1
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Tomato Xylem Sap Hydrophobins Vdh4 and Vdh5 Are Important for Late Stages of Verticillium dahliae Plant Infection. J Fungi (Basel) 2022; 8:jof8121252. [PMID: 36547586 PMCID: PMC9783231 DOI: 10.3390/jof8121252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Verticillium dahliae causes economic losses to a wide range of crops as a vascular fungal pathogen. This filamentous ascomycete spends long periods of its life cycle in the plant xylem, a unique environment that requires adaptive processes. Specifically, fungal proteins produced in the xylem sap of the plant host may play important roles in colonizing the plant vasculature and in inducing disease symptoms. RNA sequencing revealed over 1500 fungal transcripts that are significantly more abundant in cells grown in tomato xylem sap compared with pectin-rich medium. Of the 85 genes that are strongly induced in the xylem sap, four genes encode the hydrophobins Vdh1, Vdh2, Vdh4 and Vdh5. Vdh4 and Vhd5 are structurally distinct from each other and from the three other hydrophobins (Vdh1-3) annotated in V. dahliae JR2. Their functions in the life cycle and virulence of V. dahliae were explored using genetics, cell biology and plant infection experiments. Our data revealed that Vdh4 and Vdh5 are dispensable for V. dahliae development and stress response, while both contribute to full disease development in tomato plants by acting at later colonization stages. We conclude that Vdh4 and Vdh5 are functionally specialized fungal hydrophobins that support pathogenicity against plants.
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2
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Naeimi WR, Serio TR. Beyond Amyloid Fibers: Accumulation, Biological Relevance, and Regulation of Higher-Order Prion Architectures. Viruses 2022; 14:v14081635. [PMID: 35893700 PMCID: PMC9332770 DOI: 10.3390/v14081635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/14/2022] [Accepted: 07/23/2022] [Indexed: 12/19/2022] Open
Abstract
The formation of amyloid fibers is associated with a diverse range of disease and phenotypic states. These amyloid fibers often assemble into multi-protofibril, high-order architectures in vivo and in vitro. Prion propagation in yeast, an amyloid-based process, represents an attractive model to explore the link between these aggregation states and the biological consequences of amyloid dynamics. Here, we integrate the current state of knowledge, highlight opportunities for further insight, and draw parallels to more complex systems in vitro. Evidence suggests that high-order fibril architectures are present ex vivo from disease relevant environments and under permissive conditions in vivo in yeast, including but not limited to those leading to prion formation or instability. The biological significance of these latter amyloid architectures or how they may be regulated is, however, complicated by inconsistent experimental conditions and analytical methods, although the Hsp70 chaperone Ssa1/2 is likely involved. Transition between assembly states could form a mechanistic basis to explain some confounding observations surrounding prion regulation but is limited by a lack of unified methodology to biophysically compare these assembly states. Future exciting experimental entryways may offer opportunities for further insight.
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3
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Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Structure and Polymorphism of Amyloid and Amyloid-Like Aggregates. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:450-463. [PMID: 35790379 DOI: 10.1134/s0006297922050066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Amyloids are protein aggregates with the cross-β structure. The interest in amyloids is explained, on the one hand, by their role in the development of socially significant human neurodegenerative diseases, and on the other hand, by the discovery of functional amyloids, whose formation is an integral part of cellular processes. To date, more than a hundred proteins with the amyloid or amyloid-like properties have been identified. Studying the structure of amyloid aggregates has revealed a wide variety of protein conformations. In the review, we discuss the diversity of protein folds in the amyloid-like aggregates and the characteristic features of amyloid aggregates that determine their unusual properties, including stability and interaction with amyloid-specific dyes. The review also describes the diversity of amyloid aggregates and its significance for living organisms.
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Affiliation(s)
- Anton B Matiiv
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Nina P Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Bioinformatics Institute, Saint Petersburg, 197342, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
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4
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Cretenoud J, Giffin M, Özen B, Fadaei-Tirani F, Scopelliti R, Plummer CJG, Frauenrath H. Semiaromatic Polyamides with Re-Entrant Chain Folding Templated by “U-Turn” Repeat Units. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julien Cretenoud
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Michael Giffin
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Bilal Özen
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Farzaneh Fadaei-Tirani
- Institute of Chemical Science and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Rosario Scopelliti
- Institute of Chemical Science and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Holger Frauenrath
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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5
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Pathak BK, Dey S, Mozumder S, Sengupta J. The role of membranes in function and dysfunction of intrinsically disordered amyloidogenic proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:397-434. [PMID: 35034725 DOI: 10.1016/bs.apcsb.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Membrane-protein interactions play a major role in human physiology as well as in diseases pathology. Interaction of a protein with the membrane was previously thought to be dependent on well-defined three-dimensional structure of the protein. In recent decades, however, it has become evident that a large fraction of the proteome, particularly in eukaryotes, stays disordered in solution and these proteins are termed as intrinsically disordered proteins (IDPs). Also, a vast majority of human proteomes have been reported to contain substantially long disordered regions, called intrinsically disordered regions (IDRs), in addition to the structurally ordered regions. IDPs exist in an ensemble of conformations and the conformational flexibility enables IDPs to achieve functional diversity. IDPs (and IDRs) are found to be important players in cell signaling, where biological membranes act as anchors for signaling cascades. Therefore, IDPs modulate the membrane architectures, at the same time membrane composition also affects the binding of IDPs. Because of intrinsic disorders, misfolding of IDPs often leads to formation of oligomers, protofibrils and mature fibrils through progressive self-association. Accumulation of amyloid-like aggregates of some of the IDPs is a known causative agent for numerous diseases. In this chapter we highlight recent advances in understanding membrane interactions of some of the intrinsically disordered proteins involved in the pathogenesis of human diseases.
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Affiliation(s)
- Bani Kumar Pathak
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sandip Dey
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sukanya Mozumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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6
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Sawaya MR, Hughes MP, Rodriguez JA, Riek R, Eisenberg DS. The expanding amyloid family: Structure, stability, function, and pathogenesis. Cell 2021; 184:4857-4873. [PMID: 34534463 PMCID: PMC8772536 DOI: 10.1016/j.cell.2021.08.013] [Citation(s) in RCA: 164] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/26/2021] [Accepted: 08/11/2021] [Indexed: 02/05/2023]
Abstract
The hidden world of amyloid biology has suddenly snapped into atomic-level focus, revealing over 80 amyloid protein fibrils, both pathogenic and functional. Unlike globular proteins, amyloid proteins flatten and stack into unbranched fibrils. Stranger still, a single protein sequence can adopt wildly different two-dimensional conformations, yielding distinct fibril polymorphs. Thus, an amyloid protein may define distinct diseases depending on its conformation. At the heart of this conformational variability lies structural frustrations. In functional amyloids, evolution tunes frustration levels to achieve either stability or sensitivity according to the fibril's biological function, accounting for the vast versatility of the amyloid fibril scaffold.
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Affiliation(s)
- Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Michael P Hughes
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Jose A Rodriguez
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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7
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Gao Y, Saccuzzo EG, Hill SE, Huard DJE, Robang AS, Lieberman RL, Paravastu AK. Structural Arrangement within a Peptide Fibril Derived from the Glaucoma-Associated Myocilin Olfactomedin Domain. J Phys Chem B 2021; 125:2886-2897. [PMID: 33683890 DOI: 10.1021/acs.jpcb.0c11460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myocilin-associated glaucoma is a new addition to the list of diseases linked to protein misfolding and amyloid formation. Single point variants of the ∼257-residue myocilin olfactomedin domain (mOLF) lead to mutant myocilin aggregation. Here, we analyze the 12-residue peptide P1 (GAVVYSGSLYFQ), corresponding to residues 326-337 of mOLF, previously shown to form amyloid fibrils in vitro and in silico. We applied solid-state NMR structural measurements to test the hypothesis that P1 fibrils adopt one of three predicted structures. Our data are consistent with a U-shaped fibril arrangement for P1, one that is related to the U-shape predicted previously in silico. Our data are also consistent with an antiparallel fibril arrangement, likely driven by terminal electrostatics. Our proposed structural model is reminiscent of fibrils formed by the Aβ(1-40) Iowa mutant peptide, but with a different arrangement of molecular turn regions. Taken together, our results strengthen the connection between mOLF fibrils and the broader amylome and contribute to our understanding of the fundamental molecular interactions governing fibril architecture and stability.
