1
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Lewkowicz E, Jayaraman S, Gursky O. Molecular basis for non-invasive diagnostics of cardiac amyloids using bone tracers. Biomater Sci 2024; 12:4275-4282. [PMID: 39046441 PMCID: PMC11334954 DOI: 10.1039/d4bm00816b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 07/19/2024] [Indexed: 07/25/2024]
Abstract
Amyloid diseases including Alzheimer's, Parkinson's and over 30 others are incurable life-threatening disorders caused by abnormal protein deposition as fibrils in various organs. Cardiac amyloidosis is particularly challenging to diagnose and treat. Identification of the fibril-forming protein, which in the heart is usually amyloid transthyretin (ATTR) or amyloid immunoglobulin light chain (AL), is paramount to treatment. A transformative non-invasive diagnostic modality is imaging using technetium-labeled pyrophosphate or diphosphonate bone tracers, 99mTc-PYP/DPD/HMDP. For unknown reasons, these tracers show preferential uptake by ATTR deposits. The tracer-binding moiety is unknown and potentially involves amyloid fibrils and/or amyloid-associated calcific deposits. We propose that, like in the bone, the tracers chelate to surface-bound Ca2+ in amyloid. In high-affinity protein sites, Ca2+ is coordinated by pairs of acidic residues. To identify such residues on amyloids, we harnessed atomic structures of patient-derived cardiac amyloids determined using cryogenic electron microscopy since 2019. These structures help explain why most but not all ATTR deposits uptake 99mTc-PYP/DPD/HMDP radiotracers, while in AL the opposite is true. Moreover, fibril structures help explain greater microcalcification observed in ATTR vs. AL deposits. These findings may aid the diagnostics and therapeutic targeting of cardiac amyloidosis and are relevant to other amyloids.
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Affiliation(s)
- Emily Lewkowicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
| | - Shobini Jayaraman
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
| | - Olga Gursky
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
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2
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Schulte T, Chaves-Sanjuan A, Speranzini V, Sicking K, Milazzo M, Mazzini G, Rognoni P, Caminito S, Milani P, Marabelli C, Corbelli A, Diomede L, Fiordaliso F, Anastasia L, Pappone C, Merlini G, Bolognesi M, Nuvolone M, Fernández-Busnadiego R, Palladini G, Ricagno S. Helical superstructures between amyloid and collagen in cardiac fibrils from a patient with AL amyloidosis. Nat Commun 2024; 15:6359. [PMID: 39069558 PMCID: PMC11284220 DOI: 10.1038/s41467-024-50686-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 07/18/2024] [Indexed: 07/30/2024] Open
Abstract
Systemic light chain (LC) amyloidosis (AL) is a disease where organs are damaged by an overload of a misfolded patient-specific antibody-derived LC, secreted by an abnormal B cell clone. The high LC concentration in the blood leads to amyloid deposition at organ sites. Indeed, cryogenic electron microscopy (cryo-EM) has revealed unique amyloid folds for heart-derived fibrils taken from different patients. Here, we present the cryo-EM structure of heart-derived AL amyloid (AL59) from another patient with severe cardiac involvement. The double-layered structure displays a u-shaped core that is closed by a β-arc lid and extended by a straight tail. Noteworthy, the fibril harbours an extended constant domain fragment, thus ruling out the variable domain as sole amyloid building block. Surprisingly, the fibrils were abundantly concatenated with a proteinaceous polymer, here identified as collagen VI (COLVI) by immuno-electron microscopy (IEM) and mass-spectrometry. Cryogenic electron tomography (cryo-ET) showed how COLVI wraps around the amyloid forming a helical superstructure, likely stabilizing and protecting the fibrils from clearance. Thus, here we report structural evidence of interactions between amyloid and collagen, potentially signifying a distinct pathophysiological mechanism of amyloid deposits.
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Affiliation(s)
- Tim Schulte
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097, San Donato Milanese, Italy
- Dept of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121, Solna, Sweden
| | | | - Valentina Speranzini
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Kevin Sicking
- University Medical Center Göttingen, Institute for Neuropathology, Göttinge, 37077, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Melissa Milazzo
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Giulia Mazzini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia, 27100, Italy
| | - Paola Rognoni
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia, 27100, Italy
| | - Serena Caminito
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia, 27100, Italy
| | - Paolo Milani
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia, 27100, Italy
| | - Chiara Marabelli
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Alessandro Corbelli
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, Milano, 20156, Italy
| | - Luisa Diomede
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, Milano, 20156, Italy
| | - Fabio Fiordaliso
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, Milano, 20156, Italy
| | - Luigi Anastasia
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097, San Donato Milanese, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, 20132, Italy
| | - Carlo Pappone
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097, San Donato Milanese, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, 20132, Italy
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, San Donato, Milan, 20097, Italy
| | - Giampaolo Merlini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia, 27100, Italy
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Mario Nuvolone
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia, 27100, Italy
| | - Rubén Fernández-Busnadiego
- University Medical Center Göttingen, Institute for Neuropathology, Göttinge, 37077, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, 37077, Germany
- Faculty of Physics, University of Göttingen, Göttingen, 37077, Germany
| | - Giovanni Palladini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia, 27100, Italy
| | - Stefano Ricagno
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097, San Donato Milanese, Italy.
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy.
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3
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Karimi-Farsijani S, Pfeiffer PB, Banerjee S, Baur J, Kuhn L, Kupfer N, Hegenbart U, Schönland SO, Wiese S, Haupt C, Schmidt M, Fändrich M. Light chain mutations contribute to defining the fibril morphology in systemic AL amyloidosis. Nat Commun 2024; 15:5121. [PMID: 38879609 PMCID: PMC11180120 DOI: 10.1038/s41467-024-49520-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/06/2024] [Indexed: 06/19/2024] Open
Abstract
Systemic AL amyloidosis is one of the most frequently diagnosed forms of systemic amyloidosis. It arises from mutational changes in immunoglobulin light chains. To explore whether these mutations may affect the structure of the formed fibrils, we determine and compare the fibril structures from several patients with cardiac AL amyloidosis. All patients are affected by light chains that contain an IGLV3-19 gene segment, and the deposited fibrils differ by the mutations within this common germ line background. Using cryo-electron microscopy, we here find different fibril structures in each patient. These data establish that the mutations of amyloidogenic light chains contribute to defining the fibril architecture and hence the structure of the pathogenic agent.
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Affiliation(s)
| | | | | | - Julian Baur
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
| | - Lukas Kuhn
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
| | - Niklas Kupfer
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
| | - Ute Hegenbart
- Medicinal Department V, Amyloidosis Centre, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan O Schönland
- Medicinal Department V, Amyloidosis Centre, Heidelberg University Hospital, Heidelberg, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, Ulm, Germany
| | - Christian Haupt
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
| | | | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
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4
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Pelaez-Aguilar AE, Mata-Salgado F, Morales-Ortiz A, Millán-Pacheco C, Olvera-Carranza C, Salgado-Delgado J, Pastor N, Rivillas-Acevedo L. Cu(II) binding to the λ6aJL2-R24G antibody light chain protein associated with light chain amyloidosis disease: The role of histidines. Int J Biol Macromol 2024; 270:132393. [PMID: 38761898 DOI: 10.1016/j.ijbiomac.2024.132393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/29/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Light chain amyloidosis is a conformational disease caused by the abnormal proliferation and deposition of antibody light chains as amyloid fibers in organs and tissues. The effect of Cu(II) binding to the model recombinant protein 6aJL2-R24G was previously characterized in our group, and we found an acceleration of the aggregation kinetics of the protein. In this study, in order to confirm the Cu(II) binding sites, histidine variants of 6aJL2-R24G were prepared and the effects of their interaction with Cu(II) were analyzed by circular dichroism, fluorescence spectroscopy, isothermal calorimetry titrations, and molecular dynamics simulations. Confirming our earlier work, we found that His8 and His99 are the highest affinity Cu(II) binding sites, and that Cu(II) binding to both sites is a cooperative event.
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Affiliation(s)
- Angel E Pelaez-Aguilar
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Fernanda Mata-Salgado
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Alan Morales-Ortiz
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - César Millán-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Clarita Olvera-Carranza
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Jesus Salgado-Delgado
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico.
| | - Lina Rivillas-Acevedo
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico.
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5
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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6
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Wong S, West ME, Morgan GJ. Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains. Protein Sci 2024; 33:e4871. [PMID: 38100259 PMCID: PMC10868443 DOI: 10.1002/pro.4871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
Aggregation of antibody light chain proteins is associated with the progressive disease light chain amyloidosis. Patient-derived amyloid fibrils are formed from light chain variable domain residues in non-native conformations, highlighting a requirement that light chains unfold from their native structures in order to aggregate. However, mechanistic studies of amyloid formation have primarily focused on the self-assembly of natively unstructured peptides, and the role of native state unfolding is less well understood. Using a well-studied light chain variable domain protein known as WIL, which readily aggregates in vitro under conditions where the native state predominates, we asked how the protein concentration and addition of pre-formed fibril "seeds" alter the kinetics of aggregation. Monitoring aggregation with thioflavin T fluorescence revealed a distinctly non-linear dependence on concentration, with a maximum aggregation rate observed at 8 μM protein. This behavior is consistent with formation of alternate aggregate structures in the early phases of amyloid formation. Addition of N- or C-terminal peptide tags, which did not greatly affect the folding or stability of the protein, altered the concentration dependence of aggregation. Aggregation rates increased in the presence of pre-formed seeds, but this effect did not eliminate the delay before aggregation and became saturated when the proportion of seeds added was greater than 1 in 1600. The complexity of aggregation observed in vitro highlights how multiple species may contribute to amyloid pathology in patients.
