201
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Ragonis-Bachar P, Landau M. Functional and pathological amyloid structures in the eyes of 2020 cryo-EM. Curr Opin Struct Biol 2021; 68:184-193. [PMID: 33631463 DOI: 10.1016/j.sbi.2021.01.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/16/2021] [Accepted: 01/18/2021] [Indexed: 12/18/2022]
Abstract
The amyloid state of protein aggregation is associated with neurodegenerative and systemic diseases but can play physiological roles in many organisms, including as stress granules and virulence determinants. The recent resolution revolution in cryogenic electron microscopy (cryo-EM) has significantly expanded the repertoire of high-resolution amyloid structures, to include, for the first-time, fibrils extracted ex vivo in addition to those formed, or seeded, in vitro. Here, we review recently solved cryo-EM amyloid structures, and compare amino acid prevalence, in efforts to systematically distinguish between pathological and functional amyloids, even though such structural classification is hindered by extensive polymorphism even among fibrils of the same protein, and by dual functioning of some human amyloids in both physiological activities and disease mechanisms. Forthcoming structures of bacterial amyloids may expose specific, evolutionary-designed properties specific to functional fibrils.
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Affiliation(s)
- Peleg Ragonis-Bachar
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany.
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202
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Jarmuła A, Ludwiczak J, Stępkowski D. β-sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β-amyloid fibrils. Proteins 2021; 89:762-780. [PMID: 33550630 DOI: 10.1002/prot.26057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/28/2020] [Accepted: 01/31/2021] [Indexed: 12/27/2022]
Abstract
β-sheet breakers (BSB) constitute a class of peptide inhibitors of amyloidogenesis, a process which is a hallmark of many diseases called amyloidoses, including Alzheimer's disease (AD); however, the molecular details of their action are still not fully understood. Here we describe the results of the computational investigation of the three BSBs, iaβ6 (LPFFFD), iaβ5 (LPFFD), and iaβ6_Gly (LPFGFD), in complex with the fibril model of Aβ42 and propose the kinetically probable mechanism of their action. The mechanism involves the binding of BSB to the central hydrophobic core (CHC) region (LVFFA) of Aβ fibril and the π-stacking of its Phe rings both internally and with the Aβ fibril. In the process, the Aβ fibril undergoes distortion accumulating on the side of chain A (located on the odd tip of the fibril). In a single replica of extended molecular dynamics run of one of the iaβ6 poses, the distortion concludes in a dissociation of chain A from the fibril model of Aβ42. Altogether, we postulate that including consecutive Phe residues into BSBs docked around Phe 20 in the CHC region of Aβ42 improve their potency for dissolution of fibrils.
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Affiliation(s)
- Adam Jarmuła
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology PAS, Warszawa, Poland
| | - Jan Ludwiczak
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology PAS, Warszawa, Poland.,Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warszawa, Poland
| | - Dariusz Stępkowski
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology PAS, Warszawa, Poland
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203
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Protofibril–Fibril Interactions Inhibit Amyloid Fibril Assembly by Obstructing Secondary Nucleation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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204
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Hasecke F, Niyangoda C, Borjas G, Pan J, Matthews G, Muschol M, Hoyer W. Protofibril-Fibril Interactions Inhibit Amyloid Fibril Assembly by Obstructing Secondary Nucleation. Angew Chem Int Ed Engl 2021; 60:3016-3021. [PMID: 33095508 PMCID: PMC7898819 DOI: 10.1002/anie.202010098] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/16/2020] [Indexed: 12/29/2022]
Abstract
Amyloid-β peptides (Aβ) assemble into both rigid amyloid fibrils and metastable oligomers termed AβO or protofibrils. In Alzheimer's disease, Aβ fibrils constitute the core of senile plaques, but Aβ protofibrils may represent the main toxic species. Aβ protofibrils accumulate at the exterior of senile plaques, yet the protofibril-fibril interplay is not well understood. Applying chemical kinetics and atomic force microscopy to the assembly of Aβ and lysozyme, protofibrils are observed to bind to the lateral surfaces of amyloid fibrils. When utilizing Aβ variants with different critical oligomer concentrations, the interaction inhibits the autocatalytic proliferation of amyloid fibrils by secondary nucleation on the fibril surface. Thus, metastable oligomers antagonize their replacement by amyloid fibrils both by competing for monomers and blocking secondary nucleation sites. The protofibril-fibril interaction governs their temporal evolution and potential to exert specific toxic activities.
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Affiliation(s)
- Filip Hasecke
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40204DüsseldorfGermany
| | | | - Gustavo Borjas
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | - Jianjun Pan
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | | | - Martin Muschol
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | - Wolfgang Hoyer
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40204DüsseldorfGermany
- Strukturbiochemie (IBI-7)Forschungszentrum Jülich52425JülichGermany
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205
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Yoon A, Zhen J, Guo Z. Segmental structural dynamics in Aβ42 globulomers. Biochem Biophys Res Commun 2021; 545:119-124. [PMID: 33548624 DOI: 10.1016/j.bbrc.2021.01.081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/23/2021] [Indexed: 02/06/2023]
Abstract
Aβ42 aggregation plays a central role in the pathogenesis of Alzheimer's disease. In addition to the insoluble fibrils that comprise the amyloid plaques, Aβ42 also forms soluble aggregates collectively called oligomers, which are more toxic and pathogenic than fibrils. Understanding the structure and dynamics of Aβ42 oligomers is critical for developing effective therapeutic interventions against these oligomers. Here we studied the structural dynamics of Aβ42 globulomers, a type of Aβ42 oligomers prepared in the presence of sodium dodecyl sulfate, using site-directed spin labeling. Spin labels were introduced, one at a time, at all 42 residue positions of Aβ42 sequence. Electron paramagnetic resonance spectra of spin-labeled samples reveal four structural segments based on site-dependent spin label mobility pattern. Segment-1 consists of residues 1-6, which have the highest mobility that is consistent with complete disorder. Segment-3 is the most immobilized region, including residues 31-34. Segment-2 and -4 have intermediate mobility and are composed of residues 7-30 and 35-42, respectively. Considering the inverse relationship between protein dynamics and stability, our results suggest that residues 31-34 are the most stable segment in Aβ42 oligomers. At the same time, the EPR spectral lineshape suggests that Aβ42 globulomers lack a well-packed structural core akin to that of globular proteins.
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Affiliation(s)
- Allison Yoon
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - James Zhen
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
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206
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Mrdenovic D, Zarzycki P, Majewska M, Pieta IS, Nowakowski R, Kutner W, Lipkowski J, Pieta P. Inhibition of Amyloid β-Induced Lipid Membrane Permeation and Amyloid β Aggregation by K162. ACS Chem Neurosci 2021; 12:531-541. [PMID: 33478212 PMCID: PMC7877724 DOI: 10.1021/acschemneuro.0c00754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/07/2021] [Indexed: 01/17/2023] Open
Abstract
Alzheimer's disease (AD) is characterized by progressive neurodegeneration associated with amyloid β (Aβ) peptide aggregation. The aggregation of Aβ monomers (AβMs) leads to the formation of Aβ oligomers (AβOs), the neurotoxic Aβ form, capable of permeating the cell membrane. Here, we investigated the effect of a fluorene-based active drug candidate, named K162, on both Aβ aggregation and AβO toxicity toward the bilayer lipid membrane (BLM). Electrochemical impedance spectroscopy (EIS), atomic force microscopy (AFM), and molecular dynamics (MD) were employed to show that K162 inhibits AβOs-induced BLM permeation, thus preserving BLM integrity. In the presence of K162, only shallow defects on the BLM surface were formed. Apparently, K162 modifies Aβ aggregation by bypassing the formation of toxic AβOs, and only nontoxic AβMs, dimers (AβDs), and fibrils (AβFs) are produced. Unlike other Aβ toxicity inhibitors, K162 preserves neurologically beneficial AβMs. This unique K162 inhibition mechanism provides an alternative AD therapeutic strategy that could be explored in the future.
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Affiliation(s)
- Dusan Mrdenovic
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Department
of Chemistry, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Piotr Zarzycki
- Energy Geosciences
Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Marta Majewska
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Izabela S. Pieta
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Robert Nowakowski
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Wlodzimierz Kutner
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Faculty
of Mathematics and Natural Sciences, School of Sciences, Cardinal Stefan Wyszynski University in Warsaw, Wóycickiego 1/3, 01-815 Warsaw, Poland
| | - Jacek Lipkowski
- Department
of Chemistry, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Piotr Pieta
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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207
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Seuma M, Faure AJ, Badia M, Lehner B, Bolognesi B. The genetic landscape for amyloid beta fibril nucleation accurately discriminates familial Alzheimer's disease mutations. eLife 2021; 10:e63364. [PMID: 33522485 PMCID: PMC7943193 DOI: 10.7554/elife.63364] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/01/2021] [Indexed: 12/20/2022] Open
Abstract
Plaques of the amyloid beta (Aß) peptide are a pathological hallmark of Alzheimer's disease (AD), the most common form of dementia. Mutations in Aß also cause familial forms of AD (fAD). Here, we use deep mutational scanning to quantify the effects of >14,000 mutations on the aggregation of Aß. The resulting genetic landscape reveals mechanistic insights into fibril nucleation, including the importance of charge and gatekeeper residues in the disordered region outside of the amyloid core in preventing nucleation. Strikingly, unlike computational predictors and previous measurements, the empirical nucleation scores accurately identify all known dominant fAD mutations in Aß, genetically validating that the mechanism of nucleation in a cell-based assay is likely to be very similar to the mechanism that causes the human disease. These results provide the first comprehensive atlas of how mutations alter the formation of any amyloid fibril and a resource for the interpretation of genetic variation in Aß.