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8
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Dangerous Stops: Nonsense Mutations Can Dramatically Increase Frequency of Prion Conversion. Int J Mol Sci 2021; 22:ijms22041542. [PMID: 33546497 PMCID: PMC7913716 DOI: 10.3390/ijms22041542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/26/2022] Open
Abstract
Amyloid formation is associated with many incurable diseases. For some of these, sporadic cases are much more common than familial ones. Some reports point to the role of somatic cell mosaicism in these cases via origination of amyloids in a limited number of cells, which can then spread through tissues. However, specific types of sporadic mutations responsible for such effects are unknown. In order to identify mutations capable of increasing the de novo appearance of amyloids, we searched for such mutants in the yeast prionogenic protein Sup35. We introduced to yeast cells an additional copy of the SUP35 gene with mutated amyloidogenic domain and observed that some nonsense mutations increased the incidence of prions by several orders of magnitude. This effect was related to exposure at the C-terminus of an internal amyloidogenic region of Sup35. We also discovered that SUP35 mRNA could undergo splicing, although inefficiently, causing appearance of a shortened Sup35 isoform lacking its functional domain, which was also highly prionogenic. Our data suggest that truncated forms of amyloidogenic proteins, resulting from nonsense mutations or alternative splicing in rare somatic cells, might initiate spontaneous localized formation of amyloids, which can then spread, resulting in sporadic amyloid disease.
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9
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Fomicheva A, Ross ED. From Prions to Stress Granules: Defining the Compositional Features of Prion-Like Domains That Promote Different Types of Assemblies. Int J Mol Sci 2021; 22:ijms22031251. [PMID: 33513942 PMCID: PMC7865556 DOI: 10.3390/ijms22031251] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Stress granules are ribonucleoprotein assemblies that form in response to cellular stress. Many of the RNA-binding proteins found in stress granule proteomes contain prion-like domains (PrLDs), which are low-complexity sequences that compositionally resemble yeast prion domains. Mutations in some of these PrLDs have been implicated in neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia, and are associated with persistent stress granule accumulation. While both stress granules and prions are macromolecular assemblies, they differ in both their physical properties and complexity. Prion aggregates are highly stable homopolymeric solids, while stress granules are complex dynamic biomolecular condensates driven by multivalent homotypic and heterotypic interactions. Here, we use stress granules and yeast prions as a paradigm to examine how distinct sequence and compositional features of PrLDs contribute to different types of PrLD-containing assemblies.
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10
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Konstantoulea K, Louros N, Rousseau F, Schymkowitz J. Heterotypic interactions in amyloid function and disease. FEBS J 2021; 289:2025-2046. [PMID: 33460517 DOI: 10.1111/febs.15719] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 11/27/2022]
Abstract
Amyloid aggregation results from the self-assembly of identical aggregation-prone sequences into cross-beta-sheet structures. The process is best known for its association with a wide range of human pathologies but also as a functional mechanism in all kingdoms of life. Less well elucidated is the role of heterotypic interactions between amyloids and other proteins and macromolecules and how this contributes to disease. We here review current data with a focus on neurodegenerative amyloid-associated diseases. Evidence indicates that heterotypic interactions occur in a wide range of amyloid processes and that these interactions modify fundamental aspects of amyloid aggregation including seeding, aggregation rates and toxicity. More work is required to understand the mechanistic origin of these interactions, but current understanding suggests that both supersaturation and sequence-specific binding can contribute to heterotypic amyloid interactions. Further unravelling these mechanisms may help to answer outstanding questions in the field including the selective vulnerability of cells types and tissues and the stereotypical spreading patterns of amyloids in disease.
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Affiliation(s)
- Katerina Konstantoulea
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Nikolaos Louros
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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11
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Wang W, Azizyan RA, Garro A, Kajava AV, Ventura S. Multifunctional Amyloid Oligomeric Nanoparticles for Specific Cell Targeting and Drug Delivery. Biomacromolecules 2020; 21:4302-4312. [PMID: 32885960 DOI: 10.1021/acs.biomac.0c01103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural selection has endorsed proteins with amazing structures and functionalities that cannot be matched by synthetic means, explaining the exponential interest in developing protein-based materials. Protein self-assembly allows fabricating complex supramolecular structures from relatively simple building blocks, a bottom-up strategy naturally employed by amyloid fibrils. However, the design of amyloid-inspired materials with biological activity is inherently difficult. Here, we exploit a modular procedure to generate functional amyloid nanostructures with tight control of their mesoscopic properties. The soft amyloid core of a yeast prion was fused to dihydrofolate reductase through flexible linkers of different sizes. This enabled us to produce, for the first time, biocompatible protein-only amyloid-like oligomeric nanoparticles with defined dimensions in which the embedded enzyme remained highly active, as assessed by biophysical and enzymatic assays. The modular design allowed one to obtain multifunctional nanoparticles by incorporating the antibody-binding Z-domain to the protein fusion. We show how these assemblies can be exploited for antibody-directed targeting of specific cell types and the localized delivery of methotrexate, resulting in the intracellular uptake of the drug by cancer cells and their death. Overall, the novel protein particles we describe in this work might find applications in areas as diverse as biocatalysis, bioimaging, or targeted therapies.
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Affiliation(s)
- Weiqiang Wang
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Rafayel A Azizyan
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université Montpellier, Montpellier 34090, France.,Institut de Biologie Computationnelle, Université Montpellier, Montpellier 34090, France
| | - Adriana Garro
- Universidad Nacional de San Luis IMASL-CONICET, San Luis D5702, Argentina
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université Montpellier, Montpellier 34090, France.,Institut de Biologie Computationnelle, Université Montpellier, Montpellier 34090, France
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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12
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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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13
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Sulatskaya AI, Bondarev SA, Sulatsky MI, Trubitsina NP, Belousov MV, Zhouravleva GA, Llanos MA, Kajava AV, Kuznetsova IM, Turoverov KK. Point mutations affecting yeast prion propagation change the structure of its amyloid fibrils. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Wang J, Park G, Lee YK, Nguyen M, San Fung T, Lin TY, Hsu F, Guo Z. Spin Label Scanning Reveals Likely Locations of β-Strands in the Amyloid Fibrils of the Ure2 Prion Domain. ACS OMEGA 2020; 5:5984-5993. [PMID: 32226879 PMCID: PMC7098000 DOI: 10.1021/acsomega.9b04358] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
In yeast, the formation of Ure2 fibrils underlies the prion state [URE3], in which the yeast loses the ability to distinguish good nitrogen sources from bad ones. The Ure2 prion domain is both necessary and sufficient for the formation of amyloid fibrils. Understanding the structure of Ure2 fibrils is important for understanding the propagation not only of the [URE3] prion but also of other yeast prions whose prion domains share similar features, such as the enrichment of asparagine and glutamine residues. Here, we report a structural study of the amyloid fibrils formed by the Ure2 prion domain using site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy. We completed a spin label scanning of all the residue positions between 2 and 80 of the Ure2 prion domain. The EPR data show that the Ure2 fibril core consists of residues 8-68 and adopts a parallel in-register β-sheet structure. Most of the residues show strong spin-exchange interactions, suggesting that there are only short turns and no long loops in the fibril core. Based on the strength of spin-exchange interactions, we determined the likely locations of the β-strands. EPR data also show that the C-terminal region of the Ure2 prion domain is more disordered than the N-terminal region. The roles of hydrophobic and charged residues are analyzed. Overall, the structure of Ure2 fibrils appears to involve a balance of stabilizing interactions, such as asparagine ladders, and destabilizing interactions, such as stacking of charged residues.
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15
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Abstract
Amyloids and their infectious subset, prions, represent fibrillary aggregates with regular structure. They are formed by proteins that are soluble in their normal state. In amyloid form, all or part of the polypeptide sequence of the protein is resistant to treatment with proteinase K (PK). Amyloids can have structural variants, which can be distinguished by the patterns of their digestion by PK. In this review, we describe and compare studies of the resistant cores of various amyloids from different organisms. These data provide insight into the fine structure of amyloids and their variants as well as raise interesting questions, such as those concerning the differences between amyloids obtained ex vivo and in vitro, as well as the manner in which folding of one region of the amyloid can affect other regions.
