1
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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: 1.8] [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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2
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Siddiqi MK, Kim C, Haldiman T, Kacirova M, Wang B, Bohon J, Chance MR, Kiselar J, Safar JG. Structurally distinct external solvent-exposed domains drive replication of major human prions. PLoS Pathog 2021; 17:e1009642. [PMID: 34138981 PMCID: PMC8211289 DOI: 10.1371/journal.ppat.1009642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/13/2021] [Indexed: 12/01/2022] Open
Abstract
There is a limited understanding of structural attributes that encode the iatrogenic transmissibility and various phenotypes of prions causing the most common human prion disease, sporadic Creutzfeldt-Jakob disease (sCJD). Here we report the detailed structural differences between major sCJD MM1, MM2, and VV2 prions determined with two complementary synchrotron hydroxyl radical footprinting techniques—mass spectrometry (MS) and conformation dependent immunoassay (CDI) with a panel of Europium-labeled antibodies. Both approaches clearly demonstrate that the phenotypically distant prions differ in a major way with regard to their structural organization, and synchrotron-generated hydroxyl radicals progressively inhibit their seeding potency in a strain and structure-specific manner. Moreover, the seeding rate of sCJD prions is primarily determined by strain-specific structural organization of solvent-exposed external domains of human prion particles that control the seeding activity. Structural characteristics of human prion strains suggest that subtle changes in the organization of surface domains play a critical role as a determinant of human prion infectivity, propagation rate, and targeting of specific brain structures. Sporadic human prion diseases are conceivably the most heterogenous neurodegenerative disorders and a growing body of research indicates that they are caused by distinct strains of prions. By parallel monitoring their replication potency and progressive hydroxyl radical modification of amino acid side chains during synchrotron irradiation, we identified major differences in the structural organization that correlate with distinct inactivation susceptibility of a given human prion strain. Furthermore, our data demonstrated, for the first time, that seeding activity of different strains of infectious brain-derived human prions is primarily function of distinct solvent-exposed structural domains, and implicate them in the initial binding of cellular isoform of prion protein (PrPC) as a critical step in human prion replication and infectivity.
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Affiliation(s)
| | - Chae Kim
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Tracy Haldiman
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Miroslava Kacirova
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Benlian Wang
- Department of Nutrition, Case Western Reserve University, Cleveland, Ohio, United States of America.,Center for Proteomics and Bioinformatics, Case Center for Synchrotron Biosciences, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Jen Bohon
- Department of Nutrition, Case Western Reserve University, Cleveland, Ohio, United States of America.,Center for Proteomics and Bioinformatics, Case Center for Synchrotron Biosciences, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Mark R Chance
- Department of Nutrition, Case Western Reserve University, Cleveland, Ohio, United States of America.,Center for Proteomics and Bioinformatics, Case Center for Synchrotron Biosciences, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Janna Kiselar
- Department of Nutrition, Case Western Reserve University, Cleveland, Ohio, United States of America.,Center for Proteomics and Bioinformatics, Case Center for Synchrotron Biosciences, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Jiri G Safar
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America.,Department of Neurology, Case Western Reserve University, Cleveland, Ohio, United States of America
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3
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Spagnolli G, Requena JR, Biasini E. Understanding prion structure and conversion. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 175:19-30. [PMID: 32958233 DOI: 10.1016/bs.pmbts.2020.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Since their original identification, prions have represented enigmatic agents that defy the classical concept of genetic inheritance. For almost four decades, the high-resolution structure of PrPSc, the infectious and misfolded counterpart of the cellular prion protein (PrPC), has remained elusive, mostly due to technical challenges posed by its high insolubility and aggregation propensity. As a result, such a lack of information has critically hampered the search for an effective therapy against prion diseases. Nevertheless, multiple attempts to get insights into the structure of PrPSc have provided important experimental constraints that, despite being at limited resolution, are paving the way for the application of computer-aided technologies to model the three-dimensional architecture of prions and their templated replication mechanism. Here, we review the most relevant studies carried out so far to elucidate the conformation of infectious PrPSc and offer an overview of the most advanced molecular models to explain prion structure and conversion.
