1
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Santos J, Cuellar J, Pallarès I, Byrd EJ, Lends A, Moro F, Abdul-Shukkoor MB, Pujols J, Velasco-Carneros L, Sobott F, Otzen DE, Calabrese AN, Muga A, Pedersen JS, Loquet A, Valpuesta JM, Radford SE, Ventura S. A Targetable N-Terminal Motif Orchestrates α-Synuclein Oligomer-to-Fibril Conversion. J Am Chem Soc 2024; 146:12702-12711. [PMID: 38683963 PMCID: PMC11082882 DOI: 10.1021/jacs.4c02262] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Oligomeric species populated during α-synuclein aggregation are considered key drivers of neurodegeneration in Parkinson's disease. However, the development of oligomer-targeting therapeutics is constrained by our limited knowledge of their structure and the molecular determinants driving their conversion to fibrils. Phenol-soluble modulin α3 (PSMα3) is a nanomolar peptide binder of α-synuclein oligomers that inhibits aggregation by blocking oligomer-to-fibril conversion. Here, we investigate the binding of PSMα3 to α-synuclein oligomers to discover the mechanistic basis of this protective activity. We find that PSMα3 selectively targets an α-synuclein N-terminal motif (residues 36-61) that populates a distinct conformation in the mono- and oligomeric states. This α-synuclein region plays a pivotal role in oligomer-to-fibril conversion as its absence renders the central NAC domain insufficient to prompt this structural transition. The hereditary mutation G51D, associated with early onset Parkinson's disease, causes a conformational fluctuation in this region, leading to delayed oligomer-to-fibril conversion and an accumulation of oligomers that are resistant to remodeling by molecular chaperones. Overall, our findings unveil a new targetable region in α-synuclein oligomers, advance our comprehension of oligomer-to-amyloid fibril conversion, and reveal a new facet of α-synuclein pathogenic mutations.
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Affiliation(s)
- Jaime Santos
- Institut
de Biotecnologia i Biomedicina and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Jorge Cuellar
- Department
of Macromolecular Structures, Centro Nacional
de Biotecnología (CNB-CSIC), Madrid 28049, Spain
| | - Irantzu Pallarès
- Institut
de Biotecnologia i Biomedicina and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Emily J. Byrd
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Alons Lends
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac 33600, France
| | - Fernando Moro
- Instituto
Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología
Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, Leioa 48940, Spain
| | | | - Jordi Pujols
- Institut
de Biotecnologia i Biomedicina and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Lorea Velasco-Carneros
- Instituto
Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología
Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, Leioa 48940, Spain
| | - Frank Sobott
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Daniel E. Otzen
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, Gustav Wieds Vej 14, Aarhus C 8000, Denmark
| | - Antonio N. Calabrese
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Arturo Muga
- Instituto
Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología
Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, Leioa 48940, Spain
| | - Jan Skov Pedersen
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, Aarhus C 8000, Denmark
| | - Antoine Loquet
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac 33600, France
| | - Jose María Valpuesta
- Department
of Macromolecular Structures, Centro Nacional
de Biotecnología (CNB-CSIC), Madrid 28049, Spain
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Salvador Ventura
- Institut
de Biotecnologia i Biomedicina and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
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2
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Louros N, Wilkinson M, Tsaka G, Ramakers M, Morelli C, Garcia T, Gallardo R, D'Haeyer S, Goossens V, Audenaert D, Thal DR, Mackenzie IR, Rademakers R, Ranson NA, Radford SE, Rousseau F, Schymkowitz J. Local structural preferences in shaping tau amyloid polymorphism. Nat Commun 2024; 15:1028. [PMID: 38310108 PMCID: PMC10838331 DOI: 10.1038/s41467-024-45429-2] [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: 10/23/2023] [Accepted: 01/23/2024] [Indexed: 02/05/2024] Open
Abstract
Tauopathies encompass a group of neurodegenerative disorders characterised by diverse tau amyloid fibril structures. The persistence of polymorphism across tauopathies suggests that distinct pathological conditions dictate the adopted polymorph for each disease. However, the extent to which intrinsic structural tendencies of tau amyloid cores contribute to fibril polymorphism remains uncertain. Using a combination of experimental approaches, we here identify a new amyloidogenic motif, PAM4 (Polymorphic Amyloid Motif of Repeat 4), as a significant contributor to tau polymorphism. Calculation of per-residue contributions to the stability of the fibril cores of different pathologic tau structures suggests that PAM4 plays a central role in preserving structural integrity across amyloid polymorphs. Consistent with this, cryo-EM structural analysis of fibrils formed from a synthetic PAM4 peptide shows that the sequence adopts alternative structures that closely correspond to distinct disease-associated tau strains. Furthermore, in-cell experiments revealed that PAM4 deletion hampers the cellular seeding efficiency of tau aggregates extracted from Alzheimer's disease, corticobasal degeneration, and progressive supranuclear palsy patients, underscoring PAM4's pivotal role in these tauopathies. Together, our results highlight the importance of the intrinsic structural propensity of amyloid core segments to determine the structure of tau in cells, and in propagating amyloid structures in disease.
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Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Grigoria Tsaka
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Chiara Morelli
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Teresa Garcia
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Rodrigo Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sam D'Haeyer
- VIB Screening Core, Ghent, Belgium
- Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Vera Goossens
- VIB Screening Core, Ghent, Belgium
- Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Dominique Audenaert
- VIB Screening Core, Ghent, Belgium
- Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Dietmar Rudolf Thal
- KU Leuven, Leuven Brain Institute, 3000, Leuven, Belgium
- Laboratory for Neuropathology, KU Leuven, and Department of Pathology, UZ Leuven, 3000, Leuven, Belgium
| | - Ian R Mackenzie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rosa Rademakers
- Applied and Translational Neurogenomics, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
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3
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Aubrey LD, Ninkina N, Ulamec SM, Abramycheva NY, Vasili E, Devine OM, Wilkinson M, Mackinnon E, Limorenko G, Walko M, Muwanga S, Amadio L, Peters OM, Illarioshkin SN, Outeiro TF, Ranson NA, Brockwell DJ, Buchman VL, Radford SE. Substitution of Met-38 to Ile in γ-synuclein found in two patients with amyotrophic lateral sclerosis induces aggregation into amyloid. Proc Natl Acad Sci U S A 2024; 121:e2309700120. [PMID: 38170745 PMCID: PMC10786281 DOI: 10.1073/pnas.2309700120] [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: 06/08/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
α-, β-, and γ-Synuclein are intrinsically disordered proteins implicated in physiological processes in the nervous system of vertebrates. α-synuclein (αSyn) is the amyloidogenic protein associated with Parkinson's disease and certain other neurodegenerative disorders. Intensive research has focused on the mechanisms that cause αSyn to form amyloid structures, identifying its NAC region as being necessary and sufficient for amyloid assembly. Recent work has shown that a 7-residue sequence (P1) is necessary for αSyn amyloid formation. Although γ-synuclein (γSyn) is 55% identical in sequence to αSyn and its pathological deposits are also observed in association with neurodegenerative conditions, γSyn is resilient to amyloid formation in vitro. Here, we report a rare single nucleotide polymorphism (SNP) in the SNCG gene encoding γSyn, found in two patients with amyotrophic lateral sclerosis (ALS). The SNP results in the substitution of Met38 with Ile in the P1 region of the protein. These individuals also had a second, common and nonpathological, SNP in SNCG resulting in the substitution of Glu110 with Val. In vitro studies demonstrate that the Ile38 variant accelerates amyloid fibril assembly. Contrastingly, Val110 retards fibril assembly and mitigates the effect of Ile38. Substitution of residue 38 with Leu had little effect, while Val retards, and Ala increases the rate of amyloid formation. Ile38 γSyn also results in the formation of γSyn-containing inclusions in cells. The results show how a single point substitution can enhance amyloid formation of γSyn and highlight the P1 region in driving amyloid formation in another synuclein family member.
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Affiliation(s)
- Liam D. Aubrey
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Natalia Ninkina
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod308015, Russian Federation
| | - Sabine M. Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Natalia Y. Abramycheva
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow125367, Russia
| | - Eftychia Vasili
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Oliver M. Devine
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Eilish Mackinnon
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Galina Limorenko
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Sarah Muwanga
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Leonardo Amadio
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Owen M. Peters
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Sergey N. Illarioshkin
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow125367, Russia
| | - Tiago F. Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen37075, Germany
- Max Planck Institute for Multidisciplinary Sciences, Goettingen37075, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon TyneNE2 4HH, United Kingdom
- Scientific employee with a honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen, Göttingen37075, Germany
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Vladimir L. Buchman
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod308015, Russian Federation
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
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4
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Crossley JA, Allen WJ, Watkins DW, Sabir T, Radford SE, Tuma R, Collinson I, Fessl T. Dynamic coupling of fast channel gating with slow ATP-turnover underpins protein transport through the Sec translocon. EMBO J 2024; 43:1-13. [PMID: 38177311 PMCID: PMC10883268 DOI: 10.1038/s44318-023-00004-1] [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: 06/30/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024] Open
Abstract
The Sec translocon is a highly conserved membrane assembly for polypeptide transport across, or into, lipid bilayers. In bacteria, secretion through the core channel complex-SecYEG in the inner membrane-is powered by the cytosolic ATPase SecA. Here, we use single-molecule fluorescence to interrogate the conformational state of SecYEG throughout the ATP hydrolysis cycle of SecA. We show that the SecYEG channel fluctuations between open and closed states are much faster (~20-fold during translocation) than ATP turnover, and that the nucleotide status of SecA modulates the rates of opening and closure. The SecY variant PrlA4, which exhibits faster transport but unaffected ATPase rates, increases the dwell time in the open state, facilitating pre-protein diffusion through the pore and thereby enhancing translocation efficiency. Thus, rapid SecYEG channel dynamics are allosterically coupled to SecA via modulation of the energy landscape, and play an integral part in protein transport. Loose coupling of ATP-turnover by SecA to the dynamic properties of SecYEG is compatible with a Brownian-rachet mechanism of translocation, rather than strict nucleotide-dependent interconversion between different static states of a power stroke.