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Affiliation(s)
- Vitaly V Kushnirov
- Research Center of Biotechnology of Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, Moscow, Russia
| | - Alexander A Dergalev
- Research Center of Biotechnology of Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, Moscow, Russia
| | - Alexander I Alexandrov
- Research Center of Biotechnology of Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, Moscow, Russia
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16
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Danilov LG, Matveenko AG, Ryzhkova VE, Belousov MV, Poleshchuk OI, Likholetova DV, Sokolov PA, Kasyanenko NA, Kajava AV, Zhouravleva GA, Bondarev SA. Design of a New [ PSI +]-No-More Mutation in SUP35 With Strong Inhibitory Effect on the [ PSI +] Prion Propagation. Front Mol Neurosci 2019; 12:274. [PMID: 31803017 PMCID: PMC6877606 DOI: 10.3389/fnmol.2019.00274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/28/2019] [Indexed: 12/04/2022] Open
Abstract
A number of [PSI+]-no-more (PNM) mutations, eliminating [PSI+] prion, were previously described in SUP35. In this study, we designed and analyzed a new PNM mutation based on the parallel in-register β-structure of Sup35 prion fibrils suggested by the known experimental data. In such an arrangement, substitution of non-charged residues by charged ones may destabilize the fibril structure. We introduced Q33K/A34K amino acid substitutions into the Sup35 protein, corresponding allele was called sup35-M0. The mutagenized residues were chosen based on ArchCandy in silico prediction of high inhibitory effect on the amyloidogenic potential of Sup35. The experiments confirmed that Sup35-M0 leads to the elimination of [PSI+] with high efficiency. Our data suggested that the elimination of the [PSI+] prion is associated with the decreased aggregation properties of the protein. The new mutation can induce the prion with very low efficiency and is able to propagate only weak [PSI+] prion variants. We also showed that Sup35-M0 protein co-aggregates with the wild-type Sup35 in vivo. Moreover, our data confirmed the utility of the strategy of substitution of non-charged residues by charged ones to design new mutations to inhibit a prion formation.
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Affiliation(s)
- Lavrentii G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Varvara E Ryzhkova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
| | - Olga I Poleshchuk
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Daria V Likholetova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Petr A Sokolov
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University, St. Petersburg, Russia
| | - Nina A Kasyanenko
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University, St. Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, Montpellier, France.,Institut de Biologie Computationnelle (IBC), Universitè Montpellier, Montpellier, France
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
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17
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Iadanza MG, Jackson MP, Hewitt EW, Ranson NA, Radford SE. A new era for understanding amyloid structures and disease. Nat Rev Mol Cell Biol 2019; 19:755-773. [PMID: 30237470 DOI: 10.1038/s41580-018-0060-8] [Citation(s) in RCA: 580] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aggregation of proteins into amyloid fibrils and their deposition into plaques and intracellular inclusions is the hallmark of amyloid disease. The accumulation and deposition of amyloid fibrils, collectively known as amyloidosis, is associated with many pathological conditions that can be associated with ageing, such as Alzheimer disease, Parkinson disease, type II diabetes and dialysis-related amyloidosis. However, elucidation of the atomic structure of amyloid fibrils formed from their intact protein precursors and how fibril formation relates to disease has remained elusive. Recent advances in structural biology techniques, including cryo-electron microscopy and solid-state NMR spectroscopy, have finally broken this impasse. The first near-atomic-resolution structures of amyloid fibrils formed in vitro, seeded from plaque material and analysed directly ex vivo are now available. The results reveal cross-β structures that are far more intricate than anticipated. Here, we describe these structures, highlighting their similarities and differences, and the basis for their toxicity. We discuss how amyloid structure may affect the ability of fibrils to spread to different sites in the cell and between organisms in a prion-like manner, along with their roles in disease. These molecular insights will aid in understanding the development and spread of amyloid diseases and are inspiring new strategies for therapeutic intervention.
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Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Eric W Hewitt
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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18
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Yeast Sup35 Prion Structure: Two Types, Four Parts, Many Variants. Int J Mol Sci 2019; 20:ijms20112633. [PMID: 31146333 PMCID: PMC6600473 DOI: 10.3390/ijms20112633] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022] Open
Abstract
The yeast [PSI+] prion, formed by the Sup35 (eRF3) protein, has multiple structural variants differing in the strength of nonsense suppressor phenotype. Structure of [PSI+] and its variation are characterized poorly. Here, we mapped Sup35 amyloid cores of 26 [PSI+] ex vivo prions of different origin using proteinase K digestion and mass spectrometric identification of resistant peptides. In all [PSI+] variants the Sup35 amino acid residues 2-32 were fully resistant and the region up to residue 72 was partially resistant. Proteinase K-resistant structures were also found within regions 73-124, 125-153, and 154-221, but their presence differed between [PSI+] isolates. Two distinct digestion patterns were observed for region 2-72, which always correlated with the "strong" and "weak" [PSI+] nonsense suppressor phenotypes. Also, all [PSI+] with a weak pattern were eliminated by multicopy HSP104 gene and were not toxic when combined with multicopy SUP35. [PSI+] with a strong pattern showed opposite properties, being resistant to multicopy HSP104 and lethal with multicopy SUP35. Thus, Sup35 prion cores can be composed of up to four elements. [PSI+] variants can be divided into two classes reliably distinguishable basing on structure of the first element and the described assays.
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19
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Bondarev SA, Bondareva OV, Zhouravleva GA, Kajava AV. BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures. Bioinformatics 2018; 34:599-608. [PMID: 29444233 DOI: 10.1093/bioinformatics/btx629] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/03/2017] [Indexed: 11/12/2022] Open
Abstract
Motivation Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics. Results We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments. Availability and implementation BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine). Contact stanislavspbgu@gmail.com or andrey.kajava@crbm.cnrs.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stanislav A Bondarev
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Olga V Bondareva
- Laboratory of Molecular Systematics, Zoological Institute RAS, Saint Petersburg 199034, Russia
| | - Galina A Zhouravleva
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Andrey V Kajava
- Structural Bioinformatics and Molecular Modeling, Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France.,Institut de Biologie Computationnelle, Montpellier 34095, France.,Bioengineering Department, University ITMO, Saint Petersburg, 197101, Russia
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20
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Villain E, Nikekhin AA, Kajava AV. Porins and Amyloids are Coded by Similar Sequence Motifs. Proteomics 2018; 19:e1800075. [DOI: 10.1002/pmic.201800075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/27/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Etienne Villain
- Centre de Recherche en Biologie cellulaire de MontpellierUMR 5237 CNRSUniversité Montpellier 1919 Route de MendeCEDEX 5 34293 Montpellier France
- Institut de Biologie Computationnelle 34095 Montpellier France
| | | | - Andrey V. Kajava
- Centre de Recherche en Biologie cellulaire de MontpellierUMR 5237 CNRSUniversité Montpellier 1919 Route de MendeCEDEX 5 34293 Montpellier France
- Institut de Biologie Computationnelle 34095 Montpellier France
- Institute of BioengineeringITMO University St. Petersburg 197101 Russia
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21
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Establishment of Constraints on Amyloid Formation Imposed by Steric Exclusion of Globular Domains. J Mol Biol 2018; 430:3835-3846. [DOI: 10.1016/j.jmb.2018.05.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/15/2018] [Accepted: 05/27/2018] [Indexed: 11/18/2022]
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22
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Schmuck B, Sandgren M, Härd T. The kinetics of TEM1 antibiotic degrading enzymes that are displayed on Ure2 protein nanofibrils in a flow reactor. PLoS One 2018; 13:e0196250. [PMID: 29684061 PMCID: PMC5912753 DOI: 10.1371/journal.pone.0196250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/09/2018] [Indexed: 01/31/2023] Open
Abstract
Enzymatic functionalization of cross-β structured protein nanofibrils has hitherto resulted in a severe reduction of the catalytic efficiency of high turnover biocatalysts. It has been speculated that steric restrictions and mass transport pose limits on the attached enzymes, but detailed kinetics analyzing this have not yet been reported. For a more comprehensive understanding, we studied protein nanofibrils endowed with TEM1, a β-lactamase from Escherichia coli. The packing density of TEM1 along the fibrils was controlled by co-fibrillation; in other words, the N-terminal ureidosuccinate transporter Ure2(1–80) from Saccharomyces cerevisiae was simultaneously aggregated with the chimeric proteins TEM1-Ure2(1–80). The mature fibrils were trapped in a column, and the rate of ampicillin hydrolysis was recorded using a continuous substrate flow. The turnover rate was plotted as a function of substrate molecules available per enzyme per second, which demonstrated that an elevated substrate availability counteracts mass transport limitations. To analyze this data set, we derived a kinetic model, which makes it possible to easily characterize and compare enzymes packed in columns. The functional TEM1 nanofibrils possess 80% of the catalytic turnover rate compared to free TEM1 in solution. Altogether, we have created protein nanofibrils that can effectively hydrolyze β-lactam antibiotic contaminations and provided a groundwork strategy for other highly functional enzymatic nanofibrils.