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Affiliation(s)
- Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, TN, Italy; Dulbecco Telethon Institute, University of Trento, Trento, TN, Italy
| | - Jesús R Requena
- CIMUS Biomedical Research Institute & Department of Medical Sciences, University of Santiago de Compostela-IDIS, Santiago, Spain
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, TN, Italy; Dulbecco Telethon Institute, University of Trento, Trento, TN, Italy.
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4
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Lathe R, Darlix JL. Prion protein PrP nucleic acid binding and mobilization implicates retroelements as the replicative component of transmissible spongiform encephalopathy. Arch Virol 2020; 165:535-556. [PMID: 32025859 PMCID: PMC7024060 DOI: 10.1007/s00705-020-04529-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 12/21/2022]
Abstract
The existence of more than 30 strains of transmissible spongiform encephalopathy (TSE) and the paucity of infectivity of purified PrPSc, as well as considerations of PrP structure, are inconsistent with the protein-only (prion) theory of TSE. Nucleic acid is a strong contender as a second component. We juxtapose two key findings: (i) PrP is a nucleic-acid-binding antimicrobial protein that is similar to retroviral Gag proteins in its ability to trigger reverse transcription. (ii) Retroelement mobilization is widely seen in TSE disease. Given further evidence that PrP also mediates nucleic acid transport into and out of the cell, a strong case is to be made that a second element – retroelement nucleic acid – bound to PrP constitutes the second component necessary to explain the multiple strains of TSE.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, University of Edinburgh School of Medicine, Edinburgh, UK. .,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow, Moscow Region, Russia.
| | - Jean-Luc Darlix
- Faculté de Pharmacie, Centre Nationale de la Recherche Scientifique (CNRS) Laboratory of Bioimaging and Pathologies (Unité Mixte de Recherche 7021), Université de Strasbourg, Illkirch, France.
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5
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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: 19] [Impact Index Per Article: 3.2] [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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6
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Chacon SS, Reardon PN, Burgess CJ, Purvine S, Chu RK, Clauss TR, Walter E, Myrold DD, Washton N, Kleber M. Mineral Surfaces as Agents of Environmental Proteolysis: Mechanisms and Controls. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3018-3026. [PMID: 30767514 DOI: 10.1021/acs.est.8b05583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We investigated the extent to which contact with mineral surfaces affected the molecular integrity of a model protein, with an emphasis on identifying the mechanisms (hydrolysis, oxidation) and conditions leading to protein alteration. To this end, we studied the ability of four mineral surface archetypes (negatively charged, positively charged, neutral, redox-active) to abiotically fragment a well-characterized protein (GB1) as a function of pH and contact time. GB1 was exposed to the soil minerals montmorillonite, goethite, kaolinite, and birnessite at pH 5 and pH 7 for 1, 8, 24, and 168 h and the supernatant was screened for peptide fragments using Tandem Mass Spectrometry. To distinguish between products of oxidative and hydrolytic cleavage, we combined results from the SEQUEST algorithm, which identifies protein fragments that were cleaved hydrolytically, with the output of a deconvolution algorithm (DECON-Routine) designed to identify oxidation fragments. All four minerals were able to induce protein cleavage. Manganese oxide was effective at both hydrolytic and oxidative cleavage. The fact that phyllosilicates-which are not redox active-induced oxidative cleavage indicates that surfaces acted as catalysts and not as reactants. Our results extend previous observations of proteolytic capabilities in soil minerals to the groups of phyllosilicates and Fe-oxides. We identified structural regions of the protein with particularly high susceptibility to cleavage (loops and β strands) as well as regions that were entirely unaffected (α helix).
