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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Goto Y, Nakajima K, Yamamoto S, Yamaguchi K. Supersaturation, a Critical Factor Underlying Proteostasis of Amyloid Fibril Formation. J Mol Biol 2024; 436:168475. [PMID: 38311232 DOI: 10.1016/j.jmb.2024.168475] [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: 10/03/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
From a physicochemical viewpoint, amyloid fibril formation is a phase transition from soluble to crystal-like sates limited by supersaturation. It occurs only above solubility (i.e., the solubility limit) coupled with a breakdown of supersaturation. Although many studies have examined the role of molecular chaperones in the context of proteostasis, the role of supersaturation has not been addressed. Moreover, although molecular chaperone-dependent disaggregations have been reported for preformed amyloid fibrils, amyloid fibrils will not dissolve above the solubility of monomers, even if agitations fragment long fibrils to shorter amyloid particles. On the other hand, on considering a reversible and coupled equilibrium of interactions, folding/unfolding and amyloid formation/disaggregation, molecules stabilizing native states can work as a disaggregase reversing the amyloid fibrils to monomers. It is likely that the proteostasis network has various intra- and extracellular components which disaggregate preformed amyloid fibrils as well as prevent amyloid formation. Further studies with a view of solubility and supersaturation will be essential for comprehensive understanding of proteostasis.
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Affiliation(s)
- Yuji Goto
- Microsonochemistry Joint Research Chair, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Kichitaro Nakajima
- Microsonochemistry Joint Research Chair, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Suguru Yamamoto
- Division of Clinical Nephrology and Rheumatology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Keiichi Yamaguchi
- Microsonochemistry Joint Research Chair, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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4
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Yamamoto S, Yamamoto K, Hirao Y, Yamaguchi K, Nakajima K, Sato M, Kawachi M, Domon M, Goto K, Omori K, Iino N, Shimada H, Aoyagi R, Ei I, Goto S, Goto Y, Gejyo F, Yamamoto T, Narita I. Mass spectrometry-based proteomic analysis of proteins adsorbed by hexadecyl-immobilized cellulose bead column for the treatment of dialysis-related amyloidosis. Amyloid 2024; 31:105-115. [PMID: 38343068 DOI: 10.1080/13506129.2024.2315148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND Dialysis-related amyloidosis (DRA) is a severe complication in end-stage kidney disease (ESKD) patients undergoing long-term dialysis treatment, characterized by the deposition of β2-microglobulin-related amyloids (Aβ2M amyloid). To inhibit DRA progression, hexadecyl-immobilized cellulose bead (HICB) columns are employed to adsorb circulating β2-microglobulin (β2M). However, it is possible that the HICB also adsorbs other molecules involved in amyloidogenesis. METHODS We enrolled 14 ESKD patients using HICB columns for DRA treatment; proteins were extracted from HICBs following treatment and identified using liquid chromatography-linked mass spectrometry. We measured the removal rate of these proteins and examined the effect of those molecules on Aβ2M amyloid fibril formation in vitro. RESULTS We identified 200 proteins adsorbed by HICBs. Of these, 21 were also detected in the amyloid deposits in the carpal tunnels of patients with DRA. After passing through the HICB column and hemodialyzer, the serum levels of proteins such as β2M, lysozyme, angiogenin, complement factor D and matrix Gla protein were reduced. These proteins acted in the Aβ2M amyloid fibril formation. CONCLUSIONS HICBs adsorbed diverse proteins in ESKD patients with DRA, including those detected in amyloid lesions. Direct hemoperfusion utilizing HICBs may play a role in acting Aβ2M amyloidogenesis by reducing the amyloid-related proteins.