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Affiliation(s)
- Sherry Wong
- Boston University Amyloidosis Center, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Madeline E West
- Boston University Amyloidosis Center, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Gareth J Morgan
- Boston University Amyloidosis Center, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
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7
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Andreotti G, Baur J, Ugrina M, Pfeiffer PB, Hartmann M, Wiese S, Miyahara H, Higuchi K, Schwierz N, Schmidt M, Fändrich M. Insights into the Structural Basis of Amyloid Resistance Provided by Cryo-EM Structures of AApoAII Amyloid Fibrils. J Mol Biol 2024; 436:168441. [PMID: 38199491 DOI: 10.1016/j.jmb.2024.168441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Amyloid resistance is the inability or the reduced susceptibility of an organism to develop amyloidosis. In this study we have analysed the molecular basis of the resistance to systemic AApoAII amyloidosis, which arises from the formation of amyloid fibrils from apolipoprotein A-II (ApoA-II). The disease affects humans and animals, including SAMR1C mice that express the C allele of ApoA-II protein, whereas other mouse strains are resistant to development of amyloidosis due to the expression of other ApoA-II alleles, such as ApoA-IIF. Using cryo-electron microscopy, molecular dynamics simulations and other methods, we have determined the structures of pathogenic AApoAII amyloid fibrils from SAMR1C mice and analysed the structural effects of ApoA-IIF-specific mutational changes. Our data show that these changes render ApoA-IIF incompatible with the specific fibril morphologies, with which ApoA-II protein can become pathogenic in vivo.
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Affiliation(s)
- Giada Andreotti
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany.
| | - Julian Baur
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Marijana Ugrina
- Institute of Physics, University of Augsburg, 86159 Augsburg, Germany
| | | | - Max Hartmann
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Hiroki Miyahara
- Institute for Biomedical Science, Shinshu University, Matsumoto 390-8621, Japan
| | - Keiichi Higuchi
- Institute for Biomedical Science, Shinshu University, Matsumoto 390-8621, Japan; Faculty of Human Health Sciences, Meio University, Nago 905-8585, Japan
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, 86159 Augsburg, Germany
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
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8
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Bai J, Li X, Zhao J, Zong H, Yuan Y, Wang L, Zhang X, Ke Y, Han L, Xu J, Ma B, Zhang B, Zhu J. Re-Engineering Therapeutic Anti-Aβ Monoclonal Antibody to Target Amyloid Light Chain. Int J Mol Sci 2024; 25:1593. [PMID: 38338870 PMCID: PMC10855199 DOI: 10.3390/ijms25031593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Amyloidosis involves the deposition of misfolded proteins. Even though it is caused by different pathogenic mechanisms, in aggregate, it shares similar features. Here, we tested and confirmed a hypothesis that an amyloid antibody can be engineered by a few mutations to target a different species. Amyloid light chain (AL) and β-amyloid peptide (Aβ) are two therapeutic targets that are implicated in amyloid light chain amyloidosis and Alzheimer's disease, respectively. Though crenezumab, an anti-Aβ antibody, is currently unsuccessful, we chose it as a model to computationally design and prepare crenezumab variants, aiming to discover a novel antibody with high affinity to AL fibrils and to establish a technology platform for repurposing amyloid monoclonal antibodies. We successfully re-engineered crenezumab to bind both Aβ42 oligomers and AL fibrils with high binding affinities. It is capable of reversing Aβ42-oligomers-induced cytotoxicity, decreasing the formation of AL fibrils, and alleviating AL-fibrils-induced cytotoxicity in vitro. Our research demonstrated that an amyloid antibody could be engineered by a few mutations to bind new amyloid sequences, providing an efficient way to reposition a therapeutic antibody to target different amyloid diseases.
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Affiliation(s)
- Jingyi Bai
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (J.B.); (X.L.); (H.Z.); (Y.Y.); (L.W.); (X.Z.); (Y.K.); (J.Z.)
| | - Xi Li
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (J.B.); (X.L.); (H.Z.); (Y.Y.); (L.W.); (X.Z.); (Y.K.); (J.Z.)
| | - Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA;
| | - Huifang Zong
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (J.B.); (X.L.); (H.Z.); (Y.Y.); (L.W.); (X.Z.); (Y.K.); (J.Z.)
- Jecho Biopharmaceutical Institute, Shanghai 200240, China;
| | - Yuan Yuan
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (J.B.); (X.L.); (H.Z.); (Y.Y.); (L.W.); (X.Z.); (Y.K.); (J.Z.)
| | - Lei Wang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (J.B.); (X.L.); (H.Z.); (Y.Y.); (L.W.); (X.Z.); (Y.K.); (J.Z.)
| | - Xiaoshuai Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (J.B.); (X.L.); (H.Z.); (Y.Y.); (L.W.); (X.Z.); (Y.K.); (J.Z.)
| | - Yong Ke
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (J.B.); (X.L.); (H.Z.); (Y.Y.); (L.W.); (X.Z.); (Y.K.); (J.Z.)
| | - Lei Han
- Jecho Biopharmaceutical Institute, Shanghai 200240, China;
| | - Jianrong Xu
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China;
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (J.B.); (X.L.); (H.Z.); (Y.Y.); (L.W.); (X.Z.); (Y.K.); (J.Z.)
| | - Baohong Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (J.B.); (X.L.); (H.Z.); (Y.Y.); (L.W.); (X.Z.); (Y.K.); (J.Z.)
| | - Jianwei Zhu
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (J.B.); (X.L.); (H.Z.); (Y.Y.); (L.W.); (X.Z.); (Y.K.); (J.Z.)
- Jecho Biopharmaceutical Institute, Shanghai 200240, China;
- Jecho Laboratories, Inc., Frederick, MD 21704, USA
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9
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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] [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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10
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Saccuzzo EG, Mebrat MD, Scelsi HF, Kim M, Ma MT, Su X, Hill SE, Rheaume E, Li R, Torres MP, Gumbart JC, Van Horn WD, Lieberman RL. Competition between inside-out unfolding and pathogenic aggregation in an amyloid-forming β-propeller. Nat Commun 2024; 15:155. [PMID: 38168102 PMCID: PMC10762032 DOI: 10.1038/s41467-023-44479-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Studies of folded-to-misfolded transitions using model protein systems reveal a range of unfolding needed for exposure of amyloid-prone regions for subsequent fibrillization. Here, we probe the relationship between unfolding and aggregation for glaucoma-associated myocilin. Mutations within the olfactomedin domain of myocilin (OLF) cause a gain-of-function, namely cytotoxic intracellular aggregation, which hastens disease progression. Aggregation by wild-type OLF (OLFWT) competes with its chemical unfolding, but only below the threshold where OLF loses tertiary structure. Representative moderate (OLFD380A) and severe (OLFI499F) disease variants aggregate differently, with rates comparable to OLFWT in initial stages of unfolding, and variants adopt distinct partially folded structures seen along the OLFWT urea-unfolding pathway. Whether initiated with mutation or chemical perturbation, unfolding propagates outward to the propeller surface. In sum, for this large protein prone to amyloid formation, the requirement for a conformational change to promote amyloid fibrillization leads to direct competition between unfolding and aggregation.
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Affiliation(s)
- Emily G Saccuzzo
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Mubark D Mebrat
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, USA
- School of Molecular Sciences, Arizona State University, Tempe, USA
| | - Hailee F Scelsi
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Minjoo Kim
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, USA
- School of Molecular Sciences, Arizona State University, Tempe, USA
| | - Minh Thu Ma
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Xinya Su
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - Shannon E Hill
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Elisa Rheaume
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, USA
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, USA
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - James C Gumbart
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
- School of Physics, Georgia Institute of Technology, Atlanta, USA
| | - Wade D Van Horn
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, USA.
- School of Molecular Sciences, Arizona State University, Tempe, USA.
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA.
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11
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Broggini L, Barzago MM, Speranzini V, Schulte T, Sonzini F, Giono M, Romeo M, Milani P, Caminito S, Mazzini G, Rognoni P, Merlini G, Pappone C, Anastasia L, Nuvolone M, Palladini G, Diomede L, Ricagno S. Nanobodies counteract the toxicity of an amyloidogenic light chain by stabilizing a partially open dimeric conformation. J Mol Biol 2023; 435:168320. [PMID: 37865287 DOI: 10.1016/j.jmb.2023.168320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/18/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
Abstract
Light chain amyloidosis (AL) is a systemic disease where fibrillar deposition of misfolded immunoglobulin light chains (LCs) severely affects organ function and results in poor prognosis for patients, especially when heart involvement is severe. Particularly relevant in this context is the cardiotoxicity exerted by still uncharacterized soluble LC species. Here, with the final goal of identifying alternative therapeutic strategies to tackle AL amyloidosis, we produced five llama-derived nanobodies (Nbs) specific against H3, a well-characterized amyloidogenic and cardiotoxic LC from an AL patient with severe cardiac involvement. We found that Nbs are specific and potent agents capable of abolishing H3 soluble toxicity in C. elegans in vivo model. Structural characterization of H3-Nb complexes revealed that the protective effect of Nbs is related to their ability to bind to the H3 VL domain and stabilise an unexpected partially open LC dimer in which the two VL domains no longer interact with each other. Thus, while identifying potent inhibitors of LC soluble toxicity, we also describe the first non-native structure of an amyloidogenic LC that may represent a crucial step in toxicity and aggregation mechanisms.
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Affiliation(s)
- Luca Broggini
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy
| | - Maria Monica Barzago
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, Milano 20156, Italy
| | | | - Tim Schulte
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy
| | - Federica Sonzini
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy; Department of Biosciences, Università degli Studi di Milano, Milan 20133, Italy
| | - Matteo Giono
- Department of Biosciences, Università degli Studi di Milano, Milan 20133, Italy
| | - Margherita Romeo
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, Milano 20156, Italy
| | - Paolo Milani
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Serena Caminito
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Giulia Mazzini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Paola Rognoni
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Giampaolo Merlini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Carlo Pappone
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy; Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, San Donato, Milan 20097, Italy; Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Luigi Anastasia
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy; Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Mario Nuvolone
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Giovanni Palladini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Luisa Diomede
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, Milano 20156, Italy
| | - Stefano Ricagno
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy; Department of Biosciences, Università degli Studi di Milano, Milan 20133, Italy.