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Affiliation(s)
- Stephany S Chacon
- Department of Crop and Soil Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Patrick N Reardon
- Environmental Molecular Science Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
- Oregon State University Nuclear Magnetic Resonance Facility , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Christopher J Burgess
- Department of Crop and Soil Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Samuel Purvine
- Environmental Molecular Science Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Rosalie K Chu
- Environmental Molecular Science Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Therese R Clauss
- Environmental Molecular Science Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Eric Walter
- Environmental Molecular Science Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - David D Myrold
- Department of Crop and Soil Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Nancy Washton
- Environmental Molecular Science Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Markus Kleber
- Department of Crop and Soil Science , Oregon State University , Corvallis , Oregon 97331 , United States
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7
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Gielbert A, Thorne JK, Plater JM, Thorne L, Griffiths PC, Simmons MM, Cassar CA. Molecular characterisation of atypical BSE prions by mass spectrometry and changes following transmission to sheep and transgenic mouse models. PLoS One 2018; 13:e0206505. [PMID: 30408075 PMCID: PMC6224059 DOI: 10.1371/journal.pone.0206505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/14/2018] [Indexed: 11/18/2022] Open
Abstract
The prion hypothesis proposes a causal relationship between the misfolded prion protein (PrPSc) molecular entity and the disease transmissible spongiform encephalopathy (TSE). Variations in the conformation of PrPSc are associated with different forms of TSE and different risks to animal and human health. Since the discovery of atypical forms of bovine spongiform encephalopathy (BSE) in 2003, scientists have progressed the molecular characterisation of the associated PrPSc in order to better understand these risks, both in cattle as the natural host and following experimental transmission to other species. Here we report the development of a mass spectrometry based assay for molecular characterisation of bovine proteinase K (PK) treated PrPSc (PrPres) by quantitative identification of its N-terminal amino acid profiles (N-TAAPs) and tryptic peptides. We have applied the assay to classical, H-type and L-type BSE prions purified from cattle, transgenic (Tg) mice expressing the bovine (Tg110 and Tg1896) or ovine (TgEM16) prion protein gene, and sheep brain. We determined that, for classical BSE in cattle, the G96 N-terminal cleavage site dominated, while the range of cleavage sites was wider following transmission to Tg mice and sheep. For L-BSE in cattle and Tg bovinised mice, a C-terminal shift was identified in the N-TAAP distribution compared to classical BSE, consistent with observations by Western blot (WB). For L-BSE transmitted to sheep, both N-TAAP and tryptic peptide profiles were found to be changed compared to cattle, but less so following transmission to Tg ovinised mice. Relative abundances of aglycosyl peptides were found to be significantly different between the atypical BSE forms in cattle as well as in other hosts. The enhanced resolution provided by molecular analysis of PrPres using mass spectrometry has improved insight into the molecular changes following transmission of atypical BSE to other species.