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Affiliation(s)
- Benjamin Schmuck
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Torleif Härd
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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23
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Upadhyay A, Mishra A. Amyloids of multiple species: are they helpful in survival? Biol Rev Camb Philos Soc 2018; 93:1363-1386. [DOI: 10.1111/brv.12399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 01/13/2018] [Accepted: 01/18/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Arun Upadhyay
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan 342011 India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan 342011 India
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24
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Yang J, Dear AJ, Michaels TCT, Dobson CM, Knowles TPJ, Wu S, Perrett S. Direct Observation of Oligomerization by Single Molecule Fluorescence Reveals a Multistep Aggregation Mechanism for the Yeast Prion Protein Ure2. J Am Chem Soc 2018; 140:2493-2503. [PMID: 29357227 PMCID: PMC5880511 DOI: 10.1021/jacs.7b10439] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
The self-assembly of polypeptides
into amyloid structures is associated
with a range of increasingly prevalent neurodegenerative diseases
as well as with a select set of functional processes in biology. The
phenomenon of self-assembly results in species with dramatically different
sizes, from small oligomers to large fibrils; however, the kinetic
relationship between these species is challenging to characterize.
In the case of prion aggregates, these structures can self-replicate
and act as infectious agents. Here we use single molecule spectroscopy
to obtain quantitative information on the oligomer populations formed
during aggregation of the yeast prion protein Ure2. Global analysis
of the aggregation kinetics reveals the molecular mechanism underlying
oligomer formation and depletion. Quantitative characterization indicates
that the majority of Ure2 oligomers are relatively short-lived, and
their rate of dissociation is much higher than their rate of conversion
into growing fibrils. We identify an initial metastable oligomer,
which can subsequently convert into a structurally distinct oligomer,
which in turn converts into growing fibrils. We also show that fragmentation
is responsible for the autocatalytic self-replication of Ure2 fibrils,
but that preformed fibrils do not promote oligomer formation, indicating
that secondary nucleation of the type observed for peptides and proteins
associated with neurodegenerative disease does not occur at a significant
rate for Ure2. These results establish a framework for elucidating
the temporal and causal relationship between oligomers and larger
fibrillar species in amyloid forming systems, and provide insights
into why functional amyloid systems are not toxic to their host organisms.
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Affiliation(s)
- Jie Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , 15 Datun Road, Chaoyang District, Beijing 100101, China.,University of the Chinese Academy of Sciences , 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Alexander J Dear
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Cavendish Laboratory , J J Thomson Avenue, Cambridge CB3 1HE, United Kingdom
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , 15 Datun Road, Chaoyang District, Beijing 100101, China.,University of the Chinese Academy of Sciences , 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , 15 Datun Road, Chaoyang District, Beijing 100101, China.,University of the Chinese Academy of Sciences , 19A Yuquan Road, Shijingshan District, Beijing 100049, China
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25
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Meier BH, Riek R, Böckmann A. Emerging Structural Understanding of Amyloid Fibrils by Solid-State NMR. Trends Biochem Sci 2017; 42:777-787. [PMID: 28916413 DOI: 10.1016/j.tibs.2017.08.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 11/28/2022]
Abstract
Amyloid structures at atomic resolution have remained elusive mainly because of their extensive polymorphism and because their polymeric properties have hampered structural studies by classical approaches. Progress in sample preparation, as well as solid-state NMR methods, recently enabled the determination of high-resolution 3D structures of fibrils such as the amyloid-β fibril, which is involved in Alzheimer's disease. Notably, the simultaneous but independent structure determination of Aβ1-42, a peptide that forms fibrillar deposits in the brain of Alzheimer patients, by two independent laboratories, which yielded virtually identical results, has highlighted how structures can be obtained that allow further functional investigation.
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Affiliation(s)
- Beat H Meier
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
| | - Roland Riek
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon,7 passage du Vercors, 69367 Lyon, France.
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26
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Roche DB, Villain E, Kajava AV. Usage of a dataset of NMR resolved protein structures to test aggregation versus solubility prediction algorithms. Protein Sci 2017; 26:1864-1869. [PMID: 28685932 DOI: 10.1002/pro.3225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/21/2017] [Accepted: 06/29/2017] [Indexed: 01/08/2023]
Abstract
There has been an increased interest in computational methods for amyloid and (or) aggregate prediction, due to the prevalence of these aggregates in numerous diseases and their recently discovered functional importance. To evaluate these methods, several datasets have been compiled. Typically, aggregation-prone regions of proteins, which form aggregates or amyloids in vivo, are more than 15 residues long and intrinsically disordered. However, the number of such experimentally established amyloid forming and non-forming sequences are limited, not exceeding one hundred entries in existing databases. In this work, we parsed all available NMR-resolved protein structures from the PDB and assembled a new, sevenfold larger, dataset of unfolded sequences, soluble at high concentrations. We proposed to use these sequences as a negative set for evaluating methods for predicting aggregation in vivo. We also present the results of benchmarking cutting edge tools for the prediction of aggregation versus solubility propensity.
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Affiliation(s)
- Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
| | - Etienne Villain
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France.,University ITMO, 49 Kronverksky Pr, 197101, St. Petersburg, Russia
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27
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Abstract
Prions are infectious protein polymers that have been found to cause fatal diseases in mammals. Prions have also been identified in fungi (yeast and filamentous fungi), where they behave as cytoplasmic non-Mendelian genetic elements. Fungal prions correspond in most cases to fibrillary β-sheet-rich protein aggregates termed amyloids. Fungal prion models and, in particular, yeast prions were instrumental in the description of fundamental aspects of prion structure and propagation. These models established the "protein-only" nature of prions, the physical basis of strain variation, and the role of a variety of chaperones in prion propagation and amyloid aggregate handling. Yeast and fungal prions do not necessarily correspond to harmful entities but can have adaptive roles in these organisms.
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28
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Abstract
Protein aggregation is a hallmark of neurodegenerative disorders. In this group of brain-related disorders, a disease-specific "host" protein or fragment misfolds and adopts a metastatic, aggregate-prone conformation. Often, this misfolded conformation is structurally and thermodynamically different from its native state. Intermolecular contacts, which arise in this non-native state, promote aggregation. In this regard, understanding the molecular principles and mechanisms that lead to the formation of such a non-native state and further promote the formation of the critical nucleus for fiber growth is essential. In this study, the authors analyze the aggregation propensity of Huntingtin headpiece (httNT), which is known to facilitate the polyQ aggregation, in relation to the helix mediated aggregation mechanism proposed by the Wetzel group. The authors demonstrate that even though httNT displays a degenerate conformational spectrum on its own, interfaces of macroscopic or molecular origin can promote the α-helix conformation, eliminating all other alternatives in the conformational phase space. Our findings indicate that httNT molecules do not have a strong orientational preference for parallel or antiparallel orientation of the helices within the aggregate. However, a parallel packed bundle of helices would support the idea of increased polyglutamine concentration, to pave the way for cross-β structures.