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Affiliation(s)
- Joel A Crossley
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
- School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, LS1 3HE, UK
| | - William J Allen
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK
| | - Tara Sabir
- School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, LS1 3HE, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK.
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic.
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5
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Wilkinson M, Xu Y, Thacker D, Taylor AIP, Fisher DG, Gallardo RU, Radford SE, Ranson NA. Structural evolution of fibril polymorphs during amyloid assembly. Cell 2023; 186:5798-5811.e26. [PMID: 38134875 DOI: 10.1016/j.cell.2023.11.025] [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: 10/29/2022] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Cryoelectron microscopy (cryo-EM) has provided unprecedented insights into amyloid fibril structures, including those associated with disease. However, these structures represent the endpoints of long assembly processes, and their relationship to fibrils formed early in assembly is unknown. Consequently, whether different fibril architectures, with potentially different pathological properties, form during assembly remains unknown. Here, we used cryo-EM to determine structures of amyloid fibrils at different times during in vitro fibrillation of a disease-related variant of human islet amyloid polypeptide (IAPP-S20G). Strikingly, the fibrils formed in the lag, growth, and plateau phases have different structures, with new forms appearing and others disappearing as fibrillation proceeds. A time course with wild-type hIAPP also shows fibrils changing with time, suggesting that this is a general property of IAPP amyloid assembly. The observation of transiently populated fibril structures has implications for understanding amyloid assembly mechanisms with potential new insights into amyloid progression in disease.
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Affiliation(s)
- Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Dev Thacker
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alexander I P Taylor
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Declan G Fisher
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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6
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Berhanu S, Majumder S, Müntener T, Whitehouse J, Berner C, Bera AK, Kang A, Liang B, Khan GN, Sankaran B, Tamm LK, Brockwell DJ, Hiller S, Radford SE, Baker D, Vorobieva AA. Sculpting conducting nanopore size and shape through de novo protein design. bioRxiv 2023:2023.12.20.572500. [PMID: 38187764 PMCID: PMC10769293 DOI: 10.1101/2023.12.20.572500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Transmembrane β-barrels (TMBs) are widely used for single molecule DNA and RNA sequencing and have considerable potential for a broad range of sensing and sequencing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels such as CsgG, which have evolved to carry out functions very different from sensing, and hence provide sub-optimal starting points. In contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to the design of transmembrane β-barrel pores with different diameter and pore geometry. NMR and crystallographic characterization shows that the designs are stably folded with structures close to the design models. We report the first examples of de novo designed TMBs with 10, 12 and 14 stranded β-barrels. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 pS (~0.5 nm pore diameter) to 430 pS (~1.1 nm pore diameter), and can be converted into sensitive small-molecule sensors with high signal to noise ratio. The capability to generate on demand β-barrel pores of defined geometry opens up fundamentally new opportunities for custom engineering of sequencing and sensing technologies.
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Affiliation(s)
- Samuel Berhanu
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sagardip Majumder
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - James Whitehouse
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT
| | - Carolin Berner
- Structural Biology Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- VUB-VIB Center for Structural Biology, Brussels, Belgium
| | - Asim K. Bera
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lukas K. Tamm
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT
| | | | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT
| | - David Baker
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Anastassia A. Vorobieva
- Structural Biology Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- VUB-VIB Center for Structural Biology, Brussels, Belgium
- VIB Center for AI and Computational Biology, Belgium
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7
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Machin JM, Kalli AC, Ranson NA, Radford SE. Protein-lipid charge interactions control the folding of outer membrane proteins into asymmetric membranes. Nat Chem 2023; 15:1754-1764. [PMID: 37710048 PMCID: PMC10695831 DOI: 10.1038/s41557-023-01319-6] [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: 08/09/2022] [Accepted: 08/08/2023] [Indexed: 09/16/2023]
Abstract
Biological membranes consist of two leaflets of phospholipid molecules that form a bilayer, each leaflet comprising a distinct lipid composition. This asymmetry is created and maintained in vivo by dedicated biochemical pathways, but difficulties in creating stable asymmetric membranes in vitro have restricted our understanding of how bilayer asymmetry modulates the folding, stability and function of membrane proteins. In this study, we used cyclodextrin-mediated lipid exchange to generate liposomes with asymmetric bilayers and characterize the stability and folding kinetics of two bacterial outer membrane proteins (OMPs), OmpA and BamA. We found that excess negative charge in the outer leaflet of a liposome impedes their insertion and folding, while excess negative charge in the inner leaflet accelerates their folding relative to symmetric liposomes with the same membrane composition. Using molecular dynamics, mutational analysis and bioinformatics, we identified a positively charged patch critical for folding and stability. These results rationalize the well-known 'positive-outside' rule of OMPs and suggest insights into the mechanisms that drive OMP folding and assembly in vitro and in vivo.
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Affiliation(s)
- Jonathan M Machin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Antreas C Kalli
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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8
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Haysom SF, Machin J, Whitehouse JM, Horne JE, Fenn K, Ma Y, El Mkami H, Böhringer N, Schäberle TF, Ranson NA, Radford SE, Pliotas C. Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. Angew Chem Weinheim Bergstr Ger 2023; 135:e202218783. [PMID: 38515502 PMCID: PMC10952338 DOI: 10.1002/ange.202218783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Indexed: 03/23/2024]
Abstract
The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
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Affiliation(s)
- Samuel F. Haysom
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jonathan Machin
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - James M. Whitehouse
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jim E. Horne
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Katherine Fenn
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Yue Ma
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Hassane El Mkami
- School of Physics and AstronomyUniversity of St. AndrewsSt. AndrewsKY16 9SSUK
| | - Nils Böhringer
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
| | - Till F. Schäberle
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
- Natural Product DepartmentFraunhofer-Institute for Molecular Biology and Applied Ecology (IME)Ohlebergsweg 1235392GiessenGermany
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
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9
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Haysom SF, Machin J, Whitehouse JM, Horne JE, Fenn K, Ma Y, El Mkami H, Böhringer N, Schäberle TF, Ranson NA, Radford SE, Pliotas C. Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. Angew Chem Int Ed Engl 2023; 62:e202218783. [PMID: 37162386 PMCID: PMC10952311 DOI: 10.1002/anie.202218783] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/26/2023] [Accepted: 05/09/2023] [Indexed: 05/11/2023]
Abstract
The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
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Affiliation(s)
- Samuel F. Haysom
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jonathan Machin
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - James M. Whitehouse
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jim E. Horne
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Katherine Fenn
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Yue Ma
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Hassane El Mkami
- School of Physics and AstronomyUniversity of St. AndrewsSt. AndrewsKY16 9SSUK
| | - Nils Böhringer
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
| | - Till F. Schäberle
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
- Natural Product DepartmentFraunhofer-Institute for Molecular Biology and Applied Ecology (IME)Ohlebergsweg 1235392GiessenGermany
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
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10
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Radford SE, Summers MF. Changing Shape of Molecules. J Mol Biol 2023; 435:168092. [PMID: 37330281 DOI: 10.1016/j.jmb.2023.168092] [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: 06/19/2023]
Affiliation(s)
- Sheena E Radford
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Michael F Summers
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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11
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Leistner C, Wilkinson M, Burgess A, Lovatt M, Goodbody S, Xu Y, Deuchars S, Radford SE, Ranson NA, Frank RAW. The in-tissue molecular architecture of β-amyloid pathology in the mammalian brain. Nat Commun 2023; 14:2833. [PMID: 37198197 PMCID: PMC10192217 DOI: 10.1038/s41467-023-38495-5] [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: 11/06/2022] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
Amyloid plaques composed of Aβ fibrils are a hallmark of Alzheimer's disease (AD). However, the molecular architecture of amyloid plaques in the context of fresh mammalian brain tissue is unknown. Here, using cryogenic correlated light and electron tomography we report the in situ molecular architecture of Aβ fibrils in the AppNL-G-F familial AD mouse model containing the Arctic mutation and an atomic model of ex vivo purified Arctic Aβ fibrils. We show that in-tissue Aβ fibrils are arranged in a lattice or parallel bundles, and are interdigitated by subcellular compartments, extracellular vesicles, extracellular droplets and extracellular multilamellar bodies. The Arctic Aβ fibril differs significantly from an earlier AppNL-F fibril structure, indicating a striking effect of the Arctic mutation. These structural data also revealed an ensemble of additional fibrillar species, including thin protofilament-like rods and branched fibrils. Together, these results provide a structural model for the dense network architecture that characterises β-amyloid plaque pathology.