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Affiliation(s)
- Adriana Gielbert
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
- * E-mail:
| | - Jemma K. Thorne
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
| | - Jane M. Plater
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
| | - Leigh Thorne
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
| | - Peter C. Griffiths
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
| | - Marion M. Simmons
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
| | - Claire A. Cassar
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
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8
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Katorcha E, Gonzalez-Montalban N, Makarava N, Kovacs GG, Baskakov IV. Prion replication environment defines the fate of prion strain adaptation. PLoS Pathog 2018; 14:e1007093. [PMID: 29928047 PMCID: PMC6013019 DOI: 10.1371/journal.ppat.1007093] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/14/2018] [Indexed: 11/18/2022] Open
Abstract
The main risk of emergence of prion diseases in humans is associated with a cross-species transmission of prions of zoonotic origin. Prion transmission between species is regulated by a species barrier. Successful cross-species transmission is often accompanied by strain adaptation and result in stable changes of strain-specific disease phenotype. Amino acid sequences of host PrPC and donor PrPSc as well as strain-specific structure of PrPSc are believed to be the main factors that control species barrier and strain adaptation. Yet, despite our knowledge of the primary structures of mammalian prions, predicting the fate of prion strain adaptation is very difficult if possible at all. The current study asked the question whether changes in cofactor environment affect the fate of prions adaptation. To address this question, hamster strain 263K was propagated under normal or RNA-depleted conditions using serial Protein Misfolding Cyclic Amplification (PMCA) conducted first in mouse and then hamster substrates. We found that 263K propagated under normal conditions in mouse and then hamster substrates induced the disease phenotype similar to the original 263K. Surprisingly, 263K that propagated first in RNA-depleted mouse substrate and then normal hamster substrate produced a new disease phenotype upon serial transmission. Moreover, 263K that propagated in RNA-depleted mouse and then RNA-depleted hamster substrates failed to induce clinical diseases for three serial passages despite a gradual increase of PrPSc in animals. To summarize, depletion of RNA in prion replication reactions changed the rate of strain adaptation and the disease phenotype upon subsequent serial passaging of PMCA-derived materials in animals. The current studies suggest that replication environment plays an important role in determining the fate of prion strain adaptation. The main risk of emergence of prion diseases in humans is associated with a cross-species transmission of prions of zoonotic origin. Prion transmission between species is regulated by a species barrier. Amino acid sequences of host prion protein and donor prions are believed to be the main factors that control species barrier and strain adaptation. Yet, despite our knowledge of the primary structures of mammalian prions, predicting the fate of prion strain adaptation is very difficult. The current study asked the question whether changes in cofactor environment affect the fate of prions adaptation. To address this question, hamster prion strain was propagated under normal or RNA-depleted conditions in vitro first using mouse and then hamster substrates. This work demonstrated that depletion of RNA in prion replication reactions changed the rate of strain adaptation and the disease phenotype upon subsequent serial passaging in animals. The current studies suggest that replication environment plays an important role in determining the fate of prion strain adaptation.
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Affiliation(s)
- Elizaveta Katorcha
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Nuria Gonzalez-Montalban
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Natallia Makarava
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Gabor G. Kovacs
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Ilia V. Baskakov
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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9
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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: 60] [Impact Index Per Article: 8.6] [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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10
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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: 2.4] [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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11
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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: 17] [Impact Index Per Article: 2.1] [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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12
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Srivastava S, Makarava N, Katorcha E, Savtchenko R, Brossmer R, Baskakov IV. Post-conversion sialylation of prions in lymphoid tissues. Proc Natl Acad Sci U S A 2015; 112:E6654-62. [PMID: 26627256 PMCID: PMC4672809 DOI: 10.1073/pnas.1517993112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sialylated glycans on the surface of mammalian cells act as part of a "self-associated molecular pattern," helping the immune system to recognize "self" from "altered self" or "nonself." To escape the host immune system, some bacterial pathogens have evolved biosynthetic pathways for host-like sialic acids, whereas others recruited host sialic acids for decorating their surfaces. Prions lack nucleic acids and are not conventional pathogens. Nevertheless, prions might use a similar strategy for invading and colonizing the lymphoreticular system. Here we show that the sialylation status of the infectious, disease-associated state of the prion protein (PrP(Sc)) changes with colonization of secondary lymphoid organs (SLOs). As a result, spleen-derived PrP(Sc) is more sialylated than brain-derived PrP(Sc). Enhanced sialylation of PrP(Sc) is recapitulated in vitro by incubating brain-derived PrP(Sc) with primary splenocytes or cultured macrophage RAW 264.7 cells. General inhibitors of sialyltranserases (STs), the enzymes that transfer sialic acid residues onto terminal positions of glycans, suppressed extrasialylation of PrP(Sc). A fluorescently labeled precursor of sialic acid revealed ST activity associated with RAW macrophages. This study illustrates that, upon colonization of SLOs, the sialylation status of prions changes by host STs. We propose that this mechanism is responsible for camouflaging prions in SLOs and has broad implications.