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29
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Schmuck B, Sandgren M, Härd T. A fine-tuned composition of protein nanofibrils yields an upgraded functionality of displayed antibody binding domains. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/02/2017] [Accepted: 03/31/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Benjamin Schmuck
- Department of Molecular Sciences; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Mats Sandgren
- Department of Molecular Sciences; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Torleif Härd
- Department of Molecular Sciences; Swedish University of Agricultural Sciences; Uppsala Sweden
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30
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DeBenedictis EP, Ma D, Keten S. Structural predictions for curli amyloid fibril subunits CsgA and CsgB. RSC Adv 2017. [DOI: 10.1039/c7ra08030a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CsgA are the building blocks of curli fibrils.
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Affiliation(s)
- E. P. DeBenedictis
- Department of Civil and Environmental Engineering and Mechanical Engineering
- Northwestern University
- Evanston
- USA
| | - D. Ma
- Department of Civil and Environmental Engineering and Mechanical Engineering
- Northwestern University
- Evanston
- USA
| | - S. Keten
- Department of Civil and Environmental Engineering and Mechanical Engineering
- Northwestern University
- Evanston
- USA
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31
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Sulatskaya AI, Kuznetsova IM, Belousov MV, Bondarev SA, Zhouravleva GA, Turoverov KK. Stoichiometry and Affinity of Thioflavin T Binding to Sup35p Amyloid Fibrils. PLoS One 2016; 11:e0156314. [PMID: 27228180 PMCID: PMC4882037 DOI: 10.1371/journal.pone.0156314] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/12/2016] [Indexed: 11/25/2022] Open
Abstract
In this work two modes of binding of the fluorescent probe thioflavin T to yeast prion protein Sup35p amyloid fibrils were revealed by absorption spectrometry of solutions prepared by equilibrium microdialysis. These binding modes exhibited significant differences in binding affinity and stoichiometry. Moreover, the absorption spectrum and the molar extinction coefficient of the dye bound in each mode were determined. The fluorescence quantum yield of the dye bound in each mode was determined via a spectrofluorimetric study of the same solutions in which the recorded fluorescence intensity was corrected for the primary inner filter effect. As previously predicted, the existence of one of the detected binding modes may be due to the incorporation of the dye into the grooves along the fiber axis perpendicular to the β-sheets of the fibrils. It was assumed that the second type of binding with higher affinity may be due to the existence of ThT binding sites that are localized to areas where amyloid fibrils are clustered.
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Affiliation(s)
- Anna I. Sulatskaya
- Laboratory for Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Tikhoretsky Ave. 4, 194064, Russia
| | - Irina M. Kuznetsova
- Laboratory for Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Tikhoretsky Ave. 4, 194064, Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Universitetskaya Emb. 7–9, 199034, Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Universitetskaya Emb. 7–9, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Universitetskaya Emb. 7–9, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Konstantin K. Turoverov
- Laboratory for Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Tikhoretsky Ave. 4, 194064, Russia
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St.-Petersburg Polytechnic University, St. Petersburg, Polytechnicheskaya 29, 195251, Russia
- * E-mail:
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32
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Huang YW, Chang YC, Diaz-Avalos R, King CY. W8, a new Sup35 prion strain, transmits distinctive information with a conserved assembly scheme. Prion 2016; 9:207-27. [PMID: 26038983 DOI: 10.1080/19336896.2015.1039217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Prion strains are different self-propagating conformers of the same infectious protein. Three strains of the [PSI] prion, infectious forms of the yeast Sup35 protein, have been previously characterized in our laboratory. Here we report the discovery of a new [PSI] strain, named W8. We demonstrate its robust cellular propagation as well as the protein-only transmission. To reveal strain-specific sequence requirement, mutations that interfered with the propagation of W8 were identified by consecutive substitution of residues 5-55 of Sup35 by proline and insertion of glycine at alternate sites in this segment. Interestingly, propagating W8 with single mutations at residues 5-7 and around residue 43 caused the strain to transmute. In contrast to the assertion that [PSI] existed as a dynamic cloud of sub-structures, no random drift in transmission characteristics was detected in mitotically propagated W8 populations. Electron diffraction and mass-per-length measurements indicate that, similar to the 3 previously characterized strains, W8 fibers are composed of about 1 prion molecule per 4.7-Å cross-β repeat period. Thus differently folded single Sup35 molecules, not dimeric and trimeric assemblies, form the basic repeating units to build the 4 [PSI] strains.
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Key Words
- 5-FOA, 5-fluoroorotic acid
- Aβ, amyloid β-protein
- GFP, green fluorescent protein
- PrP, prion protein
- SC, synthetic complete
- STEM, scanning transmission electron microscopy
- YPD, yeast extract, peptone, dextrose
- amyloid, prion strain, [PSI+], SUP35, yeast
- mpl, mass per length
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Affiliation(s)
- Yu-Wen Huang
- a Molecular and Cell Biology; Taiwan International Graduate Program; Academia Sinica and National Defense Medical Center ; Taipei , Taiwan
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Torbeev V, Grogg M, Ruiz J, Boehringer R, Schirer A, Hellwig P, Jeschke G, Hilvert D. Chiral recognition in amyloid fiber growth. J Pept Sci 2016; 22:290-304. [DOI: 10.1002/psc.2861] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/05/2016] [Accepted: 01/11/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires; International Center for Frontier Research in Chemistry, UMR 7006, Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Marcel Grogg
- Laboratory of Organic Chemistry, ETH Zurich; Vladimir-Prelog-Weg 1-5/10; Zürich CH-8093 Switzerland
| | - Jérémy Ruiz
- Institut de Science et d'Ingénierie Supramoléculaires; International Center for Frontier Research in Chemistry, UMR 7006, Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Régis Boehringer
- Institut de Science et d'Ingénierie Supramoléculaires; International Center for Frontier Research in Chemistry, UMR 7006, Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Alicia Schirer
- Laboratoire de Bioélectrochimie et Spectroscopie; Chimie de la Matière Complexe, UMR 7140, Université de Strasbourg-CNRS; 1 rue Blaise Pascal 67070 Strasbourg France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie; Chimie de la Matière Complexe, UMR 7140, Université de Strasbourg-CNRS; 1 rue Blaise Pascal 67070 Strasbourg France
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry; ETH Zurich, Vladimir-Prelog-Weg 1-5/10; Zürich CH-8093 Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich; Vladimir-Prelog-Weg 1-5/10; Zürich CH-8093 Switzerland
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Dearborn AD, Wall JS, Cheng N, Heymann JB, Kajava AV, Varkey J, Langen R, Steven AC. α-Synuclein Amyloid Fibrils with Two Entwined, Asymmetrically Associated Protofibrils. J Biol Chem 2015; 291:2310-8. [PMID: 26644467 DOI: 10.1074/jbc.m115.698787] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Indexed: 11/06/2022] Open
Abstract
Parkinson disease and other progressive neurodegenerative conditions are characterized by the intracerebral presence of Lewy bodies, containing amyloid fibrils of α-synuclein. We used cryo-electron microscopy and scanning transmission electron microscopy (STEM) to study in vitro-assembled fibrils. These fibrils are highly polymorphic. Focusing on twisting fibrils with an inter-crossover spacing of 77 nm, our reconstructions showed them to consist of paired protofibrils. STEM mass per length data gave one subunit per 0.47 nm axial rise per protofibril, consistent with a superpleated β-structure. The STEM images show two thread-like densities running along each of these fibrils, which we interpret as ladders of metal ions. These threads confirmed the two-protofibril architecture of the 77-nm twisting fibrils and allowed us to identify this morphotype in STEM micrographs. Some other, but not all, fibril morphotypes also exhibit dense threads, implying that they also present a putative metal binding site. We propose a molecular model for the protofibril and suggest that polymorphic variant fibrils have different numbers of protofibrils that are associated differently.