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Affiliation(s)
- Mireia Seuma
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Andre J Faure
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Marta Badia
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Ben Lehner
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREA, Pg. Lluís CompanysBarcelonaSpain
| | - Benedetta Bolognesi
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and TechnologyBarcelonaSpain
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208
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Barz B, Buell AK, Nath S. Compact fibril-like structure of amyloid β-peptide (1-42) monomers. Chem Commun (Camb) 2021; 57:947-950. [PMID: 33399148 DOI: 10.1039/d0cc06607a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amyloid β (Aβ) monomers are the smallest assembly units, and play an important role in most of the individual processes involved in amyloid fibril formation. An important question is whether the monomer can adopt transient fibril-like conformations in solution. Here we use enhanced sampling simulations to study the Aβ42 monomer structural flexibility. We show that the monomer frequently adopts conformations with the N-terminus region structured very similarly to the conformation it adopts inside the fibril. This intrinsic propensity of monomeric Aβ to adopt fibril-like conformations could explain the low free energy barrier for Aβ42 fibril elongation.
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Affiliation(s)
- Bogdan Barz
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany and Institute of Biological Information Processing - Structural Biochemistry (IBI-7), Research Centre Jülich, Jülich, Germany.
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Soumav Nath
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany and Institute of Biological Information Processing - Structural Biochemistry (IBI-7), Research Centre Jülich, Jülich, Germany.
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209
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Zhang X, Forster MC, Nimerovsky E, Movellan KT, Andreas LB. Transferred-Rotational-Echo Double Resonance. J Phys Chem A 2021; 125:754-769. [PMID: 33464081 PMCID: PMC7884007 DOI: 10.1021/acs.jpca.0c09033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/11/2020] [Indexed: 12/21/2022]
Abstract
Internuclear distance determination is the foundation for NMR-based structure calculation. However, high-precision distance measurement is a laborious process requiring lengthy data acquisitions due to the large set of multidimensional spectra needed at different mixing times. This prevents application to large or challenging molecular systems. Here, we present a new approach, transferred-rotational-echo double resonance (TREDOR), a heteronuclear transfer method in which we simultaneously detect both starting and transferred signals in a single spectrum. This co-acquisition is used to compensate for coherence decay, resulting in accurate and precise distance determination by a single parameter fit using a single spectrum recorded at an ideal mixing time. We showcase TREDOR with the microcrystalline SH3 protein using 3D spectra to resolve resonances. By combining the measured N-C and H-C distances, we calculate the structure of SH3, which converges to the correct fold, with a root-mean-square deviation of 2.1 Å compared to a reference X-ray structure. The TREDOR data used in the structure calculation were acquired in only 4 days on a 600 MHz instrument. This is achieved due to the more than 2-fold time saving afforded by co-acquisition of additional information and demonstrates TREDOR as a fast and straightforward method for determining structures via magic-angle spinning NMR.
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Affiliation(s)
| | | | - Evgeny Nimerovsky
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Kumar Tekwani Movellan
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Loren B. Andreas
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
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210
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Fu Z, Van Nostrand WE, Smith SO. Anti-Parallel β-Hairpin Structure in Soluble Aβ Oligomers of Aβ40-Dutch and Aβ40-Iowa. Int J Mol Sci 2021; 22:ijms22031225. [PMID: 33513738 PMCID: PMC7865275 DOI: 10.3390/ijms22031225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 11/16/2022] Open
Abstract
The amyloid-β (Aβ) peptides are associated with two prominent diseases in the brain, Alzheimer’s disease (AD) and cerebral amyloid angiopathy (CAA). Aβ42 is the dominant component of cored parenchymal plaques associated with AD, while Aβ40 is the predominant component of vascular amyloid associated with CAA. There are familial CAA mutations at positions Glu22 and Asp23 that lead to aggressive Aβ aggregation, drive vascular amyloid deposition and result in degradation of vascular membranes. In this study, we compared the transition of the monomeric Aβ40-WT peptide into soluble oligomers and fibrils with the corresponding transitions of the Aβ40-Dutch (E22Q), Aβ40-Iowa (D23N) and Aβ40-Dutch, Iowa (E22Q, D23N) mutants. FTIR measurements show that in a fashion similar to Aβ40-WT, the familial CAA mutants form transient intermediates with anti-parallel β-structure. This structure appears before the formation of cross-β-sheet fibrils as determined by thioflavin T fluorescence and circular dichroism spectroscopy and occurs when AFM images reveal the presence of soluble oligomers and protofibrils. Although the anti-parallel β-hairpin is a common intermediate on the pathway to Aβ fibrils for the four peptides studied, the rate of conversion to cross-β-sheet fibril structure differs for each.
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Affiliation(s)
- Ziao Fu
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA;
| | - William E. Van Nostrand
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA;
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Steven O. Smith
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA;
- Correspondence: ; Tel.: +1-631-632-1210
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211
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Reif B, Ashbrook SE, Emsley L, Hong M. Solid-state NMR spectroscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:2. [PMID: 34368784 PMCID: PMC8341432 DOI: 10.1038/s43586-020-00002-1] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.
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Affiliation(s)
- Bernd Reif
- Technische Universität München, Department Chemie, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sharon E. Ashbrook
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie chimiques, CH-1015 Lausanne, Switzerland
| | - Mei Hong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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212
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Masuda Y. Bioactive 3D structures of naturally occurring peptides and their application in drug design. Biosci Biotechnol Biochem 2021; 85:24-32. [PMID: 33577656 DOI: 10.1093/bbb/zbaa008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/10/2020] [Indexed: 11/14/2022]
Abstract
Naturally occurring peptides form unique 3D structures, which are critical for their bioactivities. To gain useful insights into drug design, the relationship between the 3D structure and bioactivity of the peptides has been studied. Solid-state nuclear magnetic resonance (NMR) analysis of the 42-residue amyloid β-protein (Aβ42) suggested the presence of toxic conformers with a turn structure at positions 22 and 23 in the aggregates. Antibodies specific to this turn structure could be utilized for immunotherapy and early diagnosis of Alzheimer's disease. Solution NMR analysis of apratoxin A, a cyclic depsipeptide with potent cytotoxicity, proposed an accurate structural model with an important bend structure, which led to the development of highly active mimetics. X-ray crystal analysis of PF1171F, a cyclic hexapeptide with insecticidal activity, indicated the formation of 4 intramolecular hydrogen bonds, which play an important role in cell membrane permeability of PF1171F.
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Affiliation(s)
- Yuichi Masuda
- Graduate School of Bioresources, Mie University, Tsu, Japan
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213
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Bari KJ. The structural biology of crystallin aggregation: challenges and outlook. FEBS J 2021; 288:5888-5902. [DOI: 10.1111/febs.15684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/11/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Khandekar Jishan Bari
- Center for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad India
- Department of Chemical Sciences Indian Institute of Science Education and Research Berhampur India
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214
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Söldner CA, Sticht H, Horn AH. Molecular Simulations and Alzheimer׳s Disease. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11541-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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215
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Jahan I, Nayeem SM. Destabilization of Alzheimer's Aβ 42 protofibrils with acyclovir, carmustine, curcumin, and tetracycline: insights from molecular dynamics simulations. NEW J CHEM 2021. [DOI: 10.1039/d1nj04453b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Among the neurodegenerative diseases, one of the most common dementia is Alzheimer's disease (AD).
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Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Shahid M. Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India
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216
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Kakeshpour T, Ramanujam V, Barnes CA, Shen Y, Ying J, Bax A. A lowly populated, transient β-sheet structure in monomeric Aβ 1-42 identified by multinuclear NMR of chemical denaturation. Biophys Chem 2020; 270:106531. [PMID: 33453683 DOI: 10.1016/j.bpc.2020.106531] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023]
Abstract
Chemical denaturation is a well-established approach for probing the equilibrium between folded and unfolded states of proteins. We demonstrate applicability of this method to the detection of a small population of a transiently folded structural element in a system that is often considered to be intrinsically fully disordered. The 1HN, 15N, 13Cα, and 13C' chemical shifts of Aβ1-40 and Aβ1-42 peptides and their M35-oxidized variants were monitored as a function of urea concentration and compared to analogous urea titrations of synthetic pentapeptides of homologous sequence. Fitting of the chemical shift titrations yields a 10 ± 1% population for a structured element at the C-terminus of Aβ1-42 that folds with a cooperativity of m = 0.06 kcal/mol·M. The fit also yields the chemical shifts of the folded state and, using a database search, for Aβ1-42 these shifts identified an antiparallel intramolecular β-sheet for residues I32-A42, linked by a type I' β-turn at G37 and G38. The structure is destabilized by oxidation of M35. Paramagnetic relaxation rates and two previously reported weak, medium-range NOE interactions are consistent with this transient β-sheet. Introduction of the requisite A42C mutation and tagging with MTSL resulted in a small stabilization of this β-sheet. Chemical shift analysis suggests a C-terminal β-sheet may be present in Aβ1-40 too, but the turn type at G37 is not type I'. The approach to derive Transient Structure from chemical Denaturation by NMR (TSD-NMR), demonstrated here for Aβ peptides, provides a sensitive tool for identifying the presence of lowly populated, transiently ordered elements in proteins that are considered to be intrinsically disordered, and permits extraction of structural data for such elements.
