101
|
ATR-FTIR: A “rejuvenated” tool to investigate amyloid proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2328-38. [DOI: 10.1016/j.bbamem.2013.04.012] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/20/2013] [Accepted: 04/02/2013] [Indexed: 12/24/2022]
|
102
|
Yang S, Ravikumar KM, Levine H. Energy Evaluation of β-Strand Packing in a Fibril-Forming SH3 Domain. J Phys Chem B 2013; 117:13051-7. [DOI: 10.1021/jp402442p] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sichun Yang
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United
States
| | - Krishnakumar M. Ravikumar
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United
States
| | - Herbert Levine
- Center for Theoretical
Biological Physics and Department of Bioengineering, Rice University, Houston, Texas, United States
| |
Collapse
|
103
|
GhattyVenkataKrishna PK, Uberbacher EC, Cheng X. Effect of the amyloid β hairpin's structure on the handedness of helices formed by its aggregates. FEBS Lett 2013; 587:2649-55. [PMID: 23845280 DOI: 10.1016/j.febslet.2013.06.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/16/2013] [Accepted: 06/21/2013] [Indexed: 11/16/2022]
Abstract
Various structural models for amyloid β fibrils have been derived from a variety of experimental techniques. However, these models cannot differentiate between the relative position of the two arms of the β hairpin called the stagger. Amyloid fibrils of various hierarchical levels form left-handed helices composed of β sheets. However it is unclear if positive, negative and zero staggers all form the macroscopic left-handed helices. To address this issue we have conducted extensive molecular dynamics simulations of amyloid β sheets of various staggers and shown that only negative staggers lead to the experimentally observed left-handed helices while positive staggers generate the incorrect right-handed helices. This result suggests that the negative staggers are physiologically relevant structure of the amyloid β fibrils.
Collapse
|
104
|
Cheng H, Huang WYC, Tsai TWT, Mou Y, Chao JCH, Chan JCC. Depletion of Water Molecules Near the End Stage of Steric Zipper Formation. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201300073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hsin‐Mei Cheng
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - William Y. C. Huang
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Tim W. T. Tsai
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - John Chin Hao Chao
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Jerry C. C. Chan
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| |
Collapse
|
105
|
Comellas G, Rienstra CM. Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils. Annu Rev Biophys 2013; 42:515-36. [DOI: 10.1146/annurev-biophys-083012-130356] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology,
- Department of Chemistry, and
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; ,
| |
Collapse
|
106
|
Baftizadeh F, Pietrucci F, Biarnés X, Laio A. Nucleation process of a fibril precursor in the C-terminal segment of amyloid-β. PHYSICAL REVIEW LETTERS 2013; 110:168103. [PMID: 23679641 DOI: 10.1103/physrevlett.110.168103] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Indexed: 06/02/2023]
Abstract
By extended atomistic simulations in explicit solvent and bias-exchange metadynamics, we study the aggregation process of 18 chains of the C-terminal segment of amyloid-β, an intrinsically disordered protein involved in Alzheimer's disease and prone to form fibrils. Starting from a disordered aggregate, we are able to observe the formation of an ordered nucleus rich in beta sheets. The rate limiting step in the nucleation pathway involves crossing a barrier of approximately 40 kcal/mol and is associated with the formation of a very specific interdigitation of the side chains belonging to different sheets. This structural pattern is different from the one observed experimentally in a microcrystal of the same system, indicating that the structure of a "nascent" fibril may differ from the one of an "extended" fibril.
Collapse
|
107
|
Andreas LB, Barnes AB, Corzilius B, Chou JJ, Miller EA, Caporini M, Rosay M, Griffin RG. Dynamic nuclear polarization study of inhibitor binding to the M2(18-60) proton transporter from influenza A. Biochemistry 2013; 52:2774-82. [PMID: 23480101 DOI: 10.1021/bi400150x] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We demonstrate the use of dynamic nuclear polarization (DNP) to elucidate ligand binding to a membrane protein using dipolar recoupling magic angle spinning (MAS) NMR. In particular, we detect drug binding in the proton transporter M2(18-60) from influenza A using recoupling experiments at room temperature and with cryogenic DNP. The results indicate that the pore binding site of rimantadine is correlated with previously reported widespread chemical shift changes, suggesting functional binding in the pore. Futhermore, the (15)N-labeled ammonium of rimantadine was observed near A30 (13)Cβ and G34 (13)Cα, suggesting a possible hydrogen bond to A30 carbonyl. Cryogenic DNP was required to observe the weaker external binding site(s) in a ZF-TEDOR spectrum. This approach is generally applicable, particularly for weakly bound ligands, in which case the application of MAS NMR dipolar recoupling requires the low temperatures to quench dynamic exchange processes. For the fully protonated samples investigated, we observed DNP signal enhancements of ~10 at 400 MHz using only 4-6 mM of the polarizing agent TOTAPOL. At 600 MHz and with DNP, we measured a distance between the drug and the protein to a precision of 0.2 Å.
Collapse
Affiliation(s)
- Loren B Andreas
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | |
Collapse
|
108
|
Raveendra BL, Siemer AB, Puthanveettil SV, Hendrickson WA, Kandel ER, McDermott AE. Characterization of prion-like conformational changes of the neuronal isoform of Aplysia CPEB. Nat Struct Mol Biol 2013; 20:495-501. [PMID: 23435382 DOI: 10.1038/nsmb.2503] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 12/28/2012] [Indexed: 11/09/2022]
Abstract
The neuronal isoform of cytoplasmic polyadenylation element-binding protein (CPEB) is a regulator of local protein synthesis at synapses and is critical in maintaining learning-related synaptic plasticity in Aplysia. Previous studies indicate that the function of Aplysia CPEB can be modulated by conversion to a stable prion-like state, thus contributing to the stabilization of long-term memory on a molecular level. Here, we used biophysical methods to demonstrate that Aplysia CPEB, like other prions, undergoes a conformational switch from soluble α-helix-rich oligomer to β-sheet-rich fiber in vitro. Solid-state NMR analyses of the fibers indicated a relatively rigid N-terminal prion domain. The fiber form of Aplysia CPEB showed enhanced binding to target mRNAs as compared to the soluble form. Consequently, we propose a model for the Aplysia CPEB fibers that may have relevance for functional prions in general.