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12
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Klimtchuk ES, Peterle D, Bullitt EA, Connors LH, Engen JR, Gursky O. Role of complementarity-determining regions 1 and 3 in pathologic amyloid formation by human immunoglobulin κ1 light chains. Amyloid 2023; 30:364-378. [PMID: 37216473 PMCID: PMC10663386 DOI: 10.1080/13506129.2023.2212397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Immunoglobulin light chain (LC) amyloidosis is a life-threatening disease complicated by vast numbers of patient-specific mutations. We explored 14 patient-derived and engineered proteins related to κ1-family germline genes IGKVLD-33*01 and IGKVLD-39*01. METHODS Hydrogen-deuterium exchange mass spectrometry analysis of conformational dynamics in recombinant LCs and their fragments was integrated with studies of thermal stability, proteolytic susceptibility, amyloid formation and amyloidogenic sequence propensity. The results were mapped on the structures of native and fibrillary proteins. RESULTS Proteins from two κ1 subfamilies showed unexpected differences. Compared to their germline counterparts, amyloid LC related to IGKVLD-33*01 was less stable and formed amyloid faster, whereas amyloid LC related to IGKVLD-39*01 had similar stability and formed amyloid slower, suggesting different major factors influencing amyloidogenesis. In 33*01-related amyloid LC, these factors involved destabilization of the native structure and probable stabilization of amyloid. The atypical behavior of 39*01-related amyloid LC stemmed from increased dynamics/exposure of amyloidogenic segments in βC'V and βEV that could initiate aggregation and decreased dynamics/exposure near the Cys23-Cys88 disulfide. CONCLUSIONS The results suggest distinct amyloidogenic pathways for closely related LCs and point to the complementarity-defining regions CDR1 and CDR3, linked via the conserved internal disulfide, as key factors in amyloid formation.
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Affiliation(s)
- Elena S. Klimtchuk
- Amyloidosis Center, Boston University Chobanian and Avedisian School of Medicine, Boston MA 02118, United States
| | - Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States
| | - Esther A. Bullitt
- Department of Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
| | - Lawreen H. Connors
- Amyloidosis Center, Boston University Chobanian and Avedisian School of Medicine, Boston MA 02118, United States
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States
| | - Olga Gursky
- Amyloidosis Center, Boston University Chobanian and Avedisian School of Medicine, Boston MA 02118, United States
- Department of Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
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13
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Louros N, Schymkowitz J, Rousseau F. Mechanisms and pathology of protein misfolding and aggregation. Nat Rev Mol Cell Biol 2023; 24:912-933. [PMID: 37684425 DOI: 10.1038/s41580-023-00647-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
Despite advances in machine learning-based protein structure prediction, we are still far from fully understanding how proteins fold into their native conformation. The conventional notion that polypeptides fold spontaneously to their biologically active states has gradually been replaced by our understanding that cellular protein folding often requires context-dependent guidance from molecular chaperones in order to avoid misfolding. Misfolded proteins can aggregate into larger structures, such as amyloid fibrils, which perpetuate the misfolding process, creating a self-reinforcing cascade. A surge in amyloid fibril structures has deepened our comprehension of how a single polypeptide sequence can exhibit multiple amyloid conformations, known as polymorphism. The assembly of these polymorphs is not a random process but is influenced by the specific conditions and tissues in which they originate. This observation suggests that, similar to the folding of native proteins, the kinetics of pathological amyloid assembly are modulated by interactions specific to cells and tissues. Here, we review the current understanding of how intrinsic protein conformational propensities are modulated by physiological and pathological interactions in the cell to shape protein misfolding and aggregation pathology.
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Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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14
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Puri S, Schulte T, Chaves-Sanjuan A, Mazzini G, Caminito S, Pappone C, Anastasia L, Milani P, Merlini G, Bolognesi M, Nuvolone M, Palladini G, Ricagno S. The Cryo-EM STRUCTURE of Renal Amyloid Fibril Suggests Structurally Homogeneous Multiorgan Aggregation in AL Amyloidosis. J Mol Biol 2023; 435:168215. [PMID: 37516426 DOI: 10.1016/j.jmb.2023.168215] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/15/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
Immunoglobulin light chain amyloidosis (AL) is caused by the aberrant production of amyloidogenic light chains (LC) that accumulate as amyloid deposits in vital organs. Distinct LC sequences in each patient yield distinct amyloid structures. However different tissue microenvironments may also cause identical protein precursors to adopt distinct amyloid structures. To address the impact of the tissue environment on the structural polymorphism of amyloids, we extracted fibrils from the kidney of an AL patient (AL55) whose cardiac amyloid structure was previously determined by our group. Here we show that the 4.0 Å resolution cryo-EM structure of the renal fibril is virtually identical to that reported for the cardiac fibril. These results provide the first structural evidence that LC amyloids independently deposited in different organs of the same AL patient share a common fold.
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Affiliation(s)
- Sarita Puri
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy. https://twitter.com/@Saritapuri1504
| | - Tim Schulte
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy. https://twitter.com/@timpaul81
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy; Pediatric Research Center Fondazione R.E. Invernizzi and NOLIMITS Center, Università degli Studi di Milano, Milan, Italy. https://twitter.com/@ChavesSanjuan
| | - Giulia Mazzini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Serena Caminito
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Carlo Pappone
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; Faculty of Medicine, University of Vita-Salute San Raffaele, 20132 Milan, Italy; Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, San Donato, 20097 Milan, Italy
| | - Luigi Anastasia
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; Faculty of Medicine, University of Vita-Salute San Raffaele, 20132 Milan, Italy. https://twitter.com/@skinski74
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy; Pediatric Research Center Fondazione R.E. Invernizzi and NOLIMITS Center, Università degli Studi di Milano, Milan, Italy. https://twitter.com/@Martinobologne2
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stefano Ricagno
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy; Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy.
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15
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Wang L, Hall CE, Uchikawa E, Chen D, Choi E, Zhang X, Bai XC. Structural basis of insulin fibrillation. SCIENCE ADVANCES 2023; 9:eadi1057. [PMID: 37713485 PMCID: PMC10881025 DOI: 10.1126/sciadv.adi1057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/14/2023] [Indexed: 09/17/2023]
Abstract
Insulin is a hormone responsible for maintaining normal glucose levels by activating insulin receptor (IR) and is the primary treatment for diabetes. However, insulin is prone to unfolding and forming cross-β fibers. Fibrillation complicates insulin storage and therapeutic application. Molecular details of insulin fibrillation remain unclear, hindering efforts to prevent fibrillation process. Here, we characterized insulin fibrils using cryo-electron microscopy (cryo-EM), showing multiple forms that contain one or more of the protofilaments containing both the A and B chains of insulin linked by disulfide bonds. We solved the cryo-EM structure of one of the fibril forms composed of two protofilaments at 3.2-Å resolution, which reveals both the β sheet conformation of the protofilament and the packing interaction between them that underlie the fibrillation. On the basis of this structure, we designed several insulin mutants that display reduced fibrillation while maintaining native IR signaling activity. These designed insulin analogs may be developed into more effective therapeutics for type 1 diabetes.
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Affiliation(s)
- Liwei Wang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Catherine E. Hall
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Emiko Uchikawa
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dailu Chen
- Center for Alzheimer’s and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eunhee Choi
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiao-chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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16
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Berghaus N, Schreiner S, Poos AM, Raab MS, Goldschmidt H, Mai EK, Salwender HJ, Bernhard H, Thurner L, Müller-Tidow C, Weinhold N, Hegenbart U, Schönland SO, Huhn S. Comparison of IGLV2-14 light chain sequences of patients with AL amyloidosis or multiple myeloma. FEBS J 2023; 290:4256-4267. [PMID: 37097223 DOI: 10.1111/febs.16805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/24/2023] [Accepted: 04/25/2023] [Indexed: 04/26/2023]
Abstract
Light chain amyloidosis (AL) is one of the most common forms of systemic amyloidosis and is caused by the deposition of insoluble fibrils derived from misfolded and aggregated immunoglobulin light chains (LC). To uncover the causes leading to this aggregation, we compared AL LC sequences with those of patients with the related disease multiple myeloma (MM), which do not aggregate in insoluble fibrils in vivo. IGLV2-14 is one of the most common AL-associated IGLV subfamilies. Here, we analysed IGLV2-14 LC sequences of 13 AL and eight MM patients in detail. We found that AL-associated LCs presented a lower median mutation count (7.0 vs. 11.5 in MM; P = 0.045), as well as an overall composition of less charged amino acids than MM LCs. However, we did not find a mutation that was present in ≥ 50% of the AL and not in the MM sequences. Furthermore, we did not find a significant difference in the isoelectric point (pI) in general, suggesting similar stability of the LCs in AL and MM. However, the subgroup of patients without a detectable heavy chain stood out. Surprisingly, they are characterized by an increase in mutation count (median 7.0 vs. 5.5) and pI (median 7.82 vs. 6.44, P = 0.043). In conclusion, our data suggest that the amount of mutations and the introduction of charges play a crucial role in AL fibril formation, as well as the absence or presence of a potential heavy chain binding partner.
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Affiliation(s)
- Natalie Berghaus
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Germany
| | - Sarah Schreiner
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Germany
| | - Alexandra M Poos
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, Germany
| | - Marc S Raab
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, Germany
- National Centre for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hartmut Goldschmidt
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, Germany
| | - Elias K Mai
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, Germany
- National Centre for Tumor Diseases (NCT), Heidelberg, Germany
| | | | - Helga Bernhard
- Medical Department V, Hematology/Oncology, Hospital Darmstadt GmbH, Germany
| | - Lorenz Thurner
- Internal Medicine I, University Hospital Saarland, Homburg/ Saar, Germany
| | | | - Niels Weinhold
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, Germany
| | - Ute Hegenbart
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Germany
| | - Stefan O Schönland
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Germany
| | - Stefanie Huhn
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, Germany
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17
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Wong S, West ME, Morgan GJ. Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555139. [PMID: 37693524 PMCID: PMC10491100 DOI: 10.1101/2023.08.28.555139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Aggregation of antibody light chain proteins is associated with the progressive disease light chain amyloidosis. Patient-derived amyloid fibrils are formed from light chain variable domain residues in non-native conformations, highlighting a requirement that light chains unfold from their native structures in order to aggregate. However, mechanistic studies of amyloid formation have primarily focused on the self-assembly of natively unstructured peptides, and the role of native state unfolding is less well understood. Using a well-studied light chain variable domain protein known as WIL, which readily aggregates in vitro under conditions where the native state predominates, we asked how the protein concentration and addition of pre-formed fibril "seeds" alter the kinetics of aggregation. Monitoring aggregation with thioflavin T fluorescence revealed a distinctly non-linear dependence on concentration, with a maximum aggregation rate observed at 8 μM protein. This behavior is consistent with formation of alternate aggregate structures in the early phases of amyloid formation. Addition of N- or C-terminal peptide tags, which did not greatly affect the folding or stability of the protein, altered the concentration dependence of aggregation. Aggregation rates increased in the presence of pre-formed seeds, but this effect did not eliminate the delay before aggregation and became saturated when the proportion of seeds added was greater than 1 in 1600. The complexity of aggregation observed in vitro highlights how multiple species may contribute to amyloid pathology in patients.