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Affiliation(s)
- Altaira D Dearborn
- From the Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Joseph S Wall
- the Department of Biology, Brookhaven National Laboratory, Upton, New York 19973
| | - Naiqian Cheng
- From the Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - J Bernard Heymann
- From the Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrey V Kajava
- the Centre de Recherches de Biochimie Macromoléculaire, CNRS, University of Montpellier, Montpellier 34172, France, the University ITMO, Institute of Bioengineering, 197101 St. Petersburg, Russia
| | - Jobin Varkey
- the Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90033, and Karunya University, Coimbatore, Tamil Nadu 641 114, India
| | - Ralf Langen
- the Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90033, and
| | - Alasdair C Steven
- From the Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892,
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Wong SH, King CY. Amino Acid Proximities in Two Sup35 Prion Strains Revealed by Chemical Cross-linking. J Biol Chem 2015; 290:25062-71. [PMID: 26265470 DOI: 10.1074/jbc.m115.676379] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 12/26/2022] Open
Abstract
Strains of the yeast prion [PSI] are different folding patterns of the same Sup35 protein, which stacks up periodically to form a prion fiber. Chemical cross-linking is employed here to probe different fiber structures assembled with a mutant Sup35 fragment. The photo-reactive cross-linker, p-benzoyl-l-phenylalanine (pBpa), was biosynthetically incorporated into bacterially prepared recombinant Sup(1-61)-GFP, containing the first 61 residues of Sup35, followed by the green fluorescent protein. Four methionine substitutions and two alanine substitutions were introduced at fixed positions in Sup(1-61) to allow cyanogen bromide cleavage to facilitate subsequent mass spectrometry analysis. Amyloid fibers of pBpa and Met/Ala-substituted Sup(1-61)-GFP were nucleated from purified yeast prion particles of two different strains, namely VK and VL, and shown to faithfully transmit specific strain characteristics to yeast expressing the wild type Sup35 protein. Intra- and intermolecular cross-linking were distinguished by tandem mass spectrometry analysis on fibers seeded from solutions containing equal amounts of (14)N- and (15)N-labeled protein. Fibers propagating the VL strain type exhibited intra- and intermolecular cross-linking between amino acid residues 3 and 28, as well as intra- and intermolecular linking between 32 and 55. Inter- and intramolecular cross-linking between residues 32 and 55 were detected in fibers propagating the VK strain type. Adjacencies of amino acid residues in space revealed by cross-linking were used to constrain possible chain folds of different [PSI] strains.
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Affiliation(s)
- Shenq-Huey Wong
- From the Molecular Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan and the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Yen King
- the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
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Computational Approaches to Identification of Aggregation Sites and the Mechanism of Amyloid Growth. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:213-39. [DOI: 10.1007/978-3-319-17344-3_9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Bondarev SA, Zhouravleva GA, Belousov MV, Kajava AV. Structure-based view on [PSI(+)] prion properties. Prion 2015; 9:190-9. [PMID: 26030475 PMCID: PMC4601339 DOI: 10.1080/19336896.2015.1044186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/17/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022] Open
Abstract
Yeast [PSI(+)] prion is one of the most suitable and well characterized system for the investigation of the prion phenomenon. However, until recently, the lack of data on the 3D arrangement of Sup35p prion fibrils hindered progress in this area. The recent arrival in this field of new experimental techniques led to the parallel and in-register superpleated β-structure as a consensus model for Sup35p fibrils. Here, we analyzed the effect of amino acid substitutions of the Sup35 protein through the prism of this structural model. Application of a newly developed computational approach, called ArchCandy, gives us a better understanding of the effect caused by mutations on the fibril forming potential of Sup35 protein. This bioinformatics tool can be used for the design of new mutations with desired modification of prion properties. Thus, we provide examples of how today, having progress toward elucidation of the structural arrangement of Sup35p fibrils, researchers can advance more efficiently to a better understanding of prion [PSI(+)] stability and propagation.
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Key Words
- Asu mutations, antisupressor mutations
- EM, electron microscopy
- NMR, nuclear magnetic resonance
- PNM, [PSI+] no more
- STEM, scanning transmission electron microscopy
- amyloid, prion, protein misfolding, protein structure, Saccharomyces cerevisiae, superpleated β-structure, [PSI+]
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Affiliation(s)
- Stanislav A Bondarev
- Department of Genetics and Biotechnology; St. Petersburg State University; St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology; St. Petersburg State University; St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology; St. Petersburg State University; St. Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire; CNRS; Université Montpellier; Montpellier, Cedex 5, France
- University ITMO; St. Petersburg, Russia
- Institut de Biologie Computationnelle; Montpellier, Cedex 5, France
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Evolutionary link between metazoan RHIM motif and prion-forming domain of fungal heterokaryon incompatibility factor HET-s/HET-s. Sci Rep 2014; 4:7436. [PMID: 25500536 PMCID: PMC4262963 DOI: 10.1038/srep07436] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 11/21/2014] [Indexed: 11/30/2022] Open
Abstract
The Rip homotypic interaction motif (RHIM) is a short, non-globular sequence stretch that mediates a key interaction of mammalian necroptosis signaling. In order to understand its unusual oligomerization properties, we set out to trace the evolutionary origins of the RHIM motif by identifying distantly related protein motifs that might employ the same binding mode. The RHIM motif was found to be related to the prion-forming domain of the HET-s protein, which oligomerizes by forming structurally well-characterized fibrils and is involved in fungal heterokaryon incompatibility. This evolutionary relationship explains the recently reported propensity of mammalian RHIM motifs to form amyloid fibrils, but suggests that these fibrils have a different structural architecture than currently assumed. These findings, together with numerous observations of RHIM-like motifs in immunity proteins from a wide range of species, provide insight to the modern innate immunity pathways in animals, plants and fungi.
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Ahmed AB, Znassi N, Château MT, Kajava AV. A structure-based approach to predict predisposition to amyloidosis. Alzheimers Dement 2014; 11:681-90. [PMID: 25150734 DOI: 10.1016/j.jalz.2014.06.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/22/2014] [Accepted: 06/06/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Neurodegenerative diseases and other amyloidoses are linked to the formation of amyloid fibrils. It has been shown that the ability to form these fibrils is coded by the amino acid sequence. Existing methods for the prediction of amyloidogenicity generate an unsatisfactory high number of false positives when tested against sequences of the disease-related proteins. METHODS Recently, it has been shown that the three-dimensional structure of a majority of disease-related amyloid fibrils contains a β-strand-loop-β-strand motif called β-arch. Using this information, we have developed a novel bioinformatics approach for the prediction of amyloidogenicity. RESULTS The benchmark results show the superior performance of our method over the existing programs. CONCLUSIONS As genome sequencing becomes more affordable, our method provides an opportunity to create individual risk profiles for the neurodegenerative, age-related, and other diseases ushering in an era of personalized medicine. It will also be used in the large-scale analysis of proteomes to find new amyloidogenic proteins.
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Affiliation(s)
- Abdullah B Ahmed
- Centre de Recherches de Biochimie Macromoléculaire, UMR5237, CNRS, Université Montpellier 1 et 2, Montpellier, France; Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Nadia Znassi
- Centre de Recherches de Biochimie Macromoléculaire, UMR5237, CNRS, Université Montpellier 1 et 2, Montpellier, France; Institut de Biologie Computationnelle, Montpellier, France
| | - Marie-Thérèse Château
- Centre de Recherches de Biochimie Macromoléculaire, UMR5237, CNRS, Université Montpellier 1 et 2, Montpellier, France; UFR des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
| | - Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, UMR5237, CNRS, Université Montpellier 1 et 2, Montpellier, France; Institut de Biologie Computationnelle, Montpellier, France.
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Huang RK, Baxa U, Aldrian G, Ahmed AB, Wall JS, Mizuno N, Antzutkin O, Steven AC, Kajava AV. Conformational switching in PolyGln amyloid fibrils resulting from a single amino acid insertion. Biophys J 2014; 106:2134-42. [PMID: 24853742 PMCID: PMC4052364 DOI: 10.1016/j.bpj.2014.03.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/18/2014] [Accepted: 03/25/2014] [Indexed: 11/16/2022] Open
Abstract
The established correlation between neurodegenerative disorders and intracerebral deposition of polyglutamine aggregates motivates attempts to better understand their fibrillar structure. We designed polyglutamines with a few lysines inserted to overcome the hindrance of extreme insolubility and two D-lysines to limit the lengths of β-strands. One is 33 amino acids long (PolyQKd-33) and the other has one fewer glutamine (PolyQKd-32). Both form well-dispersed fibrils suitable for analysis by electron microscopy. Electron diffraction confirmed cross-β structures in both fibrils. Remarkably, the deletion of just one glutamine residue from the middle of the peptide leads to substantially different amyloid structures. PolyQKd-32 fibrils are consistently 10-20% wider than PolyQKd-33, as measured by negative staining, cryo-electron microscopy, and scanning transmission electron microscopy. Scanning transmission electron microscopy analysis revealed that the PolyQKd-32 fibrils have 50% higher mass-per-length than PolyQKd-33. This distinction can be explained by a superpleated β-structure model for PolyQKd-33 and a model with two β-solenoid protofibrils for PolyQKd-32. These data provide evidence for β-arch-containing structures in polyglutamine fibrils and open future possibilities for structure-based drug design.
