1
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Esmaili M, Eldeeb M. Cellular toxicity of scrapie prions in prion diseases; a biochemical and molecular overview. Mol Biol Rep 2023; 50:1743-1752. [PMID: 36446981 DOI: 10.1007/s11033-022-07806-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 12/03/2022]
Abstract
Transmissible spongiform encephalopathies (TSEs) or prion diseases consist of a broad range of fatal neurological disorders affecting humans and animals. Contrary to Watson and Crick's 'central dogma', prion diseases are caused by a protein, devoid of DNA involvement. Herein, we briefly review various cellular and biological aspects of prions and prion pathogenesis focusing mainly on historical milestones, biosynthesis, degradation, structure-function of cellular and scrapie forms of prions .
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Affiliation(s)
- Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
| | - Mohamed Eldeeb
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt.
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2
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Jheng CP, Lee CI. Combination of structure-based virtual screening, molecular docking and molecular dynamics approaches for the discovery of anti-prion fibril flavonoids. Front Mol Biosci 2023; 9:1088733. [PMID: 36685276 PMCID: PMC9849400 DOI: 10.3389/fmolb.2022.1088733] [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: 11/03/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Prion diseases are a group of rare neurodegenerative diseases caused by the structural conversion of cellular prion into Scrapie prion resulting aggregated fibrils. Therapy of prion diseases has been developed for several decades, especially drug designs based on the structure of prion monomers. Unfortunately, none of the designed anti-prion drugs function well clinically. To fight against prion fibrils, a drug design based on the precise structure of mammalian prion fibrils is highly required. Fortunately, based on the advantage of newly advanced cryo-electron microscopy (cryo-EM) in the deconvolution of large complexes, three prion fibril structures were resolved in the last 2 years. Based on the cryo-EM solved prion fibril structures, we are able to find some molecules fighting against prion fibrils. Quercetin, one flavonoid molecule in the polyphenol group, has been found to disaggregate the prion fibrils in vitro. In this study, we performed the molecular docking and molecular dynamics simulation on quercetin-like molecules possessing pharmacological properties to evaluate the anti-prion ability of tested molecules. As a result, four quercetin-like molecules interact with prion fibril and decrease the β-strand content by converting some β-strands into loop and helical structures to disintegrate the existing fibril structure. The results of this study are significant in the treatment of prion diseases, and the approaches used in this study are applicable to other amyloid diseases.
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Affiliation(s)
- Cheng-Ping Jheng
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan
| | - Cheng-I Lee
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan,Center for Nano Bio-Detections, National Chung Cheng University, Chia-Yi, Taiwan,Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chia-Yi, Taiwan,*Correspondence: Cheng-I Lee,
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3
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Quercetin binding accelerates prion fibrillation into proteinase sensitive and loosely structured amyloids. Biomed Pharmacother 2022; 151:113177. [PMID: 35676783 DOI: 10.1016/j.biopha.2022.113177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/18/2022] [Accepted: 05/22/2022] [Indexed: 11/23/2022] Open
Abstract
Amyloidoses are caused by the deposition of amyloid fibrils ascribed to protein misfolding. In this study, we examined the antiamyloidogenic and antioxidative activities of quercetin, a plant flavonol from the flavonoid group of polyphenols, on mouse prion protein (moPrP) with biophysical approaches. As the results show, quercetin binds to the C-terminal region of moPrP, and quercetin binding does not affect the structure of moPrP. However, quercetin binding accelerates moPrP fibrillation and changes the structure of moPrP fibrils. Unlike typical prion fibrils, quercetin-bound fibrils are sensitive to proteinase K and are loosely structured. Moreover, due to high antioxidant activity of flavonoid, quercetin-bound fibrils lack imbalance of free radicals and, therefore, they are nontoxic towards neuroblastoma cells. The quercetin shows its uniqueness from typical antiamyloidogenic drugs which either suppress the development of amyloid or eliminate formed amyloids. Quercetin binding converts moPrP into protease-sensitive and non-cytotoxic fibrils. This work provides a powerful resolution in the advancement of antiamyloidogenic treatment.
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Khadka A, Spiers JG, Cheng L, Hill AF. Extracellular vesicles with diagnostic and therapeutic potential for prion diseases. Cell Tissue Res 2022; 392:247-267. [PMID: 35394216 PMCID: PMC10113352 DOI: 10.1007/s00441-022-03621-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/25/2022] [Indexed: 12/14/2022]
Abstract
Prion diseases (PrD) or transmissible spongiform encephalopathies (TSE) are invariably fatal and pathogenic neurodegenerative disorders caused by the self-propagated misfolding of cellular prion protein (PrPC) to the neurotoxic pathogenic form (PrPTSE) via a yet undefined but profoundly complex mechanism. Despite several decades of research on PrD, the basic understanding of where and how PrPC is transformed to the misfolded, aggregation-prone and pathogenic PrPTSE remains elusive. The primary clinical hallmarks of PrD include vacuolation-associated spongiform changes and PrPTSE accumulation in neural tissue together with astrogliosis. The difficulty in unravelling the disease mechanisms has been related to the rare occurrence and long incubation period (over decades) followed by a very short clinical phase (few months). Additional challenge in unravelling the disease is implicated to the unique nature of the agent, its complexity and strain diversity, resulting in the heterogeneity of the clinical manifestations and potentially diverse disease mechanisms. Recent advances in tissue isolation and processing techniques have identified novel means of intercellular communication through extracellular vesicles (EVs) that contribute to PrPTSE transmission in PrD. This review will comprehensively discuss PrPTSE transmission and neurotoxicity, focusing on the role of EVs in disease progression, biomarker discovery and potential therapeutic agents for the treatment of PrD.
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Affiliation(s)
- Arun Khadka
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Jereme G Spiers
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Lesley Cheng
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Andrew F Hill
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia. .,Institute for Health and Sport, Victoria University, Footscray, VIC, Australia.
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5
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Restrepo-Pineda S, Sánchez-Puig N, Pérez NO, García-Hernández E, Valdez-Cruz NA, Trujillo-Roldán MA. The pre-induction temperature affects recombinant HuGM-CSF aggregation in thermoinducible Escherichia coli. Appl Microbiol Biotechnol 2022; 106:2883-2902. [PMID: 35412129 PMCID: PMC9002048 DOI: 10.1007/s00253-022-11908-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
The overproduction of recombinant proteins in Escherichia coli leads to insoluble aggregates of proteins called inclusion bodies (IBs). IBs are considered dynamic entities that harbor high percentages of the recombinant protein, which can be found in different conformational states. The production conditions influence the properties of IBs and recombinant protein recovery and solubilization. The E. coli growth in thermoinduced systems is generally carried out at 30 °C and then recombinant protein production at 42 °C. Since the heat shock response in E. coli is triggered above 34 °C, the synthesis of heat shock proteins can modify the yields of the recombinant protein and the structural quality of IBs. The objective of this work was to evaluate the effect of different pre-induction temperatures (30 and 34 °C) on the growth of E. coli W3110 producing the human granulocyte-macrophage colony-stimulating factor (rHuGM-CSF) and on the IBs structure in a λpL/pR-cI857 thermoinducible system. The recombinant E. coli cultures growing at 34 °C showed a ~ 69% increase in the specific growth rate compared to cultures grown at 30 °C. The amount of rHuGM-CSF in IBs was significantly higher in cultures grown at 34 °C. Main folding chaperones (DnaK and GroEL) were associated with IBs and their co-chaperones (DnaJ and GroES) with the soluble protein fraction. Finally, IBs from cultures that grew at 34 °C had a lower content of amyloid-like structure and were more sensitive to proteolytic degradation than IBs obtained from cultures at 30 °C. Our study presents evidence that increasing the pre-induction temperature in a thermoinduced system allows obtaining higher recombinant protein and reducing amyloid contents of the IBs. KEY POINTS: • Pre-induction temperature determines inclusion bodies architecture • In pre-induction (above 34 °C), the heat shock response increases recombinant protein production • Inclusion bodies at higher pre-induction temperature show a lower amyloid content.