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Affiliation(s)
- Sherry Wong
- Boston University Amyloidosis Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Madeline E West
- Boston University Amyloidosis Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Gareth J Morgan
- Boston University Amyloidosis Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
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18
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Del Pozo-Yauner L, Herrera GA, Perez Carreon JI, Turbat-Herrera EA, Rodriguez-Alvarez FJ, Ruiz Zamora RA. Role of the mechanisms for antibody repertoire diversification in monoclonal light chain deposition disorders: when a friend becomes foe. Front Immunol 2023; 14:1203425. [PMID: 37520549 PMCID: PMC10374031 DOI: 10.3389/fimmu.2023.1203425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
The adaptive immune system of jawed vertebrates generates a highly diverse repertoire of antibodies to meet the antigenic challenges of a constantly evolving biological ecosystem. Most of the diversity is generated by two mechanisms: V(D)J gene recombination and somatic hypermutation (SHM). SHM introduces changes in the variable domain of antibodies, mostly in the regions that form the paratope, yielding antibodies with higher antigen binding affinity. However, antigen recognition is only possible if the antibody folds into a stable functional conformation. Therefore, a key force determining the survival of B cell clones undergoing somatic hypermutation is the ability of the mutated heavy and light chains to efficiently fold and assemble into a functional antibody. The antibody is the structural context where the selection of the somatic mutations occurs, and where both the heavy and light chains benefit from protective mechanisms that counteract the potentially deleterious impact of the changes. However, in patients with monoclonal gammopathies, the proliferating plasma cell clone may overproduce the light chain, which is then secreted into the bloodstream. This places the light chain out of the protective context provided by the quaternary structure of the antibody, increasing the risk of misfolding and aggregation due to destabilizing somatic mutations. Light chain-derived (AL) amyloidosis, light chain deposition disease (LCDD), Fanconi syndrome, and myeloma (cast) nephropathy are a diverse group of diseases derived from the pathologic aggregation of light chains, in which somatic mutations are recognized to play a role. In this review, we address the mechanisms by which somatic mutations promote the misfolding and pathological aggregation of the light chains, with an emphasis on AL amyloidosis. We also analyze the contribution of the variable domain (VL) gene segments and somatic mutations on light chain cytotoxicity, organ tropism, and structure of the AL fibrils. Finally, we analyze the most recent advances in the development of computational algorithms to predict the role of somatic mutations in the cardiotoxicity of amyloidogenic light chains and discuss the challenges and perspectives that this approach faces.
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Affiliation(s)
- Luis Del Pozo-Yauner
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | - Guillermo A. Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | | | - Elba A. Turbat-Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
- Mitchell Cancer Institute, University of South Alabama-College of Medicine, Mobile, AL, United States
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19
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Sizova DV, Raiker S, Lakheram D, Rao V, Proffitt A, Jmeian Y, Voegtli W, Batonick M. Producing amyloid fibrils in vitro: A tool for studying AL amyloidosis. Biochem Biophys Rep 2023; 34:101442. [PMID: 36875796 PMCID: PMC9982448 DOI: 10.1016/j.bbrep.2023.101442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/03/2023] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Amyloid light-chain (AL) amyloidosis is the second most common form of systemic amyloidosis which is characterized by a high level of mortality and no effective treatment to remove fibril deposition. This disorder is caused by malfunctioning of B-cells resulting in production of abnormal protein fibrils composed of immunoglobulin light chain fragments that tend to deposit on various organs and tissues. AL amyloidosis is set apart from other forms of amyloidosis in that no specific sequences have been identified in the immunoglobulin light chains that are amyloid fibril formation causative and patient specific. This unusual feature hinders the therapeutic progress and requires either direct access to patient samples (which is not always possible) or a source of in vitro produced fibrils. While isolated reports of successful AL amyloid fibril formation from various patient-specific protein sequences can be found in literature, no systematic research on this topic was performed since 1999. In the present study we have developed a generalized approach to in vitro fibril production from various types of previously reported [[1], [2], [3]] amyloidogenic immunoglobulin light chains and their fragments. We describe the procedure from selection and generation of starting material, through finding of optimal assay conditions, to applying a panel of methods to confirm successful fibril formation. Procedure details are discussed in the light of the most recent findings and theories on amyloid fibril formation. The reported protocol produces high quality AL amyloid fibrils that can subsequently be used in the development of the much-needed amyloid-targeting diagnostic and therapeutic approaches.
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20
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Björk L, Klingstedt T, Nilsson KPR. Thiophene-Based Ligands: Design, Synthesis and Their Utilization for Optical Assignment of Polymorphic-Disease-Associated Protein Aggregates. Chembiochem 2023; 24:e202300044. [PMID: 36891883 PMCID: PMC10404026 DOI: 10.1002/cbic.202300044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 03/10/2023]
Abstract
The development of ligands for detecting protein aggregates is of great interest, as these aggregated proteinaceous species are the pathological hallmarks of several devastating diseases, including Alzheimer's disease. In this regard, thiophene-based ligands have emerged as powerful tools for fluorescent assessment of these pathological entities. The intrinsic conformationally sensitive photophysical properties of poly- and oligothiophenes have allowed optical assignment of disease-associated protein aggregates in tissue sections, as well as real-time in vivo imaging of protein deposits. Herein, we recount the chemical evolution of different generations of thiophene-based ligands, and exemplify their use for the optical distinction of polymorphic protein aggregates. Furthermore, the chemical determinants for achieving a superior fluorescent thiophene-based ligand, as well as the next generation of thiophene-based ligands targeting distinct aggregated species are described. Finally, the directions for future research into the chemical design of thiophene-based ligands that can aid in resolving the scientific challenges around protein aggregation diseases are discussed.
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Affiliation(s)
- Linnea Björk
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Therése Klingstedt
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - K Peter R Nilsson
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
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21
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Nakamura K. Molecular Research on Amyloidosis. Int J Mol Sci 2023; 24:ijms24086980. [PMID: 37108144 PMCID: PMC10139197 DOI: 10.3390/ijms24086980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Amyloidosis is a large group of diseases that are caused by the deposition of insoluble amyloid fibrils formed by misfolded soluble proteins in organs or tissues [...].
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Affiliation(s)
- Kazufumi Nakamura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
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22
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Miserez A, Yu J, Mohammadi P. Protein-Based Biological Materials: Molecular Design and Artificial Production. Chem Rev 2023; 123:2049-2111. [PMID: 36692900 PMCID: PMC9999432 DOI: 10.1021/acs.chemrev.2c00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.
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Affiliation(s)
- Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,School of Biological Sciences, NTU, Singapore637551
| | - Jing Yu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 50 Nanyang Avenue, Singapore637553
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., Espoo, UusimaaFI-02044, Finland
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23
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Meunier-Carmenate Y, Valdés-García G, Maya-Martinez R, French-Pacheco L, Fernández-Silva A, González-Onofre Y, Millan-Pacheco C, Pastor N, Amero C. Unfolding and Aggregation Pathways of Variable Domains from Immunoglobulin Light Chains. Biochemistry 2023; 62:1000-1011. [PMID: 36802343 DOI: 10.1021/acs.biochem.2c00704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Light chain amyloidosis is the most common form of systemic amyloidosis. This disease is caused by the formation and deposition of amyloid fibers made from immunoglobulin light chains. Environmental conditions such as pH and temperature can affect protein structure and induce the development of these fibers. Several studies have shed light on the native state, stability, dynamics, and final amyloid state of these proteins; however, the initiation process and the fibril formation pathway remain poorly understood structurally and kinetically. To study this, we analyzed the unfolding and aggregation process of the 6aJL2 protein under acidic conditions, with temperature changes, and upon mutation, using biophysical and computational techniques. Our results suggest that the differences in amyloidogenicity displayed by 6aJL2 under these conditions are caused by traversing different aggregation pathways, including unfolded intermediates and the formation of oligomers.
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Affiliation(s)
- Yadira Meunier-Carmenate
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Gilberto Valdés-García
- Centro de Investigacion en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Roberto Maya-Martinez
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Leidys French-Pacheco
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Arline Fernández-Silva
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Yoselin González-Onofre
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Cesar Millan-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Nina Pastor
- Centro de Investigacion en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Carlos Amero
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
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24
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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] [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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25
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Baur J, Berghaus N, Schreiner S, Hegenbart U, Schönland SO, Wiese S, Huhn S, Haupt C. Identification of AL proteins from 10 λ-AL amyloidosis patients by mass spectrometry extracted from abdominal fat and heart tissue. Amyloid 2023; 30:27-37. [PMID: 35792725 DOI: 10.1080/13506129.2022.2095618] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND Systemic AL amyloidosis arises from the misfolding of patient-specific immunoglobulin light chains (LCs). Potential drivers of LC amyloid formation are mutational changes and post-translational modifications (PTMs). However, little information is available on the exact primary structure of the AL proteins and their precursor LCs. OBJECTIVE We analyse the exact primary structure of AL proteins extracted from 10 λ AL amyloidosis patients and their corresponding precursor LCs. MATERIALS AND METHODS By cDNA sequencing of the precursor LC genes in combination with mass spectrometry of the AL proteins, the exact primary structure and PTMs were determined. This information was used to analyse their biochemical properties. RESULTS All AL proteins comprise the VL and a small part of the CL with a common C-terminal truncation region. While all AL proteins retain the conserved native disulphide bond of the VL, we found no evidence for presence of other common PTMs. The analysis of the biochemical properties revealed that the isoelectric point of the VL is significantly increased due to introduced mutations. CONCLUSION Our data imply that mutational changes influence the surface charge properties of the VL and that common proteolytic processes are involved in the generation of the cleavage sites of AL proteins.