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Affiliation(s)
- Rick K Huang
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, Maryland
| | - Ulrich Baxa
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, Maryland; Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Gudrun Aldrian
- Centre de Recherches de Biochimie Macromoléculaire, CNRS, University of Montpellier 1 and 2, Montpellier, France
| | - Abdullah B Ahmed
- Centre de Recherches de Biochimie Macromoléculaire, CNRS, University of Montpellier 1 and 2, Montpellier, France
| | - Joseph S Wall
- Department of Biology, Brookhaven National Laboratory, Upton New York
| | - Naoko Mizuno
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, Maryland; Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Oleg Antzutkin
- Chemistry of Interfaces, Luleå University of Technology, Luleå, Sweden; Department of Physics, Warwick University, Coventry, United Kingdom
| | - Alasdair C Steven
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, Maryland.
| | - Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, CNRS, University of Montpellier 1 and 2, Montpellier, France; Institut de Biologie Computationnelle, Montpellier, France; University ITMO, 197101 St. Petersburg, Russia.
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41
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French KC, Roan NR, Makhatadze GI. Structural characterization of semen coagulum-derived SEM1(86-107) amyloid fibrils that enhance HIV-1 infection. Biochemistry 2014; 53:3267-77. [PMID: 24811874 PMCID: PMC4039337 DOI: 10.1021/bi500427r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
SEM1(86–107)
is a 22-residue peptide corresponding to residues
86–107 in the semenogelin I protein. SEM1(86–107) is
an abundant component of freshly liquefied semen and forms amyloid
fibrils capable of enhancing HIV infection. To probe the factors affecting
fibril formation and gain a better understanding of how differences
in pH between semen and vaginal fluid affect fibril stability, this
study determined the effect of pH on SEM1(86–107) fibril formation
and dissociation. The SEM1(86–107) fibril structure (i.e.,
residues that comprise the fibrillar core) was also probed using hydrogen–deuterium
exchange mass spectrometry (HDXMS) and hydroxyl radical-mediated protein
modification. The average percent exposure to hydroxyl radical-mediated
modification in the SEM1(86–107) fibrils was determined without
requiring tandem mass spectrometry spectral acquisition or complete
separation of modified peptides. It was found that the residue exposures
calculated from HDXMS and hydroxyl radical-mediated modification were
similar. These techniques demonstrated that three regions of SEM1(86–107)
comprise the amyloid fibril core and that positively charged residues
are exposed, suggesting that electrostatic interactions between SEM1(86–107)
and HIV or the cell surface may be responsible for mediating HIV infection
enhancement by the SEM1(86–107) fibrils.
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Affiliation(s)
- Kinsley C French
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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Miettinen MS, Monticelli L, Nedumpully-Govindan P, Knecht V, Ignatova Z. Stable polyglutamine dimers can contain β-hairpins with interdigitated side chains-but not α-helices, β-nanotubes, β-pseudohelices, or steric zippers. Biophys J 2014; 106:1721-8. [PMID: 24739171 PMCID: PMC4008795 DOI: 10.1016/j.bpj.2014.02.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/03/2014] [Accepted: 02/25/2014] [Indexed: 10/25/2022] Open
Abstract
A common thread connecting nine fatal neurodegenerative protein aggregation diseases is an abnormally expanded polyglutamine tract found in the respective proteins. Although the structure of this tract in the large mature aggregates is increasingly well described, its structure in the small early aggregates remains largely unknown. As experimental evidence suggests that the most toxic species along the aggregation pathway are the small early ones, developing strategies to alleviate disease pathology calls for understanding the structure of polyglutamine peptides in the early stages of aggregation. Here, we present a criterion, grounded in available experimental data, that allows for using kinetic stability of dimers to assess whether a given polyglutamine conformer can be on the aggregation path. We then demonstrate that this criterion can be assessed using present-day molecular dynamics simulations. We find that although the α-helical conformer of polyglutamine is very stable, dimers of α-helices lack the kinetic stability necessary to support further oligomerization. Dimers of steric zipper, β-nanotube, and β-pseudohelix conformers are also too short-lived to initiate aggregation. The β-hairpin-containing conformers, instead, invariably form very stable dimers when their side chains are interdigitated. Combining these findings with the implications of recent solid-state NMR data on mature fibrils, we propose a possible pathway for the initial stages of polyglutamine aggregation, in which β-hairpin-containing conformers act as templates for fibril formation.
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Affiliation(s)
- Markus S Miettinen
- Fachbereich Physik, Freie Universität Berlin, Berlin, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
| | - Luca Monticelli
- Institut National de la santé et de la recherche medicale, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | | | - Volker Knecht
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Bondarev SA, Shirokolobova ED, Trubitsina NP, Zhouravleva GA. Modification of [PSI +] prion properties by combining amino acid changes in N-terminal domain of Sup35 protein. Mol Biol 2014. [DOI: 10.1134/s0026893314020034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bondarev SA, Shchepachev VV, Kajava AV, Zhouravleva GA. Effect of charged residues in the N-domain of Sup35 protein on prion [PSI+] stability and propagation. J Biol Chem 2013; 288:28503-13. [PMID: 23965990 DOI: 10.1074/jbc.m113.471805] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Recent studies have shown that Sup35p prion fibrils probably have a parallel in-register β-structure. However, the part(s) of the N-domain critical for fibril formation and maintenance of the [PSI(+)] phenotype remains unclear. Here we designed a set of five SUP35 mutant alleles (sup35(KK)) with lysine substitutions in each of five N-domain repeats, and investigated their effect on infectivity and ability of corresponding proteins to aggregate and coaggregate with wild type Sup35p in the [PSI(+)] strain. Alleles sup35-M1 (Y46K/Q47K) and sup35-M2 (Q61K/Q62K) led to prion loss, whereas sup35-M3 (Q70K/Q71K), sup35-M4 (Q80K/Q81K), and sup35-M5 (Q89K/Q90K) were able to maintain the [PSI(+)] prion. This suggests that the critical part of the parallel in-register β-structure for the studied [PSI(+)] prion variant lies in the first 63-69 residues. Our study also reveals an unexpected interplay between the wild type Sup35p and proteins expressed from the sup35(KK) alleles during prionization. Both Sup35-M1p and Sup35-M2p coaggregated with Sup35p, but only sup35-M2 led to prion loss in a dominant manner. We suggest that in the fibrils, Sup35p can bind to Sup35-M1p in the same conformation, whereas Sup35-M2p only allowed the Sup35p conformation that leads to the non-heritable fold. Mutations sup35-M4 and sup35-M5 influence the structure of the prion forming region to a lesser extent, and can lead to the formation of new prion variants.
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Affiliation(s)
- Stanislav A Bondarev
- From the Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg, Russia
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Ahmed AB, Kajava AV. Breaking the amyloidogenicity code: methods to predict amyloids from amino acid sequence. FEBS Lett 2012; 587:1089-95. [PMID: 23262221 DOI: 10.1016/j.febslet.2012.12.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 12/11/2012] [Accepted: 12/11/2012] [Indexed: 11/18/2022]
Abstract
Numerous studies have shown that the ability to form amyloid fibrils is an inherent property of the polypeptide chain. This has lead to the development of several computational approaches to predict amyloidogenicity by amino acid sequences. Here, we discuss the principles governing these methods, and evaluate them using several datasets. They deliver excellent performance in the tests made using short peptides (~6 residues). However, there is a general tendency towards a high number of false positives when tested against longer sequences. This shortcoming needs to be addressed as these longer sequences are linked to diseases. Recent structural studies have shown that the core element of the majority of disease-related amyloid fibrils is a β-strand-loop-β-strand motif called β-arch. This insight provides an opportunity to substantially improve the prediction of amyloids produced by natural proteins, ushering in an era of personalized medicine based on genome analysis.