Collapse
Affiliation(s)
- Bindu L Raveendra
- Department of Neuroscience, Columbia University, New York, New York, USA
| | | | | | | | | | | |
Collapse
|
109
|
Sabate R, Rodriguez-Santiago L, Sodupe M, Saupe SJ, Ventura S. Thioflavin-T excimer formation upon interaction with amyloid fibers. Chem Commun (Camb) 2013; 49:5745-7. [DOI: 10.1039/c3cc42040j] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
110
|
Morris RJ, Eden K, Yarwood R, Jourdain L, Allen RJ, Macphee CE. Mechanistic and environmental control of the prevalence and lifetime of amyloid oligomers. Nat Commun 2013; 4:1891. [PMID: 23695685 PMCID: PMC3796876 DOI: 10.1038/ncomms2909] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 04/18/2013] [Indexed: 11/22/2022] Open
Abstract
Amyloid fibrils are self-assembled protein aggregates implicated in a number of human diseases. Fragmentation-dominated models for the self-assembly of amyloid fibrils have had important successes in explaining the kinetics of amyloid fibril formation but predict fibril length distributions that do not match experiments. Here we resolve this inconsistency using a combination of experimental kinetic measurements and computer simulations. We provide evidence for a structural transition that occurs at a critical fibril mass concentration, or CFC, above which fragmentation of fibrils is suppressed. Our simulations predict the formation of distinct fibril length distributions above and below the CFC, which we confirm by electron microscopy. These results point to a new picture of amyloid fibril growth in which structural transitions that occur during self-assembly have strong effects on the final population of aggregate species with small, and potentially cytotoxic, oligomers dominating for long periods of time at protein concentrations below the CFC.
Collapse
Affiliation(s)
- Ryan J Morris
- SUPA, The School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ, UK
| | | | | | | | | | | |
Collapse
|
111
|
Abstract
Solid-state NMR spectroscopy proved to be a versatile tool for characterization of structure and dynamics of complex biochemical systems. In particular, magic angle spinning (MAS) solid-state NMR came to maturity for application towards structural elucidation of biological macromolecules. Current challenges in applying solid-state NMR as well as progress achieved recently will be discussed in the following chapter focusing on conceptual aspects important for structural elucidation of proteins.
Collapse
Affiliation(s)
- Henrik Müller
- Institute of Physical Biology, Heinrich-Heine-University of Düsseldorf, 40225, Düsseldorf, Germany
| | | | | |
Collapse
|
112
|
|
113
|
Fowler DM, Kelly JW. Functional amyloidogenesis and cytotoxicity-insights into biology and pathology. PLoS Biol 2012; 10:e1001459. [PMID: 23300381 PMCID: PMC3531510 DOI: 10.1371/journal.pbio.1001459] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 11/13/2012] [Indexed: 12/22/2022] Open
Abstract
Prions are self-templating protein structures that can be transferred from organism to organism. The [Het-s] prion propagates as a functional amyloid aggregate in the filamentous fungi Podospora anserina, and is involved in mediating heterokaryon incompatibility. Fusion of a P. anserina strain harboring the [Het-s] prion with another strain expressing the soluble Het-S protein results in cell death. The mechanism of Het-s/Het-S-mediated cell death has now been revealed in a paper just published in PLOS Biology. The study shows that Het-s and Het-S C-terminal domain co-amyloidogenesis induces a profound conformational rearrangement in the N-terminal Het-S HeLo domain, resulting in the exposure of a nascent transmembrane helix. Oligomerization of these helices leads to pore formation, leakage of the cytosolic contents, and subsequent cell death. Thus, Het-s amyloid plays a major role in the life cycle of P. anserina by orchestrating a complex conformational change in the Het-S protein, resulting in cytotoxicity by compromising membrane integrity. This ability of Het-s functional amyloid to initiate programmed cytotoxicity by mediating a conformational change in another protein significantly expands the functional repertoire of amyloid. Moreover, the mechanism of Het-S cell killing may be similar to the mechanism by which some pathological amyloid proteins lead to the demise of post-mitotic tissue.
Collapse
Affiliation(s)
- Douglas M. Fowler
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail: (DMF); (JWK)
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (DMF); (JWK)
| |
Collapse
|
114
|
Seuring C, Greenwald J, Wasmer C, Wepf R, Saupe SJ, Meier BH, Riek R. The mechanism of toxicity in HET-S/HET-s prion incompatibility. PLoS Biol 2012; 10:e1001451. [PMID: 23300377 PMCID: PMC3531502 DOI: 10.1371/journal.pbio.1001451] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 11/05/2012] [Indexed: 12/20/2022] Open
Abstract
The HET-s protein from the filamentous fungus Podospora anserina is a prion involved in a cell death reaction termed heterokaryon incompatibility. This reaction is observed at the point of contact between two genetically distinct strains when one harbors a HET-s prion (in the form of amyloid aggregates) and the other expresses a soluble HET-S protein (96% identical to HET-s). How the HET-s prion interaction with HET-S brings about cell death remains unknown; however, it was recently shown that this interaction leads to a relocalization of HET-S from the cytoplasm to the cell periphery and that this change is associated with cell death. Here, we present detailed insights into this mechanism in which a non-toxic HET-s prion converts a soluble HET-S protein into an integral membrane protein that destabilizes membranes. We observed liposomal membrane defects of approximately 10 up to 60 nm in size in transmission electron microscopy images of freeze-fractured proteoliposomes that were formed in mixtures of HET-S and HET-s amyloids. In liposome leakage assays, HET-S has an innate ability to associate with and disrupt lipid membranes and that this activity is greatly enhanced when HET-S is exposed to HET-s amyloids. Solid-state nuclear magnetic resonance (NMR) analyses revealed that HET-s induces the prion-forming domain of HET-S to adopt the β-solenoid fold (previously observed in HET-s) and this change disrupts the globular HeLo domain. These data indicate that upon interaction with a HET-s prion, the HET-S HeLo domain partially unfolds, thereby exposing a previously buried ∼34-residue N-terminal transmembrane segment. The liberation of this segment targets HET-S to the membrane where it further oligomerizes, leading to a loss of membrane integrity. HET-S thus appears to display features that are reminiscent of pore-forming toxins.