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Affiliation(s)
- Tayeb Kakeshpour
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Venkat Ramanujam
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - C Ashley Barnes
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
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217
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Scheidt HA, Das A, Korn A, Krueger M, Maiti S, Huster D. Structural characteristics of oligomers formed by pyroglutamate-modified amyloid β peptides studied by solid-state NMR. Phys Chem Chem Phys 2020; 22:16887-16895. [PMID: 32666970 DOI: 10.1039/d0cp02307h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neuronal plaques of amyloid β (Aβ) peptides of varying length carrying different posttranslational modifications represent a molecular hallmark of Alzheimer's disease. It is believed that transient oligomeric Aβ assemblies associating in early fibrillation events represent particularly cytotoxic peptide aggregates. Also, N-terminally truncated (in position 3 or 11) and pyroglutamate modified peptides exhibited an increased toxicity compared to the wildtype. In the current study, the molecular structure of oligomeric species of pGlu3-Aβ(3-40) and pGlu11-Aβ(11-40) was investigated using solid-state NMR spectroscopy. On the secondary structure level, for both modified peptides a large similarity between oligomers and mature fibrils of the modified peptides was found mainly based on 13C NMR chemical shift data. Some smaller structural differences were detected in the vicinity of the respective modification site. Also, the crucial early folding molecular contact between residues Phe19 and Leu34 could be observed for the oligomers of both modified peptide species. Therefore, it has to be concluded that the major secondary structure elements of Aβ are already present in oligomers of pGlu3-Aβ(3-40) and pGlu11-Aβ(11-40). These posttranslationally modified peptides arrange in a similar fashion as observed for wild type Aβ(1-40).
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Affiliation(s)
- Holger A Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University Härtelstr. 16-18, D-04107 Leipzig, Germany.
| | - Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Alexander Korn
- Institute for Medical Physics and Biophysics, Leipzig University Härtelstr. 16-18, D-04107 Leipzig, Germany.
| | - Martin Krueger
- Institute of Anatomy, Leipzig University, Liebigstraße 13, 04103 Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University Härtelstr. 16-18, D-04107 Leipzig, Germany. and Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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218
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Naito A. Fibril Formation by Glucagon in Solution and in Membrane Environments. Mol Pharmacol 2020. [DOI: 10.5772/intechopen.91681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Glucagon is a 29-amino acid peptide hormone secreted by pancreatic α-cells and interacts with specific receptors located in various organs. Glucagon tends to form gel-like fibril aggregates that are cytotoxic because they activate apoptotic signaling pathways. First, fibril formation by glucagon in acidic solution is discussed in light of morphological and structural changes during elapsed time. Second, we provide kinetic analyses using a two-step autocatalytic reaction mechanism; the first step is a homogeneous nuclear formation process, and the second step is an autocatalytic heterogeneous fibril elongation process. Third, the processes of fibril formation by glucagon in a membrane environment are discussed based on the structural changes in the fibrils. In the presence of bicelles in acidic solution, glucagon interacts with the bicelles and forms fibril intermediates on the bicelle surface and grows into elongated fibrils. Glucagon-dimyristoylphosphatidylcholine (DMPC) bilayers in neutral solution mimic the environment for fibril formation by glucagon under near-physiological condition. Under these conditions, glucagon forms fibril intermediates that grow into elongated fibrils inside the lipid bilayer. Many days after preparing the glucagon-DMPC bilayer sample, the fibrils form networks inside and outside the bilayer. Furthermore, fibril intermediates strongly interact with lipid bilayers to form small particles.
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219
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Rationally designed peptide-based inhibitor of Aβ42 fibril formation and toxicity: a potential therapeutic strategy for Alzheimer's disease. Biochem J 2020; 477:2039-2054. [PMID: 32427336 PMCID: PMC7293109 DOI: 10.1042/bcj20200290] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 12/22/2022]
Abstract
Amyloid beta peptide (Aβ42) aggregation in the brain is thought to be responsible for the onset of Alzheimer's disease, an insidious condition without an effective treatment or cure. Hence, a strategy to prevent aggregation and subsequent toxicity is crucial. Bio-inspired peptide-based molecules are ideal candidates for the inhibition of Aβ42 aggregation, and are currently deemed to be a promising option for drug design. In this study, a hexapeptide containing a self-recognition component unique to Aβ42 was designed to mimic the β-strand hydrophobic core region of the Aβ peptide. The peptide is comprised exclusively of D-amino acids to enhance specificity towards Aβ42, in conjunction with a C-terminal disruption element to block the recruitment of Aβ42 monomers on to fibrils. The peptide was rationally designed to exploit the synergy between the recognition and disruption components, and incorporates features such as hydrophobicity, β-sheet propensity, and charge, that all play a critical role in the aggregation process. Fluorescence assays, native ion-mobility mass spectrometry (IM-MS) and cell viability assays were used to demonstrate that the peptide interacts with Aβ42 monomers and oligomers with high specificity, leading to almost complete inhibition of fibril formation, with essentially no cytotoxic effects. These data define the peptide-based inhibitor as a potentially potent anti-amyloid drug candidate for this hitherto incurable disease.
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220
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Dong X, Tang Y, Zhan C, Wei G. Green tea extract EGCG plays a dual role in Aβ 42 protofibril disruption and membrane protection: A molecular dynamic study. Chem Phys Lipids 2020; 234:105024. [PMID: 33278382 DOI: 10.1016/j.chemphyslip.2020.105024] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/13/2020] [Accepted: 11/29/2020] [Indexed: 11/18/2022]
Abstract
Amyloid plaques accumulated by the amyloid-β (Aβ) fibrillar aggregates are the major pathological hallmark of the Alzheimer's disease (AD). Inhibiting aggregation and disassembling preformed fibrils of Aβ by natural small molecules have developed into a promising therapeutic strategy for AD. Previous experiments reported that the green tea extract epigallocatechin-3-gallate (EGCG) can disrupt Aβ fibril and reduce Aβ cytotoxicity. The inhibitory ability of EGCG can also be affected by cellular membranes. Thus, it is essential to consider the membrane influences in the investigation of protofibril-disruptive capability of EGCG. Here, we performed multiple all-atom molecular dynamic simulations to investigate the effect of EGCG on the Aβ42 protofibril in the presence of a mixed POPC/POPG (7:3) lipid bilayer and the underlying molecular mechanisms of action. Our simulations show that in the presence of membrane bilayers, EGCG has a preference to bind to the membrane, and this binding alters the binding modes between Aβ42 protofibril and the lipid bilayer, leading to a reduced membrane thinning, indicative of a protective effect of EGCG on the membrane. And EGCG still displays a disruptive effect on Aβ42 protofibril, albeit with a lesser extent of disruption than that in the membrane-free environment. EGCG destabilizes the two hydrophobic core regions (L17-F19-I31 and F4-L34-V36), and disrupts the intrachain K28-A42 salt bridges. Our results reveal that in the presence of lipid bilayers, EGCG plays a dual role in Aβ42 protofibril disruption and membrane protection, suggesting that EGCG could be a potential effective drug candidate for the treatment of AD.
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Affiliation(s)
- Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, 200438, People's Republic of China.
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, 200438, People's Republic of China
| | - Chendi Zhan
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, 200438, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, 200438, People's Republic of China.
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221
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Ulamec SM, Brockwell DJ, Radford SE. Looking Beyond the Core: The Role of Flanking Regions in the Aggregation of Amyloidogenic Peptides and Proteins. Front Neurosci 2020; 14:611285. [PMID: 33335475 PMCID: PMC7736610 DOI: 10.3389/fnins.2020.611285] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
Amyloid proteins are involved in many neurodegenerative disorders such as Alzheimer’s disease [Tau, Amyloid β (Aβ)], Parkinson’s disease [alpha-synuclein (αSyn)], and amyotrophic lateral sclerosis (TDP-43). Driven by the early observation of the presence of ordered structure within amyloid fibrils and the potential to develop inhibitors of their formation, a major goal of the amyloid field has been to elucidate the structure of the amyloid fold at atomic resolution. This has now been achieved for a wide variety of sequences using solid-state NMR, microcrystallography, X-ray fiber diffraction and cryo-electron microscopy. These studies, together with in silico methods able to predict aggregation-prone regions (APRs) in protein sequences, have provided a wealth of information about the ordered fibril cores that comprise the amyloid fold. Structural and kinetic analyses have also shown that amyloidogenic proteins often contain less well-ordered sequences outside of the amyloid core (termed here as flanking regions) that modulate function, toxicity and/or aggregation rates. These flanking regions, which often form a dynamically disordered “fuzzy coat” around the fibril core, have been shown to play key parts in the physiological roles of functional amyloids, including the binding of RNA and in phase separation. They are also the mediators of chaperone binding and membrane binding/disruption in toxic amyloid assemblies. Here, we review the role of flanking regions in different proteins spanning both functional amyloid and amyloid in disease, in the context of their role in aggregation, toxicity and cellular (dys)function. Understanding the properties of these regions could provide new opportunities to target disease-related aggregation without disturbing critical biological functions.