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Affiliation(s)
- Saurabh Srivastava
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Natallia Makarava
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Elizaveta Katorcha
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Regina Savtchenko
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Reinhard Brossmer
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ilia V Baskakov
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201;
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13
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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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14
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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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15
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Hosokawa-Muto J, Yamaguchi KI, Kamatari YO, Kuwata K. Synthesis of double-fluorescent labeled prion protein for FRET analysis. Biosci Biotechnol Biochem 2015; 79:1802-9. [PMID: 26035019 DOI: 10.1080/09168451.2015.1050991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
An abnormal form of prion protein (PrP) is considered to be the pathogen in prion diseases. However, the structural details of this abnormal form are not known. To characterize the non-native structure of PrP, we synthesized position-specific double-fluorescent labeled PrP for a fluorescence resonance energy transfer (FRET) experiment. Using FRET, we observed a conformational change in the labeled PrP associated with amyloid fibril formation. The FRET analysis indicated that the distance between fluorescent labeled N- and C-terminal sites of PrP increased upon the formation of amyloid fibrils compared with that of the native state. This approach using FRET analysis is useful for elucidating the structure of abnormal PrP.
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Affiliation(s)
| | - Kei-ichi Yamaguchi
- a Center for Emerging Infectious Diseases , Gifu University.,b United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University
| | - Yuji O Kamatari
- a Center for Emerging Infectious Diseases , Gifu University.,c Life Science Research Center , Gifu University
| | - Kazuo Kuwata
- a Center for Emerging Infectious Diseases , Gifu University.,b United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University.,d Department of Gene Development, Graduate School of Medicine , Gifu University , Gifu , Japan
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16
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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: 3.6] [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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17
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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: 0.9] [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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18
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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: 7.1] [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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19
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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: 1.5] [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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20
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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: 132] [Impact Index Per Article: 12.0] [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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21
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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: 1.4] [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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22
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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: 1.4] [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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23
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Wilson C, Ramai D, Serjanov D, Lama N, Levinger L, Chang EJ. Tethered domains and flexible regions in tRNase Z(L), the long form of tRNase Z. PLoS One 2013; 8:e66942. [PMID: 23874404 PMCID: PMC3714273 DOI: 10.1371/journal.pone.0066942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/13/2013] [Indexed: 11/30/2022] Open
Abstract
tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes the pre-tRNA 3′ trailer in a step central to tRNA maturation. The short form (tRNase ZS) is the only one found in bacteria and archaebacteria and is also present in some eukaryotes. The homologous long form (tRNase ZL), exclusively found in eukaryotes, consists of related amino- and carboxy-domains, suggesting that tRNase ZL arose from a tandem duplication of tRNase ZS followed by interdependent divergence of the domains. X-ray crystallographic structures of tRNase ZS reveal a flexible arm (FA) extruded from the body of tRNase Z remote from the active site that binds tRNA far from the scissile bond. No tRNase ZL structures have been solved; alternative biophysical studies are therefore needed to illuminate its functional characteristics. Structural analyses of tRNase ZL performed by limited proteolysis, two dimensional gel electrophoresis and mass spectrometry establish stability of the amino and carboxy domains and flexibility of the FA and inter-domain tether, with implications for tRNase ZL function.