Collapse
Affiliation(s)
- Carolin Seuring
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Christian Wasmer
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Roger Wepf
- Electron Microscopy ETH Zurich (EMEZ), Zürich, Switzerland
| | - Sven J. Saupe
- Laboratoire de Génétique Moléculaire des Champignons, Institut de Biochimie et Génétique Cellulaires, UMR-5095 CNRS/Université de Bordeaux 2, Bordeaux, France
| | - Beat H. Meier
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
115
|
Lee YH, Goto Y. Kinetic intermediates of amyloid fibrillation studied by hydrogen exchange methods with nuclear magnetic resonance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1307-23. [DOI: 10.1016/j.bbapap.2012.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/24/2012] [Accepted: 07/26/2012] [Indexed: 01/28/2023]
|
116
|
Sousa AA, Leapman RD. Development and application of STEM for the biological sciences. Ultramicroscopy 2012; 123:38-49. [PMID: 22749213 PMCID: PMC3500455 DOI: 10.1016/j.ultramic.2012.04.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 04/06/2012] [Accepted: 04/13/2012] [Indexed: 01/06/2023]
Abstract
The design of the scanning transmission electron microscope (STEM), as conceived originally by Crewe and coworkers, enables the highly efficient and flexible collection of different elastic and inelastic signals resulting from the interaction of a focused probe of incident electrons with a specimen. In the present paper we provide a brief review for how the STEM today can be applied towards a range of different problems in the biological sciences, emphasizing four main areas of application. (1) For three decades, the most widely used STEM technique has been the mass determination of proteins and other macromolecular assemblies. Such measurements can be performed at low electron dose by collecting the high-angle dark-field signal using an annular detector. STEM mass mapping has proven valuable for characterizing large protein assemblies such as filamentous proteins with a well-defined mass per length. (2) The annular dark-field signal can also be used to image ultrasmall, functionalized nanoparticles of heavy atoms for labeling specific amino-acid sequences in protein assemblies. (3) By acquiring electron energy loss spectra (EELS) at each pixel in a hyperspectral image, it is possible to map the distributions of specific bound elements like phosphorus, calcium and iron in isolated macromolecular assemblies or in compartments within sectioned cells. Near single atom sensitivity is feasible provided that the specimen can tolerate a very high incident electron dose. (4) Electron tomography is a new application of STEM that enables three-dimensional reconstruction of micrometer-thick sections of cells. In this technique a probe of small convergence angle gives a large depth of field throughout the thickness of the specimen while maintaining a probe diameter of <2 nm; and the use of an on-axis bright-field detector reduces the effects of beam broadening and thus improves the spatial resolution compared to that attainable by STEM dark-field tomography.
Collapse
Affiliation(s)
- Alioscka A. Sousa
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard D. Leapman
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
117
|
Surmacz-Chwedoruk W, Nieznańska H, Wójcik S, Dzwolak W. Cross-seeding of fibrils from two types of insulin induces new amyloid strains. Biochemistry 2012; 51:9460-9. [PMID: 23127165 DOI: 10.1021/bi301144d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The irreversibility and autocatalytic character of amyloidogenesis and the polymorphism of amyloid fibrils underlie the phenomenon of self-propagating strains, wherein the mother seed, rather than the seeding environment, determines the properties of daughter fibrils. Here we study the formation of amyloid fibrils from bovine insulin and the recombinant Lys(B31)-Arg(B32) human insulin analog. The two polypeptides are similar enough to cross-seed but, upon spontaneous aggregation, form amyloid fibrils with distinct spectral features in the infrared amide I' band region. When bovine insulin is cross-seeded with the analog amyloid (and vice versa), the shape, absorption maximum, and even fine fingerprint features of the amide I' band are passed from the mother to daughter fibrils with a high degree of fidelity. Although the differences in primary structure between bovine insulin and the Lys(B31)-Arg(B32) analog of human insulin lie outside of the polypeptide's critical amyloidogenic regions, they affect the secondary structure of fibrils, possibly the formation of intermolecular salt bridges, and the susceptibility to dissection and denaturation with dimethyl sulfoxide (DMSO). All these phenotypic features of mother fibrils are imprinted in daughter amyloid upon cross-seeding. Analysis of noncooperative DMSO-induced denaturation of daughter fibrils suggests that the self-propagating polymorphism underlying the emergence of new amyloid strains is encoded on the level of secondary structure. Our findings have been discussed in the context of polymorphism of fibrils, amyloid strains, and possible implications for mechanisms of amyloidogenesis.
Collapse
|
118
|
Skora L, Zweckstetter M. Determination of amyloid core structure using chemical shifts. Protein Sci 2012; 21:1948-53. [PMID: 23033250 DOI: 10.1002/pro.2170] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 12/18/2022]
Abstract
Amyloid fibrils are the pathological hallmark of a large variety of neurodegenerative disorders. The structural characterization of amyloid fibrils, however, is challenging due to their non-crystalline, heterogeneous, and often dynamic nature. Thus, the structure of amyloid fibrils of many proteins is still unknown. We here show that the structure calculation program CS-Rosetta can be used to obtain insight into the core structure of amyloid fibrils. Driven by experimental solid-state NMR chemical shifts and taking into account the polymeric nature of fibrils CS-Rosetta allows modeling of the core of amyloid fibrils. Application to the Y145X stop mutant of the human prion protein reveals a left-handed β-helix.