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Affiliation(s)
- Sara Restrepo-Pineda
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CP, 04510, México
| | - Nuria Sánchez-Puig
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Ciudad de México, 04510, México
| | - Néstor O Pérez
- Probiomed S.A. de C.V. Planta Tenancingo, Cruce de Carreteras Acatzingo-Zumpahuacan SN, Tenancingo, CP 52400, Estado de México, México
| | - Enrique García-Hernández
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Ciudad de México, 04510, México
| | - Norma A Valdez-Cruz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CP, 04510, México
| | - Mauricio A Trujillo-Roldán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CP, 04510, México.
- Departamento de Biología Molecular y Biotecnología, Unidad de Bioprocesos, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CP, 04510, México.
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6
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Serpa JJ, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. Proteomics 2021; 21:e2000298. [PMID: 34482645 PMCID: PMC9285417 DOI: 10.1002/pmic.202000298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/10/2021] [Accepted: 08/27/2021] [Indexed: 11/08/2022]
Abstract
The conversion of the native monomeric cellular prion protein (PrPC ) into an aggregated pathological β-oligomeric form (PrPβ ) and an infectious form (PrPSc ) is the central element in the development of prion diseases. The structure of the aggregates and the molecular mechanisms of the conformational changes involved in the conversion are still unknown. We applied mass spectrometry combined with chemical crosslinking, hydrogen/deuterium exchange, limited proteolysis, and surface modification for the differential characterization of the native and the urea+acid-converted prion β-oligomer structures to obtain insights into the mechanisms of conversion and aggregation. For the determination of the structure of the monomer and the dimer unit of the β-oligomer, we applied a recently-developed approach for de novo protein structure determination which is based on the incorporation of zero-length and short-distance crosslinking data as intra- and inter-protein constraints in discrete molecular dynamics simulations (CL-DMD). Based on all of the structural-proteomics experimental data and the computationally predicted structures of the monomer units, we propose the potential mode of assembly of the β-oligomer. The proposed β-oligomer assembly provides a clue on the β-sheet nucleation site, and how template-based conversion of the native prion molecule occurs, growth of the prion aggregates, and maturation into fibrils may occur.
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Affiliation(s)
- Jason J Serpa
- University of Victoria -Genome British Columbia Proteomics Centre, Victoria, British Columbia, Canada
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Evgeniy V Petrotchenko
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
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7
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Silva CJ, Erickson-Beltran ML, Dynin IC. Quantifying the Role of Lysine in Prion Replication by Nano-LC Mass Spectrometry and Bioassay. Front Bioeng Biotechnol 2020; 8:562953. [PMID: 33072723 PMCID: PMC7542330 DOI: 10.3389/fbioe.2020.562953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/24/2020] [Indexed: 11/26/2022] Open
Abstract
Prions propagate by a template driven process, inducing the normal cellular isoform (PrPC) to adopt the prion (PrPSc) conformation. In PrPC, the positions of lysines are highly conserved and strongly influence prion propagation. In this study, covalent modification was used to quantitate the role of lysines in the PrPSc template that drives prion replication. The ε-amino group of lysines in the PrPSc (hamster-adapted scrapie Sc237) template was acetylated by either acetic anhydride (Ac2O) or the N-hydroxysuccinimide ester of acetic acid (Ac-NHS). The extent of lysine acetylation in PrPSc was quantitated by mass spectrometry or Western blot-based analysis. Identical samples were bioassayed to quantitate the loss of infectivity associated with lysine acetylation. The reduction of infectivity at the highest reagent concentration was approximately 90% (∼10-fold). Ten of the eleven prion lysines were acetylated to a greater extent (25−400-fold) than the observed loss of infectivity. Only one lysine, at position 220 (K220), had a reactivity that is consistent with the loss of infectivity. Although lysines are highly conserved and play a crucial role in converting PrPC into the PrPSc conformation, once that conformation is adopted, the lysines present in the PrPSc template play only a limited role in prion replication. In principle, this approach could be used to clarify the role of other amino acids in the replication of prions and other prion-like protein misfolding diseases.
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Affiliation(s)
- Christopher J Silva
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, CA, United States
| | - Melissa L Erickson-Beltran
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, CA, United States
| | - Irina C Dynin
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, CA, United States
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8
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Eraña H, Charco JM, Di Bari MA, Díaz-Domínguez CM, López-Moreno R, Vidal E, González-Miranda E, Pérez-Castro MA, García-Martínez S, Bravo S, Fernández-Borges N, Geijo M, D’Agostino C, Garrido J, Bian J, König A, Uluca-Yazgi B, Sabate R, Khaychuk V, Vanni I, Telling GC, Heise H, Nonno R, Requena JR, Castilla J. Development of a new largely scalable in vitro prion propagation method for the production of infectious recombinant prions for high resolution structural studies. PLoS Pathog 2019; 15:e1008117. [PMID: 31644574 PMCID: PMC6827918 DOI: 10.1371/journal.ppat.1008117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/04/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
The resolution of the three-dimensional structure of infectious prions at the atomic level is pivotal to understand the pathobiology of Transmissible Spongiform Encephalopathies (TSE), but has been long hindered due to certain particularities of these proteinaceous pathogens. Difficulties related to their purification from brain homogenates of disease-affected animals were resolved almost a decade ago by the development of in vitro recombinant prion propagation systems giving rise to highly infectious recombinant prions. However, lack of knowledge about the molecular mechanisms of the misfolding event and the complexity of systems such as the Protein Misfolding Cyclic Amplification (PMCA), have limited generating the large amounts of homogeneous recombinant prion preparations required for high-resolution techniques such as solid state Nuclear Magnetic Resonance (ssNMR) imaging. Herein, we present a novel recombinant prion propagation system based on PMCA that substitutes sonication with shaking thereby allowing the production of unprecedented amounts of multi-labeled, infectious recombinant prions. The use of specific cofactors, such as dextran sulfate, limit the structural heterogeneity of the in vitro propagated prions and makes possible, for the first time, the generation of infectious and likely homogeneous samples in sufficient quantities for studies with high-resolution structural techniques as demonstrated by the preliminary ssNMR spectrum presented here. Overall, we consider that this new method named Protein Misfolding Shaking Amplification (PMSA), opens new avenues to finally elucidate the three-dimensional structure of infectious prions.
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Affiliation(s)
- Hasier Eraña
- CIC bioGUNE, Derio (Bizkaia), Spain
- ATLAS Molecular Pharma S. L. Derio (Bizkaia), Spain
| | | | - Michele A. Di Bari
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Enric Vidal
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Barcelona, Spain
| | | | | | | | - Susana Bravo
- Proteomics Lab, IDIS, Santiago de Compostela, Spain
| | | | - Mariví Geijo
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio (Bizkaia), Spain
| | - Claudia D’Agostino
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Joseba Garrido
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio (Bizkaia), Spain
| | - Jifeng Bian
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Anna König
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Boran Uluca-Yazgi
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Raimon Sabate
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Spain
| | - Vadim Khaychuk
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Ilaria Vanni
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Glenn C. Telling
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Henrike Heise
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Romolo Nonno
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Spain
| | - Joaquín Castilla
- CIC bioGUNE, Derio (Bizkaia), Spain
- IKERBasque, Basque Foundation for Science, Bilbao (Bizkaia), Spain
- * E-mail:
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Spagnolli G, Rigoli M, Orioli S, Sevillano AM, Faccioli P, Wille H, Biasini E, Requena JR. Full atomistic model of prion structure and conversion. PLoS Pathog 2019; 15:e1007864. [PMID: 31295325 PMCID: PMC6622554 DOI: 10.1371/journal.ppat.1007864] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/23/2019] [Indexed: 11/19/2022] Open
Abstract
Prions are unusual protein assemblies that propagate their conformationally-encoded information in absence of nucleic acids. The first prion identified, the scrapie isoform (PrPSc) of the cellular prion protein (PrPC), caused epidemic and epizootic episodes [1]. Most aggregates of other misfolding-prone proteins are amyloids, often arranged in a Parallel-In-Register-β-Sheet (PIRIBS) [2] or β-solenoid conformations [3]. Similar folding models have also been proposed for PrPSc, although none of these have been confirmed experimentally. Recent cryo-electron microscopy (cryo-EM) and X-ray fiber-diffraction studies provided evidence that PrPSc is structured as a 4-rung β-solenoid (4RβS) [4, 5]. Here, we combined different experimental data and computational techniques to build the first physically-plausible, atomic resolution model of mouse PrPSc, based on the 4RβS architecture. The stability of this new PrPSc model, as assessed by Molecular Dynamics (MD) simulations, was found to be comparable to that of the prion forming domain of Het-s, a naturally-occurring β-solenoid. Importantly, the 4RβS arrangement allowed the first simulation of the sequence of events underlying PrPC conversion into PrPSc. This study provides the most updated, experimentally-driven and physically-coherent model of PrPSc, together with an unprecedented reconstruction of the mechanism underlying the self-catalytic propagation of prions.