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Affiliation(s)
- Sabine M Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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222
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Abstract
Self-assembly of proteins and peptides into the amyloid fold is a widespread phenomenon in the natural world. The structural hallmark of self-assembly into amyloid fibrillar assemblies is the cross-beta motif, which conveys distinct morphological and mechanical properties. The amyloid fibril formation has contrasting results depending on the organism, in the sense that it can bestow an organism with the advantages of mechanical strength and improved functionality or, on the contrary, could give rise to pathological states. In this chapter we review the existing information on amyloid-like peptide aggregates, which could either be derived from protein sequences, but also could be rationally or de novo designed in order to self-assemble into amyloid fibrils under physiological conditions. Moreover, the development of self-assembled fibrillar biomaterials that are tailored for the desired properties towards applications in biomedical or environmental areas is extensively analyzed. We also review computational studies predicting the amyloid propensity of the natural amino acid sequences and the structure of amyloids, as well as designing novel functional amyloid materials.
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Affiliation(s)
- C. Kokotidou
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
| | - P. Tamamis
- Texas A&M University, Artie McFerrin Department of Chemical Engineering College Station Texas 77843-3122 USA
| | - A. Mitraki
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
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223
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Nguyen H, Linh HQ, Matteini P, La Penna G, Li MS. Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study. J Phys Chem B 2020; 124:10617-10631. [PMID: 33180492 PMCID: PMC7735726 DOI: 10.1021/acs.jpcb.0c05508] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/29/2020] [Indexed: 12/20/2022]
Abstract
Amyloid-β (Aβ) peptides form assemblies that are pathological hallmarks of Alzheimer's disease. Aβ oligomers are soluble, mobile, and toxic forms of the peptide that act in the extracellular space before assembling into protofibrils and fibrils. Therefore, oligomers play an important role in the mechanism of Alzheimer's disease. Since it is difficult to determine by experiment the atomic structures of oligomers, which accumulate fast and are polymorphic, computer simulation is a useful tool to investigate elusive oligomers' structures. In this work, we report extended all-atom molecular dynamics simulations, both canonical and replica exchange, of Aβ(1-42) trimer starting from two different initial conformations: (i) the pose produced by the best docking of a monomer aside of a dimer (simulation 1), representing oligomers freshly formed by assembling monomers, and (ii) a configuration extracted from an experimental mature fibril structure (simulation 2), representing settled oligomers in equilibrium with extended fibrils. We showed that in simulation 1, regions with small β-barrels are populated, indicating the chance of spontaneous formation of domains resembling channel-like structures. These structural domains are alternative to those more representative of mature fibrils (simulation 2), the latter showing a stable bundle of C-termini that is not sampled in simulation 1. Moreover, trimer of Aβ(1-42) can form internal pores that are large enough to be accessed by water molecules and Ca2+ ions.
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Affiliation(s)
- Hoang
Linh Nguyen
- Institute
for Computational Science and Technology, SBI Building, Quang Trung Software
City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Ho
Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Huynh Quang Linh
- Ho
Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Paolo Matteini
- Institute
of Applied Physics “Nello Carrara”, National Research Council, Via Madonna Del Piano 10, I-50019 Sesto Fiorentino, Italy
| | - Giovanni La Penna
- National
Research Council of Italy (CNR), Institute
for Chemistry of Organometallic Compounds (ICCOM), 50019 Florence, Italy
- National Institute for Nuclear Physics
(INFN), Section of Roma-Tor
Vergata Institute of Physics, Polish Academy of
Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- National Institute for Nuclear Physics
(INFN), Section of Roma-Tor
Vergata Institute of Physics, Polish Academy of
Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
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224
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Emerging Roles of Functional Bacterial Amyloids in Gene Regulation, Toxicity, and Immunomodulation. Microbiol Mol Biol Rev 2020; 85:85/1/e00062-20. [PMID: 33239434 DOI: 10.1128/mmbr.00062-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacteria often reside in multicellular communities, called biofilms, held together by an extracellular matrix. In many bacteria, the major proteinaceous component of the biofilm are amyloid fibers. Amyloids are highly stable and structured protein aggregates which were known mostly to be associated with neurodegenerative diseases, such as Alzheimer's, Parkinson's, and Huntington's diseases. In recent years, microbial amyloids were identified also in other species and shown to play major roles in microbial physiology and virulence. For example, amyloid fibers assemble on the bacterial cell surface as a part of the extracellular matrix and are extremely important to the scaffolding and structural integrity of biofilms, which contribute to microbial resilience and resistance. Furthermore, microbial amyloids play fundamental nonscaffold roles that contribute to the development of biofilms underlying numerous persistent infections. Here, we review several nonscaffold roles of bacterial amyloid proteins, including bridging cells during collective migration, acting as regulators of cell fate, as toxins against other bacteria or against host immune cells, and as modulators of the hosts' immune system. These overall points on the complexity of the amyloid fold in encoding numerous activities, which offer approaches for the development of a novel repertoire of antivirulence therapeutics.
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225
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Matsushima Y, Yanagita RC, Irie K. Control of the toxic conformation of amyloid β42 by intramolecular disulfide bond formation. Chem Commun (Camb) 2020; 56:4118-4121. [PMID: 32163091 DOI: 10.1039/d0cc01053g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a method to fix the conformation of Aβ42 to the toxic or non-toxic form by intramolecular disulfide bonds. We found that an Aβ42 analog crosslinked within the molecule at the 17th and 28th amino acid residues exhibited high aggregative ability and potent neurotoxicity comparable to those of E22P-Aβ42. This analog would be useful in the research of Aβ42 oligomers and to develop reliable antibodies for early diagnosis of Alzheimer's disease.
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Affiliation(s)
- Yuka Matsushima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| | - Ryo C Yanagita
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa 761-0795, Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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226
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Ostermeier L, de Oliveira GAP, Dzwolak W, Silva JL, Winter R. Exploring the polymorphism, conformational dynamics and function of amyloidogenic peptides and proteins by temperature and pressure modulation. Biophys Chem 2020; 268:106506. [PMID: 33221697 DOI: 10.1016/j.bpc.2020.106506] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 11/15/2022]
Abstract
Our understanding of amyloid structures and the mechanisms by which disease-associated peptides and proteins self-assemble into these fibrillar aggregates, has advanced considerably in recent years. It is also established that amyloid fibrils are generally polymorphic. The molecular structures of the aggregation intermediates and the causes of molecular and structural polymorphism are less understood, however. Such information is mandatory to explain the pathological diversity of amyloid diseases. What is also clear is that not only protein mutations, but also the physiological milieu, i.e. pH, cosolutes, crowding and surface interactions, have an impact on fibril formation. In this minireview, we focus on the effect of the less explored physical parameters temperature and pressure on the fibrillization propensity of proteins and how these variables can be used to reveal additional mechanistic information about intermediate states of fibril formation and molecular and structural polymorphism. Generally, amyloids are very stable and can resist harsh environmental conditions, such as extreme pH, high temperature and high pressure, and can hence serve as valuable functional amyloid. As an example, we discuss the effect of temperature and pressure on the catalytic activity of peptide amyloid fibrils that exhibit enzymatic activity.
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Affiliation(s)
- Lena Ostermeier
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur 1 Str., 02-093 Warsaw, Poland.
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil.
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany.
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227
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Architecture of the flexible tail tube of bacteriophage SPP1. Nat Commun 2020; 11:5759. [PMID: 33188213 PMCID: PMC7666168 DOI: 10.1038/s41467-020-19611-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail tube of phage SPP1. Our hybrid structure is based on the integration of structural restraints from solid-state nuclear magnetic resonance (NMR) and a density map from cryo-EM. We show that the tail tube protein gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. Additionally, we assess the dynamics of the system by combining relaxation measurements with variances in density maps. Bacteriophages of the Siphoviridae family have a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, the authors present the atomic structure of the tail tube of one of these phages, showing a hollow flexible tube formed by hexameric rings stacked by flexible linkers.
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228
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Lee M, Ghosh U, Thurber KR, Kato M, Tycko R. Molecular structure and interactions within amyloid-like fibrils formed by a low-complexity protein sequence from FUS. Nat Commun 2020; 11:5735. [PMID: 33184287 PMCID: PMC7665218 DOI: 10.1038/s41467-020-19512-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Protein domains without the usual distribution of amino acids, called low complexity (LC) domains, can be prone to self-assembly into amyloid-like fibrils. Self-assembly of LC domains that are nearly devoid of hydrophobic residues, such as the 214-residue LC domain of the RNA-binding protein FUS, is particularly intriguing from the biophysical perspective and is biomedically relevant due to its occurrence within neurons in amyotrophic lateral sclerosis, frontotemporal dementia, and other neurodegenerative diseases. We report a high-resolution molecular structural model for fibrils formed by the C-terminal half of the FUS LC domain (FUS-LC-C, residues 111-214), based on a density map with 2.62 Å resolution from cryo-electron microscopy (cryo-EM). In the FUS-LC-C fibril core, residues 112-150 adopt U-shaped conformations and form two subunits with in-register, parallel cross-β structures, arranged with quasi-21 symmetry. All-atom molecular dynamics simulations indicate that the FUS-LC-C fibril core is stabilized by a plethora of hydrogen bonds involving sidechains of Gln, Asn, Ser, and Tyr residues, both along and transverse to the fibril growth direction, including diverse sidechain-to-backbone, sidechain-to-sidechain, and sidechain-to-water interactions. Nuclear magnetic resonance measurements additionally show that portions of disordered residues 151-214 remain highly dynamic in FUS-LC-C fibrils and that fibrils formed by the N-terminal half of the FUS LC domain (FUS-LC-N, residues 2-108) have the same core structure as fibrils formed by the full-length LC domain. These results contribute to our understanding of the molecular structural basis for amyloid formation by FUS and by LC domains in general.