Collapse
Affiliation(s)
- Lukasz Skora
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, Germany
| | | |
Collapse
|
119
|
López LC, Dos-Reis S, Espargaró A, Carrodeguas JA, Maddelein ML, Ventura S, Sancho J. Discovery of Novel Inhibitors of Amyloid β-Peptide 1–42 Aggregation. J Med Chem 2012; 55:9521-30. [DOI: 10.1021/jm301186p] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laura C. López
- Departamento de Bioquímica
y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza,
Spain
- Joint Unit BIFI-IQFR,
CSIC,
Biocomputation and Complex Systems Physics Institute (BIFI), Universidad de Zaragoza, Mariano Esquillor, Edificio
I + D, 50018 Zaragoza, Spain
| | - Suzana Dos-Reis
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route
de Narbonne BP64182, F-31077 Toulouse, France
- UPS, IPBS, Université de Toulouse, F-31077 Toulouse, France
| | - Alba Espargaró
- Institut de Biotecnologia i
Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra,
Barcelona, Spain
| | - José A. Carrodeguas
- Departamento de Bioquímica
y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza,
Spain
- Joint Unit BIFI-IQFR,
CSIC,
Biocomputation and Complex Systems Physics Institute (BIFI), Universidad de Zaragoza, Mariano Esquillor, Edificio
I + D, 50018 Zaragoza, Spain
| | - Marie-Lise Maddelein
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route
de Narbonne BP64182, F-31077 Toulouse, France
- UPS, IPBS, Université de Toulouse, F-31077 Toulouse, France
| | - Salvador Ventura
- Institut de Biotecnologia i
Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra,
Barcelona, Spain
| | - Javier Sancho
- Departamento de Bioquímica
y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza,
Spain
- Joint Unit BIFI-IQFR,
CSIC,
Biocomputation and Complex Systems Physics Institute (BIFI), Universidad de Zaragoza, Mariano Esquillor, Edificio
I + D, 50018 Zaragoza, Spain
| |
Collapse
|
120
|
Antony H, Wiegmans AP, Wei MQ, Chernoff YO, Khanna KK, Munn AL. Potential roles for prions and protein-only inheritance in cancer. Cancer Metastasis Rev 2012; 31:1-19. [PMID: 22138778 DOI: 10.1007/s10555-011-9325-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inherited mutations are known to cause familial cancers. However, the cause of sporadic cancers, which likely represent the majority of cancers, is yet to be elucidated. Sporadic cancers contain somatic mutations (including oncogenic mutations); however, the origin of these mutations is unclear. An intriguing possibility is that a stable alteration occurs in somatic cells prior to oncogenic mutations and promotes the subsequent accumulation of oncogenic mutations. This review explores the possible role of prions and protein-only inheritance in cancer. Genetic studies using lower eukaryotes, primarily yeast, have identified a large number of proteins as prions that confer dominant phenotypes with cytoplasmic (non-Mendelian) inheritance. Many of these have mammalian functional homologs. The human prion protein (PrP) is known to cause neurodegenerative diseases and has now been found to be upregulated in multiple cancers. PrP expression in cancer cells contributes to cancer progression and resistance to various cancer therapies. Epigenetic changes in the gene expression and hyperactivation of MAP kinase signaling, processes that in lower eukaryotes are affected by prions, play important roles in oncogenesis in humans. Prion phenomena in yeast appear to be influenced by stresses, and there is considerable evidence of the association of some amyloids with biologically positive functions. This suggests that if protein-only somatic inheritance exists in mammalian cells, it might contribute to cancer phenotypes. Here, we highlight evidence in the literature for an involvement of prion or prion-like mechanisms in cancer and how they may in the future be viewed as diagnostic markers and potential therapeutic targets.
Collapse
Affiliation(s)
- H Antony
- Griffith Health Institute, Griffith University, Southport, Queensland, Australia.
| | | | | | | | | | | |
Collapse
|
121
|
Hettiarachchi CA, Melton LD, Gerrard JA, Loveday SM. Formation of β-Lactoglobulin Nanofibrils by Microwave Heating Gives a Peptide Composition Different from Conventional Heating. Biomacromolecules 2012; 13:2868-80. [DOI: 10.1021/bm300896r] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Charith A. Hettiarachchi
- Riddet Institute, Private Bag 11222, Palmerston North
4442, New Zealand
- School
of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland
1142, New Zealand
| | - Laurence D. Melton
- Riddet Institute, Private Bag 11222, Palmerston North
4442, New Zealand
- School
of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland
1142, New Zealand
| | - Juliet A. Gerrard
- Riddet Institute, Private Bag 11222, Palmerston North
4442, New Zealand
- Biomolecular
Interaction Centre
and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
- Industrial Research Limited,
PO Box 31310, Lower Hutt 5040, New Zealand
| | - Simon M. Loveday
- Riddet Institute, Private Bag 11222, Palmerston North
4442, New Zealand
| |
Collapse
|
122
|
Abstract
The concept of a prion as an infectious self-propagating protein isoform was initially proposed to explain certain mammalian diseases. It is now clear that yeast also has heritable elements transmitted via protein. Indeed, the "protein only" model of prion transmission was first proven using a yeast prion. Typically, known prions are ordered cross-β aggregates (amyloids). Recently, there has been an explosion in the number of recognized prions in yeast. Yeast continues to lead the way in understanding cellular control of prion propagation, prion structure, mechanisms of de novo prion formation, specificity of prion transmission, and the biological roles of prions. This review summarizes what has been learned from yeast prions.
Collapse
Affiliation(s)
- Susan W Liebman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA.
| | | |
Collapse
|
123
|
Gardiennet C, Schütz AK, Hunkeler A, Kunert B, Terradot L, Böckmann A, Meier BH. Hochaufgelöste Festkörper-NMR-Spektren einer sedimentierten, nichtkristallinen dodekameren Helicase (59 kDa). Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200779] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
124
|
Gardiennet C, Schütz AK, Hunkeler A, Kunert B, Terradot L, Böckmann A, Meier BH. A Sedimented Sample of a 59 kDa Dodecameric Helicase Yields High-Resolution Solid-State NMR Spectra. Angew Chem Int Ed Engl 2012; 51:7855-8. [DOI: 10.1002/anie.201200779] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 04/10/2012] [Indexed: 11/10/2022]
|
125
|
Espargaró A, Villar-Piqué A, Sabaté R, Ventura S. Yeast prions form infectious amyloid inclusion bodies in bacteria. Microb Cell Fact 2012; 11:89. [PMID: 22731490 PMCID: PMC3520751 DOI: 10.1186/1475-2859-11-89] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 05/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prions were first identified as infectious proteins associated with fatal brain diseases in mammals. However, fungal prions behave as epigenetic regulators that can alter a range of cellular processes. These proteins propagate as self-perpetuating amyloid aggregates being an example of structural inheritance. The best-characterized examples are the Sup35 and Ure2 yeast proteins, corresponding to [PSI+] and [URE3] phenotypes, respectively. RESULTS Here we show that both the prion domain of Sup35 (Sup35-NM) and the Ure2 protein (Ure2p) form inclusion bodies (IBs) displaying amyloid-like properties when expressed in bacteria. These intracellular aggregates template the conformational change and promote the aggregation of homologous, but not heterologous, soluble prionogenic molecules. Moreover, in the case of Sup35-NM, purified IBs are able to induce different [PSI+] phenotypes in yeast, indicating that at least a fraction of the protein embedded in these deposits adopts an infectious prion fold. CONCLUSIONS An important feature of prion inheritance is the existence of strains, which are phenotypic variants encoded by different conformations of the same polypeptide. We show here that the proportion of infected yeast cells displaying strong and weak [PSI+] phenotypes depends on the conditions under which the prionogenic aggregates are formed in E. coli, suggesting that bacterial systems might become useful tools to generate prion strain diversity.