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Affiliation(s)
- Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology (CIBIO)–University of Trento, Povo TN, ITALY
- * E-mail: (GS); (EB); (JRR)
| | - Marta Rigoli
- Department of Cellular, Computational and Integrative Biology (CIBIO)–University of Trento, Povo TN, ITALY
- Department of Physics, Povo, Trento TN, ITALY
| | - Simone Orioli
- Department of Physics, Povo, Trento TN, ITALY
- INFN-TIFPA, Povo (Trento), ITALY
| | - Alejandro M. Sevillano
- Department of Pathology–University of California—San Diego, San Diego, California, United States of America
| | - Pietro Faccioli
- Department of Physics, Povo, Trento TN, ITALY
- INFN-TIFPA, Povo (Trento), ITALY
| | - Holger Wille
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases–University of Alberta, Edmonton (AB), CANADA
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology (CIBIO)–University of Trento, Povo TN, ITALY
- * E-mail: (GS); (EB); (JRR)
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute & Department of Medical Sciences, University of Santiago de Compostela-IDIS, Santiago, SPAIN
- * E-mail: (GS); (EB); (JRR)
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10
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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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11
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Rigoli M, Spagnolli G, Faccioli P, Requena JR, Biasini E. Ok Google, how could I design therapeutics against prion diseases? Curr Opin Pharmacol 2019; 44:39-45. [PMID: 31059982 DOI: 10.1016/j.coph.2019.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 02/06/2023]
Abstract
A number of previous successful attempts in the search for therapeutics for a variety of human pathologies highlight the importance of computational technologies in the drug discovery pipeline. This approach, often referred to as computer-aided drug design, is unfortunately inapplicable when the precise information regarding the three-dimensional structure of disease-associated proteins or the mechanism by which they are altered to generate misfolded isoforms are missing. A typical example is represented by prion diseases, fatal pathologies of the nervous system characterized by the conformational conversion of a physiological protein called PrPC into a misfolded and infectious isoform referred to as PrPSc. Missing information regarding the atomic structure of PrPSc as well as the mechanism of templated conversion of PrPC has severely halted the discovery of effective therapies for prion diseases. In this manuscript, we review emerging opportunities to apply computer-aided techniques to target PrPC, PrPSc or to design inhibitors of prion replication, and discuss how these fast-evolving technologies could lay the groundwork for the application of entirely novel rational drug design schemes for these devastating pathologies.
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Affiliation(s)
- Marta Rigoli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Jesús R Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain; Department of Medical Sciences, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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Baskakov IV, Caughey B, Requena JR, Sevillano AM, Surewicz WK, Wille H. The prion 2018 round tables (I): the structure of PrP Sc. Prion 2019; 13:46-52. [PMID: 30646817 PMCID: PMC6422368 DOI: 10.1080/19336896.2019.1569450] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/26/2018] [Indexed: 01/26/2023] Open
Abstract
Understanding the structure of PrPSc is without doubt a sine qua non to understand not only PrPSc propagation, but also critical features of that process such as the strain phenomenon and transmission barriers. While elucidation of the PrPSc structure has been full of difficulties, we now have a large amount of structural information that allows us to begin to understand it. This commentary article summarizes a round table that took place within the Prion 2018 meeting held in Santiago de Compostela to discuss the state of the art in this matter. Two alternative models of PrPSc exist: the PIRIBS and the 4-rung β-solenoid models. Both of them have relevant features. The 4-rung β-solenoid model agrees with experimental constraints of brain derived PrPSc obtained from cryo-EM and X-ray fiber diffraction studies. Furthermore, it allows facile accommodation of the bulky glycans that decorate brain-derived PrPSc. On the other hand, the infectious PrP23-144 amyloid exhibits a PIRIBS architecture. Perhaps, both types of structure co-exist.
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Affiliation(s)
- Ilia V. Baskakov
- Center for Biomedical Engineering and Technology and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute and Department of Medical Sciences, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Alejandro M. Sevillano
- Departments of Pathology and Medicine, University of California San Diego, La Jolla, CA, USA
| | - Witold K. Surewicz
- Departments of Pathology, and of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Holger Wille
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada
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Flores-Fernández JM, Rathod V, Wille H. Comparing the Folds of Prions and Other Pathogenic Amyloids. Pathogens 2018; 7:E50. [PMID: 29734684 PMCID: PMC6027354 DOI: 10.3390/pathogens7020050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 04/29/2018] [Accepted: 05/02/2018] [Indexed: 01/13/2023] Open
Abstract
Pathogenic amyloids are the main feature of several neurodegenerative disorders, such as Creutzfeldt⁻Jakob disease, Alzheimer’s disease, and Parkinson’s disease. High resolution structures of tau paired helical filaments (PHFs), amyloid-β(1-42) (Aβ(1-42)) fibrils, and α-synuclein fibrils were recently reported using cryo-electron microscopy. A high-resolution structure for the infectious prion protein, PrPSc, is not yet available due to its insolubility and its propensity to aggregate, but cryo-electron microscopy, X-ray fiber diffraction, and other approaches have defined the overall architecture of PrPSc as a 4-rung β-solenoid. Thus, the structure of PrPSc must have a high similarity to that of the fungal prion HET-s, which is part of the fungal heterokaryon incompatibility system and contains a 2-rung β-solenoid. This review compares the structures of tau PHFs, Aβ(1-42), and α-synuclein fibrils, where the β-strands of each molecule stack on top of each other in a parallel in-register arrangement, with the β-solenoid folds of HET-s and PrPSc.
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Affiliation(s)
- José Miguel Flores-Fernández
- Department of Biochemistry & Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB T6G 2M8, Canada.
| | - Vineet Rathod
- Department of Biochemistry & Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB T6G 2M8, Canada.
| | - Holger Wille
- Department of Biochemistry & Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB T6G 2M8, Canada.
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14
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The Structure of PrP Sc Prions. Pathogens 2018; 7:pathogens7010020. [PMID: 29414853 PMCID: PMC5874746 DOI: 10.3390/pathogens7010020] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 01/31/2018] [Accepted: 02/03/2018] [Indexed: 12/14/2022] Open
Abstract
PrPSc (scrapie isoform of the prion protein) prions are the infectious agent behind diseases such as Creutzfeldt–Jakob disease in humans, bovine spongiform encephalopathy in cattle, chronic wasting disease in cervids (deer, elk, moose, and reindeer), as well as goat and sheep scrapie. PrPSc is an alternatively folded variant of the cellular prion protein, PrPC, which is a regular, GPI-anchored protein that is present on the cell surface of neurons and other cell types. While the structure of PrPC is well studied, the structure of PrPSc resisted high-resolution determination due to its general insolubility and propensity to aggregate. Cryo-electron microscopy, X-ray fiber diffraction, and a variety of other approaches defined the structure of PrPSc as a four-rung β-solenoid. A high-resolution structure of PrPSc still remains to be solved, but the four-rung β-solenoid architecture provides a molecular framework for the autocatalytic propagation mechanism that gives rise to the alternative conformation of PrPSc. Here, we summarize the current knowledge regarding the structure of PrPSc and speculate about the molecular conversion mechanisms that leads from PrPC to PrPSc.