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Affiliation(s)
- Julian Baur
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
| | - Natalie Berghaus
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Sarah Schreiner
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Ute Hegenbart
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan O Schönland
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Medical Faculty, Ulm University, Ulm, Germany
| | - Stefanie Huhn
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Haupt
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
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26
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Absmeier RM, Rottenaicher GJ, Svilenov HL, Kazman P, Buchner J. Antibodies gone bad - the molecular mechanism of light chain amyloidosis. FEBS J 2023; 290:1398-1419. [PMID: 35122394 DOI: 10.1111/febs.16390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/19/2022] [Accepted: 02/03/2022] [Indexed: 12/19/2022]
Abstract
Light chain amyloidosis (AL) is a systemic disease in which abnormally proliferating plasma cells secrete large amounts of mutated antibody light chains (LCs) that eventually form fibrils. The fibrils are deposited in various organs, most often in the heart and kidney, and impair their function. The prognosis for patients diagnosed with AL is generally poor. The disease is set apart from other amyloidoses by the huge number of patient-specific mutations in the disease-causing and fibril-forming protein. The molecular mechanisms that drive the aggregation of mutated LCs into fibrils have been enigmatic, which hindered the development of efficient diagnostics and therapies. In this review, we summarize our current knowledge on AL amyloidosis and discuss open issues.
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Affiliation(s)
- Ramona M Absmeier
- Center for Functional Protein Assemblies and Department of Chemistry, Technische Universität München, Garching, Germany
| | - Georg J Rottenaicher
- Center for Functional Protein Assemblies and Department of Chemistry, Technische Universität München, Garching, Germany
| | - Hristo L Svilenov
- Center for Functional Protein Assemblies and Department of Chemistry, Technische Universität München, Garching, Germany
| | - Pamina Kazman
- Center for Functional Protein Assemblies and Department of Chemistry, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Functional Protein Assemblies and Department of Chemistry, Technische Universität München, Garching, Germany
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27
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Role of Triggers on the Structural and Functional Facets of TAR DNA-binding Protein 43. Neuroscience 2023; 511:110-130. [PMID: 36442745 DOI: 10.1016/j.neuroscience.2022.11.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/15/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Nuclear TAR DNA-binding protein 43 (TDP-43) mitigates cellular function, but the dynamic nucleus-cytoplasm shuttling of TDP-43 is disrupted in diseases, such as Amyotrophic Lateral Sclerosis (ALS). The polymorphic nature of the TDP-43 structures in vitro and in vivo is a result of environmental factors leading to the protein pathogenesis. Once the triggers which mitigate TDP-43 biochemistry are identified, new therapies can be developed. This review aims to illustrate recent discoveries in the diversity of TDP-43 structures (amyloidogenic and non-amyloidogenic) and highlight the triggers which result in their formation.
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28
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Sternke-Hoffmann R, Pauly T, Norrild RK, Hansen J, Tucholski F, Høie MH, Marcatili P, Dupré M, Duchateau M, Rey M, Malosse C, Metzger S, Boquoi A, Platten F, Egelhaaf SU, Chamot-Rooke J, Fenk R, Nagel-Steger L, Haas R, Buell AK. Widespread amyloidogenicity potential of multiple myeloma patient-derived immunoglobulin light chains. BMC Biol 2023; 21:21. [PMID: 36737754 PMCID: PMC9898917 DOI: 10.1186/s12915-022-01506-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/15/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND In a range of human disorders such as multiple myeloma (MM), immunoglobulin light chains (IgLCs) can be produced at very high concentrations. This can lead to pathological aggregation and deposition of IgLCs in different tissues, which in turn leads to severe and potentially fatal organ damage. However, IgLCs can also be highly soluble and non-toxic. It is generally thought that the cause for this differential solubility behaviour is solely found within the IgLC amino acid sequences, and a variety of individual sequence-related biophysical properties (e.g. thermal stability, dimerisation) have been proposed in different studies as major determinants of the aggregation in vivo. Here, we investigate biophysical properties underlying IgLC amyloidogenicity. RESULTS We introduce a novel and systematic workflow, Thermodynamic and Aggregation Fingerprinting (ThAgg-Fip), for detailed biophysical characterisation, and apply it to nine different MM patient-derived IgLCs. Our set of pathogenic IgLCs spans the entire range of values in those parameters previously proposed to define in vivo amyloidogenicity; however, none actually forms amyloid in patients. Even more surprisingly, we were able to show that all our IgLCs are able to form amyloid fibrils readily in vitro under the influence of proteolytic cleavage by co-purified cathepsins. CONCLUSIONS We show that (I) in vivo aggregation behaviour is unlikely to be mechanistically linked to any single biophysical or biochemical parameter and (II) amyloidogenic potential is widespread in IgLC sequences and is not confined to those sequences that form amyloid fibrils in patients. Our findings suggest that protein sequence, environmental conditions and presence and action of proteases all determine the ability of light chains to form amyloid fibrils in patients.
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Affiliation(s)
- Rebecca Sternke-Hoffmann
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.5991.40000 0001 1090 7501Department of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Thomas Pauly
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XForschungszentrum Jülich GmbH, IBI-7, Jülich, Germany
| | - Rasmus K. Norrild
- grid.5170.30000 0001 2181 8870Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jan Hansen
- grid.411327.20000 0001 2176 9917Condensed Matter Physics Laboratory, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Florian Tucholski
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Magnus Haraldson Høie
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Paolo Marcatili
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Mathieu Dupré
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Magalie Duchateau
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Martial Rey
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Christian Malosse
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Sabine Metzger
- grid.6190.e0000 0000 8580 3777Cologne Biocenter, Cluster of Excellence on Plant Sciences, Mass Spectrometry Platform, University of Cologne, Cologne, Germany
| | - Amelie Boquoi
- grid.411327.20000 0001 2176 9917Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Florian Platten
- grid.411327.20000 0001 2176 9917Condensed Matter Physics Laboratory, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XForschungszentrum Jülich GmbH, IBI-4, Jülich, Germany
| | - Stefan U. Egelhaaf
- grid.411327.20000 0001 2176 9917Condensed Matter Physics Laboratory, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Julia Chamot-Rooke
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Roland Fenk
- grid.411327.20000 0001 2176 9917Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XForschungszentrum Jülich GmbH, IBI-7, Jülich, Germany
| | - Rainer Haas
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany.
| | - Alexander K. Buell
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.5170.30000 0001 2181 8870Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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Klimtchuk ES, Peterle D, Bullitt EA, Connors LH, Engen JR, Gursky O. Role of Complementarity-Determining Regions 1 and 3 in Pathologic Amyloid Formation by Human Immunoglobulin κ1 Light Chains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526662. [PMID: 36778378 PMCID: PMC9915687 DOI: 10.1101/2023.02.01.526662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Immunoglobulin light chain (LC) amyloidosis is a life-threatening disease whose understanding and treatment is complicated by vast numbers of patient-specific mutations. To address molecular origins of the disease, we explored 14 patient-derived and engineered proteins related to κ1-family germline genes IGKVLD-33*01 and IGKVLD-39*01. Hydrogen-deuterium exchange mass spectrometry analysis of local conformational dynamics in full-length recombinant LCs and their fragments was integrated with studies of thermal stability, proteolytic susceptibility, amyloid formation, and amyloidogenic sequence propensities using spectroscopic, electron microscopic and bioinformatics tools. The results were mapped on the atomic structures of native and fibrillary proteins. Proteins from two κ1 subfamilies showed unexpected differences. Compared to their germline counterparts, amyloid LC related to IGKVLD-33*01 was less stable and formed amyloid faster, whereas amyloid LC related to IGKVLD-39*01 had similar stability and formed amyloid slower. These and other differences suggest different major factors influencing amyloid formation. In 33*01-related amyloid LC, these factors involved mutation-induced destabilization of the native structure and probable stabilization of amyloid. The atypical behaviour of 39*01-related amyloid LC tracked back to increased dynamics/exposure of amyloidogenic segments in βC' V and βE V that could initiate aggregation, combined with decreased dynamics/exposure near the Cys23-Cys88 disulfide whose rearrangement is rate-limiting to amyloidogenesis. The results suggest distinct amyloidogenic pathways for closely related LCs and point to the antigen-binding, complementarity-determining regions CDR1 and CDR3, which are linked via the conserved internal disulfide, as key factors in amyloid formation by various LCs.
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30
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Diagnosis and Treatment of AL Amyloidosis. Drugs 2023; 83:203-216. [PMID: 36652193 DOI: 10.1007/s40265-022-01830-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 01/19/2023]
Abstract
Systemic light chain (AL) amyloidosis is caused by an usually small B cell clone that produces a toxic light chain forming amyloid deposits in tissue. The heart and kidney are the major organs affected, but all others, with the exception of the CNS, can be involved. The disease is rapidly progressive, and it is still diagnosed late. Screening programs in patients followed by hematologists for plasma cell dyscrasias should be considered. The diagnosis requires demonstration in a tissue biopsy of amyloid deposits formed by immunoglobulin light chains. The workup of patients with AL amyloidosis requires adequate technology and expertise, and patients should be referred to specialized centers whenever possible. Stagings are based on cardiac and renal biomarkers and guides the choice of treatment. The combination of daratumumab, cyclophosphamide, bortezomib and dexamethasone (dara-CyBorD) is the current standard of care. Autologous stem cell transplant is performed in eligible patients, especially those who do not attain a satisfactory response to dara-CyBorD. Passive immunotherapy targeting the amyloid deposits combined with chemo-/immune-therapy targeting the amyloid clone is currently being tested in controlled clinical trials. Response to therapy is assessed based on validated criteria. Profound hematologic response is the early goal of treatment and should be accompanied over time by deepening organ response. Many relapsed/refractory patients are also treated with daratumumab combination, but novel regimens will be needed to rescue daratumumab-exposed subjects. Immunomodulatory drugs are the current cornerstone of rescue therapy, while immunotherapy targeting B-cell maturation antigen and inhibitors of Bcl-2 are promising alternatives.