Collapse
Affiliation(s)
- Alba Espargaró
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | | | | |
Collapse
|
126
|
Genomic clustering and homology between HET-S and the NWD2 STAND protein in various fungal genomes. PLoS One 2012; 7:e34854. [PMID: 22493719 PMCID: PMC3321046 DOI: 10.1371/journal.pone.0034854] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 03/08/2012] [Indexed: 12/23/2022] Open
Abstract
Background Prions are infectious proteins propagating as self-perpetuating amyloid polymers. The [Het-s] prion of Podospora anserina is involved in a cell death process associated with non-self recognition. The prion forming domain (PFD) of HET-s adopts a β-solenoid amyloid structure characterized by the two fold repetition of an elementary triangular motif. [Het-s] induces cell death when interacting with HET-S, an allelic variant of HET-s. When templated by [Het-s], HET-S undergoes a trans-conformation, relocates to the cell membrane and induces toxicity. Methodology/Principal Findings Here, comparing HET-s homologs from different species, we devise a consensus for the HET-s elementary triangular motif. We use this motif to screen genomic databases and find a match to the N-terminus of NWD2, a STAND protein, encoded by the gene immediately adjacent to het-S. STAND proteins are signal transducing ATPases which undergo ligand-induced oligomerisation. Homology modelling predicts that the NWD2 N-terminal region adopts a HET-s-like fold. We propose that upon NWD2 oligomerisation, these N-terminal extensions adopt the β-solenoid fold and template HET-S to adopt the amyloid fold and trigger toxicity. We extend this model to a putative prion, the σ infectious element in Nectria haematococca, because the s locus controlling propagation of σ also encodes a STAND protein and displays analogous features. Comparative genomic analyses indicate evolutionary conservation of these STAND/prion-like gene pairs, identify a number of novel prion candidates and define, in addition to the HET-s PFD motif, two distinct, novel putative PFD-like motifs. Conclusions/Significance We suggest the existence, in the fungal kingdom, of a widespread and evolutionarily conserved mode of signal transduction based on the transmission of an amyloid-fold from a NOD-like STAND receptor protein to an effector protein.
Collapse
|
127
|
Reif B. Deuterated peptides and proteins: structure and dynamics studies by MAS solid-state NMR. Methods Mol Biol 2012; 831:279-301. [PMID: 22167680 DOI: 10.1007/978-1-61779-480-3_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Perdeuteration and back substitution of exchangeable protons in microcrystalline proteins, in combination with recrystallization from D(2)O-containing buffers, significantly reduce (1)H, (1)H dipolar interactions. This way, amide proton line widths on the order of 20 Hz are obtained. Aliphatic protons are accessible either via specifically protonated precursors or by using low amounts of H(2)O in the bacterial growth medium. The labeling scheme enables characterization of structure and dynamics in the solid-state without dipolar truncation artifacts.
Collapse
Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM) at Department Chemie, Technische Universität München, Garching, Germany.
| |
Collapse
|
128
|
Vilar M, Wang L, Riek R. Structural studies of amyloids by quenched hydrogen-deuterium exchange by NMR. Methods Mol Biol 2012; 849:185-198. [PMID: 22528091 DOI: 10.1007/978-1-61779-551-0_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The elucidation of the structure of amyloid fibrils and related aggregates is an important step towards understanding the pathogenesis of diseases such as Alzheimer's and Parkinson's, which feature protein misfolding and/or aggregation. However, the large size and poor solubility of amyloid-like fibrils make them resistant to high-resolution structure determination. Here, we describe the use of hydrogen-deuterium exchange coupled with NMR as an indirect strategy to determine the folding regions of amyloid-forming proteins at residue level resolution.
Collapse
Affiliation(s)
- Marçal Vilar
- Neurodegeneration Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.
| | | | | |
Collapse
|
129
|
Abstract
We detail some of the genetic, biochemical, and physical methods useful in studying amyloids in yeast, particularly the yeast prions. These methods include cytoduction (cytoplasmic mixing), infection of cells with prion amyloids, use of green fluorescent protein fusions with amyloid-forming proteins for cytology, protein purification and amyloid formation, and electron microscopy of filaments.
Collapse
|
130
|
Srinivasan A. Experimental inhibition of peptide fibrillogenesis by synthetic peptides, carbohydrates and drugs. Subcell Biochem 2012; 65:271-94. [PMID: 23225008 DOI: 10.1007/978-94-007-5416-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Peptide fibrillogenesis generally begins by the transformation of normally soluble proteins into elongated aggregates which are called as amyloid. These fibrils mainly consist of ß-sheets. They share certain common characteristics such as a cross-ß x-ray diffraction pattern, association with other common proteins and typical staining by the dye Congo Red. The individual form of the deposit consists of a disease-specific peptide/protein. The disease-specific protein serves as the basis for the classification of the amyloids. The association of fibril-forming peptides/proteins with diseases makes them primary disease-targets. Understanding the molecular interactions involved in the fibril formation becomes the foremost requirement to characterize the target. Interference with these interactions of ß-sheets in vitro prevents and sometimes reverses the fibril assembly. A small molecule capable of interfering with the formation of fibril could have therapeutic applications in these diseases. This anti-aggregation approach appears to be a viable treatment option. A search for such a molecule is pursued actively world over. All types of compounds and approaches to slow down or prevent the aggregation process have been described in the literature. These efforts are reviewed in this chapter.
Collapse
|
131
|
Staniforth GL, Tuite MF. Fungal prions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 107:417-56. [PMID: 22482457 DOI: 10.1016/b978-0-12-385883-2.00007-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
For both mammalian and fungal prion proteins, conformational templating drives the phenomenon of protein-only infectivity. The conformational conversion of a protein to its transmissible prion state is associated with changes to host cellular physiology. In mammals, this change is synonymous with disease, whereas in fungi no notable detrimental effect on the host is typically observed. Instead, fungal prions can serve as epigenetic regulators of inheritance in the form of partial loss-of-function phenotypes. In the presence of environmental challenges, the prion state [PRION(+)], with its resource for phenotypic plasticity, can be associated with a growth advantage. The growing number of yeast proteins that can switch to a heritable [PRION(+)] form represents diverse and metabolically penetrating cellular functions, suggesting that the [PRION(+)] state in yeast is a functional one, albeit rarely found in nature. In this chapter, we introduce the biochemical and genetic properties of fungal prions, many of which are shared by the mammalian prion protein PrP, and then outline the major contributions that studies on fungal prions have made to prion biology.