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Affiliation(s)
- Conny Leistner
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Ailidh Burgess
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Megan Lovatt
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Stanley Goodbody
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Susan Deuchars
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - René A W Frank
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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12
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Marcuccio F, Soulias D, Chau CCC, Radford SE, Hewitt E, Actis P, Edwards MA. Mechanistic Study of the Conductance and Enhanced Single-Molecule Detection in a Polymer-Electrolyte Nanopore. ACS Nanosci Au 2023; 3:172-181. [PMID: 37096230 PMCID: PMC10119975 DOI: 10.1021/acsnanoscienceau.2c00050] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 04/26/2023]
Abstract
Solid-state nanopores have been widely employed in the detection of biomolecules, but low signal-to-noise ratios still represent a major obstacle in the discrimination of nucleic acid and protein sequences substantially smaller than the nanopore diameter. The addition of 50% poly(ethylene) glycol (PEG) to the external solution is a simple way to enhance the detection of such biomolecules. Here, we demonstrate with finite-element modeling and experiments that the addition of PEG to the external solution introduces a strong imbalance in the transport properties of cations and anions, drastically affecting the current response of the nanopore. We further show that the strong asymmetric current response is due to a polarity-dependent ion distribution and transport at the nanopipette tip region, leading to either ion depletion or enrichment for few tens of nanometers across its aperture. We provide evidence that a combination of the decreased/increased diffusion coefficients of cations/anions in the bath outside the nanopore and the interaction between a translocating molecule and the nanopore-bath interface is responsible for the increase in the translocation signals. We expect this new mechanism to contribute to further developments in nanopore sensing by suggesting that tuning the diffusion coefficients of ions could enhance the sensitivity of the system.
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Affiliation(s)
- Fabio Marcuccio
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
| | - Dimitrios Soulias
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
| | - Chalmers C. C. Chau
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, LeedsLS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, LeedsLS2 9JT, U.K.
| | - Eric Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, LeedsLS2 9JT, U.K.
| | - Paolo Actis
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
| | - Martin Andrew Edwards
- Department
of Chemistry and Biochemistry, University
of Arkansas, Fayetteville, Arkansas72701, United States
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13
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Wilkinson M, Gallardo RU, Martinez RM, Guthertz N, So M, Aubrey LD, Radford SE, Ranson NA. Disease-relevant β 2-microglobulin variants share a common amyloid fold. Nat Commun 2023; 14:1190. [PMID: 36864041 PMCID: PMC9981686 DOI: 10.1038/s41467-023-36791-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 02/16/2023] [Indexed: 03/04/2023] Open
Abstract
β2-microglobulin (β2m) and its truncated variant ΔΝ6 are co-deposited in amyloid fibrils in the joints, causing the disorder dialysis-related amyloidosis (DRA). Point mutations of β2m result in diseases with distinct pathologies. β2m-D76N causes a rare systemic amyloidosis with protein deposited in the viscera in the absence of renal failure, whilst β2m-V27M is associated with renal failure, with amyloid deposits forming predominantly in the tongue. Here we use cryoEM to determine the structures of fibrils formed from these variants under identical conditions in vitro. We show that each fibril sample is polymorphic, with diversity arising from a 'lego-like' assembly of a common amyloid building block. These results suggest a 'many sequences, one amyloid fold' paradigm in contrast with the recently reported 'one sequence, many amyloid folds' behaviour of intrinsically disordered proteins such as tau and Aβ.
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Affiliation(s)
- Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Aelin Therapeutics, Bio-Incubator Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Roberto Maya Martinez
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Peak Proteins, Birchwood House, Larkwood Way, Macclesfield, Cheshire, SK10 2XR, UK
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Bicycle Therapeutics, Blocks A & B, Portway Building, Grant Park, Abingdon, Cambridge, CB21 6GS, UK
| | - Masatomo So
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Liam D Aubrey
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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14
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Byrd E, Wilkinson M, Radford SE, Sobott F. Taking Charge: Metal Ions Accelerate Amyloid Aggregation in Sequence Variants of α-Synuclein. J Am Soc Mass Spectrom 2023; 34:493-504. [PMID: 36794792 PMCID: PMC9983014 DOI: 10.1021/jasms.2c00379] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/29/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Αlpha-synuclein (αS) is an intrinsically disordered protein which exhibits a high degree of conformational heterogeneity. In vivo, αS experiences various environments which cause adaptation of its structural ensemble. Divalent metal ions are prominent in synaptic terminals where αS is located and are thought to bind to the αS C-terminal region. Herein, we used native nanoelectrospray ionization ion mobility-mass spectrometry to investigate changes in the charge state distribution and collision cross sections of wild-type N-terminally acetylated (NTA) αS, along with a deletion variant (ΔΔNTA) which inhibits amyloid formation and a C-terminal truncated variant (119NTA) which increases the rate of amyloid formation. We also examine the effect of the addition of divalent metal ions, Ca2+, Mn2+, and Zn2+, and correlate the conformational properties of the αS monomer with the ability to aggregate into amyloid, measured using Thioflavin T fluorescence and negative stain transmission electron microscopy. We find a correlation between the population of species with a low collision cross section and accelerated amyloid assembly kinetics, with the presence of metal ions resulting in protein compaction and causing ΔΔ to regain its ability to form an amyloid. The results portray how the αS conformational ensemble is governed by specific intramolecular interactions that influence its amyloidogenic behavior.
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Affiliation(s)
- Emily
J. Byrd
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Martin Wilkinson
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Frank Sobott
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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15
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Horne JE, Fenn K, Crossley JA, Radford SE, Ranson NA. The delivery complex in outer membrane protein biogenesis: How the SurA chaperone interacts with the BAM enzyme. Biophys J 2023; 122:343a. [PMID: 36783740 DOI: 10.1016/j.bpj.2022.11.1910] [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: 02/12/2023] Open
Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Katherine Fenn
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Joel A Crossley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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16
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Crossley JA, Fessl T, Collinson I, Tuma R, Radford SE. Single-molecule fluorescence: Elucidating ATP driven protein transport in the sec complex. Biophys J 2023; 122:50a. [PMID: 36784632 DOI: 10.1016/j.bpj.2022.11.482] [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: 02/12/2023] Open
Affiliation(s)
- Joel A Crossley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Tomas Fessl
- Chemistry, University of South Bohemia Ceske Budejovice, Ceske Budejovice, Czech Republic
| | | | - Roman Tuma
- Chemistry, University of South Bohemia Ceske Budejovice, Ceske Budejovice, Czech Republic
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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17
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Chau C, Marcuccio F, Soulias D, Edwards MA, Tuplin A, Radford SE, Hewitt E, Actis P. Probing RNA Conformations Using a Polymer-Electrolyte Solid-State Nanopore. ACS Nano 2022; 16:20075-20085. [PMID: 36279181 PMCID: PMC9798860 DOI: 10.1021/acsnano.2c08312] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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] [Indexed: 05/10/2023]
Abstract
Nanopore systems have emerged as a leading platform for the analysis of biomolecular complexes with single-molecule resolution. The conformation of biomolecules, such as RNA, is highly dependent on the electrolyte composition, but solid-state nanopore systems often require high salt concentration to operate, precluding analysis of macromolecular conformations under physiologically relevant conditions. Here, we report the implementation of a polymer-electrolyte solid-state nanopore system based on alkali metal halide salts dissolved in 50% w/v poly(ethylene) glycol (PEG) to augment the performance of our system. We show that polymer-electrolyte bath governs the translocation dynamics of the analyte which correlates with the physical properties of the salt used in the bath. This allowed us to identify CsBr as the optimal salt to complement PEG to generate the largest signal enhancement. Harnessing the effects of the polymer-electrolyte, we probed the conformations of the Chikungunya virus (CHIKV) RNA genome fragments under physiologically relevant conditions. Our system was able to fingerprint CHIKV RNA fragments ranging from ∼300 to ∼2000 nt length and subsequently distinguish conformations between the co-transcriptionally folded and the natively refolded ∼2000 nt CHIKV RNA. We envision that the polymer-electrolyte solid-state nanopore system will further enable structural and conformational analyses of individual biomolecules under physiologically relevant conditions.
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Affiliation(s)
- Chalmers Chau
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Fabio Marcuccio
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Dimitrios Soulias
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Martin Andrew Edwards
- Department
of Chemistry & Biochemistry, University
of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Andrew Tuplin
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Eric Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
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18
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Maya-Martinez R, Xu Y, Guthertz N, Walko M, Karamanos TK, Sobott F, Breeze AL, Radford SE. Dimers of D76N-β 2-microglobulin display potent antiamyloid aggregation activity. J Biol Chem 2022; 298:102659. [PMID: 36328246 PMCID: PMC9712992 DOI: 10.1016/j.jbc.2022.102659] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/05/2022] Open
Abstract
Self-association of WT β2-microglobulin (WT-β2m) into amyloid fibrils is associated with the disorder dialysis related amyloidosis. In the familial variant D76N-β2m, the single amino acid substitution enhances the aggregation propensity of the protein dramatically and gives rise to a disorder that is independent of renal dysfunction. Numerous biophysical and structural studies on WT- and D76N-β2m have been performed in order to better understand the structure and dynamics of the native proteins and their different potentials to aggregate into amyloid. However, the structural properties of transient D76N-β2m oligomers and their role(s) in assembly remained uncharted. Here, we have utilized NMR methods, combined with photo-induced crosslinking, to detect, trap, and structurally characterize transient dimers of D76N-β2m. We show that the crosslinked D76N-β2m dimers have different structures from those previously characterized for the on-pathway dimers of ΔN6-β2m and are unable to assemble into amyloid. Instead, the crosslinked D76N-β2m dimers are potent inhibitors of amyloid formation, preventing primary nucleation and elongation/secondary nucleation when added in substoichiometric amounts with D76N-β2m monomers. The results highlight the specificity of early protein-protein interactions in amyloid formation and show how mapping these interfaces can inform new strategies to inhibit amyloid assembly.