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15
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Sevillano AM, Fernández-Borges N, Younas N, Wang F, R. Elezgarai S, Bravo S, Vázquez-Fernández E, Rosa I, Eraña H, Gil D, Veiga S, Vidal E, Erickson-Beltran ML, Guitián E, Silva CJ, Nonno R, Ma J, Castilla J, R. Requena J. Recombinant PrPSc shares structural features with brain-derived PrPSc: Insights from limited proteolysis. PLoS Pathog 2018; 14:e1006797. [PMID: 29385212 PMCID: PMC5809102 DOI: 10.1371/journal.ppat.1006797] [Citation(s) in RCA: 17] [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: 04/06/2017] [Revised: 02/12/2018] [Accepted: 12/08/2017] [Indexed: 11/18/2022] Open
Abstract
Very solid evidence suggests that the core of full length PrPSc is a 4-rung β-solenoid, and that individual PrPSc subunits stack to form amyloid fibers. We recently used limited proteolysis to map the β-strands and connecting loops that make up the PrPSc solenoid. Using high resolution SDS-PAGE followed by epitope analysis, and mass spectrometry, we identified positions ~116/118, 133-134, 141, 152-153, 162, 169 and 179 (murine numbering) as Proteinase K (PK) cleavage sites in PrPSc. Such sites likely define loops and/or borders of β-strands, helping us to predict the threading of the β-solenoid. We have now extended this approach to recombinant PrPSc (recPrPSc). The term recPrPSc refers to bona fide recombinant prions prepared by PMCA, exhibiting infectivity with attack rates of ~100%. Limited proteolysis of mouse and bank vole recPrPSc species yielded N-terminally truncated PK-resistant fragments similar to those seen in brain-derived PrPSc, albeit with varying relative yields. Along with these fragments, doubly N- and C-terminally truncated fragments, in particular ~89/97-152, were detected in some recPrPSc preparations; similar fragments are characteristic of atypical strains of brain-derived PrPSc. Our results suggest a shared architecture of recPrPSc and brain PrPSc prions. The observed differences, in particular the distinct yields of specific PK-resistant fragments, are likely due to differences in threading which result in the specific biochemical characteristics of recPrPSc. Furthermore, recombinant PrPSc offers exciting opportunities for structural studies unachievable with brain-derived PrPSc.
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Affiliation(s)
- Alejandro M. Sevillano
- CIMUS Biomedical Research Institute and Department of Medical Sciences University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
- * E-mail: (AMS); (JRR)
| | | | - Neelam Younas
- CIMUS Biomedical Research Institute and Department of Medical Sciences University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Fei Wang
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | | | - Susana Bravo
- Proteomics Lab, IDIS, Santiago de Compostela, Spain
| | | | - Isaac Rosa
- CIMUS Biomedical Research Institute and Department of Medical Sciences University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | | | | | - Sonia Veiga
- CIMUS Biomedical Research Institute and Department of Medical Sciences University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Enric Vidal
- Priocat Laboratory, Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Barcelona, Catalonia, Spain
| | | | - Esteban Guitián
- Mass spectrometry Core Facility, RIAIDT, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Christopher J. Silva
- USDA, ARS Western Regional Research Center, Albany, California, United States of America
| | - Romolo Nonno
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Jiyan Ma
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | | | - Jesús R. Requena
- CIMUS Biomedical Research Institute and Department of Medical Sciences University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
- * E-mail: (AMS); (JRR)
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16
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Elezgarai SR, Fernández-Borges N, Eraña H, Sevillano AM, Charco JM, Harrathi C, Saá P, Gil D, Kong Q, Requena JR, Andréoletti O, Castilla J. Generation of a new infectious recombinant prion: a model to understand Gerstmann-Sträussler-Scheinker syndrome. Sci Rep 2017; 7:9584. [PMID: 28851967 PMCID: PMC5575253 DOI: 10.1038/s41598-017-09489-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/10/2017] [Indexed: 12/15/2022] Open
Abstract
Human transmissible spongiform encephalopathies (TSEs) or prion diseases are a group of fatal neurodegenerative disorders that include Kuru, Creutzfeldt-Jakob disease, Gerstmann-Sträussler-Scheinker syndrome (GSS), and fatal familial insomnia. GSS is a genetically determined TSE caused by a range of mutations within the prion protein (PrP) gene. Several animal models, based on the expression of PrPs carrying mutations analogous to human heritable prion diseases, support that mutations might predispose PrP to spontaneously misfold. An adapted Protein Misfolding Cyclic Amplification methodology based on the use of human recombinant PrP (recPMCA) generated different self-propagating misfolded proteins spontaneously. These were characterized biochemically and structurally, and the one partially sharing some of the GSS PrPSc molecular features was inoculated into different animal models showing high infectivity. This constitutes an infectious recombinant prion which could be an invaluable model for understanding GSS. Moreover, this study proves the possibility to generate recombinant versions of other human prion diseases that could provide a further understanding on the molecular features of these devastating disorders.
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Affiliation(s)
- Saioa R Elezgarai
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio, 48160, Bizkaia, Spain
| | | | - Hasier Eraña
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio, 48160, Bizkaia, Spain
| | - Alejandro M Sevillano
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Jorge M Charco
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio, 48160, Bizkaia, Spain
| | - Chafik Harrathi
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio, 48160, Bizkaia, Spain
| | - Paula Saá
- American Red Cross, Gaithersburg, MD, USA
| | - David Gil
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio, 48160, Bizkaia, Spain
| | - Qingzhong Kong
- Department of Pathology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jesús R Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Olivier Andréoletti
- Ecole Nationale du Veterinaire, Service de Pathologie du Bétail, Toulouse, 31076, France
| | - Joaquín Castilla
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio, 48160, Bizkaia, Spain. .,IKERBASQUE, Basque Foundation for Science, Bilbao, 48011, Bizkaia, Spain.
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Requena JR, Wille H. The Structure of the Infectious Prion Protein and Its Propagation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 150:341-359. [PMID: 28838667 DOI: 10.1016/bs.pmbts.2017.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The prion diseases, which include Creutzfeldt-Jakob disease in humans, chronic wasting disease in cervids (i.e., deer, elk, moose, and reindeer), bovine spongiform encephalopathy in cattle, as well as sheep and goat scrapie, are caused by the conversion of the cellular prion protein (PrPC) into a disease-causing conformer (PrPSc). PrPC is a regular, GPI-anchored protein that is expressed on the cell surface of neurons and many other cell types. The structure of PrPC is well studied, based on analyses of recombinant PrP, which is thought to mimic the structure of native PrPC. The mature protein contains an N-terminal, unfolded domain and a C-terminal, globular domain that consists of three α-helices and only a small, two-stranded β-sheet. In contrast, PrPSc was found to contain predominantly β-structure and to aggregate into a variety of quaternary structures, such as oligomers, amorphous aggregates, amyloid fibrils, and two-dimensional crystals. The tendency of PrPSc to aggregate into these diverse forms is also responsible for our incomplete knowledge about its molecular structure. Nevertheless, the repeating nature of the more regular PrPSc aggregates has provided informative insights into the structure of the infectious conformer, albeit at limited resolution. These data established a four-rung β-solenoid architecture as the main element of its structure. Moreover, the four-rung β-solenoid architecture provides a molecular framework for an autocatalytic propagation mechanism, which could explain the conversion of PrPC into PrPSc.
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Affiliation(s)
- Jesús R Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Holger Wille
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada.
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18
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Abstract
Prion diseases are characterized by the deposition of amyloids, misfolded conformers of the prion protein. The misfolded conformation is self-replicating, by a mechanism solely enciphered in the conformation of the protein. Because of low solubility and heterogeneous aggregate sizes, the detailed atomic structure of the infectious isoform is still unknown. Progress has, however, been made, and has allowed insights into the structural and disease-related mechanisms of prions. Many structural models have been proposed, and a number of them support a consensus trimeric β-helical model, significantly more complex than simple amyloid models. There is evidence that such complexity may be a necessary property of prion structure. Knowledge of the structure of prions will provide a greater understanding of the protein isoform conversion mechanism, and could eventually lead to rationally designed intervention strategies.