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Affiliation(s)
- Christopher Wilson
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Daryl Ramai
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
| | - Dmitri Serjanov
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Neema Lama
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
| | - Louis Levinger
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Emmanuel J. Chang
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
- * E-mail:
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24
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Structural similarity of wild-type and ALS-mutant superoxide dismutase-1 fibrils using limited proteolysis and atomic force microscopy. Proc Natl Acad Sci U S A 2013; 110:10934-9. [PMID: 23781106 DOI: 10.1073/pnas.1309613110] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Abnormal assemblies formed by misfolded superoxide dismutase-1 (SOD1) proteins are the likely cause of SOD1-linked familial amyotrophic lateral sclerosis (fALS) and may be involved in some cases of sporadic ALS. To analyze the structure of the insoluble SOD1 amyloid fibrils, we first used limited proteolysis followed by mass spectrometric analysis. Digestion of amyloid fibrils formed from full-length N-acetylated WT SOD1 with trypsin, chymotrypsin, or Pronase revealed that the first 63 residues of the N terminus were protected from protease digestion by fibril formation. Furthermore, every tested ALS-mutant SOD1 protein (G37R, L38V, G41D, G93A, G93S, and D101N) showed a similar protected fragment after trypsin digestion. Our second approach to structural characterization used atomic force microscopy to image the SOD1 fibrils and revealed that WT and mutants showed similar twisted morphologies. WT fibrils had a consistent average helical pitch distance of 62.1 nm. The ALS-mutant SOD1 proteins L38V, G93A, and G93S formed fibrils with helical twist patterns very similar to those of WT, whereas small but significant structural deviations were observed for the mutant proteins G37R, G41D, and D101N. Overall, our studies suggest that human WT SOD1 and ALS-mutants tested have a common intrinsic propensity to fibrillate through the N terminus and that single amino acid substitutions can lead to changes in the helical twist pattern.
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Gielbert A, Davis LA, Sayers AR, Tang Y, Hope J, Sauer MJ. Quantitative profiling of PrPSc peptides by high-performance liquid chromatography mass spectrometry to investigate the diversity of prions. Anal Biochem 2013; 436:36-44. [DOI: 10.1016/j.ab.2013.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/11/2013] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
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Zweckstetter M. Conserved amyloid core structure of stop mutants of the human prion protein. Prion 2013; 7:193-7. [PMID: 23406905 DOI: 10.4161/pri.23956] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Prion diseases are associated with misfolding of the natively α-helical prion protein into isoforms that are rich in cross β-structure. However, both the mechanism by which pathological conformations are produced and their structural properties remain unclear. Using a combination of nuclear magnetic resonance spectroscopy, computation, hydroxyl radical probing combined with mass-spectrometry and site-directed mutagenesis, we showed that prion stop mutants that accumulate in amyloidogenic plaque-forming aggregates fold into a β-helix. The polymorphic residue 129 is located in the hydrophobic core of the β-helix in line with a critical role of the 129 region in the packing of protein chains into prion particles. Together with electron microscopy our data support a trimeric left-handed β-helix model in which the trimer interface is formed by residues L125, Y128 and L130. Different prion types or strains might be related to different aggregate structures or filament assemblies.
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Affiliation(s)
- Markus Zweckstetter
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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27
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Vázquez-Fernández E, Alonso J, Pastrana MA, Ramos A, Stitz L, Vidal E, Dynin I, Petsch B, Silva CJ, Requena JR. Structural organization of mammalian prions as probed by limited proteolysis. PLoS One 2012. [PMID: 23185550 PMCID: PMC3502352 DOI: 10.1371/journal.pone.0050111] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Elucidation of the structure of PrPSc continues to be one major challenge in prion research. The mechanism of propagation of these infectious agents will not be understood until their structure is solved. Given that high resolution techniques such as NMR or X-ray crystallography cannot be used, a number of lower resolution analytical approaches have been attempted. Thus, limited proteolysis has been successfully used to pinpoint flexible regions within prion multimers (PrPSc). However, the presence of covalently attached sugar antennae and glycosylphosphatidylinositol (GPI) moieties makes mass spectrometry-based analysis impractical. In order to surmount these difficulties we analyzed PrPSc from transgenic mice expressing prion protein (PrP) lacking the GPI membrane anchor. Such animals produce prions that are devoid of the GPI anchor and sugar antennae, and, thereby, permit the detection and location of flexible, proteinase K (PK) susceptible regions by Western blot and mass spectrometry-based analysis. GPI-less PrPSc samples were digested with PK. PK-resistant peptides were identified, and found to correspond to molecules cleaved at positions 81, 85, 89, 116, 118, 133, 134, 141, 152, 153, 162, 169 and 179. The first 10 peptides (to position 153), match very well with PK cleavage sites we previously identified in wild type PrPSc. These results reinforce the hypothesis that the structure of PrPSc consists of a series of highly PK-resistant β-sheet strands connected by short flexible PK-sensitive loops and turns. A sizeable C-terminal stretch of PrPSc is highly resistant to PK and therefore perhaps also contains β-sheet secondary structure.