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Affiliation(s)
- Abdullah B Ahmed
- Centre de Recherches de Biochimie Macromoléculaire, UMR5237 CNRS, Montpellier 1 et 2, 1919, Route de Mende, 34293 Montpellier Cédex 5, France
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Ngo S, Chiang V, Guo Z. Quantitative analysis of spin exchange interactions to identify β strand and turn regions in Ure2 prion domain fibrils with site-directed spin labeling. J Struct Biol 2012; 180:374-81. [PMID: 22967940 DOI: 10.1016/j.jsb.2012.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 08/23/2012] [Accepted: 08/24/2012] [Indexed: 12/21/2022]
Abstract
Amyloid formation is associated with a range of debilitating human disorders including Alzheimer's and prion diseases. The amyloid structure is essential for understanding the role of amyloids in these diseases. Amyloid formation of Ure2 protein underlies the yeast prion [URE3]. Here we use site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy to investigate the structure of amyloid fibrils formed by the Ure2 prion domain. The Ure2 prion domain under study contains a Sup35M domain at C-terminus as a solubilization element. We introduced spin labels at every residue from positions 2-15, and every 5th residue from positions 20-80 in Ure2 prion domain. EPR spectra at most labeling sites show strong spin exchange interactions, suggesting a parallel in-register β structure. With quantitative analysis of spin exchange interactions, we show that residues 8-12 form the first β strand, followed by a turn at residues 13-14, and then the second β strand from residue 15 to at least residue 20. Comparison of the spin exchange frequency for the fibrils formed under quiescent and agitated conditions also revealed differences in the fibril structures. Currently there is a lack of techniques for in-depth structural studies of amyloid fibrils. Detailed structural information is obtained almost exclusively from solid-state NMR. The identification of β-strand and turn regions in this work suggests that quantitative analysis of spin exchange interactions in spin-labeled amyloid fibrils is a powerful approach for identifying the β-strand and turn/loop residues and for studying structural differences of different fibril polymorphs.
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Affiliation(s)
- Sam Ngo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, 710 Westwood Plaza, Los Angeles, CA 90095, USA
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Miettinen MS, Knecht V, Monticelli L, Ignatova Z. Assessing polyglutamine conformation in the nucleating event by molecular dynamics simulations. J Phys Chem B 2012; 116:10259-65. [PMID: 22770401 DOI: 10.1021/jp305065c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polyglutamine (polyQ) diseases comprise a group of dominantly inherited pathology caused by an expansion of an unstable polyQ stretch which is presumed to form β-sheets. Similar to other amyloid pathologies, polyQ amyloidogenesis occurs via a nucleated polymerization mechanism, and proceeds through energetically unfavorable nucleus whose existence and structure are difficult to detect. Here, we use atomistic molecular dynamics simulations in explicit solvent to assess the conformation of the polyQ stretch in the nucleus that initiates polyQ fibrillization. Comparison of the kinetic stability of various structures of polyQ peptide with a Q-length in the pathological range (Q40) revealed that steric zipper or nanotube-like structures (β-nanotube or β-pseudohelix) are not kinetically stable enough to serve as a template to initiate polyQ fibrillization as opposed to β-hairpin-based (β-sheet and β-sheetstack) or α-helical conformations. The selection of different structures of the polyQ stretch in the aggregation-initiating event may provide an alternative explanation for polyQ aggregate polymorphism.
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Affiliation(s)
- Markus S Miettinen
- Institute of Biochemistry and Biology, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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48
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Lyubchenko YL, Krasnoslobodtsev AV, Luca S. Fibrillogenesis of huntingtin and other glutamine containing proteins. Subcell Biochem 2012; 65:225-51. [PMID: 23225006 PMCID: PMC4226413 DOI: 10.1007/978-94-007-5416-4_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This chapter focuses on the aggregation of glutamine containing peptides and proteins with an emphasis on huntingtin protein, whose aggregation leads to the development of Huntington's disease. The kinetics that leads to the formation of amyloids, the structure of aggregates of various types and the morphological mechanical properties of amyloid fibrils are described. The kinetics of amyloid fibril formation has been proposed to follow a nucleation dependent polymerization model, dependent upon the size of the nucleus. This model and the effect of the polyglutamine length on the nucleus size are reviewed. Aggregate structure is characterized at two different levels. The atomic-scale resolution structure of fibrillar and crystalline aggregates of polyglutamine containing proteins and peptides was determined by X-ray crystallography and solid-state nuclear magnetic resonance (NMR). The chapter outlines the results obtained by both these techniques. Atomic force microscopy (AFM) was instrumental in elucidating the morphology of fibrils, their organization and assembly. The chapter also discusses the high stability of amyloid fibrils, including their mechanical properties as revealed by AFM.
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Affiliation(s)
- Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, Nanoimaging Core Facility College of Pharmacy, University of Nebraska Medical Center, COP 1012, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Alexey V. Krasnoslobodtsev
- Department of Pharmaceutical Sciences, Nanoimaging Core Facility College of Pharmacy, University of Nebraska Medical Center, COP 1012, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Sorin Luca
- Department of Pharmaceutical Sciences, Nanoimaging Core Facility College of Pharmacy, University of Nebraska Medical Center, COP 1012, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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Bryan AW, O'Donnell CW, Menke M, Cowen LJ, Lindquist S, Berger B. STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions. Proteins 2011; 80:410-20. [PMID: 22095906 PMCID: PMC3298606 DOI: 10.1002/prot.23203] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/25/2011] [Accepted: 09/06/2011] [Indexed: 12/21/2022]
Abstract
The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively 'stitches' strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer's amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies.
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Affiliation(s)
- Allen W Bryan
- Harvard/MIT Division of Health Science and Technology, Bioinformatics and Integrative Genomics, E25-519 Cambridge, Massachusetts 02139; Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142; MIT Computer Science and Artificial Intelligence Laboratory, The Stata Center, Cambridge, Massachusetts 02139
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Gendoo DMA, Harrison PM. Origins and evolution of the HET-s prion-forming protein: searching for other amyloid-forming solenoids. PLoS One 2011; 6:e27342. [PMID: 22096554 PMCID: PMC3214033 DOI: 10.1371/journal.pone.0027342] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/14/2011] [Indexed: 11/18/2022] Open
Abstract
The HET-s prion-forming domain from the filamentous fungus Podospora anserina is gaining considerable interest since it yielded the first well-defined atomic structure of a functional amyloid fibril. This structure has been identified as a left-handed beta solenoid with a triangular hydrophobic core. To delineate the origins of the HET-s prion-forming protein and to discover other amyloid-forming proteins, we searched for all homologs of the HET-s protein in a database of protein domains and fungal genomes, using a combined application of HMM, psi-blast and pGenThreader techniques, and performed a comparative evolutionary analysis of the N-terminal alpha-helical domain and the C-terminal prion-forming domain of HET-s. By assessing the tandem evolution of both domains, we observed that the prion-forming domain is restricted to Sordariomycetes, with a marginal additional sequence homolog in Arthroderma otae as a likely case of horizontal transfer. This suggests innovation and rapid evolution of the solenoid fold in the Sordariomycetes clade. In contrast, the N-terminal domain evolves at a slower rate (in Sordariomycetes) and spans many diverse clades of fungi. We performed a full three-dimensional protein threading analysis on all identified HET-s homologs against the HET-s solenoid fold, and present detailed structural annotations for identified structural homologs to the prion-forming domain. An analysis of the physicochemical characteristics in our set of structural models indicates that the HET-s solenoid shape can be readily adopted in these homologs, but that they are all less optimized for fibril formation than the P. anserina HET-s sequence itself, due chiefly to the presence of fewer asparagine ladders and salt bridges. Our combined structural and evolutionary analysis suggests that the HET-s shape has "limited scope" for amyloidosis across the wider protein universe, compared to the 'generic' left-handed beta helix. We discuss the implications of our findings on future identification of amyloid-forming proteins sharing the solenoid fold.
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Affiliation(s)
- Deena M. A. Gendoo
- Department of Biology, McGill University, Montreal, Quebec, Canada
- McGill Center for Bioinformatics, McGill University, Montreal, Quebec, Canada
| | - Paul M. Harrison
- Department of Biology, McGill University, Montreal, Quebec, Canada
- McGill Center for Bioinformatics, McGill University, Montreal, Quebec, Canada
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