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Affiliation(s)
- Suguru Yamamoto
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker Center, Niigata University, Niigata, Japan
| | - Yoshitoshi Hirao
- Instrumental Analysis Section, Okinawa Institute of Science and Technology, Onna, Japan
| | | | | | - Mami Sato
- Sakelogy Center, Niigata University, Niigata, Japan
| | - Miho Kawachi
- Division of Clinical Chemistry, Niigata University Graduate School of Health Sciences, Niigata, Japan
| | - Mio Domon
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kei Goto
- Division of Nephrology, Agano Municipal Hospital, Niigata, Japan
| | | | - Noriaki Iino
- Division of Nephrology, Uonuma Kikan Hospital, Niigata, Japan
| | | | - Ryuzi Aoyagi
- Department of Nephrology, Tachikawa General Hospital, Niigata, Japan
| | - Isei Ei
- Santo-Second Clinic, Niigata, Japan
| | - Shin Goto
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yuji Goto
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Fumitake Gejyo
- Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Niigata University, Niigata, Japan
- Department of Clinical Laboratory, Shinrakuen Hospital, Niigata, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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5
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Oliyantakath Hassan MS, Abdul Vahid A, Sahayaraj AE, Viswanathan R, Vijayan V. NMR Relaxation Experiments Probe Monomer-Fibril Interaction and Identify Critical Interacting Residues Responsible for Distinct Tau Fibril Morphologies. J Phys Chem Lett 2023; 14:6583-6591. [PMID: 37458827 DOI: 10.1021/acs.jpclett.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Tau aggregation is governed by secondary processes, a major pathological pathway for tau protein fibril propagation, yet its molecular mechanism remains unknown. This work uses saturation transfer and lifetime line-broadening experiments to identify the critical residues involved in these secondary processes. Distinct residue-specific NMR relaxation parameters were obtained for the truncated three repeat tau construct (K19) in equilibrium with structurally different, self-aggregated (saK19) or heparin-induced (hK19) fibrils. The interacting residues are restricted to R3 repeat for hK19 and to R3, R4, and R' repeats for saK19 fibrils. Furthermore, the relaxation profiles of tau monomers in equilibrium with the structurally comparable, in vitro pathological fibrils (tauAD and tauCTE) were similar but distinct from hK19 or saK19 fibrils. Thus, residue-specific relaxation identifies the important residues involved in the binding of monomers to the fibrils. The relaxation profile of the monomers in equilibrium with the NMR invisible fibril seeds potentially distinguishes the distinct structures of tau fibrils.
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Affiliation(s)
| | - Arshad Abdul Vahid
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Allwin Ebenezer Sahayaraj
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Renjith Viswanathan
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Vinesh Vijayan
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, Kerala 695551, India
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6
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Maya-Martinez R, Xu Y, Guthertz N, Walko M, Karamanos TK, Sobott F, Breeze AL, Radford SE. Dimers of D76N-β 2-microglobulin display potent antiamyloid aggregation activity. J Biol Chem 2022; 298:102659. [PMID: 36328246 PMCID: PMC9712992 DOI: 10.1016/j.jbc.2022.102659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/05/2022] Open
Abstract
Self-association of WT β2-microglobulin (WT-β2m) into amyloid fibrils is associated with the disorder dialysis related amyloidosis. In the familial variant D76N-β2m, the single amino acid substitution enhances the aggregation propensity of the protein dramatically and gives rise to a disorder that is independent of renal dysfunction. Numerous biophysical and structural studies on WT- and D76N-β2m have been performed in order to better understand the structure and dynamics of the native proteins and their different potentials to aggregate into amyloid. However, the structural properties of transient D76N-β2m oligomers and their role(s) in assembly remained uncharted. Here, we have utilized NMR methods, combined with photo-induced crosslinking, to detect, trap, and structurally characterize transient dimers of D76N-β2m. We show that the crosslinked D76N-β2m dimers have different structures from those previously characterized for the on-pathway dimers of ΔN6-β2m and are unable to assemble into amyloid. Instead, the crosslinked D76N-β2m dimers are potent inhibitors of amyloid formation, preventing primary nucleation and elongation/secondary nucleation when added in substoichiometric amounts with D76N-β2m monomers. The results highlight the specificity of early protein-protein interactions in amyloid formation and show how mapping these interfaces can inform new strategies to inhibit amyloid assembly.
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Affiliation(s)
- Roberto Maya-Martinez
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
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7
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Nakajima K, Yamaguchi K, Noji M, Aguirre C, Ikenaka K, Mochizuki H, Zhou L, Ogi H, Ito T, Narita I, Gejyo F, Naiki H, Yamamoto S, Goto Y. Macromolecular crowding and supersaturation protect hemodialysis patients from the onset of dialysis-related amyloidosis. Nat Commun 2022; 13:5689. [PMID: 36192385 PMCID: PMC9530240 DOI: 10.1038/s41467-022-33247-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 09/08/2022] [Indexed: 11/09/2022] Open
Abstract
Dialysis-related amyloidosis (DRA), a serious complication among long-term hemodialysis patients, is caused by amyloid fibrils of β2-microglobulin (β2m). Although high serum β2m levels and a long dialysis vintage are the primary and secondary risk factors for the onset of DRA, respectively, patients with these do not always develop DRA, indicating that there are additional risk factors. To clarify these unknown factors, we investigate the effects of human sera on β2m amyloid fibril formation, revealing that sera markedly inhibit amyloid fibril formation. Results from over 100 sera indicate that, although the inhibitory effects of sera deteriorate in long-term dialysis patients, they are ameliorated by maintenance dialysis treatments in the short term. Serum albumin prevents amyloid fibril formation based on macromolecular crowding effects, and decreased serum albumin concentration in dialysis patients is a tertiary risk factor for the onset of DRA. We construct a theoretical model assuming cumulative effects of the three risk factors, suggesting the importance of monitoring temporary and accumulated risks to prevent the development of amyloidosis, which occurs based on supersaturation-limited amyloid fibril formation in a crowded milieu.