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Affiliation(s)
- Gerald Stubbs
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 53723
| | - Jan Stöhr
- Institute for Neurodegenerative Diseases, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94143
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19
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Silva CJ, Erickson-Beltran ML, Hui C, Badiola JJ, Nicholson EM, Requena JR, Bolea R. Quantitating PrP Polymorphisms Present in Prions from Heterozygous Scrapie-Infected Sheep. Anal Chem 2016; 89:854-861. [PMID: 27936597 DOI: 10.1021/acs.analchem.6b03822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Scrapie is a prion (PrPSc) disease of sheep. The incubation period of sheep scrapie is strongly influenced by polymorphisms at positions 136, 154, and 171 of a sheep's normal cellular prion protein (PrPC). Chymotrypsin was used to digest sheep recombinant PrP to identify a set of characteristic peptides [M132LGSXMSRPL141 (X = A or V), Y153XENMY158 (X,= H or R), and Y166RPVDXY172 (X = H, K, Q, or R)] that could be used to detect and quantitate polymorphisms at positions 136, 154, and 171 of sheep PrPC or PrPSc. These peptides were used to develop a multiple reaction monitoring method (MRM) to detect the amounts of a particular polymorphism in a sample of PrPSc isolated from sheep heterozygous for their PrPC proteins. The limit of detection for these peptides was less than 50 attomole. Spinal cord tissue from heterozygous (ARQ/VRQ or ARH/ARQ) scrapie-infected Rasa Aragonesa sheep was analyzed using this MRM method. Both sets of heterozygotes show the presence of both polymorphisms in PrPSc. This was true for samples containing both proteinase K (PK)-sensitive and PK-resistant PrPSc and samples containing only the PK-resistant PrPSc. These results show that heterozygous animals contain PrPSc that is composed of significant amounts of both PrP polymorphisms.
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Affiliation(s)
- Christopher J Silva
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States
| | - Melissa L Erickson-Beltran
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States
| | - Colleen Hui
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States
| | - Juan José Badiola
- Veterinary Faculty, Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes (CIEETE), Universidad de Zaragoza , 50013, Zaragoza Spain
| | - Eric M Nicholson
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service , Ames, Iowa 50010, United States
| | - Jesús R Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS , Santiago de Compostela, 15782 Spain
| | - Rosa Bolea
- Veterinary Faculty, Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes (CIEETE), Universidad de Zaragoza , 50013, Zaragoza Spain
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20
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The Structure of Mammalian Prions and Their Aggregates. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:277-301. [PMID: 28109330 DOI: 10.1016/bs.ircmb.2016.08.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Prion diseases, such as Creutzfeldt-Jakob disease in humans, bovine spongiform encephalopathy in cattle, chronic wasting disease in cervids (i.e., deer, elk, moose, and reindeer), and sheep scrapie, are caused by the misfolding of the cellular prion protein (PrPC) into a disease-causing conformer (PrPSc). PrPC is a normal, GPI-anchored protein that is expressed on the surface of neurons and other cell types. The structure of PrPC is well understood, based on studies of recombinant PrP, which closely mimics the structure of native PrPC. In contrast, PrPSc is prone to aggregate into a variety of quaternary structures, such as oligomers, amorphous aggregates, and amyloid fibrils. The propensity of PrPSc to assemble into these diverse forms of aggregates is also responsible for our limited knowledge about its structure. Then again, the repeating nature of certain regular PrPSc aggregates has allowed (lower resolution) insights into the structure of the infectious conformer, establishing a four-rung β-solenoid structure as a key element of its architecture.
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21
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The Structural Architecture of an Infectious Mammalian Prion Using Electron Cryomicroscopy. PLoS Pathog 2016; 12:e1005835. [PMID: 27606840 PMCID: PMC5015997 DOI: 10.1371/journal.ppat.1005835] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/01/2016] [Indexed: 12/31/2022] Open
Abstract
The structure of the infectious prion protein (PrPSc), which is responsible for Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy, has escaped all attempts at elucidation due to its insolubility and propensity to aggregate. PrPSc replicates by converting the non-infectious, cellular prion protein (PrPC) into the misfolded, infectious conformer through an unknown mechanism. PrPSc and its N-terminally truncated variant, PrP 27–30, aggregate into amorphous aggregates, 2D crystals, and amyloid fibrils. The structure of these infectious conformers is essential to understanding prion replication and the development of structure-based therapeutic interventions. Here we used the repetitive organization inherent to GPI-anchorless PrP 27–30 amyloid fibrils to analyze their structure via electron cryomicroscopy. Fourier-transform analyses of averaged fibril segments indicate a repeating unit of 19.1 Å. 3D reconstructions of these fibrils revealed two distinct protofilaments, and, together with a molecular volume of 18,990 Å3, predicted the height of each PrP 27–30 molecule as ~17.7 Å. Together, the data indicate a four-rung β-solenoid structure as a key feature for the architecture of infectious mammalian prions. Furthermore, they allow to formulate a molecular mechanism for the replication of prions. Knowledge of the prion structure will provide important insights into the self-propagation mechanisms of protein misfolding. The structure of the infectious prion (PrPSc), which is responsible for Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy, has escaped all attempts at elucidation due to its propensity to aggregate. Here, we use the repetitive organization inherent in amyloid fibrils to analyze the structure of GPI-anchorless PrP 27–30 via electron cryomicroscopy. Fourier-transform analysis of averaged fibril segments indicates a repeating unit of 19.1 Å. In agreement with this observation, 3D reconstructions reveal that each fibril contains two distinct protofilaments and that the height of each PrP 27–30 molecule in these fibrils is ~17.7 Å. Together the data indicate a four-rung β-solenoid structure as a key feature for the architecture of infectious mammalian prions. The data conflict with all previous models for the structure of PrPSc and allow the formulation of a molecular mechanism for the replication of prions.
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22
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Requena JR, Kristensson K, Korth C, Zurzolo C, Simmons M, Aguilar-Calvo P, Aguzzi A, Andreoletti O, Benestad SL, Böhm R, Brown K, Calgua B, del Río JA, Espinosa JC, Girones R, Godsave S, Hoelzle LE, Knittler MR, Kuhn F, Legname G, Laeven P, Mabbott N, Mitrova E, Müller-Schiffmann A, Nuvolone M, Peters PJ, Raeber A, Roth K, Schmitz M, Schroeder B, Sonati T, Stitz L, Taraboulos A, Torres JM, Yan ZX, Zerr I. The Priority position paper: Protecting Europe's food chain from prions. Prion 2016; 10:165-81. [PMID: 27220820 PMCID: PMC4981192 DOI: 10.1080/19336896.2016.1175801] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/28/2016] [Accepted: 04/01/2016] [Indexed: 01/09/2023] Open
Abstract
Bovine spongiform encephalopathy (BSE) created a global European crisis in the 1980s and 90s, with very serious health and economic implications. Classical BSE now appears to be under control, to a great extent as a result of a global research effort that identified the sources of prions in meat and bone meal (MBM) and developed new animal-testing tools that guided policy. Priority ( www.prionpriority.eu ) was a European Union (EU) Framework Program 7 (FP7)-funded project through which 21 European research institutions and small and medium enterprises (SMEs) joined efforts between 2009 and 2014, to conduct coordinated basic and applied research on prions and prion diseases. At the end of the project, the Priority consortium drafted a position paper ( www.prionpriority.eu/Priority position paper) with its main conclusions. In the present opinion paper, we summarize these conclusions. With respect to the issue of re-introducing ruminant protein into the feed-chain, our opinion is that sustaining an absolute ban on feeding ruminant protein to ruminants is essential. In particular, the spread and impact of non-classical forms of scrapie and BSE in ruminants is not fully understood and the risks cannot be estimated. Atypical prion agents will probably continue to represent the dominant form of prion diseases in the near future in Europe. Atypical L-type BSE has clear zoonotic potential, as demonstrated in experimental models. Similarly, there are now data indicating that the atypical scrapie agent can cross various species barriers. More epidemiological data from large cohorts are necessary to reach any conclusion on the impact of its transmissibility on public health. Re-evaluations of safety precautions may become necessary depending on the outcome of these studies. Intensified searching for molecular determinants of the species barrier is recommended, since this barrier is key for important policy areas and risk assessment. Understanding the structural basis for strains and the basis for adaptation of a strain to a new host will require continued fundamental research, also needed to understand mechanisms of prion transmission, replication and how they cause nervous system dysfunction and death. Early detection of prion infection, ideally at a preclinical stage, also remains crucial for development of effective treatment strategies.
