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Jagger AM, Waudby CA, Irving JA, Christodoulou J, Lomas DA. High-resolution ex vivo NMR spectroscopy of human Z α 1-antitrypsin. Nat Commun 2020; 11:6371. [PMID: 33311470 PMCID: PMC7732992 DOI: 10.1038/s41467-020-20147-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/15/2020] [Indexed: 01/18/2023] Open
Abstract
Genetic mutations predispose the serine protease inhibitor α1-antitrypsin to misfolding and polymerisation within hepatocytes, causing liver disease and chronic obstructive pulmonary disease. This misfolding occurs via a transiently populated intermediate state, but our structural understanding of this process is limited by the instability of recombinant α1-antitrypsin variants in solution. Here we apply NMR spectroscopy to patient-derived samples of α1-antitrypsin at natural isotopic abundance to investigate the consequences of disease-causing mutations, and observe widespread chemical shift perturbations for methyl groups in Z AAT (E342K). By comparison with perturbations induced by binding of a small-molecule inhibitor of misfolding we conclude that they arise from rapid exchange between the native conformation and a well-populated intermediate state. The observation that this intermediate is stabilised by inhibitor binding suggests a paradoxical approach to the targeted treatment of protein misfolding disorders, wherein the stabilisation of disease-associated states provides selectivity while inhibiting further transitions along misfolding pathways.
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Affiliation(s)
- Alistair M Jagger
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK
| | - James A Irving
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK.
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
| | - David A Lomas
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK.
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
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Nyon MP, Prentice T, Day J, Kirkpatrick J, Sivalingam GN, Levy G, Haq I, Irving JA, Lomas DA, Christodoulou J, Gooptu B, Thalassinos K. An integrative approach combining ion mobility mass spectrometry, X-ray crystallography, and nuclear magnetic resonance spectroscopy to study the conformational dynamics of α1 -antitrypsin upon ligand binding. Protein Sci 2015; 24:1301-12. [PMID: 26011795 PMCID: PMC4534181 DOI: 10.1002/pro.2706] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/05/2015] [Accepted: 05/11/2015] [Indexed: 11/11/2022]
Abstract
Native mass spectrometry (MS) methods permit the study of multiple protein species within solution equilibria, whereas ion mobility (IM)-MS can report on conformational behavior of specific states. We used IM-MS to study a conformationally labile protein (α1 -antitrypsin) that undergoes pathological polymerization in the context of point mutations. The folded, native state of the Z-variant remains highly polymerogenic in physiological conditions despite only minor thermodynamic destabilization relative to the wild-type variant. Various data implicate kinetic instability (conformational lability within a native state ensemble) as the basis of Z α1 -antitrypsin polymerogenicity. We show the ability of IM-MS to track such disease-relevant conformational behavior in detail by studying the effects of peptide binding on α1 -antitrypsin conformation and dynamics. IM-MS is, therefore, an ideal platform for the screening of compounds that result in therapeutically beneficial kinetic stabilization of native α1 -antitrypsin. Our findings are confirmed with high-resolution X-ray crystallographic and nuclear magnetic resonance spectroscopic studies of the same event, which together dissect structural changes from dynamic effects caused by peptide binding at a residue-specific level. IM-MS methods, therefore, have great potential for further study of biologically relevant thermodynamic and kinetic instability of proteins and provide rapid and multidimensional characterization of ligand interactions of therapeutic interest.
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Affiliation(s)
- Mun Peak Nyon
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Tanya Prentice
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Jemma Day
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - John Kirkpatrick
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Ganesh N Sivalingam
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Geraldine Levy
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Imran Haq
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, United Kingdom
| | - James A Irving
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, United Kingdom
| | - David A Lomas
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, United Kingdom
| | - John Christodoulou
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, WC1E 7HX, United Kingdom
| | - Bibek Gooptu
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, WC1E 7HX, United Kingdom.,Division of Asthma, Allergy and Lung Biology, King's College London, Guy's Hospital, London, SE1 9RT, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, WC1E 7HX, United Kingdom
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Nyon M, Segu L, Cabrita L, Lévy G, Kirkpatrick J, Roussel B, Patschull A, Barrett T, Ekeowa U, Kerr R, Waudby C, Kalsheker N, Hill M, Thalassinos K, Lomas D, Christodoulou J, Gooptu B. Structural dynamics associated with intermediate formation in an archetypal conformational disease. Structure 2012; 20:504-12. [PMID: 22405009 PMCID: PMC3314904 DOI: 10.1016/j.str.2012.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 12/02/2011] [Accepted: 01/03/2012] [Indexed: 11/21/2022]
Abstract
In conformational diseases, native protein conformers convert to pathological intermediates that polymerize. Structural characterization of these key intermediates is challenging. They are unstable and minimally populated in dynamic equilibria that may be perturbed by many analytical techniques. We have characterized a forme fruste deficiency variant of α1-antitrypsin (Lys154Asn) that forms polymers recapitulating the conformer-specific neo-epitope observed in polymers that form in vivo. Lys154Asn α1-antitrypsin populates an intermediate ensemble along the polymerization pathway at physiological temperatures. Nuclear magnetic resonance spectroscopy was used to report the structural and dynamic changes associated with this. Our data highlight an interaction network likely to regulate conformational change and do not support the recent contention that the disease-relevant intermediate is substantially unfolded. Conformational disease intermediates may best be defined using powerful but minimally perturbing techniques, mild disease mutants, and physiological conditions.
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Affiliation(s)
- Mun Peak Nyon
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
| | - Lakshmi Segu
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
| | - Lisa D. Cabrita
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Géraldine R. Lévy
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - John Kirkpatrick
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Benoit D. Roussel
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
| | - Anathe O.M. Patschull
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Tracey E. Barrett
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
| | - Ugo I. Ekeowa
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
| | - Richard Kerr
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Christopher A. Waudby
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Noor Kalsheker
- Division of Clinical Chemistry, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Marian Hill
- Division of Clinical Chemistry, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - David A. Lomas
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
- Corresponding author
| | - John Christodoulou
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
- Corresponding author
| | - Bibek Gooptu
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- Corresponding author
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