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Affiliation(s)
- Roberto Maya-Martinez
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
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19
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Ruff KM, Choi YH, Cox D, Ormsby AR, Myung Y, Ascher DB, Radford SE, Pappu RV, Hatters DM. Sequence grammar underlying the unfolding and phase separation of globular proteins. Mol Cell 2022; 82:3193-3208.e8. [PMID: 35853451 PMCID: PMC10846692 DOI: 10.1016/j.molcel.2022.06.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 08/19/2021] [Revised: 05/05/2022] [Accepted: 06/15/2022] [Indexed: 12/23/2022]
Abstract
Aberrant phase separation of globular proteins is associated with many diseases. Here, we use a model protein system to understand how the unfolded states of globular proteins drive phase separation and the formation of unfolded protein deposits (UPODs). We find that for UPODs to form, the concentrations of unfolded molecules must be above a threshold value. Additionally, unfolded molecules must possess appropriate sequence grammars to drive phase separation. While UPODs recruit molecular chaperones, their compositional profiles are also influenced by synergistic physicochemical interactions governed by the sequence grammars of unfolded proteins and cellular proteins. Overall, the driving forces for phase separation and the compositional profiles of UPODs are governed by the sequence grammars of unfolded proteins. Our studies highlight the need for uncovering the sequence grammars of unfolded proteins that drive UPOD formation and cause gain-of-function interactions whereby proteins are aberrantly recruited into UPODs.
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Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering, Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yoon Hee Choi
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Dezerae Cox
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Angelique R Ormsby
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Yoochan Myung
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Systems and Computational Biology, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Systems and Computational Biology, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sheena E Radford
- Astbury Centre for Structural and Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Danny M Hatters
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.
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20
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Abstract
ATP-independent chaperones like trigger factor are generally assumed to play passive roles in protein folding by acting as holding chaperones. Here we show that trigger factor plays a more active role. Consistent with a role as an aggregation inhibiting chaperone, we find that trigger factor rapidly binds to partially folded glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and prevents it from non-productive self-association by shielding oligomeric interfaces. In the traditional view of holding chaperone action, trigger factor would then be expected to transfer its client to a chaperone foldase system for complete folding. Unexpectedly, we noticed that GAPDH folds into a monomeric but otherwise rather native-like intermediate state while trigger factor-bound. Upon release from trigger factor, the mostly folded monomeric GAPDH rapidly self-associates into its native tetramer and acquires enzymatic activity without needing additional folding factors. The mechanism we propose here for trigger factor bridges the holding and folding activities of chaperone function.
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Affiliation(s)
- Kevin Wu
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Thomas C Minshull
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
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21
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Abstract
The early stages of protein misfolding and aggregation involve disordered and partially folded protein conformers that contain a high degree of dynamic disorder. These dynamic species may undergo large-scale intra-molecular motions of intrinsically disordered protein (IDP) precursors, or flexible, low affinity inter-molecular binding in oligomeric assemblies. In both cases, generating atomic level visualization of the interconverting species that captures the conformations explored and their physico-chemical properties remains hugely challenging. How specific sub-ensembles of conformers that are on-pathway to aggregation into amyloid can be identified from their aggregation-resilient counterparts within these large heterogenous pools of rapidly moving molecules represents an additional level of complexity. Here, we describe current experimental and computational approaches designed to capture the dynamic nature of the early stages of protein misfolding and aggregation, and discuss potential challenges in describing these species because of the ensemble averaging of experimental restraints that arise from motions on the millisecond timescale. We give a perspective of how machine learning methods can be used to extract aggregation-relevant sub-ensembles and provide two examples of such an approach in which specific interactions of defined species within the dynamic ensembles of α-synuclein (αSyn) and β2-microgloblulin (β2m) can be captured and investigated.
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Affiliation(s)
- Theodoros K. Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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22
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23
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Horne JE, Radford SE. Roll out the barrel! Outer membrane tension resolves an unexpected folding intermediate. Cell 2022; 185:1107-1109. [DOI: 10.1016/j.cell.2022.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 12/01/2022]
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24
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Xu Y, Maya-Martinez R, Guthertz N, Heath GR, Manfield IW, Breeze AL, Sobott F, Foster R, Radford SE. Tuning the rate of aggregation of hIAPP into amyloid using small-molecule modulators of assembly. Nat Commun 2022; 13:1040. [PMID: 35210421 PMCID: PMC8873464 DOI: 10.1038/s41467-022-28660-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 06/28/2021] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Human islet amyloid polypeptide (hIAPP) self-assembles into amyloid fibrils which deposit in pancreatic islets of type 2 diabetes (T2D) patients. Here, we applied chemical kinetics to study the mechanism of amyloid assembly of wild-type hIAPP and its more amyloidogenic natural variant S20G. We show that the aggregation of both peptides involves primary nucleation, secondary nucleation and elongation. We also report the discovery of two structurally distinct small-molecule modulators of hIAPP assembly, one delaying the aggregation of wt hIAPP, but not S20G; while the other enhances the rate of aggregation of both variants at substoichiometric concentrations. Investigation into the inhibition mechanism(s) using chemical kinetics, native mass spectrometry, fluorescence titration, SPR and NMR revealed that the inhibitor retards primary nucleation, secondary nucleation and elongation, by binding peptide monomers. By contrast, the accelerator predominantly interacts with species formed in the lag phase. These compounds represent useful chemical tools to study hIAPP aggregation and may serve as promising starting-points for the development of therapeutics for T2D.
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Affiliation(s)
- Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Roberto Maya-Martinez
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - George R Heath
- Astbury Centre for Structural Molecular Biology, School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Richard Foster
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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25
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Good SC, Dewison KM, Radford SE, van Oosten-Hawle P. Global Proteotoxicity Caused by Human β 2 Microglobulin Variants Impairs the Unfolded Protein Response in C. elegans. Int J Mol Sci 2021; 22:10752. [PMID: 34639093 PMCID: PMC8509642 DOI: 10.3390/ijms221910752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/31/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
Aggregation of β2 microglobulin (β2m) into amyloid fibrils is associated with systemic amyloidosis, caused by the deposition of amyloid fibrils containing the wild-type protein and its truncated variant, ΔN6 β2m, in haemo-dialysed patients. A second form of familial systemic amyloidosis caused by the β2m variant, D76N, results in amyloid deposits in the viscera, without renal dysfunction. Although the folding and misfolding mechanisms of β2 microglobulin have been widely studied in vitro and in vivo, we lack a comparable understanding of the molecular mechanisms underlying toxicity in a cellular and organismal environment. Here, we established transgenic C. elegans lines expressing wild-type (WT) human β2m, or the two highly amyloidogenic naturally occurring variants, D76N β2m and ΔN6 β2m, in the C. elegans bodywall muscle. Nematodes expressing the D76N β2m and ΔN6 β2m variants exhibit increased age-dependent and cell nonautonomous proteotoxicity associated with reduced motility, delayed development and shortened lifespan. Both β2m variants cause widespread endogenous protein aggregation contributing to the increased toxicity in aged animals. We show that expression of β2m reduces the capacity of C. elegans to cope with heat and endoplasmic reticulum (ER) stress, correlating with a deficiency to upregulate BiP/hsp-4 transcripts in response to ER stress in young adult animals. Interestingly, protein secretion in all β2m variants is reduced, despite the presence of the natural signal sequence, suggesting a possible link between organismal β2m toxicity and a disrupted ER secretory metabolism.
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Affiliation(s)
| | | | | | - Patricija van Oosten-Hawle
- Faculty of Biological Sciences, School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (S.C.G.); (K.M.D.); (S.E.R.)
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26
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Cornwell O, Ault JR, Bond NJ, Radford SE, Ashcroft AE. Investigation of D76N β 2-Microglobulin Using Protein Footprinting and Structural Mass Spectrometry. J Am Soc Mass Spectrom 2021; 32:1583-1592. [PMID: 33586970 PMCID: PMC9282677 DOI: 10.1021/jasms.0c00438] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
NMR studies and X-ray crystallography have shown that the structures of the 99-residue amyloidogenic protein β2-microglobulin (β2m) and its more aggregation-prone variant, D76N, are indistinguishable, and hence, the reason for the striking difference in their aggregation propensities remains elusive. Here, we have employed two protein footprinting methods, hydrogen-deuterium exchange (HDX) and fast photochemical oxidation of proteins (FPOP), in conjunction with ion mobility-mass spectrometry, to probe the differences in conformational dynamics of the two proteins. Using HDX-MS, a clear difference in HDX protection is observed between these two proteins in the E-F loop (residues 70-77) which contains the D76N substitution, with a significantly higher deuterium uptake being observed in the variant protein. Conversely, following FPOP-MS only minimal differences in the level of oxidation between the two proteins are observed in the E-F loop region, suggesting only modest side-chain movements in that area. Together the HDX-MS and FPOP-MS data suggest that a tangible perturbation to the hydrogen-bonding network in the E-F loop has taken place in the D76N variant and furthermore illustrate the benefit of using multiple complementary footprinting methods to address subtle, but possibly biologically important, differences between highly similar proteins.