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Affiliation(s)
- Jesús R. Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela, Santiago de Compostela, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sue Godsave
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | | | - Paul Laeven
- University of Maastricht, Maastricht, The Netherlands
| | | | - Eva Mitrova
- Medical University of Slovakia, Bratislava, Slovakia
| | | | | | - Peter J. Peters
- The Maastricht Multimodal Molecular Imaging Institute, University of Maastricht, Maastricht, The Netherlands
| | | | | | | | | | | | - Lothar Stitz
- Friedrich Löffler Institut, Insel Reims, Germany
| | | | | | | | - Inga Zerr
- Universitätmedizin Göttingen, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
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23
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Abstract
Prion diseases are a heterogeneous class of fatal neurodegenerative disorders associated with misfolding of host cellular prion protein (PrP(C)) into a pathological isoform, termed PrP(Sc). Prion diseases affect various mammals, including humans, and effective treatments are not available. Prion diseases are distinguished from other protein misfolding disorders - such as Alzheimer's or Parkinson's disease - in that they are infectious. Prion diseases occur sporadically without any known exposure to infected material, and hereditary cases resulting from rare mutations in the prion protein have also been documented. The mechanistic underpinnings of prion and other neurodegenerative disorders remain poorly understood. Various proteomics techniques have been instrumental in early PrP(Sc) detection, biomarker discovery, elucidation of PrP(Sc) structure and mapping of biochemical pathways affected by pathogenesis. Moving forward, proteomics approaches will likely become more integrated into the clinical and research settings for the rapid diagnosis and characterization of prion pathogenesis.
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Affiliation(s)
- Roger A Moore
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIH,NIAID, Hamilton, MT 59840, USA
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Müller H, Brener O, Andreoletti O, Piechatzek T, Willbold D, Legname G, Heise H. Progress towards structural understanding of infectious sheep PrP-amyloid. Prion 2015; 8:344-58. [PMID: 25482596 PMCID: PMC4601355 DOI: 10.4161/19336896.2014.983754] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The still elusive structural difference of non-infectious and infectious amyloid of the mammalian prion protein (PrP) is a major pending milestone in understanding protein-mediated infectivity in neurodegenerative diseases. Preparations of PrP-amyloid proven to be infectious have never been investigated with a high-resolution technique. All available models to date have been based on low-resolution data. Here, we establish protocols for the preparation of infectious samples of full-length recombinant (rec) PrP-amyloid in NMR-sufficient amounts by spontaneous fibrillation and seeded fibril growth from brain extract. We link biological and structural data of infectious recPrP-amyloid, derived from bioassays, atomic force microscopy, and solid-state NMR spectroscopy. Our data indicate a semi-mobile N-terminus, some residues with secondary chemical shifts typical of α-helical secondary structure in the middle part between ∼115 to ∼155, and a distinct β-sheet core C-terminal of residue ∼155. These findings are not in agreement with all current models for PrP-amyloid. We also provide evidence that samples seeded from brain extract may not differ in the overall arrangement of secondary structure elements, but rather in the flexibility of protein segments outside the β-core region. Taken together, our protocols provide an essential basis for the high-resolution characterization of non-infectious and infectious PrP-amyloid in the near future.
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Affiliation(s)
- Henrik Müller
- a Institute of Complex Systems; ICS-6: Structural Biochemistry; Forschungszentrum Jülich (FZJ) ; Jülich , Germany
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Daus ML. Techniques to elucidate the conformation of prions. World J Biol Chem 2015; 6:218-222. [PMID: 26322176 PMCID: PMC4549762 DOI: 10.4331/wjbc.v6.i3.218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/04/2015] [Accepted: 06/16/2015] [Indexed: 02/05/2023] Open
Abstract
Proteinaceous infectious particles (prions) are unique pathogens as they are devoid of any coding nucleic acid. Whilst it is assumed that prion disease is transmitted by a misfolded isoform of the cellular prion protein, the structural insight of prions is still vague and research for high resolution structural information of prions is still ongoing. In this review, techniques that may contribute to the clarification of the conformation of prions are presented and discussed.
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N(ε)-Carboxymethyl Modification of Lysine Residues in Pathogenic Prion Isoforms. Mol Neurobiol 2015; 53:3102-3112. [PMID: 25983034 PMCID: PMC4902843 DOI: 10.1007/s12035-015-9200-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/27/2015] [Indexed: 12/17/2022]
Abstract
The most prominent hallmark of prion diseases is prion protein conversion and the subsequent deposition of the altered prions, PrPSc, at the pathological sites of affected individuals, particularly in the brain. A previous study has demonstrated that the N-terminus of the pathogenic prion isoform (PrPSc) is modified with advanced glycation end products (AGEs), most likely at one or more of the three Lys residues (positions 23, 24, and 27) in the N-terminus (23KKRPKP28). The current study investigated whether Nε-(carboxymethyl)lysine (CML), a major AGE form specific to Lys residues produced by nonenzymatic glycation, is an AGE adduct of the N-terminus of PrPSc. We show that CML is linked to at least one Lys residue at the N-terminus of PrPSc in 263K prion-infected hamster brains and at least one of the eight Lys residues (positions 101, 104, 106, 110, 185, 194, 204, and 220) in the proteinase K (PK)-resistant core region of PrPSc. The nonenzymatic glycation of the Lys residue(s) of PrPSc with CML likely occurs in the widespread prion-deposit areas within infected brains, particularly in some of the numerous tyrosine hydroxylase-positive thalamic and hypothalamic nuclei. CML glycation does not occur in PrPC but is seen in the pathologic PrPSc isoform. Furthermore, the modification of PrPSc with CML may be closely involved in prion propagation and deposition in pathological brain areas.
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Proteinase K and the structure of PrPSc: The good, the bad and the ugly. Virus Res 2015; 207:120-6. [PMID: 25816779 DOI: 10.1016/j.virusres.2015.03.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/14/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022]
Abstract
Infectious proteins (prions) are, ironically, defined by their resistance to proteolytic digestion. A defining characteristic of the transmissible isoform of the prion protein (PrP(Sc)) is its partial resistance to proteinase K (PK) digestion. Diagnosis of prion disease typically relies upon immunodetection of PK-digested PrP(Sc) by Western blot, ELISA or immunohistochemical detection. PK digestion has also been used to detect differences in prion strains. Thus, PK has been a crucial tool to detect and, thereby, control the spread of prions. PK has also been used as a tool to probe the structure of PrP(Sc). Mass spectrometry and antibodies have been used to identify PK cleavage sites in PrP(Sc). These results have been used to identify the more accessible, flexible stretches connecting the β-strand components in PrP(Sc). These data, combined with physical constraints imposed by spectroscopic results, were used to propose a qualitative model for the structure of PrP(Sc). Assuming that PrP(Sc) is a four rung β-solenoid, we have threaded the PrP sequence to satisfy the PK proteolysis data and other experimental constraints.
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Silva CJ. Applying the tools of chemistry (mass spectrometry and covalent modification by small molecule reagents) to the detection of prions and the study of their structure. Prion 2015; 8:42-50. [PMID: 24509645 DOI: 10.4161/pri.27891] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Prions are molecular pathogens, able to convert a normal cellular prion protein (PrP(C)) into a prion (PrP(Sc)). The information necessary for this conversion is contained in the conformation of PrP(Sc). Mass spectrometry (MS) and small-molecule covalent reactions have been used to study prions. Mass spectrometry has been used to detect and quantitate prions in the attomole range (10⁻¹⁸ mole). MS-based analysis showed that both possess identical amino acid sequences, one disulfide bond, a GPI anchor, asparagine-linked sugar antennae, and unoxidized methionines. Mass spectrometry has been used to define elements of the secondary and tertiary structure of wild-type PrP(Sc) and GPI-anchorless PrP(Sc). It has also been used to study the quaternary structure of the PrP(Sc) multimer. Small molecule reagents react differently with the same lysine in the PrP(C) conformation than in the PrP(Sc) conformation. Such differences can be detected by Western blot using mAbs with lysine-containing epitopes, such as 3F4 and 6D11. This permits the detection of PrP(Sc) without the need for proteinase K pretreatment and can be used to distinguish among prion strains. These results illustrate how two important chemical tools, mass spectrometry and covalent modification by small molecules, are being applied to the detection and structural study of prions. Furthermore these tools are or can be applied to the study of the other protein misfolding diseases such as Alzheimer Disease, Parkinson Disease, or ALS.
