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RNA recognition motifs of disease-linked RNA-binding proteins contribute to amyloid formation. Sci Rep 2019; 9:6171. [PMID: 30992467 PMCID: PMC6467989 DOI: 10.1038/s41598-019-42367-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022] Open
Abstract
Aberrant expression, dysfunction and particularly aggregation of a group of RNA-binding proteins, including TDP-43, FUS and RBM45, are associated with neurological disorders. These three disease-linked RNA-binding proteins all contain at least one RNA recognition motif (RRM). However, it is not clear if these RRMs contribute to their aggregation-prone character. Here, we compare the biophysical and fibril formation properties of five RRMs from disease-linked RNA-binding proteins and five RRMs from non-disease-associated proteins to determine if disease-linked RRMs share specific features making them prone to self-assembly. We found that most of the disease-linked RRMs exhibit reversible thermal unfolding and refolding, and have a slightly lower average thermal melting point compared to that of normal RRMs. The full domain of TDP-43 RRM1 and FUS RRM, as well as the β-peptides from these two RRMs, could self-assemble into fibril-like aggregates which are amyloids of parallel β-sheets as verified by X-ray diffraction and FT-IR spectroscopy. Our results suggest that some disease-linked RRMs indeed play important roles in amyloid formation and shed light on why RNA-binding proteins with RRMs are frequently identified in the cellular inclusions of neurodegenerative diseases.
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Tobias F, Keiderling TA. Role of Side Chains in β-Sheet Self-Assembly into Peptide Fibrils. IR and VCD Spectroscopic Studies of Glutamic Acid-Containing Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:4653-61. [PMID: 27099990 DOI: 10.1021/acs.langmuir.6b00077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Poly(glutamic acid) at low pH self-assembles after incubation at higher temperature into fibrils composed of antiparallel sheets that are stacked in a β2-type structure whose amide carbonyls have bifurcated H-bonds involving the side chains from the next sheet. Oligomers of Glu can also form such structures, and isotope labeling has provided insight into their out-of-register antiparallel structure [ Biomacromolecules 2013 , 14 , 3880 - 3891 ]. In this paper we report IR and VCD spectra and transmission electron micrograph (TEM) images for a series of alternately sequenced oligomers, Lys-(Aaa-Glu)5-Lys-NH2, where Aaa was varied over a variety of polar, aliphatic, or aromatic residues. Their spectral and TEM data show that these oligopeptides self-assemble into different structures, both local and morphological, that are dependent on both the nature of the Aaa side chains and growth conditions employed. Such alternate peptides substituted with small or polar residues, Ala and Thr, do not yield fibrils; but with β-branched aliphatic residues, Val and Ile, that could potentially pack with Glu side chains, these oligopeptides do show evidence of β2-stacking. By contrast, for Leu, with longer side chains, only β1-stacking is seen while with even larger Phe side chains, either β-form can be detected separately, depending on preparation conditions. These structures are dependent on high temperature incubation after reducing the pH and in some cases after sonication of initial fibril forms and reincubation. Some of these fibrillar peptides, but not all, show enhanced VCD, which can offer evidence for formation of long, multistrand, often twisted structures. Substitution of Glu with residues having selected side chains yields a variety of morphologies, leading to both β1- and β2-structures, that overall suggests two different packing modes for the hydrophobic side chains depending on size and type.
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Affiliation(s)
- Fernando Tobias
- Department of Chemistry, University of Illinois at Chicago , 845 W. Taylor Street (m/c111), Chicago, Illinois 60607-7061, United States
| | - Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago , 845 W. Taylor Street (m/c111), Chicago, Illinois 60607-7061, United States
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Nabers A, Ollesch J, Schartner J, Kötting C, Genius J, Haußmann U, Klafki H, Wiltfang J, Gerwert K. An infrared sensor analysing label-free the secondary structure of the Abeta peptide in presence of complex fluids. JOURNAL OF BIOPHOTONICS 2016; 9:224-234. [PMID: 25808829 DOI: 10.1002/jbio.201400145] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/19/2015] [Accepted: 03/01/2015] [Indexed: 06/04/2023]
Abstract
The secondary structure change of the Abeta peptide to beta-sheet was proposed as an early event in Alzheimer's disease. The transition may be used for diagnostics of this disease in an early state. We present an Attenuated Total Reflection (ATR) sensor modified with a specific antibody to extract minute amounts of Abeta peptide out of a complex fluid. Thereby, the Abeta peptide secondary structure was determined in its physiological aqueous environment by FTIR-difference-spectroscopy. The presented results open the door for label-free Alzheimer diagnostics in cerebrospinal fluid or blood. It can be extended to further neurodegenerative diseases. An immunologic ATR-FTIR sensor for Abeta peptide secondary structure analysis in complex fluids is presented.
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Affiliation(s)
- Andreas Nabers
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Julian Ollesch
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Jonas Schartner
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Carsten Kötting
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Just Genius
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
| | - Ute Haußmann
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
| | - Hans Klafki
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
| | - Jens Wiltfang
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
- University Medical Center, Department of Psychiatry and Psychotherapy, Georg-August-University, 37073, Göttingen, Germany
| | - Klaus Gerwert
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany.