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Affiliation(s)
- Kichitaro Nakajima
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, 565-0871, Japan.,Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Keiichi Yamaguchi
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, 565-0871, Japan.,Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masahiro Noji
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshidahonmatsu-cho, Sakyo-ku, Kyoto, 606-8316, Japan
| | - César Aguirre
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kensuke Ikenaka
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Lianjie Zhou
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hirotsugu Ogi
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Toru Ito
- Division of Clinical Nephrology and Rheumatology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, 951-8510, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, 951-8510, Japan
| | - Fumitake Gejyo
- Niigata University of Pharmacy and Applied Life Sciences, Niigata, 956-8603, Japan
| | - Hironobu Naiki
- Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Suguru Yamamoto
- Division of Clinical Nephrology and Rheumatology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, 951-8510, Japan.
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, 565-0871, Japan. .,Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
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8
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Supersaturation-Dependent Formation of Amyloid Fibrils. Molecules 2022; 27:molecules27144588. [PMID: 35889461 PMCID: PMC9321232 DOI: 10.3390/molecules27144588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 01/27/2023] Open
Abstract
The supersaturation of a solution refers to a non-equilibrium phase in which the solution is trapped in a soluble state, even though the solute’s concentration is greater than its thermodynamic solubility. Upon breaking supersaturation, crystals form and the concentration of the solute decreases to its thermodynamic solubility. Soon after the discovery of the prion phenomena, it was recognized that prion disease transmission and propagation share some similarities with the process of crystallization. Subsequent studies exploring the structural and functional association between amyloid fibrils and amyloidoses solidified this paradigm. However, recent studies have not necessarily focused on supersaturation, possibly because of marked advancements in structural studies clarifying the atomic structures of amyloid fibrils. On the other hand, there is increasing evidence that supersaturation plays a critical role in the formation of amyloid fibrils and the onset of amyloidosis. Here, we review the recent evidence that supersaturation plays a role in linking unfolding/folding and amyloid fibril formation. We also introduce the HANABI (HANdai Amyloid Burst Inducer) system, which enables high-throughput analysis of amyloid fibril formation by the ultrasonication-triggered breakdown of supersaturation. In addition to structural studies, studies based on solubility and supersaturation are essential both to developing a comprehensive understanding of amyloid fibrils and their roles in amyloidosis, and to developing therapeutic strategies.
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9
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Karamanos TK, Kalverda AP, Radford SE. Generating Ensembles of Dynamic Misfolding Proteins. Front Neurosci 2022; 16:881534. [PMID: 35431773 PMCID: PMC9008329 DOI: 10.3389/fnins.2022.881534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/08/2022] [Indexed: 01/09/2023] Open
Abstract
The early stages of protein misfolding and aggregation involve disordered and partially folded protein conformers that contain a high degree of dynamic disorder. These dynamic species may undergo large-scale intra-molecular motions of intrinsically disordered protein (IDP) precursors, or flexible, low affinity inter-molecular binding in oligomeric assemblies. In both cases, generating atomic level visualization of the interconverting species that captures the conformations explored and their physico-chemical properties remains hugely challenging. How specific sub-ensembles of conformers that are on-pathway to aggregation into amyloid can be identified from their aggregation-resilient counterparts within these large heterogenous pools of rapidly moving molecules represents an additional level of complexity. Here, we describe current experimental and computational approaches designed to capture the dynamic nature of the early stages of protein misfolding and aggregation, and discuss potential challenges in describing these species because of the ensemble averaging of experimental restraints that arise from motions on the millisecond timescale. We give a perspective of how machine learning methods can be used to extract aggregation-relevant sub-ensembles and provide two examples of such an approach in which specific interactions of defined species within the dynamic ensembles of α-synuclein (αSyn) and β2-microgloblulin (β2m) can be captured and investigated.