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Affiliation(s)
- Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA
| | - Ujjayini Ghosh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA
| | - Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75390-9152, USA
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba, 263-8555, Japan
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA.
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229
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Sun Y, Ding F. αB-Crystallin Chaperone Inhibits Aβ Aggregation by Capping the β-Sheet-Rich Oligomers and Fibrils. J Phys Chem B 2020; 124:10138-10146. [PMID: 33119314 DOI: 10.1021/acs.jpcb.0c07256] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inhibiting the cytotoxicity of amyloid aggregation by endogenous proteins is a promising strategy against degenerative amyloid diseases due to their intrinsically high biocompatibility and low immunogenicity. In this study, we investigated the inhibition mechanism of the structured core region of αB-crystallin (αBC) against Aβ fibrillization using discrete molecular dynamics simulations. Our computational results recapitulated the experimentally observed Aβ binding sites in αBC and suggested that αBC could bind to various Aβ aggregate species during the aggregation process-including monomers, dimers, and likely other high molecular weight oligomers, protofibrils, and fibrils-by capping the exposed β-sheet elongation surfaces. Thus, the nucleation of Aβ oligomers into fibrils and the fibril growth could be inhibited. Mechanistic insights obtained from our systematic computational studies may aid in the development of novel therapeutic strategies to modulate the aggregation of pathological, amyloidogenic protein in degenerative diseases.
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Affiliation(s)
- Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.,Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
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230
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Lieblein T, Zangl R, Martin J, Hoffmann J, Hutchison MJ, Stark T, Stirnal E, Schrader T, Schwalbe H, Morgner N. Structural rearrangement of amyloid-β upon inhibitor binding suppresses formation of Alzheimer's disease related oligomers. eLife 2020; 9:59306. [PMID: 33095161 PMCID: PMC7682991 DOI: 10.7554/elife.59306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/22/2020] [Indexed: 01/24/2023] Open
Abstract
The formation of oligomers of the amyloid-β peptide plays a key role in the onset of Alzheimer's disease. We describe herein the investigation of disease-relevant small amyloid-β oligomers by mass spectrometry and ion mobility spectrometry, revealing functionally relevant structural attributes. In particular, we can show that amyloid-β oligomers develop in two distinct arrangements leading to either neurotoxic oligomers and fibrils or non-toxic amorphous aggregates. Comprehending the key-attributes responsible for those pathways on a molecular level is a pre-requisite to specifically target the peptide's tertiary structure with the aim to promote the emergence of non-toxic aggregates. Here, we show for two fibril inhibiting ligands, an ionic molecular tweezer and a hydrophobic peptide that despite their different interaction mechanisms, the suppression of the fibril pathway can be deduced from the disappearance of the corresponding structure of the first amyloid-β oligomers.
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Affiliation(s)
- Tobias Lieblein
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Rene Zangl
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Janosch Martin
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Jan Hoffmann
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Marie J Hutchison
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Tina Stark
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Elke Stirnal
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Thomas Schrader
- University of Duisburg-Essen, Institute of Organic Chemistry, Essen, Germany
| | - Harald Schwalbe
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Nina Morgner
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
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231
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Puig E, Tolchard J, Riera A, Carulla N. Somatostatin, an In Vivo Binder to Aβ Oligomers, Binds to βPFO Aβ(1-42) Tetramers. ACS Chem Neurosci 2020; 11:3358-3365. [PMID: 32915532 DOI: 10.1021/acschemneuro.0c00470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Somatostatin (SST14) is strongly related to Alzheimer's disease (AD), as its levels decline during aging, it regulates the proteolytic degradation of the amyloid beta peptide (Aβ), and it binds to Aβ oligomers in vivo. Recently, the 3D structure of a membrane-associated β-sheet pore-forming tetramer (βPFOAβ(1-42) tetramer) has been reported. Here, we show that SST14 binds selectively to the βPFOAβ(1-42) tetramer with a KD value of ∼40 μM without binding to monomeric Aβ(1-42). Specific NMR chemical shift perturbations, observed during titration of SST14, define a binding site in the βPFOAβ(1-42) tetramer and are in agreement with a 2:1 stoichiometry determined by both native mass spectroscopy and isothermal titration calorimetry. These results enabled us to perform driven docking and model the binding mode for the interaction. The present study provides additional evidence on the relation between SST14 and the amyloid cascade and positions the βPFOAβ(1-42) tetramer as a relevant aggregation form of Aβ and as a potential target for AD.
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Affiliation(s)
- Eduard Puig
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- CBMN (UMR 5248), University of Bordeaux−CNRS−IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, Pessac 33600, France
| | - James Tolchard
- CBMN (UMR 5248), University of Bordeaux−CNRS−IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, Pessac 33600, France
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franqués 1, Barcelona 08028, Spain
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- CBMN (UMR 5248), University of Bordeaux−CNRS−IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, Pessac 33600, France
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232
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Noda K, Tachi Y, Okamoto Y. Structural Characteristics of Monomeric Aβ42 on Fibril in the Early Stage of Secondary Nucleation Process. ACS Chem Neurosci 2020; 11:2989-2998. [PMID: 32794732 DOI: 10.1021/acschemneuro.0c00163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Amyloid-β (Aβ) aggregates are believed to be one of the main causes of Alzheimer's disease. Aβ peptides form fibrils having cross β-sheet structures mainly through primary nucleation, secondary nucleation, and elongation. In particular, self-catalyzed secondary nucleation is of great interest. Here, we investigate the adsorption of Aβ42 peptides to the Aβ42 fibril to reveal a role of adsorption as a part of secondary nucleation. We performed extensive molecular dynamics simulations based on replica exchange with solute tempering 2 (REST2) to two systems: a monomeric Aβ42 in solution and a complex of an Aβ42 peptide and Aβ42 fibril. Results of our simulations show that the Aβ42 monomer is extended on the fibril. Furthermore, we find that the hairpin structure of the Aβ42 monomer decreases but the helix structure increases by adsorption to the fibril surface. These structural changes are preferable for forming fibril-like aggregates, suggesting that the fibril surface serves as a catalyst in the secondary nucleation process. In addition, the stabilization of the helix structure of the Aβ42 monomer on the fibril indicates that the strategy of a secondary nucleation inhibitor design for Aβ40 can also be used for Aβ42.
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Affiliation(s)
- Kohei Noda
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yuhei Tachi
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
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233
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Murakami K, Yamaguchi T, Izuo N, Kume T, Hara H, Irie K. Synthetic and Biophysical Studies on the Toxic Conformer in Amyloid β with the E22Δ Mutation in Alzheimer Pathology. ACS Chem Neurosci 2020; 11:3017-3024. [PMID: 32790274 DOI: 10.1021/acschemneuro.0c00331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The toxic conformer of the 40- or 42-mer-amyloid β-proteins (Aβ) (Aβ40, Aβ42) with a turn at positions 22 and 23 plays a role in oligomer formation, leading to neurotoxicity as part of the pathogenesis of Alzheimer's disease (AD). A deletion mutant at Glu22 (E22Δ) of Aβ, known as an Osaka mutation, accelerates oligomerization. Although E22Δ-Aβ has not been found to be toxic to cultured neuronal cells and is instead synaptotoxic in long-term potentiation, there is no information on the toxic conformer of E22Δ-Aβ in AD. The site-directed spin labeling study of E22Δ-Aβ40 by continuous wave-electron spin resonance (CW-ESR) spectroscopy in part showed the spatial proximity between positions 10 and 35, which are characteristic of the toxic conformation of Aβ, indicating the existence of a toxic conformer of Aβ with the E22Δ mutation. To obtain structural insight, E22Δ-Aβ42 substitutes with proline (F20P, A21P, D23P, and V24P), in which proline is known as a turn inducer but is a β-sheet breaker, were synthesized. An enzyme immunoassay using the 24B3 antibody recognizing toxic conformer of Aβ was carried out. 24B3 reacted with these substitutes of E22Δ-Aβ42 as well as E22Δ-Aβ42 in a similar manner to WT-Aβ42. Notably, only A21P-E22Δ-Aβ42 exhibited strong neurotoxicity in rat primary neurons after 8 days of incubation, with potent high-order oligomerization compared with E22Δ-Aβ42. These results suggest that E22Δ-Aβ42 could enhance neurotoxicity by generating a toxic oligomer conformation with a turn near position 21.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Tomomi Yamaguchi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Naotaka Izuo
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Toshiaki Kume
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Hideyuki Hara
- BioSpin Division, Bruker Japan K. K., Yokohama 221-0022, Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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234
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Azizyan RA, Wang W, Anikeenko A, Radkova Z, Bakulina A, Garro A, Charlier L, Dumas C, Ventura S, Kajava AV. Amyloidogenicity as a driving force for the formation of functional oligomers. J Struct Biol 2020; 212:107604. [PMID: 32805411 DOI: 10.1016/j.jsb.2020.107604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/28/2022]
Abstract
Insoluble amyloid fibrils formed by self-assembly of amyloidogenic regions of proteins have a cross-β-structure. In this work, by using targeted molecular dynamics and rigid body simulation, we demonstrate that if a protein consists of an amyloidogenic region and a globular domain(s) and if the linker between them is short enough, such molecules cannot assemble into amyloid fibrils, instead, they form oligomers with a defined and limited number of β-strands in the cross-β core. We show that this blockage of the amyloid growth is due to the steric repulsion of the globular structures linked to amyloidogenic regions. Furthermore, we establish a relationship between the linker length and the number of monomers in such nanoparticles. We hypothesise that such oligomerisation can be a yet unrecognised way to form natural protein complexes involved in biological processes. Our results can also be used in protein engineering for designing soluble nanoparticles carrying different functional domains.