Collapse
Affiliation(s)
- Gemma L Staniforth
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | | |
Collapse
|
132
|
Sabaté R, Villar-Piqué A, Espargaró A, Ventura S. Temperature Dependence of the Aggregation Kinetics of Sup35 and Ure2p Yeast Prions. Biomacromolecules 2011; 13:474-83. [DOI: 10.1021/bm201527m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raimon Sabaté
- Institut de Biotecnologia
i de Biomedicina and Departament
de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona),
Spain
| | - Anna Villar-Piqué
- Institut de Biotecnologia
i de Biomedicina and Departament
de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona),
Spain
| | - Alba Espargaró
- Institut de Biotecnologia
i de Biomedicina and Departament
de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona),
Spain
| | - Salvador Ventura
- Institut de Biotecnologia
i de Biomedicina and Departament
de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona),
Spain
| |
Collapse
|
133
|
Affiliation(s)
- Jozef Adamcik
- Food & Soft Materials Science, Institute of Food, Nutrition & Health, ETH Zürich, LFO23, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Raffaele Mezzenga
- Food & Soft Materials Science, Institute of Food, Nutrition & Health, ETH Zürich, LFO23, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| |
Collapse
|
134
|
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.
Collapse
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
| | | | | | | | | | | |
Collapse
|
135
|
Benkemoun L, Ness F, Sabaté R, Ceschin J, Breton A, Clavé C, Saupe SJ. Two structurally similar fungal prions efficiently cross-seed in vivo but form distinct polymers when coexpressed. Mol Microbiol 2011; 82:1392-405. [PMID: 22050595 DOI: 10.1111/j.1365-2958.2011.07893.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
HET-s is a prion protein of the filamentous fungus Podospora anserina. An orthologue of this protein, called FgHET-s has been identified in Fusarium graminearum. The region of the FgHET-s protein corresponding to the prion forming domain of HET-s, forms amyloid fibrils in vitro. These fibrils seed HET-s(218-289) fibril formation in vitro and vice versa. The amyloid fold of HET-s(218-289) and FgHET-s(218-289) are remarkably similar although they share only 38% identity. The present work corresponds to the functional characterization of the FgHET-s(218-289) region as a prion forming domain in vivo. We show that FgHET-s(218-289) is capable of prion propagation in P. anserina and is able to substitute for the HET-s PFD in the full-length HET-s protein. In accordance with the in vitro cross-seeding experiments, we detect no species barrier between P. anserina and F. graminearum PFDs. We use the yeast Saccharomyces cerevisiae as a host to compare the prion performances of the two orthologous PFDs. We find that FgHET-s(218-289) leads to higher spontaneous prion formation rates and mitotic prion stability than HET-s(218-289). Then we analysed the outcome of HET-s(218-289)/FgHET-s(218-289) coexpression. In spite of the cross-seeding ability of HET-s(218-289) and FgHET-s(218-289), in vivo, homotypic polymerization is favoured over mixed fibril formation.
Collapse
Affiliation(s)
- Laura Benkemoun
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS - Université de Bordeaux 2, 1 rue Camille St Saens, 33077 Bordeaux cedex, France
| | | | | | | | | | | | | |
Collapse
|
136
|
Localization of HET-S to the cell periphery, not to [Het-s] aggregates, is associated with [Het-s]-HET-S toxicity. Mol Cell Biol 2011; 32:139-53. [PMID: 22037764 DOI: 10.1128/mcb.06125-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prion diseases are associated with accumulation of the amyloid form of the prion protein, but the mechanisms of toxicity are unknown. Amyloid toxicity is also associated with fungal prions. In Podospora anserina, the simultaneous presence of [Het-s] prion and its allelic protein HET-S causes cell death in a self-/nonself-discrimination process. Here, using the prion form of a fragment of HET-s ([PrD(157)(+)]), we show that [Het-s]-HET-S toxicity can be faithfully recapitulated in yeast. Overexpression of Hsp40 chaperone, Sis1, rescues this toxicity by curing cells of [PrD(157)(+)]. We find no evidence for toxic [PrD(157)(+)] conformers in the presence of HET-S. Instead, [PrD(157)(+)] appears to seed HET-S to accumulate at the cell periphery and to form aggregates distinct from visible [PrD(157)(+)] aggregates. Furthermore, HET-S mutants that cause HET-S to be sequestered into [PrD(157)(+)] prion aggregates are not toxic. The localization of HET-S at the cell periphery and its association with cell death was also observed in the native host Podospora anserina. Thus, upon interaction with [Het-s], HET-S localizes to the cell periphery, and this relocalization, rather than the formation of mixed HET-s/HET-S aggregates, is associated with toxicity.
Collapse
|
137
|
Franks WT, Linden AH, Kunert B, van Rossum BJ, Oschkinat H. Solid-state magic-angle spinning NMR of membrane proteins and protein-ligand interactions. Eur J Cell Biol 2011; 91:340-8. [PMID: 22019511 DOI: 10.1016/j.ejcb.2011.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 09/09/2011] [Accepted: 09/09/2011] [Indexed: 10/15/2022] Open
Abstract
Structural biology is developing into a universal tool for visualizing biological processes in space and time at atomic resolution. The field has been built by established methodology like X-ray crystallography, electron microscopy and solution NMR and is now incorporating new techniques, such as small-angle X-ray scattering, electron tomography, magic-angle-spinning solid-state NMR and femtosecond X-ray protein nanocrystallography. These new techniques all seek to investigate non-crystalline, native-like biological material. Solid-state NMR is a relatively young technique that has just proven its capabilities for de novo structure determination of model proteins. Further developments promise great potential for investigations on functional biological systems such as membrane-integrated receptors and channels, and macromolecular complexes attached to cytoskeletal proteins. Here, we review the development and applications of solid-state NMR from the first proof-of-principle investigations to mature structure determination projects, including membrane proteins. We describe the development of the methodology by looking at examples in detail and provide an outlook towards future 'big' projects.
Collapse
Affiliation(s)
- W Trent Franks
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert Rössle Str. 10, 13125 Berlin, Germany
| | | | | | | | | |
Collapse
|
138
|
Hernandez M, Golbert S, Zhang LG, Kim JR. Creation of aggregation-defective α-synuclein variants by engineering the sequence connecting β-strand-forming domains. Chembiochem 2011; 12:2630-9. [PMID: 21998035 DOI: 10.1002/cbic.201100430] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Indexed: 12/18/2022]
Abstract
The aggregation of α-synuclein (αS), which is implicated in the pathology of Parkinson's disease, produces fibrils in which layers of parallel, in-register β-sheet-loop-β-sheets are formed. The effects of sequence variation in the loop-forming region (referred to as the linker region) on αS aggregation have yet to be systematically studied. In the study described here, we created and characterized αS variants containing mutations in the linker regions. Our results indicate that although the physicochemical properties of the linker region, evaluated based on an intrinsic property of a single amino acid, still play a significant role in aggregation, additional factors can also determine aggregation of αS linker mutants. Our analyses suggest that these factors include a pairwise potential for parallel in-register β-sheet formation. A linker variant displaying significantly reduced self-aggregation interfered with αS aggregation by inhibiting the conversion of αS soluble species to αS insoluble fibrils. We anticipate that linker mutations could serve as a novel method of creating αS variants that are aggregation-defective and/or inhibit αS aggregation.