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Affiliation(s)
- Owen Cornwell
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - James R. Ault
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Nicholas J. Bond
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Alison E. Ashcroft
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
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27
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Radford SE, Karamanos TK. Finding the sweet spot for chaperone activity. Nat Chem 2021; 13:397-399. [PMID: 33931750 DOI: 10.1038/s41557-021-00691-5] [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: 11/10/2022]
Affiliation(s)
- Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
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28
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Bunce SJ, Wang Y, Radford SE, Wilson AJ, Hall CK. Structural insights into peptide self-assembly using photo-induced crosslinking experiments and discontinuous molecular dynamics. AIChE J 2021; 67:e17101. [PMID: 33776061 PMCID: PMC7988534 DOI: 10.1002/aic.17101] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/07/2020] [Indexed: 11/09/2022]
Abstract
Determining the structure of the (oligomeric) intermediates that form during the self-assembly of amyloidogenic peptides is challenging because of their heterogeneous and dynamic nature. Thus, there is need for methodology to analyze the underlying molecular structure of these transient species. In this work, a combination of fluorescence quenching, photo-induced crosslinking (PIC) and molecular dynamics simulation was used to study the assembly of a synthetic amyloid-forming peptide, Aβ16-22. A PIC amino acid containing a trifluormethyldiazirine (TFMD) group-Fmoc(TFMD)Phe-was incorporated into the sequence (Aβ*16-22). Electrospray ionization ion-mobility spectrometry mass-spectrometry (ESI-IMS-MS) analysis of the PIC products confirmed that Aβ*16-22 forms assemblies with the monomers arranged as anti-parallel, in-register β-strands at all time points during the aggregation assay. The assembly process was also monitored separately using fluorescence quenching to profile the fibril assembly reaction. The molecular picture resulting from discontinuous molecule dynamics simulations showed that Aβ16-22 assembles through a single-step nucleation into a β-sheet fibril in agreement with these experimental observations. This study provides detailed structural insights into the Aβ16-22 self-assembly processes, paving the way to explore the self-assembly mechanism of larger, more complex peptides, including those whose aggregation is responsible for human disease.
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Affiliation(s)
- Samuel J. Bunce
- School of ChemistryUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Yiming Wang
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Department of Chemical and Biological EngineeringPrinceton UniversityPrincetonNew JerseyUSA
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
- School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Carol K. Hall
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
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29
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Nahass GR, Sun Y, Xu Y, Batchelor M, Reilly M, Benilova I, Kedia N, Spehar K, Sobott F, Sessions RB, Caughey B, Radford SE, Jat PS, Collinge J, Bieschke J. Brazilin Removes Toxic Alpha-Synuclein and Seeding Competent Assemblies from Parkinson Brain by Altering Conformational Equilibrium. J Mol Biol 2021; 433:166878. [PMID: 33610557 DOI: 10.1016/j.jmb.2021.166878] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/06/2021] [Accepted: 02/05/2021] [Indexed: 12/31/2022]
Abstract
Alpha-synuclein (α-syn) fibrils, a major constituent of the neurotoxic Lewy Bodies in Parkinson's disease, form via nucleation dependent polymerization and can replicate by a seeding mechanism. Brazilin, a small molecule derived from red cedarwood trees in Brazil, has been shown to inhibit the fibrillogenesis of amyloid-beta (Aβ) and α-syn as well as remodel mature fibrils and reduce cytotoxicity. Here we test the effects of Brazilin on both seeded and unseeded α-syn fibril formation and show that the natural polyphenol inhibits fibrillogenesis of α-syn by a unique mechanism that alters conformational equilibria in two separate points of the assembly mechanism: Brazilin preserves the natively unfolded state of α-syn by specifically binding to the compact conformation of the α-syn monomer. Brazilin also eliminates seeding competence of α-syn assemblies from Parkinson's disease patient brain tissue, and reduces toxicity of pre-formed assemblies in primary neurons by inducing the formation of large fibril clusters. Molecular docking of Brazilin shows the molecule to interact both with unfolded α-syn monomers and with the cross-β sheet structure of α-syn fibrils. Our findings suggest that Brazilin has substantial potential as a neuroprotective and therapeutic agent for Parkinson's disease.
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Affiliation(s)
- George R Nahass
- Colorado College, Colorado Springs, CO, USA; Medical Research Council Prion Unit / UCL Institute of Prion Diseases, University College London, London, UK; Washington University in St. Louis, St Louis, MO, USA; Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA
| | - Yuanzi Sun
- Medical Research Council Prion Unit / UCL Institute of Prion Diseases, University College London, London, UK
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Mark Batchelor
- Medical Research Council Prion Unit / UCL Institute of Prion Diseases, University College London, London, UK
| | - Madeleine Reilly
- Medical Research Council Prion Unit / UCL Institute of Prion Diseases, University College London, London, UK
| | - Iryna Benilova
- Medical Research Council Prion Unit / UCL Institute of Prion Diseases, University College London, London, UK
| | - Niraja Kedia
- Washington University in St. Louis, St Louis, MO, USA
| | - Kevin Spehar
- Washington University in St. Louis, St Louis, MO, USA
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | | | - Byron Caughey
- Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Parmjit S Jat
- Medical Research Council Prion Unit / UCL Institute of Prion Diseases, University College London, London, UK
| | - John Collinge
- Medical Research Council Prion Unit / UCL Institute of Prion Diseases, University College London, London, UK
| | - Jan Bieschke
- Medical Research Council Prion Unit / UCL Institute of Prion Diseases, University College London, London, UK; Washington University in St. Louis, St Louis, MO, USA.
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30
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Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D. De novo design of transmembrane β barrels. Science 2021; 371:eabc8182. [PMID: 33602829 PMCID: PMC8064278 DOI: 10.1126/science.abc8182] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [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: 05/17/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a "hypothesis, design, and test" approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.
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Affiliation(s)
- Anastassia A Vorobieva
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sinduja Marx
- Department of Molecular Engineering and Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Q Stiving
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dagan C Marx
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Karen G Fleming
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
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31
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Milardi D, Gazit E, Radford SE, Xu Y, Gallardo RU, Caflisch A, Westermark GT, Westermark P, Rosa CL, Ramamoorthy A. Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chem Rev 2021; 121:1845-1893. [PMID: 33427465 DOI: 10.1021/acs.chemrev.0c00981] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [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
The possible link between hIAPP accumulation and β-cell death in diabetic patients has inspired numerous studies focusing on amyloid structures and aggregation pathways of this hormone. Recent studies have reported on the importance of early oligomeric intermediates, the many roles of their interactions with lipid membrane, pH, insulin, and zinc on the mechanism of aggregation of hIAPP. The challenges posed by the transient nature of amyloid oligomers, their structural heterogeneity, and the complex nature of their interaction with lipid membranes have resulted in the development of a wide range of biophysical and chemical approaches to characterize the aggregation process. While the cellular processes and factors activating hIAPP-mediated cytotoxicity are still not clear, it has recently been suggested that its impaired turnover and cellular processing by proteasome and autophagy may contribute significantly toward toxic hIAPP accumulation and, eventually, β-cell death. Therefore, studies focusing on the restoration of hIAPP proteostasis may represent a promising arena for the design of effective therapies. In this review we discuss the current knowledge of the structures and pathology associated with hIAPP self-assembly and point out the opportunities for therapy that a detailed biochemical, biophysical, and cellular understanding of its aggregation may unveil.
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Affiliation(s)
- Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via P. Gaifami 18, 95126 Catania, Italy
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Gunilla T Westermark
- Department of Medical Cell Biology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 41809-1055, United States
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32
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Brown MR, Radford SE, Hewitt EW. Modulation of β-Amyloid Fibril Formation in Alzheimer's Disease by Microglia and Infection. Front Mol Neurosci 2020; 13:609073. [PMID: 33324164 PMCID: PMC7725705 DOI: 10.3389/fnmol.2020.609073] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/03/2020] [Indexed: 01/06/2023] Open
Abstract
Amyloid plaques are a pathological hallmark of Alzheimer's disease. The major component of these plaques are highly ordered amyloid fibrils formed by amyloid-β (Aβ) peptides. However, whilst Aβ amyloid fibril assembly has been subjected to detailed and extensive analysis in vitro, these studies may not reproduce how Aβ fibrils assemble in the brain. This is because the brain represents a highly complex and dynamic environment, and in Alzheimer's disease multiple cofactors may affect the assembly of Aβ fibrils. Moreover, in vivo amyloid plaque formation will reflect the balance between the assembly of Aβ fibrils and their degradation. This review explores the roles of microglia as cofactors in Aβ aggregation and in the clearance of amyloid deposits. In addition, we discuss how infection may be an additional cofactor in Aβ fibril assembly by virtue of the antimicrobial properties of Aβ peptides. Crucially, by understanding the roles of microglia and infection in Aβ amyloid fibril assembly it may be possible to identify new therapeutic targets for Alzheimer's disease.
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Affiliation(s)
- Madeleine R Brown
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Eric W Hewitt
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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33
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Iadanza MG, Schiffrin B, White P, Watson MA, Horne JE, Higgins AJ, Calabrese AN, Brockwell DJ, Tuma R, Kalli AC, Radford SE, Ranson NA. Distortion of the bilayer and dynamics of the BAM complex in lipid nanodiscs. Commun Biol 2020; 3:766. [PMID: 33318620 PMCID: PMC7736308 DOI: 10.1038/s42003-020-01419-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 02/06/2020] [Accepted: 10/12/2020] [Indexed: 11/28/2022] Open
Abstract
The β-barrel assembly machinery (BAM) catalyses the folding and insertion of β-barrel outer membrane proteins (OMPs) into the outer membranes of Gram-negative bacteria by mechanisms that remain unclear. Here, we present an ensemble of cryoEM structures of the E. coli BamABCDE (BAM) complex in lipid nanodiscs, determined using multi-body refinement techniques. These structures, supported by single-molecule FRET measurements, describe a range of motions in the BAM complex, mostly localised within the periplasmic region of the major subunit BamA. The β-barrel domain of BamA is in a 'lateral open' conformation in all of the determined structures, suggesting that this is the most energetically favourable species in this bilayer. Strikingly, the BAM-containing lipid nanodisc is deformed, especially around BAM's lateral gate. This distortion is also captured in molecular dynamics simulations, and provides direct structural evidence for the lipid 'disruptase' activity of BAM, suggested to be an important part of its functional mechanism.