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Affiliation(s)
- Rafayel A Azizyan
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France
| | - Weiqiang Wang
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193-Bellaterra, Spain
| | | | | | | | - Adriana Garro
- Universidad Nacional de San Luis IMASL-CONICET, San Luis, Argentina
| | - Landry Charlier
- Institut des Biomolécules Max Mousseron, Montpellier, France
| | - Christian Dumas
- Centre de Biochimie Structurale, CNRS, UMR5048, INSERM, U1054, Université de Montpellier, Montpellier, France
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193-Bellaterra, Spain
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.
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235
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The role of fibril structure and surface hydrophobicity in secondary nucleation of amyloid fibrils. Proc Natl Acad Sci U S A 2020; 117:25272-25283. [PMID: 33004626 PMCID: PMC7568274 DOI: 10.1073/pnas.2002956117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alzheimer’s disease affects a rapidly growing number of individuals worldwide. Key unresolved questions relate to the onset and propagation of the disease, linked to the self-assembly of amyloid β peptide into fibrillar and smaller aggregates. This study investigates the propagation of aggregates of amyloid β peptide and asks whether hydrophobic molecular features observed on the fibril surface correlate with its ability to catalyze the formation of new aggregates. This question is motivated by the associated formation of intermediate forms that are toxic to neuronal cells. The results imply that surface catalysis is independent of surface details but requires that the monomers that form the new aggregate can adopt the structure of the parent aggregate without steric clashes. Crystals, nanoparticles, and fibrils catalyze the generation of new aggregates on their surface from the same type of monomeric building blocks as the parent assemblies. This secondary nucleation process can be many orders of magnitude faster than primary nucleation. In the case of amyloid fibrils associated with Alzheimer’s disease, this process leads to the multiplication and propagation of aggregates, whereby short-lived oligomeric intermediates cause neurotoxicity. Understanding the catalytic activity is a fundamental goal in elucidating the molecular mechanisms of Alzheimer’s and associated diseases. Here we explore the role of fibril structure and hydrophobicity by asking whether the V18, A21, V40, and A42 side chains which are exposed on the Aβ42 fibril surface as continuous hydrophobic patches play a role in secondary nucleation. Single, double, and quadruple serine substitutions were made. Kinetic analyses of aggregation data at multiple monomer concentrations reveal that all seven mutants retain the dominance of secondary nucleation as the main mechanism of fibril proliferation. This finding highlights the generality of secondary nucleation and its independence of the detailed molecular structure. Cryo-electron micrographs reveal that the V18S substitution causes fibrils to adopt a distinct morphology with longer twist distance than variants lacking this substitution. Self- and cross-seeding data show that surface catalysis is only efficient between peptides of identical morphology, indicating a templating role of secondary nucleation with structural conversion at the fibril surface. Our findings thus provide clear evidence that the propagation of amyloid fibril strains is possible even in systems dominated by secondary nucleation rather than fragmentation.
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236
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Wiegand T, Malär AA, Cadalbert R, Ernst M, Böckmann A, Meier BH. Asparagine and Glutamine Side-Chains and Ladders in HET-s(218-289) Amyloid Fibrils Studied by Fast Magic-Angle Spinning NMR. Front Mol Biosci 2020; 7:582033. [PMID: 33195425 PMCID: PMC7556116 DOI: 10.3389/fmolb.2020.582033] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Asparagine and glutamine side-chains can form hydrogen-bonded ladders which contribute significantly to the stability of amyloid fibrils. We show, using the example of HET-s(218–289) fibrils, that the primary amide side-chain proton resonances can be detected in cross-polarization based solid-state NMR spectra at fast magic-angle spinning (MAS). J-coupling based experiments offer the possibility to distinguish them from backbone amide groups if the spin-echo lifetimes are long enough, which turned out to be the case for the glutamine side-chains, but not for the asparagine side-chains forming asparagine ladders. We explore the sensitivity of NMR observables to asparagine ladder formation. One of the two possible asparagine ladders in HET-s(218–289), the one comprising N226 and N262, is assigned by proton-detected 3D experiments at fast MAS and significant de-shielding of one of the NH2 proton resonances indicative of hydrogen-bond formation is observed. Small rotating-frame 15N relaxation-rate constants point to rigidified asparagine side-chains in this ladder. The proton resonances are homogeneously broadened which could indicate chemical exchange, but is presently not fully understood. The second asparagine ladder (N243 and N279) in contrast remains more flexible.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Alexander A Malär
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Riccardo Cadalbert
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Matthias Ernst
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, Lyon, France
| | - Beat H Meier
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
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237
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Kinetic fingerprints differentiate the mechanisms of action of anti-Aβ antibodies. Nat Struct Mol Biol 2020; 27:1125-1133. [PMID: 32989305 DOI: 10.1038/s41594-020-0505-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/13/2020] [Indexed: 12/28/2022]
Abstract
The amyloid cascade hypothesis, according to which the self-assembly of amyloid-β peptide (Aβ) is a causative process in Alzheimer's disease, has driven many therapeutic efforts for the past 20 years. Failures of clinical trials investigating Aβ-targeted therapies have been interpreted as evidence against this hypothesis, irrespective of the characteristics and mechanisms of action of the therapeutic agents, which are highly challenging to assess. Here, we combine kinetic analyses with quantitative binding measurements to address the mechanism of action of four clinical stage anti-Aβ antibodies, aducanumab, gantenerumab, bapineuzumab and solanezumab. We quantify the influence of these antibodies on the aggregation kinetics and on the production of oligomeric aggregates and link these effects to the affinity and stoichiometry of each antibody for monomeric and fibrillar forms of Aβ. Our results reveal that, uniquely among these four antibodies, aducanumab dramatically reduces the flux of Aβ oligomers.
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238
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Yu Y, Grazioli G, Unhelkar MH, Martin RW, Butts CT. Network Hamiltonian models reveal pathways to amyloid fibril formation. Sci Rep 2020; 10:15668. [PMID: 32973286 PMCID: PMC7515878 DOI: 10.1038/s41598-020-72260-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/27/2020] [Indexed: 12/26/2022] Open
Abstract
Amyloid fibril formation is central to the etiology of a wide range of serious human diseases, such as Alzheimer's disease and prion diseases. Despite an ever growing collection of amyloid fibril structures found in the Protein Data Bank (PDB) and numerous clinical trials, therapeutic strategies remain elusive. One contributing factor to the lack of progress on this challenging problem is incomplete understanding of the mechanisms by which these locally ordered protein aggregates self-assemble in solution. Many current models of amyloid deposition diseases posit that the most toxic species are oligomers that form either along the pathway to forming fibrils or in competition with their formation, making it even more critical to understand the kinetics of fibrillization. A recently introduced topological model for aggregation based on network Hamiltonians is capable of recapitulating the entire process of amyloid fibril formation, beginning with thousands of free monomers and ending with kinetically accessible and thermodynamically stable amyloid fibril structures. The model can be parameterized to match the five topological classes encompassing all amyloid fibril structures so far discovered in the PDB. This paper introduces a set of network statistical and topological metrics for quantitative analysis and characterization of the fibrillization mechanisms predicted by the network Hamiltonian model. The results not only provide insight into different mechanisms leading to similar fibril structures, but also offer targets for future experimental exploration into the mechanisms by which fibrils form.
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Affiliation(s)
- Yue Yu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Gianmarc Grazioli
- Department of Chemistry, San José State University, San Jose, CA, 95192, USA
| | - Megha H Unhelkar
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Rachel W Martin
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA
| | - Carter T Butts
- Department of Computer Science, University of California, Irvine, CA, 92697, USA. .,California Institute for Telecommunications and Information Technology, University of California, Irvine, CA, 92697, USA. .,Departments of Sociology, Statistics, and EECS, University of California, Irvine, CA, 92697, USA.
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239
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Ikenoue T, Aprile FA, Sormanni P, Ruggeri FS, Perni M, Heller GT, Haas CP, Middel C, Limbocker R, Mannini B, Michaels TCT, Knowles TPJ, Dobson CM, Vendruscolo M. A rationally designed bicyclic peptide remodels Aβ42 aggregation in vitro and reduces its toxicity in a worm model of Alzheimer's disease. Sci Rep 2020; 10:15280. [PMID: 32943652 PMCID: PMC7498612 DOI: 10.1038/s41598-020-69626-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/26/2020] [Indexed: 01/01/2023] Open
Abstract
Bicyclic peptides have great therapeutic potential since they can bridge the gap between small molecules and antibodies by combining a low molecular weight of about 2 kDa with an antibody-like binding specificity. Here we apply a recently developed in silico rational design strategy to produce a bicyclic peptide to target the C-terminal region (residues 31–42) of the 42-residue form of the amyloid β peptide (Aβ42), a protein fragment whose aggregation into amyloid plaques is linked with Alzheimer’s disease. We show that this bicyclic peptide is able to remodel the aggregation process of Aβ42 in vitro and to reduce its associated toxicity in vivo in a C. elegans worm model expressing Aβ42. These results provide an initial example of a computational approach to design bicyclic peptides to target specific epitopes on disordered proteins.