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31
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Aggregation mechanism and branched 3D morphologies of pathological human light chain proteins under reducing conditions. Colloids Surf B Biointerfaces 2023; 221:112983. [DOI: 10.1016/j.colsurfb.2022.112983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/31/2022] [Accepted: 10/27/2022] [Indexed: 11/17/2022]
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Martinez-Rivas G, Bender S, Sirac C. Understanding AL amyloidosis with a little help from in vivo models. Front Immunol 2022; 13:1008449. [PMID: 36458006 PMCID: PMC9707859 DOI: 10.3389/fimmu.2022.1008449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/27/2022] [Indexed: 08/01/2023] Open
Abstract
Monoclonal immunoglobulin (Ig) light chain amyloidosis (AL) is a rare but severe disease that may occur when a B or plasma cell clone secretes an excess of free Ig light chains (LCs). Some of these LCs tend to aggregate into organized fibrils with a β-sheet structure, the so-called amyloid fibrils, and deposit into the extracellular compartment of organs, such as the heart or kidneys, causing their dysfunction. Recent findings have confirmed that the core of the amyloid fibrils is constituted by the variable (V) domain of the LCs, but the mechanisms underlying the unfolding and aggregation of this fragment and its deposition are still unclear. Moreover, in addition to the mechanical constraints exerted by the massive accumulation of amyloid fibrils in organs, the direct toxicity of these variable domain LCs, full-length light chains, or primary amyloid precursors (oligomers) seems to play a role in the pathogenesis of the disease. Many in vitro studies have focused on these topics, but the variability of this disease, in which each LC presents unique properties, and the extent and complexity of affected organs make its study in vivo very difficult. Accordingly, several groups have focused on the development of animal models for years, with some encouraging but mostly disappointing results. In this review, we discuss the experimental models that have been used to better understand the unknowns of this pathology with an emphasis on in vivo approaches. We also focus on why reliable AL amyloidosis animal models remain so difficult to obtain and what this tells us about the pathophysiology of the disease.
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33
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Targeting Amyloid Fibrils by Passive Immunotherapy in Systemic Amyloidosis. BioDrugs 2022; 36:591-608. [PMID: 36094752 PMCID: PMC9466354 DOI: 10.1007/s40259-022-00550-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2022] [Indexed: 12/03/2022]
Abstract
Systemic amyloidoses are characterized by the unrelenting deposition of autologous proteins as highly ordered fibrils in target organs. The ensuing, potentially fatal organ dysfunction is the result of the combined damage caused by the proteotoxic effect of prefibrillar species and by the cytotoxicity and the structural alterations produced by the amyloid fibrils. Current therapy is focused on eliminating the amyloid protein, thus extinguishing the amyloid cascade at its origin. While this approach may end the cell damage caused by prefibrillar aggregates and prevent further amyloid accumulation, the noxious effects of the amyloid fibrils persist and may hamper the recovery of organ function, which is the ultimate goal of therapy as it is necessary to improve the quality of life and extend survival. Preclinical studies indicate that the clearance of amyloid deposits can be accelerated by specific antibodies targeting amyloid fibrils that activate complement-mediated macrophages and giant cell phagocytosis, possibly promoting the recovery of organ function. Measuring the therapeutic effect of anti-amyloid agents is still a matter of research. In recent years, several monoclonal antibodies targeting amyloid deposits have been tested in clinical trials with mixed outcomes. Recent encouraging results from phase I/II trials, new anti-amyloid agents, and new antibody engineering offer hope that effective amyloid removal will be accomplished in the near future, accelerating organ recovery and improving quality of life and survival.
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34
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Golan N, Engelberg Y, Landau M. Structural Mimicry in Microbial and Antimicrobial Amyloids. Annu Rev Biochem 2022; 91:403-422. [PMID: 35729071 DOI: 10.1146/annurev-biochem-032620-105157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The remarkable variety of microbial species of human pathogens and microbiomes generates significant quantities of secreted amyloids, which are structured protein fibrils that serve diverse functions related to virulence and interactions with the host. Human amyloids are associated largely with fatal neurodegenerative and systemic aggregation diseases, and current research has put forward the hypothesis that the interspecies amyloid interactome has physiological and pathological significance. Moreover, functional and molecular-level connections between antimicrobial activity and amyloid structures suggest a neuroimmune role for amyloids that are otherwise known to be pathological. Compared to the extensive structural information that has been accumulated for human amyloids, high-resolution structures of microbial and antimicrobial amyloids are only emerging. These recent structures reveal both similarities and surprising departures from the typical amyloid motif, in accordance with their diverse activities, and advance the discovery of novel antivirulence and antimicrobial agents. In addition, the structural information has led researchers to postulate that amyloidogenic sequences are natural targets for structural mimicry, for instance in host-microbe interactions. Microbial amyloid research could ultimately be used to fight aggressive infections and possibly processes leading to autoimmune and neurodegenerative diseases.
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Affiliation(s)
- Nimrod Golan
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
| | - Yizhaq Engelberg
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel; .,European Molecular Biology Laboratory (EMBL) and Center for Structural Systems Biology (CSSB), Hamburg, Germany
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35
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Molecular Mechanism of Pathogenesis and Treatment Strategies for AL Amyloidosis. Int J Mol Sci 2022; 23:ijms23116336. [PMID: 35683015 PMCID: PMC9181426 DOI: 10.3390/ijms23116336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 11/17/2022] Open
Abstract
In amyloid light-chain (AL) amyloidosis, small B-cell clones (mostly plasma cell clones) present in the bone marrow proliferate and secrete unstable monoclonal free light chains (FLCs), which form amyloid fibrils that deposit in the interstitial tissue, resulting in organ injury and dysfunction. AL amyloidosis progresses much faster than other types of amyloidosis, with a slight delay in diagnosis leading to a marked exacerbation of cardiomyopathy. In some cases, the resulting heart failure is so severe that chemotherapy cannot be administered, and death sometimes occurs within a few months. To date, many clinical studies have focused on therapeutics, especially chemotherapy, to treat this disease. Because it is necessary to promptly lower FLC, the causative protein of amyloid, to achieve a hematological response, various anticancer agents targeting neoplastic plasma cells are used for the treatment of this disease. In addition, many basic studies using human specimens to elucidate the pathophysiology of AL have been conducted. Gene mutations associated with AL, the characteristics of amyloidogenic LC, and the structural specificity of amyloid fibrils have been clarified. Regarding the mechanism of cellular and tissue damage, the mass effect due to amyloid deposition, as well as the toxicity of pre-fibrillar LC, is gradually being elucidated. This review outlines the pathogenesis and treatment strategies for AL amyloidosis with respect to its molecular mechanisms.
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36
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Taylor AIP, Staniforth RA. General Principles Underpinning Amyloid Structure. Front Neurosci 2022; 16:878869. [PMID: 35720732 PMCID: PMC9201691 DOI: 10.3389/fnins.2022.878869] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Amyloid fibrils are a pathologically and functionally relevant state of protein folding, which is generally accessible to polypeptide chains and differs fundamentally from the globular state in terms of molecular symmetry, long-range conformational order, and supramolecular scale. Although amyloid structures are challenging to study, recent developments in techniques such as cryo-EM, solid-state NMR, and AFM have led to an explosion of information about the molecular and supramolecular organization of these assemblies. With these rapid advances, it is now possible to assess the prevalence and significance of proposed general structural features in the context of a diverse body of high-resolution models, and develop a unified view of the principles that control amyloid formation and give rise to their unique properties. Here, we show that, despite system-specific differences, there is a remarkable degree of commonality in both the structural motifs that amyloids adopt and the underlying principles responsible for them. We argue that the inherent geometric differences between amyloids and globular proteins shift the balance of stabilizing forces, predisposing amyloids to distinct molecular interaction motifs with a particular tendency for massive, lattice-like networks of mutually supporting interactions. This general property unites previously characterized structural features such as steric and polar zippers, and contributes to the long-range molecular order that gives amyloids many of their unique properties. The shared features of amyloid structures support the existence of shared structure-activity principles that explain their self-assembly, function, and pathogenesis, and instill hope in efforts to develop broad-spectrum modifiers of amyloid function and pathology.
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37
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The effect of mutation on an aggregation-prone protein: An in vivo, in vitro, and in silico analysis. Proc Natl Acad Sci U S A 2022; 119:e2200468119. [PMID: 35613051 PMCID: PMC9295795 DOI: 10.1073/pnas.2200468119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Aggregation of initially stably structured proteins is involved in more than 20 human amyloid diseases. Despite intense research, however, how this class of proteins assembles into amyloid fibrils remains poorly understood, principally because of the complex effects of amino acid substitutions on protein stability, solubility, and aggregation propensity. We address this question using β2-microglobulin (β2m) as a model system, focusing on D76N-β2m that is involved in hereditary amyloidosis. This amino acid substitution causes the aggregation-resilient wild-type protein to become highly aggregation prone in vitro, although the mechanism by which this occurs remained elusive. Here, we identify the residues key to protecting β2m from aggregation by coupling aggregation with antibiotic resistance in E. coli using a tripartite β-lactamase assay (TPBLA). By performing saturation mutagenesis at three different sites (D53X-, D76X-, and D98X-β2m) we show that residue 76 has a unique ability to drive β2m aggregation in vivo and in vitro. Using a randomly mutated D76N-β2m variant library, we show that all of the mutations found to improve protein behavior involve residues in a single aggregation-prone region (APR) (residues 60 to 66). Surprisingly, no correlation was found between protein stability and protein aggregation rate or yield, with several mutations in the APR decreasing aggregation without affecting stability. Together, the results demonstrate the power of the TPBLA to develop proteins that are resilient to aggregation and suggest a model for D76N-β2m aggregation involving the formation of long-range couplings between the APR and Asn76 in a nonnative state.
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38
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Lövestam S, Koh FA, van Knippenberg B, Kotecha A, Murzin AG, Goedert M, Scheres SHW. Assembly of recombinant tau into filaments identical to those of Alzheimer's disease and chronic traumatic encephalopathy. eLife 2022; 11:e76494. [PMID: 35244536 PMCID: PMC8983045 DOI: 10.7554/elife.76494] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/03/2022] [Indexed: 11/22/2022] Open
Abstract
Abundant filamentous inclusions of tau are characteristic of more than 20 neurodegenerative diseases that are collectively termed tauopathies. Electron cryo-microscopy (cryo-EM) structures of tau amyloid filaments from human brain revealed that distinct tau folds characterise many different diseases. A lack of laboratory-based model systems to generate these structures has hampered efforts to uncover the molecular mechanisms that underlie tauopathies. Here, we report in vitro assembly conditions with recombinant tau that replicate the structures of filaments from both Alzheimer's disease (AD) and chronic traumatic encephalopathy (CTE), as determined by cryo-EM. Our results suggest that post-translational modifications of tau modulate filament assembly, and that previously observed additional densities in AD and CTE filaments may arise from the presence of inorganic salts, like phosphates and sodium chloride. In vitro assembly of tau into disease-relevant filaments will facilitate studies to determine their roles in different diseases, as well as the development of compounds that specifically bind to these structures or prevent their formation.