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Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew A Watson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Anna J Higgins
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Antreas C Kalli
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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34
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Ulamec SM, Brockwell DJ, Radford SE. Looking Beyond the Core: The Role of Flanking Regions in the Aggregation of Amyloidogenic Peptides and Proteins. Front Neurosci 2020; 14:611285. [PMID: 33335475 PMCID: PMC7736610 DOI: 10.3389/fnins.2020.611285] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
Amyloid proteins are involved in many neurodegenerative disorders such as Alzheimer’s disease [Tau, Amyloid β (Aβ)], Parkinson’s disease [alpha-synuclein (αSyn)], and amyotrophic lateral sclerosis (TDP-43). Driven by the early observation of the presence of ordered structure within amyloid fibrils and the potential to develop inhibitors of their formation, a major goal of the amyloid field has been to elucidate the structure of the amyloid fold at atomic resolution. This has now been achieved for a wide variety of sequences using solid-state NMR, microcrystallography, X-ray fiber diffraction and cryo-electron microscopy. These studies, together with in silico methods able to predict aggregation-prone regions (APRs) in protein sequences, have provided a wealth of information about the ordered fibril cores that comprise the amyloid fold. Structural and kinetic analyses have also shown that amyloidogenic proteins often contain less well-ordered sequences outside of the amyloid core (termed here as flanking regions) that modulate function, toxicity and/or aggregation rates. These flanking regions, which often form a dynamically disordered “fuzzy coat” around the fibril core, have been shown to play key parts in the physiological roles of functional amyloids, including the binding of RNA and in phase separation. They are also the mediators of chaperone binding and membrane binding/disruption in toxic amyloid assemblies. Here, we review the role of flanking regions in different proteins spanning both functional amyloid and amyloid in disease, in the context of their role in aggregation, toxicity and cellular (dys)function. Understanding the properties of these regions could provide new opportunities to target disease-related aggregation without disturbing critical biological functions.
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Affiliation(s)
- Sabine M Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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35
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Cawood EE, Guthertz N, Ebo JS, Karamanos TK, Radford SE, Wilson AJ. Modulation of Amyloidogenic Protein Self-Assembly Using Tethered Small Molecules. J Am Chem Soc 2020; 142:20845-20854. [PMID: 33253560 PMCID: PMC7729939 DOI: 10.1021/jacs.0c10629] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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] [Indexed: 02/06/2023]
Abstract
![]()
Protein–protein
interactions (PPIs) are involved in many
of life’s essential biological functions yet are also an underlying
cause of several human diseases, including amyloidosis. The modulation
of PPIs presents opportunities to gain mechanistic insights into amyloid
assembly, particularly through the use of methods which can trap specific
intermediates for detailed study. Such information can also provide
a starting point for drug discovery. Here, we demonstrate that covalently
tethered small molecule fragments can be used to stabilize specific
oligomers during amyloid fibril formation, facilitating the structural
characterization of these assembly intermediates. We exemplify the
power of covalent tethering using the naturally occurring truncated
variant (ΔN6) of the human protein β2-microglobulin
(β2m), which assembles into amyloid fibrils associated
with dialysis-related amyloidosis. Using this approach, we have trapped
tetramers formed by ΔN6 under conditions which would normally
lead to fibril formation and found that the degree of tetramer stabilization
depends on the site of the covalent tether and the nature of the protein–fragment
interaction. The covalent protein–ligand linkage enabled structural
characterization of these trapped, off-pathway oligomers using X-ray
crystallography and NMR, providing insight into why tetramer stabilization
inhibits amyloid assembly. Our findings highlight the power of “post-translational
chemical modification” as a tool to study biological molecular
mechanisms.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Jessica S Ebo
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
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36
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2020; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease. Methods to study structure, toxicity, and kinetics of transient amyloid oligomers. NMR and single particle methods can characterize lowly-populated oligomers. Chemical tools/antibodies stabilize oligomers for structural and toxicity studies A combination of methods is needed to fully characterize amyloid assembly pathways.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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37
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Lauwers E, Lalli G, Brandner S, Collinge J, Compernolle V, Duyckaerts C, Edgren G, Haïk S, Hardy J, Helmy A, Ivinson AJ, Jaunmuktane Z, Jucker M, Knight R, Lemmens R, Lin IC, Love S, Mead S, Perry VH, Pickett J, Poppy G, Radford SE, Rousseau F, Routledge C, Schiavo G, Schymkowitz J, Selkoe DJ, Smith C, Thal DR, Theys T, Tiberghien P, van den Burg P, Vandekerckhove P, Walton C, Zaaijer HL, Zetterberg H, De Strooper B. Potential human transmission of amyloid β pathology: surveillance and risks. Lancet Neurol 2020; 19:872-878. [PMID: 32949547 DOI: 10.1016/s1474-4422(20)30238-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 03/04/2020] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 01/05/2023]
Abstract
Studies in experimental animals show transmissibility of amyloidogenic proteins associated with prion diseases, Alzheimer's disease, Parkinson's disease, and other neurodegenerative diseases. Although these data raise potential concerns for public health, convincing evidence for human iatrogenic transmission only exists for prions and amyloid β after systemic injections of contaminated growth hormone extracts or dura mater grafts derived from cadavers. Even though these procedures are now obsolete, some reports raise the possibility of iatrogenic transmission of amyloid β through putatively contaminated neurosurgical equipment. Iatrogenic transmission of amyloid β might lead to amyloid deposition in the brain parenchyma and blood vessel walls, potentially resulting in cerebral amyloid angiopathy after several decades. Cerebral amyloid angiopathy can cause life-threatening brain haemorrhages; yet, there is no proof that the transmission of amyloid β can also lead to Alzheimer's dementia. Large, long-term epidemiological studies and sensitive, cost-efficient tools to detect amyloid are needed to better understand any potential routes of amyloid β transmission and to clarify whether other similar proteopathic seeds, such as tau or α-synuclein, can also be transferred iatrogenically.
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Affiliation(s)
- Elsa Lauwers
- VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Giovanna Lalli
- UK Dementia Research Institute, University College London, London, UK
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK; Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London National Health Service Foundation Trust, London, UK
| | - John Collinge
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, UK
| | - Veerle Compernolle
- Blood Services, Belgian Red Cross-Flanders, Mechelen, Belgium; Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Charles Duyckaerts
- Institut du Cerveau et de la Moelle épinière, Sorbonne University, INSERM, CNRS UMR, Paris, France; Laboratoire de Neuropathologie Raymond Escourolle, Hôpital de la Pitié-Salpêtrière, Assistance Publique- Hôpitaux de Paris, Paris, France
| | - Gustaf Edgren
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Department of Cardiology, Södersjukhuset, Stockholm, Sweden
| | - Stéphane Haïk
- Institut du Cerveau et de la Moelle épinière, Sorbonne University, INSERM, CNRS UMR, Paris, France; Laboratoire de Neuropathologie Raymond Escourolle, Hôpital de la Pitié-Salpêtrière, Assistance Publique- Hôpitaux de Paris, Paris, France; Cellule Nationale de Référence des maladies de Creutzfeldt-Jakob, Hôpital de la Pitié-Salpêtrière, Assistance Publique- Hôpitaux de Paris, Paris, France
| | - John Hardy
- UK Dementia Research Institute, University College London, London, UK; Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK; Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre, London, UK; Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region, China
| | - Adel Helmy
- Department of Clinical Neuroscience, Division of Neurosurgery, University of Cambridge, Cambridge, UK
| | - Adrian J Ivinson
- UK Dementia Research Institute, University College London, London, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK; Queen Square Brain Bank for Neurological Disorders, Queen Square Institute of Neurology, University College London, London, UK; Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London National Health Service Foundation Trust, London, UK
| | - Mathias Jucker
- Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Richard Knight
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK; National Creutzfeldt-Jakob Disease Research and Surveillance Unit, Western General Hospital, Edinburgh, UK
| | - Robin Lemmens
- VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium; Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - I-Chun Lin
- UK Dementia Research Institute, University College London, London, UK
| | - Seth Love
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Simon Mead
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, UK
| | - V Hugh Perry
- UK Dementia Research Institute, University College London, London, UK
| | - James Pickett
- Alzheimer's Society, London, London, UK; Epilepsy Research UK, London, UK
| | - Guy Poppy
- Biological Sciences, University of Southampton, Southampton, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Frederic Rousseau
- VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Giampietro Schiavo
- UK Dementia Research Institute, University College London, London, UK; Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Joost Schymkowitz
- VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Dennis J Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Harvard University, Boston, MA, USA
| | - Colin Smith
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Dietmar R Thal
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium; Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Tom Theys
- Department of Neurosurgery, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Tiberghien
- Etablissement Français du Sang, La Plaine St Denis, France; Unité Mixte de Recherche, INSERM, Université de Franche-Comté, Besançon, France
| | - Peter van den Burg
- European Blood Alliance, Brussels, Belgium; Department of Transfusion Medicine, Sanquin, Amsterdam, Netherlands
| | - Philippe Vandekerckhove
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium; Blood Services, Belgian Red Cross-Flanders, Mechelen, Belgium
| | - Clare Walton
- Alzheimer's Society, London, London, UK; Multiple Sclerosis International Federation, London, UK
| | - Hans L Zaaijer
- Department of Blood-borne Infections, Sanquin, Amsterdam, Netherlands
| | - Henrik Zetterberg
- UK Dementia Research Institute, University College London, London, UK; Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK; Department of Psychiatry and Neurochemistry, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bart De Strooper
- VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium; UK Dementia Research Institute, University College London, London, UK.