Collapse
Affiliation(s)
- Michael Hernandez
- Othmer-Jacobs Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
| | | | | | | |
Collapse
|
139
|
Abstract
Many, perhaps most, proteins, are capable of forming self-propagating, β-sheet (amyloid) aggregates. Amyloid-like aggregates are found in a wide range of diseases and underlie prion-based inheritance. Despite intense interest in amyloids, structural details have only recently begun to be revealed as advances in biophysical approaches, such as hydrogen-deuterium exchange, X-ray crystallography, solid-state nuclear magnetic resonance (SSNMR), and cryoelectron microscopy (cryoEM), have enabled high-resolution insights into their molecular organization. Initial studies found that despite the highly divergent primary structure of different amyloid-forming proteins, amyloids from different sources share many structural similarities. With higher-resolution information, however, it has become clear that, on the molecular level, amyloids comprise a wide diversity of structures. Particularly surprising has been the finding that identical polypeptides can fold into multiple, distinct amyloid conformations and that this structural diversity can lead to distinct heritable prion states or strains.
Collapse
Affiliation(s)
- Brandon H Toyama
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco and California Institute for Quantitative Biomedical Research, San Francisco, California 94158-2542, USA.
| | | |
Collapse
|
140
|
Wickner RB, Edskes HK, Bateman D, Kelly AC, Gorkovskiy A. The yeast prions [PSI+] and [URE3] are molecular degenerative diseases. Prion 2011; 5:258-62. [PMID: 22052353 DOI: 10.4161/pri.17748] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The yeast prions [URE3] and [PSI] are not found in wild strains, suggesting they are not an advantage. Prion-forming ability is not conserved, even within Saccharomyces, suggesting it is a disease. Prion domains have non-prion functions, explaining some conservation of sequence. However, in spite of the sequence being constrained in evolution by these non-prion functions, the prion domains vary more rapidly than the remainder of the molecule, and these changes produce a transmission barrier, suggesting that these changes were selected to block prion infection. Yeast prions [PSI] and [URE3] induce a cellular stress response (Hsp104 and Hsp70 induction), suggesting the cells are not happy about being infected. Recently, we showed that the array of [PSI] and [URE3] prions includes a majority of lethal or very toxic variants, a result not expected if either prion were an adaptive cellular response to stress.
Collapse
Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD, USA.
| | | | | | | | | |
Collapse
|
141
|
Wickner RB, Edskes HK, Bateman D, Kelly AC, Gorkovskiy A. The yeast prions [PSI+] and [URE3] are molecular degenerative diseases. Prion 2011. [PMID: 22052353 DOI: 10.4161/pri.5.4.17748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The yeast prions [URE3] and [PSI] are not found in wild strains, suggesting they are not an advantage. Prion-forming ability is not conserved, even within Saccharomyces, suggesting it is a disease. Prion domains have non-prion functions, explaining some conservation of sequence. However, in spite of the sequence being constrained in evolution by these non-prion functions, the prion domains vary more rapidly than the remainder of the molecule, and these changes produce a transmission barrier, suggesting that these changes were selected to block prion infection. Yeast prions [PSI] and [URE3] induce a cellular stress response (Hsp104 and Hsp70 induction), suggesting the cells are not happy about being infected. Recently, we showed that the array of [PSI] and [URE3] prions includes a majority of lethal or very toxic variants, a result not expected if either prion were an adaptive cellular response to stress.
Collapse
Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD, USA.
| | | | | | | | | |
Collapse
|
142
|
Dynamics of polymerization shed light on the mechanisms that lead to multiple amyloid structures of the prion protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1305-17. [DOI: 10.1016/j.bbapap.2011.05.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 05/20/2011] [Accepted: 05/25/2011] [Indexed: 11/19/2022]
|
143
|
Chimon S, Shaibat MA, Jones CR, Calero DC, Aizezi B, Ishii Y. Evidence of fibril-like β-sheet structures in a neurotoxic amyloid intermediate of Alzheimer's β-amyloid. Nat Struct Mol Biol 2011; 14:1157-64. [PMID: 18059284 DOI: 10.1038/nsmb1345] [Citation(s) in RCA: 458] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 11/01/2007] [Indexed: 01/13/2023]
Abstract
Diffusible subfibrillar aggregates of amyloid proteins are potent neurotoxins and primary suspects in amyloid diseases including Alzheimer's disease. Despite widespread interest, the molecular structures of the amyloid intermediates and the conformational conversions in amyloid misfolding are poorly understood. Here we present a molecular-level examination of sequence-specific secondary structures and supramolecular structures of a neurotoxic amyloid intermediate of the 40-residue β-amyloid (Aβ) peptide involved in Alzheimer's disease. Using solid-state NMR and electron microscopy, we show that, before fibrillization, natively unstructured monomeric Aβ is subject to large conformational changes into a spherical amyloid intermediate of 15–35 nm diameter, which has predominantly parallel β-sheet structures. Structural comparison with Aβ fibrils demonstrates that formation of this β-sheet intermediate I(β) largely defines conformational transitions in amyloid misfolding. Neurotoxicity assays on PC12 cells show that I(β) shows higher toxicity than the fibril, indicating that the β-sheet formation may trigger neurotoxicity.