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Affiliation(s)
- Sofia Lövestam
- Medical Research Council Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | | | | | - Alexey G Murzin
- Medical Research Council Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Michel Goedert
- Medical Research Council Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Sjors HW Scheres
- Medical Research Council Laboratory of Molecular BiologyCambridgeUnited Kingdom
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39
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Berghaus N, Schreiner S, Granzow M, Müller-Tidow C, Hegenbart U, Schönland SO, Huhn S. Analysis of the complete lambda light chain germline usage in patients with AL amyloidosis and dominant heart or kidney involvement. PLoS One 2022; 17:e0264407. [PMID: 35213605 PMCID: PMC8880859 DOI: 10.1371/journal.pone.0264407] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/10/2022] [Indexed: 12/20/2022] Open
Abstract
Light chain amyloidosis is one of the most common forms of systemic amyloidosis. The disease is caused by the misfolding and aggregation of immunoglobulin light chains to insoluble fibrils. These fibrils can deposit in different tissues and organs such as heart and kidney and cause organ impairments that define the clinical presentation. In this study, we present an overview of IGLV-IGLJ and IGLC germline utilization in 85 patients classified in three clinically important subgroups with dominant cardiac, renal as well as cardiac and renal involvement. We found that IGLV3 was the most frequently detected IGLV-family in patients with dominant cardiac involvement, whereas in renal patients IGLV1 were most frequently identified. For patients with dominant heart and kidney involvement IGLV6 was the most frequently detected IGLV-family. In more detailed analysis IGLV3-21 was observed as the most dominant IGLV-subfamily for patients with dominant heart involvement and IGLV1-44 as the most frequent IGLV-subfamily in the group of patients with dominant kidney involvement. For patients with dominant heart and kidney involvement IGLV6-57 was the most frequently detected IGLV-subfamily. Additionally, we were able to show an exclusive linkage between IGLJ1 and IGLC1 as well as between IGLJ2 and IGLC2 in the fully assembled IGL mRNA.
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Affiliation(s)
- Natalie Berghaus
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Sarah Schreiner
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Granzow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Medical Department V, Heidelberg University Hospital, Heidelberg, Germany
- National Centre for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ute Hegenbart
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan O. Schönland
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefanie Huhn
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, Heidelberg, Germany
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40
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Louros N, van der Kant R, Schymkowitz J, Rousseau F. StAmP-DB: A platform for structures of polymorphic amyloid fibril cores. Bioinformatics 2022; 38:2636-2638. [PMID: 35199146 DOI: 10.1093/bioinformatics/btac126] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/20/2022] [Accepted: 02/22/2022] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Amyloid polymorphism is emerging as a key property that is differentially linked to various conformational diseases, including major neurodegenerative disorders, but also as a feature that potentially relates to complex structural mechanisms mediating transmissibility barriers and selective vulnerability of amyloids. In response to the rapidly expanding number of amyloid fibril structures formed by full-length proteins, we here have developed StAmP-DB, a public database that supports the curation and cross-comparison of experimentally determined three-dimensional amyloid polymorph structures. AVAILABILITY StAmP-DB is freely accessible for queries and downloads at https://stamp.switchlab.org.
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Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, Leuven, 3000, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Leuven, box 802, 3000, Belgium
| | - Rob van der Kant
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, Leuven, 3000, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Leuven, box 802, 3000, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, Leuven, 3000, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Leuven, box 802, 3000, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, Leuven, 3000, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Leuven, box 802, 3000, Belgium
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41
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Russo R, Romeo M, Schulte T, Maritan M, Oberti L, Barzago MM, Barbiroli A, Pappone C, Anastasia L, Palladini G, Diomede L, Ricagno S. Cu(II) Binding Increases the Soluble Toxicity of Amyloidogenic Light Chains. Int J Mol Sci 2022; 23:ijms23020950. [PMID: 35055136 PMCID: PMC8780072 DOI: 10.3390/ijms23020950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 11/16/2022] Open
Abstract
Light chain amyloidosis (AL) is caused by the aberrant overproduction of immunoglobulin light chains (LCs). The resulting abnormally high LC concentrations in blood lead to deposit formation in the heart and other target organs. Organ damage is caused not only by the accumulation of bulky amyloid deposits, but extensive clinical data indicate that circulating soluble LCs also exert cardiotoxic effects. The nematode C. elegans has been validated to recapitulate LC soluble toxicity in vivo, and in such a model a role for copper ions in increasing LC soluble toxicity has been reported. Here, we applied microscale thermophoresis, isothermal calorimetry and thermal melting to demonstrate the specific binding of Cu2+ to the variable domain of amyloidogenic H7 with a sub-micromolar affinity. Histidine residues present in the LC sequence are not involved in the binding, and yet their mutation to Ala reduces the soluble toxicity of H7. Copper ions bind to and destabilize the variable domains and induce a limited stabilization in this domain. In summary, the data reported here, elucidate the biochemical bases of the Cu2+-induced toxicity; moreover, they also show that copper binding is just one of the several biochemical traits contributing to LC soluble in vivo toxicity.
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Affiliation(s)
- Rosaria Russo
- Dipartimento di Fisiopatologia Medico-Chirurgica e Dei Trapianti, Università Degli Studi di Milano, 20090 Segrate, Italy;
| | - Margherita Romeo
- Dipartimento di Biochimica e Farmacologia Molecolare, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (M.R.); (M.M.B.)
| | - Tim Schulte
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; (T.S.); (C.P.); (L.A.)
| | - Martina Maritan
- Dipartimento di Bioscienze, Università Degli Studi di Milano, 20133 Milano, Italy; (M.M.); (L.O.)
| | - Luca Oberti
- Dipartimento di Bioscienze, Università Degli Studi di Milano, 20133 Milano, Italy; (M.M.); (L.O.)
| | - Maria Monica Barzago
- Dipartimento di Biochimica e Farmacologia Molecolare, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (M.R.); (M.M.B.)
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, La Nutrizione e L’Ambiente, Università Degli Studi di Milano, 20133 Milan, Italy;
| | - Carlo Pappone
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; (T.S.); (C.P.); (L.A.)
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, San Donato, 20097 Milan, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Luigi Anastasia
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; (T.S.); (C.P.); (L.A.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Giovanni Palladini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, 27100 Pavia, Italy;
| | - Luisa Diomede
- Dipartimento di Biochimica e Farmacologia Molecolare, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (M.R.); (M.M.B.)
- Correspondence: (L.D.); (S.R.)
| | - Stefano Ricagno
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; (T.S.); (C.P.); (L.A.)
- Dipartimento di Bioscienze, Università Degli Studi di Milano, 20133 Milano, Italy; (M.M.); (L.O.)
- Correspondence: (L.D.); (S.R.)
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42
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Lewkowicz E, Gursky O. Dynamic protein structures in normal function and pathologic misfolding in systemic amyloidosis. Biophys Chem 2022; 280:106699. [PMID: 34773861 PMCID: PMC9416430 DOI: 10.1016/j.bpc.2021.106699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 02/08/2023]
Abstract
Dynamic and disordered regions in native proteins are often critical for their function, particularly in ligand binding and signaling. In certain proteins, however, such regions can contribute to misfolding and pathologic deposition as amyloid fibrils in vivo. For example, dynamic and disordered regions can promote amyloid formation by destabilizing the native structure, by directly triggering the aggregation, by promoting protein condensation, or by acting as sites of early proteolytic cleavage that favor a release of aggregation-prone fragments or facilitate fibril maturation. At the same time, enhanced dynamics in the native protein state accelerates proteolytic degradation that counteracts amyloid accumulation in vivo. Therefore, the functional need for dynamic protein regions must be balanced against their inherently labile nature. How exactly this balance is achieved and how is it shifted upon amyloidogenic mutations or post-translational modifications? To illustrate possible scenarios, here we review the beneficial and pathologic roles of dynamic and disordered regions in the native states of three families of human plasma proteins that form amyloid precursors in systemic amyloidoses: immunoglobulin light chain, apolipoproteins, and serum amyloid A. Analysis of structure, stability and local dynamics of these diverse proteins and their amyloidogenic variants exemplifies how disordered/dynamic regions can provide a functional advantage as well as an Achilles heel in pathologic amyloid formation.
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Molecular Mechanisms of Cardiac Amyloidosis. Int J Mol Sci 2021; 23:ijms23010025. [PMID: 35008444 PMCID: PMC8744761 DOI: 10.3390/ijms23010025] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/18/2021] [Accepted: 12/18/2021] [Indexed: 12/22/2022] Open
Abstract
Cardiac involvement has a profound effect on the prognosis of patients with systemic amyloidosis. Therapeutic methods for suppressing the production of causative proteins have been developed for ATTR amyloidosis and AL amyloidosis, which show cardiac involvement, and the prognosis has been improved. However, a method for removing deposited amyloid has not been established. Methods for reducing cytotoxicity caused by amyloid deposition and amyloid precursor protein to protect cardiovascular cells are also needed. In this review, we outline the molecular mechanisms and treatments of cardiac amyloidosis.
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Ng YK, Tajoddin NN, Scrosati PM, Konermann L. Mechanism of Thermal Protein Aggregation: Experiments and Molecular Dynamics Simulations on the High-Temperature Behavior of Myoglobin. J Phys Chem B 2021; 125:13099-13110. [PMID: 34808050 DOI: 10.1021/acs.jpcb.1c07210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Proteins that encounter unfavorable solvent conditions are prone to aggregation, a phenomenon that remains poorly understood. This work focuses on myoglobin (Mb) as a model protein. Upon heating, Mb produces amorphous aggregates. Thermal unfolding experiments at low concentration (where aggregation is negligible), along with centrifugation assays, imply that Mb aggregation proceeds via globally unfolded conformers. This contrasts studies on other proteins that emphasized the role of partially folded structures as aggregate precursors. Molecular dynamics (MD) simulations were performed to gain insights into the mechanism by which heat-unfolded Mb molecules associate with one another. A prerequisite for these simulations was the development of a method for generating monomeric starting structures. Periodic boundary condition artifacts necessitated the implementation of a partially immobilized water layer lining the walls of the simulation box. Aggregation simulations were performed at 370 K to track the assembly of monomeric Mb into pentameric species. Binding events were preceded by multiple unsuccessful encounters. Even after association, protein-protein contacts remained in flux. Binding was mediated by hydrophobic contacts, along with salt bridges that involved hydrophobically embedded Lys residues. Overall, this work illustrates that atomistic MD simulations are well suited for garnering insights into protein aggregation mechanisms.