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38
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Ulamec SM, Radford SE. Spot the Difference: Function versus Toxicity in Amyloid Fibrils. Trends Biochem Sci 2020; 45:635-636. [DOI: 10.1016/j.tibs.2020.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 11/29/2022]
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39
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Horne JE, Brockwell DJ, Radford SE. Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria. J Biol Chem 2020; 295:10340-10367. [PMID: 32499369 PMCID: PMC7383365 DOI: 10.1074/jbc.rev120.011473] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [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: 02/04/2020] [Revised: 06/03/2020] [Indexed: 01/09/2023] Open
Abstract
β-Barrel outer membrane proteins (OMPs) represent the major proteinaceous component of the outer membrane (OM) of Gram-negative bacteria. These proteins perform key roles in cell structure and morphology, nutrient acquisition, colonization and invasion, and protection against external toxic threats such as antibiotics. To become functional, OMPs must fold and insert into a crowded and asymmetric OM that lacks much freely accessible lipid. This feat is accomplished in the absence of an external energy source and is thought to be driven by the high thermodynamic stability of folded OMPs in the OM. With such a stable fold, the challenge that bacteria face in assembling OMPs into the OM is how to overcome the initial energy barrier of membrane insertion. In this review, we highlight the roles of the lipid environment and the OM in modulating the OMP-folding landscape and discuss the factors that guide folding in vitro and in vivo We particularly focus on the composition, architecture, and physical properties of the OM and how an understanding of the folding properties of OMPs in vitro can help explain the challenges they encounter during folding in vivo Current models of OMP biogenesis in the cellular environment are still in flux, but the stakes for improving the accuracy of these models are high. OMP folding is an essential process in all Gram-negative bacteria, and considering the looming crisis of widespread microbial drug resistance it is an attractive target. To bring down this vital OMP-supported barrier to antibiotics, we must first understand how bacterial cells build it.
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Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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40
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Smith HI, Guthertz N, Cawood EE, Maya-Martinez R, Breeze AL, Radford SE. The role of the I T-state in D76N β 2-microglobulin amyloid assembly: A crucial intermediate or an innocuous bystander? J Biol Chem 2020; 295:12474-12484. [PMID: 32661194 PMCID: PMC7458819 DOI: 10.1074/jbc.ra120.014901] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/06/2020] [Indexed: 02/05/2023] Open
Abstract
The D76N variant of human β2-microglobulin (β2m) is the causative agent of a hereditary amyloid disease. Interestingly, D76N-associated amyloidosis has a distinctive pathology compared with aggregation of WT-β2m, which occurs in dialysis-related amyloidosis. A folding intermediate of WT-β2m, known as the IT-state, which contains a nonnative trans Pro-32, has been shown to be a key precursor of WT-β2m aggregation in vitro. However, how a single amino acid substitution enhances the rate of aggregation of D76N-β2m and gives rise to a different amyloid disease remained unclear. Using real-time refolding experiments monitored by CD and NMR, we show that the folding mechanisms of WT- and D76N-β2m are conserved in that both proteins fold slowly via an IT-state that has similar structural properties. Surprisingly, however, direct measurement of the equilibrium population of IT using NMR showed no evidence for an increased population of the IT-state for D76N-β2m, ruling out previous models suggesting that this could explain its enhanced aggregation propensity. Producing a kinetically trapped analog of IT by deleting the N-terminal six amino acids increases the aggregation rate of WT-β2m but slows aggregation of D76N-β2m, supporting the view that although the folding mechanisms of the two proteins are conserved, their aggregation mechanisms differ. The results exclude the IT-state as the origin of the rapid aggregation of D76N-β2m, suggesting that other nonnative states must cause its high aggregation rate. The results highlight how a single substitution at a solvent-exposed site can affect the mechanism of aggregation and the resulting disease.
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Affiliation(s)
- Hugh I Smith
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.,School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Roberto Maya-Martinez
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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41
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Chau C, Radford SE, Hewitt EW, Actis P. Macromolecular Crowding Enhances the Detection of DNA and Proteins by a Solid-State Nanopore. Nano Lett 2020; 20:5553-5561. [PMID: 32559088 PMCID: PMC7357865 DOI: 10.1021/acs.nanolett.0c02246] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [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: 05/28/2020] [Revised: 06/18/2020] [Indexed: 05/19/2023]
Abstract
Nanopore analysis of nucleic acid is now routine, but detection of proteins remains challenging. Here, we report the systematic characterization of the effect of macromolecular crowding on the detection sensitivity of a solid-state nanopore for circular and linearized DNA plasmids, globular proteins (β-galactosidase), and filamentous proteins (α-synuclein amyloid fibrils). We observe a remarkable ca. 1000-fold increase in the molecule count for the globular protein β-galactosidase and a 6-fold increase in peak amplitude for plasmid DNA under crowded conditions. We also demonstrate that macromolecular crowding facilitates the study of the topology of DNA plasmids and the characterization of amyloid fibril preparations with different length distributions. A remarkable feature of this method is its ease of use; it simply requires the addition of a macromolecular crowding agent to the electrolyte. We therefore envision that macromolecular crowding can be applied to many applications in the analysis of biomolecules by solid-state nanopores.
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Affiliation(s)
- Chalmers
C. Chau
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Eric W. Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
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42
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Schiffrin B, Radford SE, Brockwell DJ, Calabrese AN. PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system. Protein Sci 2020; 29:1851-1857. [PMID: 32557917 PMCID: PMC7380677 DOI: 10.1002/pro.3902] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 01/01/2023]
Abstract
Chemical crosslinking‐mass spectrometry (XL‐MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL‐MS data yield inter‐residue restraints that can be compared with high‐resolution structural data. Distances greater than the crosslinker spacer‐arm can reveal lowly populated “excited” states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL‐MS, there are few tools to enable rapid and facile mapping of XL‐MS data onto high‐resolution structures or structural models. PyXlinkViewer is a user‐friendly plugin for PyMOL v2 that maps intra‐protein, inter‐protein, and dead‐end crosslinks onto protein structures/models and automates the calculation of inter‐residue distances for the detected crosslinks. This enables rapid visualization of XL‐MS data, assessment of whether a set of detected crosslinks is congruent with structural data, and easy production of high‐quality images for publication.
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Affiliation(s)
- Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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43
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Rodríguez-Alonso R, Létoquart J, Nguyen VS, Louis G, Calabrese AN, Iorga BI, Radford SE, Cho SH, Remaut H, Collet JF. Structural insight into the formation of lipoprotein-β-barrel complexes. Nat Chem Biol 2020; 16:1019-1025. [PMID: 32572278 PMCID: PMC7610366 DOI: 10.1038/s41589-020-0575-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 10/29/2019] [Accepted: 05/15/2020] [Indexed: 12/14/2022]
Abstract
The β-barrel assembly machinery (BAM) inserts outer membrane β-barrel proteins (OMPs) in the outer membrane of Gram-negative bacteria. In Enterobacteriacea, BAM also mediates export of the stress sensor lipoprotein RcsF to the cell surface by assembling RcsF-OMP complexes. Here, we report the crystal structure of the key BAM component BamA in complex with RcsF. BamA adopts an inward-open conformation, with the lateral gate to the membrane closed. RcsF is lodged deep inside the lumen of the BamA barrel, binding regions proposed to undergo an outward and lateral opening during OMP insertion. On the basis of our structural and biochemical data, we propose a push-and-pull model for RcsF export upon conformational cycling of BamA and provide a mechanistic explanation for how RcsF uses its interaction with BamA to detect envelope stress. Our data also suggest that the flux of incoming OMP substrates is involved in the control of BAM activity.
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Affiliation(s)
- Raquel Rodríguez-Alonso
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Juliette Létoquart
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Van Son Nguyen
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium
| | - Gwennaelle Louis
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Bogdan I Iorga
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium.,Université Paris-Saclay, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Seung-Hyun Cho
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium. .,de Duve Institute, Université catholique de Louvain, Brussels, Belgium.
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium. .,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium.
| | - Jean-François Collet
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium. .,de Duve Institute, Université catholique de Louvain, Brussels, Belgium.
