142794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The emergence and rapid proliferation of the novel coronavirus (SARS-CoV-2) resulted in a global pandemic, with over six million cases and nearly four hundred thousand deaths reported world-wide by the end of May 2020. A rush to find the cures prompted re-evaluation of a range of existing therapeutics vis-à-vis their potential role in treating COVID-19, placing a premium on analytical tools capable of supporting such efforts. Native mass spectrometry (MS) has long been a tool of choice in supporting the mechanistic studies of drug/therapeutic target interactions, but its applications remain limited in the cases that involve systems with a high level of structural heterogeneity. Both SARS-CoV-2 spike protein (S-protein), a critical element of the viral entry to the host cell, and ACE2, its docking site on the host cell surface, are extensively glycosylated, making them challenging targets for native MS. However, supplementing native MS with a gas-phase ion manipulation technique (limited charge reduction) allows meaningful information to be obtained on the non-covalent complexes formed by ACE2 and the receptor-binding domain (RBD) of the S-protein. Using this technique in combination with molecular modeling also allows the role of heparin in destabilizing the ACE2/RBD association to be studied, providing critical information for understanding the molecular mechanism of its interference with the virus docking to the host cell receptor. Both short (pentasaccharide) and relatively long (eicosasaccharide) heparin oligomers form 1:1 complexes with RBD, indicating the presence of a single binding site. This association alters the protein conformation (to maximize the contiguous patch of the positive charge on the RBD surface), resulting in a notable decrease of its ability to associate with ACE2. The destabilizing effect of heparin is more pronounced in the case of the longer chains due to the electrostatic repulsion between the low-p I ACE2 and the heparin segments not accommodated on the RBD surface. In addition to providing important mechanistic information on attenuation of the ACE2/RBD association by heparin, the study demonstrates the yet untapped potential of native MS coupled to gas-phase ion chemistry as a means of facilitating rational repurposing of the existing medicines for treating COVID-19. Abstract Figure
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