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Natalello A, Mangione PP, Giorgetti S, Porcari R, Marchese L, Zorzoli I, Relini A, Ami D, Faravelli G, Valli M, Stoppini M, Doglia SM, Bellotti V, Raimondi S. Co-fibrillogenesis of Wild-type and D76N β2-Microglobulin: THE CRUCIAL ROLE OF FIBRILLAR SEEDS. J Biol Chem 2016; 291:9678-89. [PMID: 26921323 PMCID: PMC4850305 DOI: 10.1074/jbc.m116.720573] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Indexed: 11/28/2022] Open
Abstract
The amyloidogenic variant of β2-microglobulin, D76N, can readily convert into genuine fibrils under physiological conditions and primes in vitro the fibrillogenesis of the wild-type β2-microglobulin. By Fourier transformed infrared spectroscopy, we have demonstrated that the amyloid transformation of wild-type β2-microglobulin can be induced by the variant only after its complete fibrillar conversion. Our current findings are consistent with preliminary data in which we have shown a seeding effect of fibrils formed from D76N or the natural truncated form of β2-microglobulin lacking the first six N-terminal residues. Interestingly, the hybrid wild-type/variant fibrillar material acquired a thermodynamic stability similar to that of homogenous D76N β2-microglobulin fibrils and significantly higher than the wild-type homogeneous fibrils prepared at neutral pH in the presence of 20% trifluoroethanol. These results suggest that the surface of D76N β2-microglobulin fibrils can favor the transition of the wild-type protein into an amyloid conformation leading to a rapid integration into fibrils. The chaperone crystallin, which is a mild modulator of the lag phase of the variant fibrillogenesis, potently inhibits fibril elongation of the wild-type even once it is absorbed on D76N β2-microglobulin fibrils.
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Affiliation(s)
- Antonino Natalello
- From the Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, the Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR Milano-Bicocca, 20126 Milan, Italy
| | - P Patrizia Mangione
- the Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London NW3 2PF, United Kingdom, the Departments of Molecular Medicine, Institute of Biochemistry, and
| | - Sofia Giorgetti
- the Departments of Molecular Medicine, Institute of Biochemistry, and
| | - Riccardo Porcari
- the Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London NW3 2PF, United Kingdom
| | - Loredana Marchese
- the Departments of Molecular Medicine, Institute of Biochemistry, and
| | - Irene Zorzoli
- the Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, Italy, and
| | - Annalisa Relini
- the Department of Physics, University of Genoa, 16146 Genoa, Italy
| | - Diletta Ami
- From the Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, the Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR Milano-Bicocca, 20126 Milan, Italy
| | - Giulia Faravelli
- the Departments of Molecular Medicine, Institute of Biochemistry, and
| | - Maurizia Valli
- the Departments of Molecular Medicine, Institute of Biochemistry, and
| | - Monica Stoppini
- the Departments of Molecular Medicine, Institute of Biochemistry, and
| | - Silvia M Doglia
- From the Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, the Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR Milano-Bicocca, 20126 Milan, Italy
| | - Vittorio Bellotti
- the Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London NW3 2PF, United Kingdom, the Departments of Molecular Medicine, Institute of Biochemistry, and
| | - Sara Raimondi
- the Departments of Molecular Medicine, Institute of Biochemistry, and
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Wild type beta-2 microglobulin and DE loop mutants display a common fibrillar architecture. PLoS One 2015; 10:e0122449. [PMID: 25803608 PMCID: PMC4372401 DOI: 10.1371/journal.pone.0122449] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/15/2015] [Indexed: 12/14/2022] Open
Abstract
Beta-2 microglobulin (β2m) is the protein responsible for a pathologic condition known as dialysis related amyloidosis. In recent years an important role has been assigned to the peptide loop linking strands D and E (DE loop) in determining β2m stability and amyloid propensity. Several mutants of the DE loop have been studied, showing a good correlation between DE loop geometrical strain, protein stability and aggregation propensity. However, it remains unclear whether the aggregates formed by wild type (wt) β2m and by the DE loop variants are of the same kind, or whether the mutations open new aggregation pathways. In order to address this question, fibrillar samples of wt and mutated β2m variants have been analysed by means of atomic force microscopy and infrared spectroscopy. The data here reported indicate that the DE loop mutants form aggregates with morphology and structural organisation very similar to the wt protein. Therefore, the main effect of β2m DE loop mutations is proposed to stem from the different stabilities of the native fold. Considerations on the structural role of the DE loop in the free monomeric β2m and as part of the Major Histocompatibility Complex are also presented.
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Abstract
β2-Microglobulin is responsible for systemic amyloidosis affecting patients undergoing long-term hemodialysis. Its genetic variant D76N causes a very rare form of familial systemic amyloidosis. These two types of amyloidoses differ significantly in terms of the tissue localization of deposits and for major pathological features. Considering how the amyloidogenesis of the β2-microglobulin mechanism has been scrutinized in depth for the last three decades, the comparative analysis of molecular and pathological properties of wild type β2-microglobulin and of the D76N variant offers a unique opportunity to critically reconsider the current understanding of the relation between the protein's structural properties and its pathologic behavior.
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Affiliation(s)
- Monica Stoppini
- From the Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, 27100 Pavia, Italy and
| | - Vittorio Bellotti
- From the Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, 27100 Pavia, Italy and the Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London NW3 2PF, United Kingdom
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