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44
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Willis LF, Kumar A, Jain T, Caffry I, Xu Y, Radford SE, Kapur N, Vásquez M, Brockwell DJ. The uniqueness of flow in probing the aggregation behavior of clinically relevant antibodies. Eng Rep 2020; 2:e12147. [PMID: 34901768 PMCID: PMC8638667 DOI: 10.1002/eng2.12147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
The development of therapeutic monoclonal antibodies (mAbs) can be hindered by their tendency to aggregate throughout their lifetime, which can illicit immunogenic responses and render mAb manufacturing unfeasible. Consequently, there is a need to identify mAbs with desirable thermodynamic stability, solubility, and lack of self-association. These behaviors are assessed using an array of in silico and in vitro assays, as no single assay can predict aggregation and developability. We have developed an extensional and shear flow device (EFD), which subjects proteins to defined hydrodynamic forces which mimic those experienced in bioprocessing. Here, we utilize the EFD to explore the aggregation propensity of 33 IgG1 mAbs, whose variable domains are derived from clinical antibodies. Using submilligram quantities of material per replicate, wide-ranging EFD-induced aggregation (9-81% protein in pellet) was observed for these mAbs, highlighting the EFD as a sensitive method to assess aggregation propensity. By comparing the EFD-induced aggregation data to those obtained previously from 12 other biophysical assays, we show that the EFD provides distinct information compared with current measures of adverse biophysical behavior. Assessing a candidate's liability to hydrodynamic force thus adds novel insight into the rational selection of developable mAbs that complements other assays.
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Affiliation(s)
- Leon F. Willis
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Amit Kumar
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
- Department of Life SciencesImperial College LondonLondonUK
| | | | - Isabelle Caffry
- Adimab LLCLebanonNew HampshireUSA
- Cornell Johnson Graduate School of ManagementIthacaNew YorkUSA
| | - Yingda Xu
- Adimab LLCLebanonNew HampshireUSA
- Biotheus Inc.ZhuhaiGuangdong ProvinceChina
| | - Sheena E. Radford
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Nikil Kapur
- School of Mechanical Engineering, Faculty of EngineeringUniversity of LeedsLeedsUK
| | | | - David J. Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
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45
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Calabrese AN, Schiffrin B, Watson M, Karamanos TK, Walko M, Humes JR, Horne JE, White P, Wilson AJ, Kalli AC, Tuma R, Ashcroft AE, Brockwell DJ, Radford SE. Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients. Nat Commun 2020; 11:2155. [PMID: 32358557 PMCID: PMC7195389 DOI: 10.1038/s41467-020-15702-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 11/24/2019] [Accepted: 03/18/2020] [Indexed: 01/11/2023] Open
Abstract
The periplasmic chaperone SurA plays a key role in outer membrane protein (OMP) biogenesis. E. coli SurA comprises a core domain and two peptidylprolyl isomerase domains (P1 and P2), but its mechanisms of client binding and chaperone function have remained unclear. Here, we use chemical cross-linking, hydrogen-deuterium exchange mass spectrometry, single-molecule FRET and molecular dynamics simulations to map the client binding site(s) on SurA and interrogate the role of conformational dynamics in OMP recognition. We demonstrate that SurA samples an array of conformations in solution in which P2 primarily lies closer to the core/P1 domains than suggested in the SurA crystal structure. OMP binding sites are located primarily in the core domain, and OMP binding results in conformational changes between the core/P1 domains. Together, the results suggest that unfolded OMP substrates bind in a cradle formed between the SurA domains, with structural flexibility between domains assisting OMP recognition, binding and release.
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Affiliation(s)
- Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew Watson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Julia R Humes
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Antreas C Kalli
- Astbury Centre for Structural Molecular Biology and School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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46
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Ebo JS, Saunders JC, Devine PWA, Gordon AM, Warwick AS, Schiffrin B, Chin SE, England E, Button JD, Lloyd C, Bond NJ, Ashcroft AE, Radford SE, Lowe DC, Brockwell DJ. An in vivo platform to select and evolve aggregation-resistant proteins. Nat Commun 2020; 11:1816. [PMID: 32286330 PMCID: PMC7156504 DOI: 10.1038/s41467-020-15667-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 11/11/2019] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Protein biopharmaceuticals are highly successful, but their utility is compromised by their propensity to aggregate during manufacture and storage. As aggregation can be triggered by non-native states, whose population is not necessarily related to thermodynamic stability, prediction of poorly-behaving biologics is difficult, and searching for sequences with desired properties is labour-intensive and time-consuming. Here we show that an assay in the periplasm of E. coli linking aggregation directly to antibiotic resistance acts as a sensor for the innate (un-accelerated) aggregation of antibody fragments. Using this assay as a directed evolution screen, we demonstrate the generation of aggregation resistant scFv sequences when reformatted as IgGs. This powerful tool can thus screen and evolve ‘manufacturable’ biopharmaceuticals early in industrial development. By comparing the mutational profiles of three different immunoglobulin scaffolds, we show the applicability of this method to investigate protein aggregation mechanisms important to both industrial manufacture and amyloid disease. Protein aggregation remains a significant challenge for manufacturing of protein biopharmaceuticals. Here, the authors demonstrate the use of directed evolution and an assay for in vivo innate protein aggregation-propensity to generate aggregation-resistant scFv fragments.
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Affiliation(s)
- Jessica S Ebo
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Janet C Saunders
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.,AstraZeneca, Granta Park, Cambridge, CB21 6GH, UK.,AstraZeneca, Granta Park, Cambridge, CB21 6GH, UK
| | - Paul W A Devine
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.,AstraZeneca, Granta Park, Cambridge, CB21 6GH, UK
| | - Alice M Gordon
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Amy S Warwick
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | | | | | | | | | | | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David C Lowe
- AstraZeneca, Granta Park, Cambridge, CB21 6GH, UK.
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. .,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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47
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Doherty CPA, Ulamec SM, Maya-Martinez R, Good SC, Makepeace J, Khan GN, van Oosten-Hawle P, Radford SE, Brockwell DJ. A short motif in the N-terminal region of α-synuclein is critical for both aggregation and function. Nat Struct Mol Biol 2020; 27:249-259. [PMID: 32157247 PMCID: PMC7100612 DOI: 10.1038/s41594-020-0384-x] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [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: 07/30/2019] [Accepted: 01/22/2020] [Indexed: 02/04/2023]
Abstract
Aggregation of human α-synuclein (αSyn) is linked to Parkinson’s disease (PD) pathology. The central region of the αSyn sequence contains the non-amyloid β-component (NAC) crucial for aggregation. However, how NAC flanking regions modulate αSyn aggregation remains unclear. Using bioinformatics, mutation, and NMR we identify a 7-residue sequence, named P1 (residues 36-42), that controls αSyn aggregation. Deletion or substitution of this ‘master-controller’ prevents aggregation at pH 7.5 in vitro. At lower pH, P1 synergises with a sequence containing the PreNAC region (P2, residues 45-57) to prevent aggregation. Deleting P1 (ΔP1) or both P1 and P2 (ΔΔ) also prevents age-dependent αSyn aggregation and toxicity in C. elegans models and prevents αSyn-mediated vesicle fusion by altering the conformational properties of the protein when lipid-bound. The results highlight the importance of a master-controller sequence motif that controls both αSyn aggregation and function- a region that could be targeted to prevent aggregation in disease.
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Affiliation(s)
- Ciaran P A Doherty
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Sabine M Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Roberto Maya-Martinez
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Sarah C Good
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Jemma Makepeace
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Patricija van Oosten-Hawle
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom.
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom.
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48
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Ebo JS, Guthertz N, Radford SE, Brockwell DJ. Using protein engineering to understand and modulate aggregation. Curr Opin Struct Biol 2020; 60:157-166. [PMID: 32087409 PMCID: PMC7132541 DOI: 10.1016/j.sbi.2020.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023]
Abstract
Protein aggregation occurs through a variety of mechanisms, initiated by the unfolded, non-native, or even the native state itself. Understanding the molecular mechanisms of protein aggregation is challenging, given the array of competing interactions that control solubility, stability, cooperativity and aggregation propensity. An array of methods have been developed to interrogate protein aggregation, spanning computational algorithms able to identify aggregation-prone regions, to deep mutational scanning to define the entire mutational landscape of a protein's sequence. Here, we review recent advances in this exciting and emerging field, focussing on protein engineering approaches that, together with improved computational methods, hold promise to predict and control protein aggregation linked to human disease, as well as facilitating the manufacture of protein-based therapeutics.
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Affiliation(s)
- Jessica S Ebo
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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49
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Abstract
In recent years our understanding of amyloid structure has been revolutionised by innovations in cryo-electron microscopy, electron diffraction and solid-state NMR. These techniques have yielded high-resolution structures of fibrils isolated from patients with neurodegenerative disease, as well as those formed from amyloidogenic proteins in vitro. The results not only show the expected cross-β amyloid structure, but also reveal that the amyloid fold is unexpectedly diverse and complex. Here, we discuss this diversity, highlighting dynamic regions, ligand binding motifs, cavities, non-protein components, and structural polymorphism. Collectively, these variations combine to allow the generic amyloid fold to be realised in three dimensions in different ways, and this diversity may be related to the roles of fibrils in disease.
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Affiliation(s)
- Rodrigo Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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Baum J, Chiti F, De Simone A, Knowles TPJ, Kumita JR, Radford SE, Robinson CV, Salvatella X, Valelli K, Vendruscolo M, Pastore A, Tartaglia GG. Homage to Chris Dobson. Front Mol Biosci 2020; 6:137. [PMID: 31921887 PMCID: PMC6921691 DOI: 10.3389/fmolb.2019.00137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 11/18/2019] [Indexed: 11/25/2022] Open
Affiliation(s)
- Jean Baum
- School of Arts and Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Janet R Kumita
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sheena E Radford
- Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Xavier Salvatella
- ICREA, Institute for Research in Biomedicine and the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Karen Valelli
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Annalisa Pastore
- Maurice Wohl Institute & Dementia Research Institute, King's College London, London, United Kingdom
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Catalan Institute for Research and Advance Studies (ICREA), Barcelona, Spain
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