Collapse
Affiliation(s)
- Sandra Chimon
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | | | | | | | | | | |
Collapse
|
144
|
Baiesi M, Seno F, Trovato A. Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for growth polarity. Proteins 2011; 79:3067-81. [DOI: 10.1002/prot.23133] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 06/23/2011] [Accepted: 07/07/2011] [Indexed: 01/24/2023]
|
145
|
Bayro MJ, Debelouchina GT, Eddy MT, Birkett NR, MacPhee CE, Rosay M, Maas WE, Dobson CM, Griffin RG. Intermolecular structure determination of amyloid fibrils with magic-angle spinning and dynamic nuclear polarization NMR. J Am Chem Soc 2011; 133:13967-74. [PMID: 21774549 DOI: 10.1021/ja203756x] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe magic-angle spinning NMR experiments designed to elucidate the interstrand architecture of amyloid fibrils. Three methods are introduced for this purpose, two being based on the analysis of long-range (13)C-(13)C correlation spectra and the third based on the identification of intermolecular interactions in (13)C-(15)N spectra. We show, in studies of fibrils formed by the 86-residue SH3 domain of PI3 kinase (PI3-SH3 or PI3K-SH3), that efficient (13)C-(13)C correlation spectra display a resonance degeneracy that establishes a parallel, in-register alignment of the proteins in the amyloid fibrils. In addition, this degeneracy can be circumvented to yield direct intermolecular constraints. The (13)C-(13)C experiments are corroborated by (15)N-(13)C correlation spectra obtained from a mixed [(15)N,(12)C]/[(14)N,(13)C] sample which directly quantify interstrand distances. Furthermore, when the spectra are recorded with signal enhancement provided by dynamic nuclear polarization (DNP) at 100 K, we demonstrate a dramatic increase (from 23 to 52) in the number of intermolecular (15)N-(13)C constraints detectable in the spectra. The increase in the information content is due to the enhanced signal intensities and to the fact that dynamic processes, leading to spectral intensity losses, are quenched at low temperatures. Thus, acquisition of low temperature spectra addresses a problem that is frequently encountered in MAS spectra of proteins. In total, the experiments provide 111 intermolecular (13)C-(13)C and (15)N-(13)C constraints that establish that the PI3-SH3 protein strands are aligned in a parallel, in-register arrangement within the amyloid fibril.
Collapse
Affiliation(s)
- Marvin J Bayro
- Francis Bitter Magnet Laboratory, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, 02139, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
146
|
Jiang P, Li W, Shea JE, Mu Y. Resveratrol inhibits the formation of multiple-layered β-sheet oligomers of the human islet amyloid polypeptide segment 22-27. Biophys J 2011; 100:1550-8. [PMID: 21402038 DOI: 10.1016/j.bpj.2011.02.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/01/2011] [Accepted: 02/03/2011] [Indexed: 11/17/2022] Open
Abstract
The abnormal self-assembly of a number of proteins or peptides is a hallmark of >20 amyloidogenic diseases. Recent studies suggest that the pathology of amyloidogenesis can be attributed primarily to cytotoxic, soluble, intermediate oligomeric species rather than to mature amyloid fibrils. Despite the lack of available structural information regarding these transient species, many therapeutic efforts have focused on inhibiting the formation of these aggregates. One of the most successful approaches has been to use small molecules, many of which have been found to inhibit toxic species with high efficacy. A significant issue that remains to be resolved is the mechanism underlying the inhibitory effects of these molecules. In this article, we present extensive replica-exchange molecular dynamics simulations to study the early aggregation of the human islet amyloid polypeptide segment 22-27 in the presence and absence of the small-molecule inhibitor resveratrol. The simulations indicate that aggregation of these peptides was hindered by resveratrol via a mechanism of blocking the lateral growth of a single-layered β-sheet oligomer (rather than preventing growth by elongation along the fibril axis). Intersheet side-chain stacking, especially stacking of the aromatic rings, was blocked by the presence of resveratrol molecules, and the overall aggregation level was reduced.
Collapse
Affiliation(s)
- Ping Jiang
- School of Biological Sciences, Nanyang Technological University, Singapore. [corrected]
| | | | | | | |
Collapse
|
147
|
Schütz AK, Soragni A, Hornemann S, Aguzzi A, Ernst M, Böckmann A, Meier BH. Die Amyloid-Kongorot-Bindungsstelle in atomarer Auflösung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008276] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
148
|
Schütz AK, Soragni A, Hornemann S, Aguzzi A, Ernst M, Böckmann A, Meier BH. The amyloid-Congo red interface at atomic resolution. Angew Chem Int Ed Engl 2011; 50:5956-60. [PMID: 21591034 DOI: 10.1002/anie.201008276] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/03/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Anne K Schütz
- Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | | | | | | | | | | | | |
Collapse
|
149
|
Greenwald J, Riek R. Biology of amyloid: structure, function, and regulation. Structure 2011; 18:1244-60. [PMID: 20947013 DOI: 10.1016/j.str.2010.08.009] [Citation(s) in RCA: 419] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 08/18/2010] [Accepted: 08/30/2010] [Indexed: 01/23/2023]
Abstract
Amyloids are highly ordered cross-β sheet protein aggregates associated with many diseases including Alzheimer's disease, but also with biological functions such as hormone storage. The cross-β sheet entity comprising an indefinitely repeating intermolecular β sheet motif is unique among protein folds. It grows by recruitment of the corresponding amyloid protein, while its repetitiveness can translate what would be a nonspecific activity as monomer into a potent one through cooperativity. Furthermore, the one-dimensional crystal-like repeat in the amyloid provides a structural framework for polymorphisms. This review summarizes the recent high-resolution structural studies of amyloid fibrils in light of their biological activities. We discuss how the unique properties of amyloids gives rise to many activities and further speculate about currently undocumented biological roles for the amyloid entity. In particular, we propose that amyloids could have existed in a prebiotic world, and may have been the first functional protein fold in living cells.
Collapse
Affiliation(s)
- Jason Greenwald
- ETH Zurich, Physical Chemistry, ETH Honggerberg, 8093 Zurich, Switzerland
| | | |
Collapse
|
150
|
Wickner RB, Edskes HK, Kryndushkin D, McGlinchey R, Bateman D, Kelly A. Prion diseases of yeast: amyloid structure and biology. Semin Cell Dev Biol 2011; 22:469-75. [PMID: 21345375 DOI: 10.1016/j.semcdb.2011.02.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Revised: 02/11/2011] [Accepted: 02/14/2011] [Indexed: 12/11/2022]
Abstract
Prion "variants" or "strains" are prions with the identical protein sequence, but different characteristics of the prion infection: e.g. different incubation periods for scrapie strains or different phenotype intensities for yeast prion variants. We have shown that infectious amyloids of the yeast prions [PSI+], [URE3] and [PIN+] each have an in-register parallel β-sheet architecture. Moreover, we have pointed out that this amyloid architecture can explain how one protein can faithfully transmit any of several conformations to new protein monomers. This explains how proteins can be genes.
Collapse
Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, United States.
| | | | | | | | | | | |
Collapse
|