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Affiliation(s)
- Theodoros K. Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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10
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Dang H, Chen Z, Chen W, Luo X, Liu P, Wang L, Chen J, Tang X, Wang Z, Liang Y. The residues 4 to 6 at the N-terminus in particular modulate fibril propagation of β-microglobulin. Acta Biochim Biophys Sin (Shanghai) 2021; 54:187-198. [PMID: 35130623 PMCID: PMC9909321 DOI: 10.3724/abbs.2021017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The ΔN6 truncation is the main posttranslational modification of β-microglobulin (βM) found in dialysis-related amyloid. Investigation of the interaction of wild-type (WT) βM with N-terminally truncated variants is therefore of medical relevance. However, it is unclear which residues among the six residues at the N-terminus are crucial to the interactions and the modulation of amyloid fibril propagation of βM. We herein analyzed homo- and heterotypic seeding of amyloid fibrils of WT human βM and its N-terminally-truncated variants ΔN1 to ΔN6, lacking up to six residues at the N-terminus. At acidic pH 2.5, we produced amyloid fibrils from recombinant, WT βM and its six truncated variants, and found that ΔN6 βM fibrils exhibit a significantly lower conformational stability than WT βM fibrils. Importantly, under more physiological conditions (pH 6.2), we assembled amyloid fibrils only from recombinant, ΔN4, ΔN5, and ΔN6 βM but not from WT βM and its three truncated variants ΔN1 to ΔN3. Notably, the removal of the six, five or four residues at the N-terminus leads to enhanced fibril formation, and homo- and heterotypic seeding of ΔN6 fibrils strongly promotes amyloid fibril formation of WT βM and its six truncated variants, including at more physiological pH 6.2. Collectively, these results demonstrated that the residues 4 to 6 at the N-terminus particularly modulate amyloid fibril propagation of βM and the interactions of WT βM with N-terminally truncated variants, potentially indicating the direct relevance to the involvement of the protein's aggregation in dialysis-related amyloidosis.
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Affiliation(s)
- Haibin Dang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Zhixian Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Wang Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Xudong Luo
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | | | - Liqiang Wang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Jie Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | | | | | - Yi Liang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China,Correspondence address. Tel: +86-27-68754902; E-mail:
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11
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Good SC, Dewison KM, Radford SE, van Oosten-Hawle P. Global Proteotoxicity Caused by Human β 2 Microglobulin Variants Impairs the Unfolded Protein Response in C. elegans. Int J Mol Sci 2021; 22:10752. [PMID: 34639093 PMCID: PMC8509642 DOI: 10.3390/ijms221910752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
Aggregation of β2 microglobulin (β2m) into amyloid fibrils is associated with systemic amyloidosis, caused by the deposition of amyloid fibrils containing the wild-type protein and its truncated variant, ΔN6 β2m, in haemo-dialysed patients. A second form of familial systemic amyloidosis caused by the β2m variant, D76N, results in amyloid deposits in the viscera, without renal dysfunction. Although the folding and misfolding mechanisms of β2 microglobulin have been widely studied in vitro and in vivo, we lack a comparable understanding of the molecular mechanisms underlying toxicity in a cellular and organismal environment. Here, we established transgenic C. elegans lines expressing wild-type (WT) human β2m, or the two highly amyloidogenic naturally occurring variants, D76N β2m and ΔN6 β2m, in the C. elegans bodywall muscle. Nematodes expressing the D76N β2m and ΔN6 β2m variants exhibit increased age-dependent and cell nonautonomous proteotoxicity associated with reduced motility, delayed development and shortened lifespan. Both β2m variants cause widespread endogenous protein aggregation contributing to the increased toxicity in aged animals. We show that expression of β2m reduces the capacity of C. elegans to cope with heat and endoplasmic reticulum (ER) stress, correlating with a deficiency to upregulate BiP/hsp-4 transcripts in response to ER stress in young adult animals. Interestingly, protein secretion in all β2m variants is reduced, despite the presence of the natural signal sequence, suggesting a possible link between organismal β2m toxicity and a disrupted ER secretory metabolism.
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Affiliation(s)
| | | | | | - Patricija van Oosten-Hawle
- Faculty of Biological Sciences, School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (S.C.G.); (K.M.D.); (S.E.R.)
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12
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Oliyantakath Hassan MS, Somasundaran SM, Abdul Shukkoor MB, Ayyappan S, Abdul Vahid A, Vijayan V. Examining the Transient Dark State in Protein-Quantum Dot Interaction by Relaxation-Based Solution NMR. J Phys Chem B 2021; 125:10119-10125. [PMID: 34473517 DOI: 10.1021/acs.jpcb.1c04853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We probed the "dark" state involved in the protein-quantum dot (QD) interaction using a relaxation-based solution nuclear magnetic resonance (NMR) approach. We examined the dynamics and exchange kinetics of the ubiquitin-CdTe model system, which undergoes a fast exchange in the transverse relaxation time scale. We applied the recently developed dark-state exchange saturation transfer (DEST), lifetime line broadening (ΔR2), and exchange-induced chemical shift (δex) solution NMR techniques to obtain a residue-specific binding behavior of the protein on the QD surface. The variation in the estimated 15N-R2bound values clearly shows the dynamic nature of bound Ub. Upon mapping the amino acid residues showing a faster relaxation rate on the electrostatic potential surface of the protein, we have determined that the interaction is preferably electrostatic, and the amino acid residues involved in binding lie on the positively charged surface of the protein. We believe that our experimental approach should provide more in-depth knowledge to engineer new hybrid protein-QD systems in the future.