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Affiliation(s)
- Yuen Ki Ng
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Nastaran N Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Pablo M Scrosati
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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Iakovleva I, Hall M, Oelker M, Sandblad L, Anan I, Sauer-Eriksson AE. Structural basis for transthyretin amyloid formation in vitreous body of the eye. Nat Commun 2021; 12:7141. [PMID: 34880242 PMCID: PMC8654999 DOI: 10.1038/s41467-021-27481-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/18/2021] [Indexed: 11/26/2022] Open
Abstract
Amyloid transthyretin (ATTR) amyloidosis is characterized by the abnormal accumulation of ATTR fibrils in multiple organs. However, the structure of ATTR fibrils from the eye is poorly understood. Here, we used cryo-EM to structurally characterize vitreous body ATTR fibrils. These structures were distinct from previously characterized heart fibrils, even though both have the same mutation and type A pathology. Differences were observed at several structural levels: in both the number and arrangement of protofilaments, and the conformation of the protein fibril in each layer of protofilaments. Thus, our results show that ATTR protein structure and its assembly into protofilaments in the type A fibrils can vary between patients carrying the same mutation. By analyzing and matching the interfaces between the amino acids in the ATTR fibril with those in the natively folded TTR, we are able to propose a mechanism for the structural conversion of TTR into a fibrillar form.
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Affiliation(s)
- Irina Iakovleva
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden.
| | - Michael Hall
- grid.12650.300000 0001 1034 3451Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Melanie Oelker
- grid.12650.300000 0001 1034 3451Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Linda Sandblad
- grid.12650.300000 0001 1034 3451Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Intissar Anan
- grid.12650.300000 0001 1034 3451Department of Public Health and Clinical Medicine, Umeå University, SE-901 87 Umeå, Sweden ,grid.12650.300000 0001 1034 3451Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
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A Conservative Point Mutation in a Dynamic Antigen-binding Loop of Human Immunoglobulin λ6 Light Chain Promotes Pathologic Amyloid Formation. J Mol Biol 2021; 433:167310. [PMID: 34678302 DOI: 10.1016/j.jmb.2021.167310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 02/07/2023]
Abstract
Immunoglobulin light chain (LC) amyloidosis (AL) is a life-threatening human disease wherein free mono-clonal LCs deposit in vital organs. To determine what makes some LCs amyloidogenic, we explored patient-based amyloidogenic and non-amyloidogenic recombinant LCs from the λ6 subtype prevalent in AL. Hydrogen-deuterium exchange mass spectrometry, structural stability, proteolysis, and amyloid growth studies revealed that the antigen-binding CDR1 loop is the least protected part in the variable domain of λ6 LC, particularly in the AL variant. N32T substitution in CRD1 is identified as a driver of amyloid formation. Substitution N32T increased the amyloidogenic propensity of CDR1 loop, decreased its protection in the native structure, and accelerated amyloid growth in the context of other AL substitutions. The destabilizing effects of N32T propagated across the molecule increasing its dynamics in regions ∼30 Å away from the substitution site. Such striking long-range effects of a conservative point substitution in a dynamic surface loop may be relevant to Ig function. Comparison of patient-derived and engineered proteins showed that N32T interactions with other substitution sites must contribute to amyloidosis. The results suggest that CDR1 is critical in amyloid formation by other λ6 LCs.
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Schönfelder J, Pfeiffer PB, Pradhan T, Bijzet J, Hazenberg BPC, Schönland SO, Hegenbart U, Reif B, Haupt C, Fändrich M. Protease resistance of ex vivo amyloid fibrils implies the proteolytic selection of disease-associated fibril morphologies. Amyloid 2021; 28:243-251. [PMID: 34338090 DOI: 10.1080/13506129.2021.1960501] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Several studies recently showed that ex vivo fibrils from patient or animal tissue were structurally different from in vitro formed fibrils from the same polypeptide chain. Analysis of serum amyloid A (SAA) and Aβ-derived amyloid fibrils additionally revealed that ex vivo fibrils were more protease stable than in vitro fibrils. These observations gave rise to the proteolytic selection hypothesis that suggested that disease-associated amyloid fibrils were selected inside the body by their ability to resist endogenous clearance mechanisms. We here show, for more than twenty different fibril samples, that ex vivo fibrils are more protease stable than in vitro fibrils. These data support the idea of a proteolytic selection of pathogenic amyloid fibril morphologies and help to explain why only few amino acid sequences lead to amyloid diseases, although many, if not all, polypeptide chains can form amyloid fibrils in vitro.
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Affiliation(s)
| | | | - Tejaswini Pradhan
- Bayerisches NMR Zentrum at the Department Chemie, Technische Universität München, Garching, Germany
| | - Johan Bijzet
- Department of Rheumatology & Clinical Immunology, AA21, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bouke P C Hazenberg
- Department of Rheumatology & Clinical Immunology, AA21, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Stefan O Schönland
- Department of Internal Medicine V (Hematology, Oncology and Rheumatology), Amyloidosis Center, University Hospital Heidelberg, Heidelberg, Germany
| | - Ute Hegenbart
- Department of Internal Medicine V (Hematology, Oncology and Rheumatology), Amyloidosis Center, University Hospital Heidelberg, Heidelberg, Germany
| | - Bernd Reif
- Bayerisches NMR Zentrum at the Department Chemie, Technische Universität München, Garching, Germany
| | - Christian Haupt
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
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48
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Dissection of the amyloid formation pathway in AL amyloidosis. Nat Commun 2021; 12:6516. [PMID: 34764275 PMCID: PMC8585945 DOI: 10.1038/s41467-021-26845-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/25/2021] [Indexed: 11/18/2022] Open
Abstract
In antibody light chain (AL) amyloidosis, overproduced light chain (LC) fragments accumulate as fibrils in organs and tissues of patients. In vitro, AL fibril formation is a slow process, characterized by a pronounced lag phase. The events occurring during this lag phase are largely unknown. We have dissected the lag phase of a patient-derived LC truncation and identified structural transitions that precede fibril formation. The process starts with partial unfolding of the VL domain and the formation of small amounts of dimers. This is a prerequisite for the formation of an ensemble of oligomers, which are the precursors of fibrils. During oligomerization, the hydrophobic core of the LC domain rearranges which leads to changes in solvent accessibility and rigidity. Structural transitions from an anti-parallel to a parallel β-sheet secondary structure occur in the oligomers prior to amyloid formation. Together, our results reveal a rate-limiting multi-step mechanism of structural transitions prior to fibril formation in AL amyloidosis, which offers, in the long run, opportunities for therapeutic intervention. AL amyloidosis is caused by the accumulation of overproduced light chain (LC) fragments as fibrils in patient organs and it is the most prevalent systemic amyloidosis. Here, the authors combine biochemical and biophysical experiments to characterise the lag phase of a patient-derived truncated LC and they identify structural transitions that precede fibril formation.
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Radamaker L, Karimi-Farsijani S, Andreotti G, Baur J, Neumann M, Schreiner S, Berghaus N, Motika R, Haupt C, Walther P, Schmidt V, Huhn S, Hegenbart U, Schönland SO, Wiese S, Read C, Schmidt M, Fändrich M. Role of mutations and post-translational modifications in systemic AL amyloidosis studied by cryo-EM. Nat Commun 2021; 12:6434. [PMID: 34741031 PMCID: PMC8571268 DOI: 10.1038/s41467-021-26553-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/01/2021] [Indexed: 12/29/2022] Open
Abstract
Systemic AL amyloidosis is a rare disease that is caused by the misfolding of immunoglobulin light chains (LCs). Potential drivers of amyloid formation in this disease are post-translational modifications (PTMs) and the mutational changes that are inserted into the LCs by somatic hypermutation. Here we present the cryo electron microscopy (cryo-EM) structure of an ex vivo λ1-AL amyloid fibril whose deposits disrupt the ordered cardiomyocyte structure in the heart. The fibril protein contains six mutational changes compared to the germ line and three PTMs (disulfide bond, N-glycosylation and pyroglutamylation). Our data imply that the disulfide bond, glycosylation and mutational changes contribute to determining the fibril protein fold and help to generate a fibril morphology that is able to withstand proteolytic degradation inside the body.
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Affiliation(s)
- Lynn Radamaker
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | | | - Giada Andreotti
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Julian Baur
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | | | - Sarah Schreiner
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Natalie Berghaus
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Raoul Motika
- Department of Asia-Africa-Studies, Middle Eastern History and Culture, University of Hamburg, 20148, Hamburg, Germany
| | - Christian Haupt
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany
| | - Volker Schmidt
- Institute of Stochastics, Ulm University, 89081, Ulm, Germany
| | - Stefanie Huhn
- Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Ute Hegenbart
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Stefan O Schönland
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Clarissa Read
- Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany
- Institute of Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.
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50
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Morgan GJ. Transient disorder along pathways to amyloid. Biophys Chem 2021; 281:106711. [PMID: 34839162 DOI: 10.1016/j.bpc.2021.106711] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/15/2023]
Abstract
High-resolution structures of amyloid fibrils formed from normally-folded proteins have revealed non-native conformations of the polypeptide chains. Attaining these conformations apparently requires transition from the native state via a highly disordered conformation, in contrast to earlier models that posited a role for assembly of partially folded proteins. Modifications or interactions that extend the lifetime or constrain the conformations of these disordered states could act to enhance or suppress amyloid formation. Understanding how the properties of both the folded and transiently disordered structural ensembles influence the process of amyloid formation is a substantial challenge, but research into the properties of intrinsically disordered proteins will deliver important insights.
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Affiliation(s)
- Gareth J Morgan
- The Amyloidosis Center and Section of Hematology and Medical Oncology, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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