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Requena JR, Wille H. The structure of the infectious prion protein: experimental data and molecular models. Prion 2015; 8:60-6. [PMID: 24583975 PMCID: PMC7030906 DOI: 10.4161/pri.28368] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The structures of the infectious prion protein, PrP(Sc), and that of its proteolytically truncated variant, PrP 27-30, have evaded experimental determination due to their insolubility and propensity to aggregate. Molecular modeling has been used to fill this void and to predict their structures, but various modeling approaches have produced significantly different models. The disagreement between the different modeling solutions indicates the limitations of this method. Over the years, in absence of a three-dimensional (3D) structure, a variety of experimental techniques have been used to gain insights into the structure of this biologically, medically, and agriculturally important isoform. Here, we present an overview of experimental results that were published in recent years, and which provided new insights into the molecular architecture of PrP(Sc) and PrP 27-30. Furthermore, we evaluate all published models in light of these recent, experimental data, and come to the conclusion that none of the models can accommodate all of the experimental constraints. Moreover, this conclusion constitutes an open invitation for renewed efforts to model the structure of PrP(Sc).
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Acevedo-Morantes CY, Wille H. The structure of human prions: from biology to structural models-considerations and pitfalls. Viruses 2014; 6:3875-92. [PMID: 25333467 PMCID: PMC4213568 DOI: 10.3390/v6103875] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 12/27/2022] Open
Abstract
Prion diseases are a family of transmissible, progressive, and uniformly fatal neurodegenerative disorders that affect humans and animals. Although cross-species transmissions of prions are usually limited by an apparent “species barrier”, the spread ofa prion disease to humans by ingestion of contaminated food, or via other routes of exposure, indicates that animal prions can pose a significant public health risk. The infectious agent responsible for the transmission of prion diseases is a misfolded conformer of the prion protein, PrPSc, a pathogenic isoform of the host-encoded, cellular prion protein,PrPC. The detailed mechanisms of prion conversion and replication, as well as the high-resolution structure of PrPSc, are unknown. This review will discuss the general background related to prion biology and assess the structural models proposed to date,while highlighting the experimental challenges of elucidating the structure of PrPSc.
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Affiliation(s)
- Claudia Y Acevedo-Morantes
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB T6G 2M8, Canada.
| | - Holger Wille
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB T6G 2M8, Canada.
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Klimova N, Makarava N, Baskakov IV. The diversity and relationship of prion protein self-replicating states. Virus Res 2014; 207:113-9. [PMID: 25312451 DOI: 10.1016/j.virusres.2014.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/15/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
Abstract
It has become evident that the prion protein (PrP) can form a diverse range of self-replicating structures in addition to bona fide PrP(Sc) or strain-specific PrP(Sc) variants. Some self-replicating states can be only produced in vitro, whereas others can be formed in vivo and in vitro. While transmissible, not all states that replicate in vivo are truly pathogenic. Some of them can replicate silently without causing symptoms or clinical diseases. In the current article we discuss the data on PK-digestion patterns of different self-replicating PrP states in connection with other structural data available to date and assess possible relationships between different self-replicating states. Even though different self-replicating PrP states appear to have significantly different global folding patterns, it seems that the C-terminal region exhibits a cross-β-sheet structure in all self-replicating states, as this region acquires the proteolytically most stable conformation. We also discuss the possibility of the transformation of self-replicating states and triggering of PrP(Sc) formation within the frame of the deformed templating model. The spread of silent self-replicating states is of a particular concern because they can lead to transmissible prion disease. Moreover, examples on how different replication requirements favor different states are discussed. This knowledge can help in designing conditions for selective amplification of a particular PrP state in vitro.
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Affiliation(s)
- Nina Klimova
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 725 W. Lombard St., Baltimore, MD 21201, USA; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, 725 W. Lombard St., Baltimore, MD 21201, USA
| | - Natallia Makarava
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 725 W. Lombard St., Baltimore, MD 21201, USA; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, 725 W. Lombard St., Baltimore, MD 21201, USA
| | - Ilia V Baskakov
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 725 W. Lombard St., Baltimore, MD 21201, USA; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, 725 W. Lombard St., Baltimore, MD 21201, USA.
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Castellanos-Mendoza A, Castro-Acosta RM, Olvera A, Zavala G, Mendoza-Vera M, García-Hernández E, Alagón A, Trujillo-Roldán MA, Valdez-Cruz NA. Influence of pH control in the formation of inclusion bodies during production of recombinant sphingomyelinase-D in Escherichia coli. Microb Cell Fact 2014; 13:137. [PMID: 25213001 PMCID: PMC4177172 DOI: 10.1186/s12934-014-0137-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/04/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Inclusion bodies (IBs) are aggregated proteins that form clusters when protein is overexpressed in heterologous expression systems. IBs have been considered as non-usable proteins, but recently they are being used as functional materials, catalytic particles, drug delivery agents, immunogenic structures, and as a raw material in recombinant therapeutic protein purification. However, few studies have been made to understand how culture conditions affect the protein aggregation and the physicochemical characteristics that lead them to cluster. The objective of our research was to understand how pH affects the physicochemical properties of IBs formed by the recombinant sphingomyelinase-D of tick expressed in E. coli BL21-Gold (DE3) by evaluating two pH culture strategies. RESULTS Uncontrolled pH culture conditions favored recombinant sphingomyelinase-D aggregation and IB formation. The IBs of sphingomyelinase-D produced under controlled pH at 7.5 and after 24 h were smaller (<500 nm) than those produced under uncontrolled pH conditions (>500 nm). Furthermore, the composition, conformation and β-structure formation of the aggregates were different. Under controlled pH conditions in comparison to uncontrolled conditions, the produced IBs presented higher resistance to denaturants and proteinase-K degradation, presented β-structure, but apparently as time passes the IBs become compacted and less sensitive to amyloid dye binding. CONCLUSIONS The manipulation of the pH has an impact on IB formation and their physicochemical characteristics. Particularly, uncontrolled pH conditions favored the protein aggregation and sphingomyelinase-D IB formation. The evidence may lead to find methodologies for bioprocesses to obtain biomaterials with particular characteristics, extending the application possibilities of the inclusion bodies.
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33
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Groveman BR, Dolan MA, Taubner LM, Kraus A, Wickner RB, Caughey B. Parallel in-register intermolecular β-sheet architectures for prion-seeded prion protein (PrP) amyloids. J Biol Chem 2014; 289:24129-42. [PMID: 25028516 DOI: 10.1074/jbc.m114.578344] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structures of the infectious form of prion protein (e.g. PrP(Sc) or PrP-Scrapie) remain poorly defined. The prevalent structural models of PrP(Sc) retain most of the native α-helices of the normal, noninfectious prion protein, cellular prion protein (PrP(C)), but evidence is accumulating that these helices are absent in PrP(Sc) amyloid. Moreover, recombinant PrP(C) can form amyloid fibrils in vitro that have parallel in-register intermolecular β-sheet architectures in the domains originally occupied by helices 2 and 3. Here, we provide solid-state NMR evidence that the latter is also true of initially prion-seeded recombinant PrP amyloids formed in the absence of denaturants. These results, in the context of a primarily β-sheet structure, led us to build detailed models of PrP amyloid based on parallel in-register architectures, fibrillar shapes and dimensions, and other available experimentally derived conformational constraints. Molecular dynamics simulations of PrP(90-231) octameric segments suggested that such linear fibrils, which are consistent with many features of PrP(Sc) fibrils, can have stable parallel in-register β-sheet cores. These simulations revealed that the C-terminal residues ∼124-227 more readily adopt stable tightly packed structures than the N-terminal residues ∼90-123 in the absence of cofactors. Variations in the placement of turns and loops that link the β-sheets could give rise to distinct prion strains capable of faithful template-driven propagation. Moreover, our modeling suggests that single PrP monomers can comprise the entire cross-section of fibrils that have previously been assumed to be pairs of laterally associated protofilaments. Together, these insights provide a new basis for deciphering mammalian prion structures.