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Affiliation(s)
- Tatsuya Ikenoue
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Francesco S Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Gabriella T Heller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christian P Haas
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christoph Middel
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Ryan Limbocker
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
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240
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Fibril structures of diabetes-related amylin variants reveal a basis for surface-templated assembly. Nat Struct Mol Biol 2020; 27:1048-1056. [PMID: 32929282 DOI: 10.1038/s41594-020-0496-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022]
Abstract
Aggregation of the peptide hormone amylin into amyloid deposits is a pathological hallmark of type-2 diabetes (T2D). While no causal link between T2D and amyloid has been established, the S20G mutation in amylin is associated with early-onset T2D. Here we report cryo-EM structures of amyloid fibrils of wild-type human amylin and its S20G variant. The wild-type fibril structure, solved to 3.6-Å resolution, contains two protofilaments, each built from S-shaped subunits. S20G fibrils, by contrast, contain two major polymorphs. Their structures, solved at 3.9-Å and 4.0-Å resolution, respectively, share a common two-protofilament core that is distinct from the wild-type structure. Remarkably, one polymorph contains a third subunit with another, distinct, cross-β conformation. The presence of two different backbone conformations within the same fibril may explain the increased aggregation propensity of S20G, and illustrates a potential structural basis for surface-templated fibril assembly.
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241
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Vadukul DM, Maina M, Franklin H, Nardecchia A, Serpell LC, Marshall KE. Internalisation and toxicity of amyloid-β 1-42 are influenced by its conformation and assembly state rather than size. FEBS Lett 2020; 594:3490-3503. [PMID: 32871611 DOI: 10.1002/1873-3468.13919] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/30/2020] [Accepted: 08/19/2020] [Indexed: 01/18/2023]
Abstract
Amyloid fibrils found in plaques in Alzheimer's disease (AD) brains are composed of amyloid-β peptides. Oligomeric amyloid-β 1-42 (Aβ42) is thought to play a critical role in neurodegeneration in AD. Here, we determine how size and conformation affect neurotoxicity and internalisation of Aβ42 assemblies using biophysical methods, immunoblotting, toxicity assays and live-cell imaging. We report significant cytotoxicity of Aβ42 oligomers and their internalisation into neurons. In contrast, Aβ42 fibrils show reduced internalisation and no toxicity. Sonicating Aβ42 fibrils generates species similar in size to oligomers but remains nontoxic. The results suggest that Aβ42 oligomers have unique properties that underlie their neurotoxic potential. Furthermore, we show that incubating cells with Aβ42 oligomers for 24 h is sufficient to trigger irreversible neurotoxicity.
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Affiliation(s)
- Devkee M Vadukul
- Dementia Research group, Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, E Sussex, UK.,CEMO-Alzheimer Dementia group, Institute of Neuroscience, Université catholique de Louvain, Brussels, Belgium
| | - Mahmoud Maina
- Dementia Research group, Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, E Sussex, UK.,College of Medical Sciences, Yobe State University, Nigeria
| | - Hannah Franklin
- Dementia Research group, Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, E Sussex, UK
| | - Astrid Nardecchia
- Dementia Research group, Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, E Sussex, UK
| | - Louise C Serpell
- Dementia Research group, Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, E Sussex, UK
| | - Karen E Marshall
- Dementia Research group, Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, E Sussex, UK
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242
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Schledorn M, Malär AA, Torosyan A, Penzel S, Klose D, Oss A, Org M, Wang S, Lecoq L, Cadalbert R, Samoson A, Böckmann A, Meier BH. Protein NMR Spectroscopy at 150 kHz Magic-Angle Spinning Continues To Improve Resolution and Mass Sensitivity. Chembiochem 2020; 21:2540-2548. [PMID: 32501630 PMCID: PMC7497035 DOI: 10.1002/cbic.202000341] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 12/21/2022]
Abstract
Spectral resolution is the key to unleashing the structural and dynamic information contained in NMR spectra. Fast magic-angle spinning (MAS) has recently revolutionized the spectroscopy of biomolecular solids. Herein, we report a further remarkable improvement in the resolution of the spectra of four fully protonated proteins and a small drug molecule by pushing the MAS rotation frequency higher (150 kHz) than the more routinely used 100 kHz. We observed a reduction in the average homogeneous linewidth by a factor of 1.5 and a decrease in the observed linewidth by a factor 1.25. We conclude that even faster MAS is highly attractive and increases mass sensitivity at a moderate price in overall sensitivity.
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Affiliation(s)
| | | | | | | | - Daniel Klose
- Physical ChemistryETH Zürich8093ZürichSwitzerland
| | - Andres Oss
- Institute of Health TechnologiesTallinn University of TechnologyAkadeemia tee 15a12618TallinnEstonia
| | - Mai‐Liis Org
- Institute of Health TechnologiesTallinn University of TechnologyAkadeemia tee 15a12618TallinnEstonia
| | - Shishan Wang
- Institut de Biologie et Chimie des Protéines MMSB UMR 5086 CNRS/Université de Lyon, Labex Ecofect7 passage du Vercors69367LyonFrance
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines MMSB UMR 5086 CNRS/Université de Lyon, Labex Ecofect7 passage du Vercors69367LyonFrance
| | | | - Ago Samoson
- Institute of Health TechnologiesTallinn University of TechnologyAkadeemia tee 15a12618TallinnEstonia
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines MMSB UMR 5086 CNRS/Université de Lyon, Labex Ecofect7 passage du Vercors69367LyonFrance
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243
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Foley AR, Raskatov JA. Assessing Reproducibility in Amyloid β Research: Impact of Aβ Sources on Experimental Outcomes. Chembiochem 2020; 21:2425-2430. [PMID: 32249510 PMCID: PMC7647053 DOI: 10.1002/cbic.202000125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/04/2020] [Indexed: 12/16/2022]
Abstract
The difficulty of synthesizing and purifying the amyloid β (Aβ) peptide, combined with its high aggregation propensity and low solubility under physiological conditions, leads to a wide variety of experimental results from kinetic assays to biological activity. Thus, it becomes challenging to reproduce outcomes, and this limits our ability to rely on reported results as the foundation for new research. This article examines variability of the Aβ peptide from different sources, comparing purity, and oligomer and fibril formation propensity side by side. The results highlight the importance of performing rigorous controls so that meaningful biophysical, biochemical, and neurobiological results can be obtained to improve our understanding on Aβ.
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Affiliation(s)
- Alejandro R Foley
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Jevgenij A Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
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244
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Gelenter MD, Dregni AJ, Hong M. Pulsed Third-Spin-Assisted Recoupling NMR for Obtaining Long-Range 13C- 13C and 15N- 13C Distance Restraints. J Phys Chem B 2020; 124:7138-7151. [PMID: 32700540 PMCID: PMC8324326 DOI: 10.1021/acs.jpcb.0c04574] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present a class of pulsed third-spin-assisted recoupling (P-TSAR) magic-angle-spinning solid-state NMR techniques that achieve efficient polarization transfer over long distances to provide important restraints for structure determination. These experiments utilize second-order cross terms between strong 1H-13C and 1H-15N dipolar couplings to achieve 13C-13C and 15N-13C polarization transfer, similar to the principle of continuous-wave (CW) TSAR experiments. However, in contrast to the CW-TSAR experiments, these P-TSAR experiments require much less radiofrequency (rf) energy and allow a much simpler routine for optimizing the rf field strength. We call the technique PULSAR (pulsed proton-assisted recoupling) for homonuclear spin pairs. For heteronuclear spin pairs, we improve the recently introduced PERSPIRATIONCP (proton-enhanced rotor-echo short pulse irradiation cross-polarization) experiment by shifting the pulse positions and removing the z-filters, which significantly broaden the bandwidth and increase the efficiency of polarization transfer. We demonstrate the PULSAR and PERSPIRATIONCP techniques on the model protein GB1 and found cross peaks for distances as long as 10 and 8 Å for 13C-13C and 15N-13C spin pairs, respectively. We then apply these methods to the amyloid fibrils formed by the peptide hormone glucagon and show that long-range correlation peaks are readily observed to constrain intermolecular packing in this cross-β fibril. We provide an analytical model for the PULSAR and PERSPIRATIONCP experiments to explain the measured and simulated chemical shift dependence and pulse flip angle dependence of polarization transfer. These two techniques are useful for measuring long-range distance restraints to determine the three-dimensional structures of proteins and other biological macromolecules.