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Affiliation(s)
| | - Sanoop Mambully Somasundaran
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala P.O, Vithura, Thiruvananthapuram, Kerala 695551, India
| | | | - Shine Ayyappan
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala P.O, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Arshad Abdul Vahid
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala P.O, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Vinesh Vijayan
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala P.O, Vithura, Thiruvananthapuram, Kerala 695551, India
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13
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Zhu H, Gu D, Rao Z, Li Y, Liu Y, Hao J. Design of gel-to-sol UCST transition peptides by controlling polypeptide β-sheet nanostructures. Polym J 2021. [DOI: 10.1038/s41428-021-00490-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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14
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Cornwell O, Ault JR, Bond NJ, Radford SE, Ashcroft AE. Investigation of D76N β 2-Microglobulin Using Protein Footprinting and Structural Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1583-1592. [PMID: 33586970 PMCID: PMC9282677 DOI: 10.1021/jasms.0c00438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
NMR studies and X-ray crystallography have shown that the structures of the 99-residue amyloidogenic protein β2-microglobulin (β2m) and its more aggregation-prone variant, D76N, are indistinguishable, and hence, the reason for the striking difference in their aggregation propensities remains elusive. Here, we have employed two protein footprinting methods, hydrogen-deuterium exchange (HDX) and fast photochemical oxidation of proteins (FPOP), in conjunction with ion mobility-mass spectrometry, to probe the differences in conformational dynamics of the two proteins. Using HDX-MS, a clear difference in HDX protection is observed between these two proteins in the E-F loop (residues 70-77) which contains the D76N substitution, with a significantly higher deuterium uptake being observed in the variant protein. Conversely, following FPOP-MS only minimal differences in the level of oxidation between the two proteins are observed in the E-F loop region, suggesting only modest side-chain movements in that area. Together the HDX-MS and FPOP-MS data suggest that a tangible perturbation to the hydrogen-bonding network in the E-F loop has taken place in the D76N variant and furthermore illustrate the benefit of using multiple complementary footprinting methods to address subtle, but possibly biologically important, differences between highly similar proteins.
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Affiliation(s)
- Owen Cornwell
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - James R. Ault
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Nicholas J. Bond
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Alison E. Ashcroft
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
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15
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NMR unveils an N-terminal interaction interface on acetylated-α-synuclein monomers for recruitment to fibrils. Proc Natl Acad Sci U S A 2021; 118:2017452118. [PMID: 33903234 DOI: 10.1073/pnas.2017452118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Amyloid fibril formation of α-synuclein (αS) is associated with multiple neurodegenerative diseases, including Parkinson's disease (PD). Growing evidence suggests that progression of PD is linked to cell-to-cell propagation of αS fibrils, which leads to seeding of endogenous intrinsically disordered monomer via templated elongation and secondary nucleation. A molecular understanding of the seeding mechanism and driving interactions is crucial to inhibit progression of amyloid formation. Here, using relaxation-based solution NMR experiments designed to probe large complexes, we probe weak interactions of intrinsically disordered acetylated-αS (Ac-αS) monomers with seeding-competent Ac-αS fibrils and seeding-incompetent off-pathway oligomers to identify Ac-αS monomer residues at the binding interface. Under conditions that favor fibril elongation, we determine that the first 11 N-terminal residues on the monomer form a common binding site for both fibrils and off-pathway oligomers. Additionally, the presence of off-pathway oligomers within a fibril seeding environment suppresses seeded amyloid formation, as observed through thioflavin-T fluorescence experiments. This highlights that off-pathway αS oligomers can act as an auto-inhibitor against αS fibril elongation. Based on these data taken together with previous results, we propose a model in which Ac-αS monomer recruitment to the fibril is driven by interactions between the intrinsically disordered monomer N terminus and the intrinsically disordered flanking regions (IDR) on the fibril surface. We suggest that this monomer recruitment may play a role in the elongation of amyloid fibrils and highlight the potential of the IDRs of the fibril as important therapeutic targets against seeded amyloid formation.
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