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Affiliation(s)
- Bradley R Groveman
- From the Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840 and
| | - Michael A Dolan
- the Computational Biology Section, Bioinformatics and Computational Biosciences Branch, NIAID, and
| | - Lara M Taubner
- From the Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840 and
| | - Allison Kraus
- From the Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840 and
| | - Reed B Wickner
- Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Byron Caughey
- From the Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840 and
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Marshall KE, Offerdahl DK, Speare JO, Dorward DW, Hasenkrug A, Carmody AB, Baron GS. Glycosylphosphatidylinositol anchoring directs the assembly of Sup35NM protein into non-fibrillar, membrane-bound aggregates. J Biol Chem 2014; 289:12245-63. [PMID: 24627481 DOI: 10.1074/jbc.m114.556639] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In prion-infected hosts, PrPSc usually accumulates as non-fibrillar, membrane-bound aggregates. Glycosylphosphatidylinositol (GPI) anchor-directed membrane association appears to be an important factor controlling the biophysical properties of PrPSc aggregates. To determine whether GPI anchoring can similarly modulate the assembly of other amyloid-forming proteins, neuronal cell lines were generated that expressed a GPI-anchored form of a model amyloidogenic protein, the NM domain of the yeast prion protein Sup35 (Sup35(GPI)). We recently reported that GPI anchoring facilitated the induction of Sup35(GPI) prions in this system. Here, we report the ultrastructural characterization of self-propagating Sup35(GPI) aggregates of either spontaneous or induced origin. Like membrane-bound PrPSc, Sup35(GPI) aggregates resisted release from cells treated with phosphatidylinositol-specific phospholipase C. Sup35(GPI) aggregates of spontaneous origin were detergent-insoluble, protease-resistant, and self-propagating, in a manner similar to that reported for recombinant Sup35NM amyloid fibrils and induced Sup35(GPI) aggregates. However, GPI-anchored Sup35 aggregates were not stained with amyloid-binding dyes, such as Thioflavin T. This was consistent with ultrastructural analyses, which showed that the aggregates corresponded to dense cell surface accumulations of membrane vesicle-like structures and were not fibrillar. Together, these results showed that GPI anchoring directs the assembly of Sup35NM into non-fibrillar, membrane-bound aggregates that resemble PrPSc, raising the possibility that GPI anchor-dependent modulation of protein aggregation might occur with other amyloidogenic proteins. This may contribute to differences in pathogenesis and pathology between prion diseases, which uniquely involve aggregation of a GPI-anchored protein, versus other protein misfolding diseases.
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Affiliation(s)
- Karen E Marshall
- From the Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840
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Shirai T, Saito M, Kobayashi A, Asano M, Hizume M, Ikeda S, Teruya K, Morita M, Kitamoto T. Evaluating prion models based on comprehensive mutation data of mouse PrP. Structure 2014; 22:560-71. [PMID: 24560805 DOI: 10.1016/j.str.2013.12.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 12/21/2013] [Accepted: 12/28/2013] [Indexed: 10/25/2022]
Abstract
The structural details of the essential entity of prion disease, fibril prion protein (PrP(Sc)), are still elusive despite the large body of evidence supporting the prion hypothesis. Five major working models of PrP(Sc) structure, which are not compatible with each other, have been proposed. However, no systematic evaluation has been performed on those models. We devised a method that combined systematic point mutation with threading on knowledge-based amino acid potentials. A comprehensive mutation experiment was performed on mouse prion protein, and the PrP(Sc) conversion efficiency of each mutant was examined. The models were evaluated based on the mutation data by using the threading method. Although the data turned out to be rather more consistent with the models that assumed a conversion of the N-terminal region of core PrP into a β helix than with others, substantial modifications were also required to further improve the current model based on recent experimental results.
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Affiliation(s)
- Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan; Bioinformatics Research Division, Japan Science and Technology Agency, 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-8666 Japan.
| | - Mihoko Saito
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan; Bioinformatics Research Division, Japan Science and Technology Agency, 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-8666 Japan
| | - Atsushi Kobayashi
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Masahiro Asano
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Masaki Hizume
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Shino Ikeda
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Kenta Teruya
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Masanori Morita
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan; Research and Development Division, Benesis Corporation, Kitahama, Chuo-Ku, Osaka 541-850, Japan
| | - Tetsuyuki Kitamoto
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
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Zanusso G, Fiorini M, Ferrari S, Meade-White K, Barbieri I, Brocchi E, Ghetti B, Monaco S. Gerstmann-Sträussler-Scheinker disease and "anchorless prion protein" mice share prion conformational properties diverging from sporadic Creutzfeldt-Jakob disease. J Biol Chem 2014; 289:4870-81. [PMID: 24398683 DOI: 10.1074/jbc.m113.531335] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The role of the GPI-anchor in prion disease pathogenesis is still a challenging issue. In vitro studies have shown that anchorless cellular prion protein (PrP(C)) undergoes aberrant post-translational processing and metabolism. Moreover, transgenic (Tg) mice overexpressing anchorless PrP(C) develop a spontaneous neurological disease accompanied with widespread brain PrP amyloid deposition, in the absence of spongiform changes. Generation of PrP forms lacking the GPI and PrP amyloidosis are striking features of human stop codon mutations in the PrP gene (PRNP), associated with PrP cerebral amyloid angiopathy (PrP-CAA) and Gerstmann-Sträussler-Scheinker (GSS) syndrome. More recently, the presence of anchorless PrP species has been also claimed in sporadic Creutzfeldt-Jakob disease (sCJD). Using a highly sensitive protein separation technique and taking advantage of reference maps of synthetic PrP peptides, we investigated brain tissues from scrapie-infected "anchorless PrP" Tg mice and wild type mice to determine the contribution of the GPI-anchor to the molecular mass and isoelectric point of PrP quasispecies under two-dimensional electrophoresis. We also assessed the conformational properties of anchorless and anchored prions under standard and inactivating conditions. These studies were extended to sCJD and GSS. At variance with GSS, characterization of PrP quasispecies in different sCJD subtypes ruled out the presence of anchorless prions. Moreover, under inactivating conditions, mice anchorless prions, but not sCJD prions, generated internal PrP fragments, cleaved at both N and C termini, similar to those found in PrP-CAA and GSS brain tissues. These findings show that anchorless PrP(Sc) generates GSS-like PrP fragments, and suggest a major role for unanchored PrP in amyloidogenesis.
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Affiliation(s)
- Gianluigi Zanusso
- From the Department of Neurological and Movement Sciences, University of Verona, Verona 37134, Italy
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37
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Amenitsch H, Benetti F, Ramos A, Legname G, Requena JR. SAXS structural study of PrP(Sc) reveals ~11 nm diameter of basic double intertwined fibers. Prion 2013; 7:496-500. [PMID: 24247356 DOI: 10.4161/pri.27190] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A sample of purified Syrian hamster PrP27-30 prion fibers was analyzed by synchrotron small-angle X-ray scattering (SAXS). The SAXS pattern obtained was fitted to a model based on infinitely long cylinders with a log-normal intensity distribution, a hard-sphere structure factor and a general Porod term for larger aggregates. The diameter calculated for the cylinders determined from the fit was 11.0 ± 0.2 nm. This measurement offers an estimation of the diameter of PrP(Sc) fibers in suspension, i.e., free of errors derived from estimations based on 2D projections in transmission electron microscopy images, subjected to further possible distortions from the negative stain. This diameter, which corresponds to a maximum diameter of approximately 5.5 nm for each of the two intertwined protofilaments making up the fibers, rules out the possibility that PrP(Sc) conforms to a stack of in-register, single-rung flat PrP(Sc) monomers; rather, PrP(Sc) subunits must necessarily coil, most likely several times, into themselves.
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Affiliation(s)
- Heinz Amenitsch
- Institute of Inorganic Chemistry; Graz University of Technology; Graz, Austria
| | - Federico Benetti
- Laboratory of Prion Biology; Department of Neuroscience; Scuola Internazionale Superiore di Studi Avanzati (SISSA); Trieste, Italy
| | - Adriana Ramos
- CIMUS Biomedical Research Institute & Department of Medicine; University of Santiago de Compostela-IDIS; Santiago de Compostela, Spain
| | - Giuseppe Legname
- Laboratory of Prion Biology; Department of Neuroscience; Scuola Internazionale Superiore di Studi Avanzati (SISSA); Trieste, Italy
| | - Jesús R Requena
- CIMUS Biomedical Research Institute & Department of Medicine; University of Santiago de Compostela-IDIS; Santiago de Compostela, Spain
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