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Affiliation(s)
- Martin D. Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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245
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Lu J, Cao Q, Hughes MP, Sawaya MR, Boyer DR, Cascio D, Eisenberg DS. CryoEM structure of the low-complexity domain of hnRNPA2 and its conversion to pathogenic amyloid. Nat Commun 2020; 11:4090. [PMID: 32796831 PMCID: PMC7427792 DOI: 10.1038/s41467-020-17905-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/14/2020] [Indexed: 01/02/2023] Open
Abstract
hnRNPA2 is a human ribonucleoprotein (RNP) involved in RNA metabolism. It forms fibrils both under cellular stress and in mutated form in neurodegenerative conditions. Previous work established that the C-terminal low-complexity domain (LCD) of hnRNPA2 fibrillizes under stress, and missense mutations in this domain are found in the disease multisystem proteinopathy (MSP). However, little is known at the atomic level about the hnRNPA2 LCD structure that is involved in those processes and how disease mutations cause structural change. Here we present the cryo-electron microscopy (cryoEM) structure of the hnRNPA2 LCD fibril core and demonstrate its capability to form a reversible hydrogel in vitro containing amyloid-like fibrils. Whereas these fibrils, like pathogenic amyloid, are formed from protein chains stacked into β-sheets by backbone hydrogen bonds, they display distinct structural differences: the chains are kinked, enabling non-covalent cross-linking of fibrils and disfavoring formation of pathogenic steric zippers. Both reversibility and energetic calculations suggest these fibrils are less stable than pathogenic amyloid. Moreover, the crystal structure of the disease-mutation-containing segment (D290V) of hnRNPA2 suggests that the replacement fundamentally alters the fibril structure to a more stable energetic state. These findings illuminate how molecular interactions promote protein fibril networks and how mutation can transform fibril structure from functional to a pathogenic form. hnRNPA2 is involved in RNA metabolism and can form both functional amyloid-like fibrils in membraneless organelles, and pathogenic fibrils in neurodegenerative conditions. Here, the authors present the cryo-EM fibril structure of the wild-type hnRNPA2 low-complexity domain (LCD) and the crystal structure of a LCD segment with the disease causing D290V variant and discuss how mutations can transform fibril structure from a functional to a pathogenic form.
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Affiliation(s)
- Jiahui Lu
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Qin Cao
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Michael P Hughes
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA.,Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - David R Boyer
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Duilio Cascio
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA. .,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA.
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246
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Ke PC, Zhou R, Serpell LC, Riek R, Knowles TPJ, Lashuel HA, Gazit E, Hamley IW, Davis TP, Fändrich M, Otzen DE, Chapman MR, Dobson CM, Eisenberg DS, Mezzenga R. Half a century of amyloids: past, present and future. Chem Soc Rev 2020; 49:5473-5509. [PMID: 32632432 PMCID: PMC7445747 DOI: 10.1039/c9cs00199a] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.
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Affiliation(s)
- Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China; Department of Chemistry, Columbia University, New York, New York, 10027, USA
| | - Louise C. Serpell
- School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Wolfgang-Pauli-Str. 10, 8093 Zurich, Switzerland
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, CB3 0HE, Cambridge, UK
| | - Hilal A. Lashuel
- Laboratory of Molecular Neurobiology and Neuroproteomics, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ian W. Hamley
- School of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Daniel Erik Otzen
- Department of Molecular Biology, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Matthew R. Chapman
- Department of Molecular, Cellular and Developmental Biology, Centre for Microbial Research, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - David S. Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Raffaele Mezzenga
- Department of Health Science & Technology, ETH Zurich, Schmelzbergstrasse 9, LFO, E23, 8092 Zurich, Switzerland
- Department of Materials, ETH Zurich, Wolfgang Pauli Strasse 10, 8093 Zurich, Switzerland
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247
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Anomalous Salt Dependence Reveals an Interplay of Attractive and Repulsive Electrostatic Interactions in α-synuclein Fibril Formation. QRB DISCOVERY 2020. [PMID: 37528959 PMCID: PMC10392692 DOI: 10.1017/qrd.2020.7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstractα-Synuclein (α-syn) is an intrinsically disordered protein with a highly asymmetric charge distribution, whose aggregation is linked to Parkinson’s disease. The effect of ionic strength was investigated at mildly acidic pH (5.5) in the presence of catalytic surfaces in the form of α-syn seeds or anionic lipid vesicles using thioflavin T fluorescence measurements. Similar trends were observed with both surfaces: increasing ionic strength reduced the rate of α-syn aggregation although the surfaces as well as α-syn have a net negative charge at pH 5.5. This anomalous salt dependence implies that short-range attractive electrostatic interactions are critical for secondary nucleation as well as heterogeneous primary nucleation. Such interactions were confirmed in Monte Carlo simulations of α-syn monomers interacting with surface-grafted C-terminal tails, and found to be weakened in the presence of salt. Thus, nucleation of α-syn aggregation depends critically on an attractive electrostatic component that is screened by salt to the extent that it outweighs the screening of the long-range repulsion between negatively charged monomers and negative surfaces. Interactions between the positively charged N-termini of α-syn monomers on the one hand, and the negatively C-termini of α-syn on fibrils or vesicles surfaces on the other hand, are thus critical for nucleation.
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248
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Proteotoxicity and Neurodegenerative Diseases. Int J Mol Sci 2020; 21:ijms21165646. [PMID: 32781742 PMCID: PMC7460676 DOI: 10.3390/ijms21165646] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/01/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative diseases are a major burden for our society, affecting millions of people worldwide. A main goal of past and current research is to enhance our understanding of the mechanisms underlying proteotoxicity, a common theme among these incurable and debilitating conditions. Cell proteome alteration is considered to be one of the main driving forces that triggers neurodegeneration, and unraveling the biological complexity behind the affected molecular pathways constitutes a daunting challenge. This review summarizes the current state on key processes that lead to cellular proteotoxicity in Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis, providing a comprehensive landscape of recent literature. A foundational understanding of how proteotoxicity affects disease etiology and progression may provide essential insight towards potential targets amenable of therapeutic intervention.
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249
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Kreutzer AG, Samdin TD, Guaglianone G, Spencer RK, Nowick JS. X-ray Crystallography Reveals Parallel and Antiparallel β-Sheet Dimers of a β-Hairpin Derived from Aβ 16-36 that Assemble to Form Different Tetramers. ACS Chem Neurosci 2020; 11:2340-2347. [PMID: 32584538 DOI: 10.1021/acschemneuro.0c00290] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
High-resolution structures of oligomers formed by the β-amyloid peptide, Aβ, are important for understanding the molecular basis of Alzheimer's disease. Dimers of Aβ are linked to the pathogenesis and progression of Alzheimer's disease, and tetramers of Aβ are neurotoxic. This paper reports the X-ray crystallographic structures of dimers and tetramers, as well as an octamer, formed by a peptide derived from the central and C-terminal regions of Aβ. In the crystal lattice, the peptide assembles to form two different dimers-an antiparallel β-sheet dimer and a parallel β-sheet dimer-that each further self-assemble to form two different tetramers-a sandwich-like tetramer and a twisted β-sheet tetramer. The structures of these dimers and tetramers derived from Aβ serve as potential models for dimers and tetramers of full-length Aβ that form in vitro and in Alzheimer's disease-afflicted brains.
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250
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Roy R, Pradhan K, Khan J, Das G, Mukherjee N, Das D, Ghosh S. Human Serum Albumin-Inspired Glycopeptide-Based Multifunctional Inhibitor of Amyloid-β Toxicity. ACS OMEGA 2020; 5:18628-18641. [PMID: 32775865 PMCID: PMC7407538 DOI: 10.1021/acsomega.0c01028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/19/2020] [Indexed: 05/07/2023]
Abstract
In Alzheimer's disease (AD), insoluble Aβ42 peptide fragments self-aggregate and form oligomers and fibrils in the brain, causing neurotoxicity. Further, the presence of redox-active metal ions such as Cu2+ enhances the aggregation process through chelation with these Aβ42 aggregates as well as generation of Aβ42-mediated reactive oxygen species (ROS). Herein, we have adopted a bioinspired strategy to design and develop a multifunctional glycopeptide hybrid molecule (Glupep), which can serve as a potential AD therapeutic. This molecule consists of a natural metal-chelating tetrapeptide motif of human serum albumin (HSA), a β-sheet breaker peptide, and a sugar moiety for better bioavailability. We performed different biophysical and docking experiments, which revealed that Glupep not only associates with Aβ42 but also prevents its self-aggregation to form toxic oligomers and fibrils. Moreover, Glupep was also shown to sequester out Cu2+ from the Aβ-Cu2+ complex, reducing the ROS formation and toxicity. Besides, this study also revealed that Glupep could protect PC12-derived neurons from Aβ-Cu2+-mediated toxicity by reducing intracellular ROS generation and stabilizing the mitochondrial membrane potential. All these exciting features show Glupep to be a potent inhibitor of Aβ42-mediated multifaceted toxicity and a prospective therapeutic lead for AD.
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Affiliation(s)
- Rajsekhar Roy
- Department
of Bioscience & Bioengineering, Indian
Institute of Technology Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Krishnangsu Pradhan
- Organic
and Medicinal Chemistry and Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical
Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, WB, India
| | - Juhee Khan
- Organic
and Medicinal Chemistry and Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical
Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, WB, India
| | - Gaurav Das
- Organic
and Medicinal Chemistry and Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical
Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, WB, India
| | - Nabanita Mukherjee
- Department
of Bioscience & Bioengineering, Indian
Institute of Technology Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Durba Das
- Department
of Bioscience & Bioengineering, Indian
Institute of Technology Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Surajit Ghosh
- Organic
and Medicinal Chemistry and Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical
Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, WB, India
- Department
of Bioscience & Bioengineering, Indian
Institute of Technology Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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