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Affiliation(s)
- Ester Vázquez-Fernández
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
- * E-mail: (EVF); (JRR)
| | - Jana Alonso
- Proteomics Unit, IDIS, Santiago de Compostela, Spain
| | - Miguel A. Pastrana
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Adriana Ramos
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Lothar Stitz
- Institute of Immunology, Friedrich Loeffler Institut, Tübingen, Germany
| | - Enric Vidal
- Priocat Laboratory, Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Barcelona, Spain
| | - Irina Dynin
- Western Regional Research Center, USDA, Albany, California, United States of America
| | - Benjamin Petsch
- Institute of Immunology, Friedrich Loeffler Institut, Tübingen, Germany
| | - Christopher J. Silva
- Western Regional Research Center, USDA, Albany, California, United States of America
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
- Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
- * E-mail: (EVF); (JRR)
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Makarava N, Savtchenko R, Baskakov IV. Selective amplification of classical and atypical prions using modified protein misfolding cyclic amplification. J Biol Chem 2012; 288:33-41. [PMID: 23168413 DOI: 10.1074/jbc.m112.419531] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
With the development of protein misfolding cyclic amplification (PMCA), the topic of faithful propagation of prion strain-specific structures has been constantly debated. Here we show that by subjecting brain material of a synthetic strain consisting of a mixture of self-replicating states to PMCAb, selective amplification of PrP(Sc) could be achieved, and that PMCAb mimicked the evolutionary trend observed during serial transmission in animals. On the other hand, using modified PMCAb conditions that employ partially deglycosylated PrP(C) (dgPMCAb), an alternative transmissible state referred to as atypical protease-resistant form of the prion protein (atypical PrPres) was selectively amplified from a mixture. Surprisingly, when hamster-adapted strains (263K and Hyper) were subjected to dgPMCAb, their proteinase K digestion profile underwent a dramatic transformation, suggesting that a mixture of atypical PrPres and PrP(Sc) might be present in brain-derived materials. However, detailed analysis revealed that the proteinase K-resistant profile of PrP(Sc) changed in response to dgPMCAb. Despite these changes, the 263K strain-specific disease phenotype was preserved after passage through dgPMCAb. This study revealed that the change in PrP(Sc) biochemical phenotype does not always represent an irreversible transformation of a strain, but rather demonstrated the existence of a wide range of variation for strain-specific physical features in response to a change in prion replication environment. The current work introduced a new PMCA technique for amplification of atypical PrPres and raised a number of questions about the need for a clever distinction between actual strain mutation and variation of strain-specific features in response to a change in the replication environment.
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Affiliation(s)
- Natallia Makarava
- Center for Biomedical Engineering and Technology and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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29
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Peoc'h K, Levavasseur E, Delmont E, De Simone A, Laffont-Proust I, Privat N, Chebaro Y, Chapuis C, Bedoucha P, Brandel JP, Laquerriere A, Kemeny JL, Hauw JJ, Borg M, Rezaei H, Derreumaux P, Laplanche JL, Haïk S. Substitutions at residue 211 in the prion protein drive a switch between CJD and GSS syndrome, a new mechanism governing inherited neurodegenerative disorders. Hum Mol Genet 2012; 21:5417-28. [DOI: 10.1093/hmg/dds377] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Mouse prion protein (PrP) segment 100 to 104 regulates conversion of PrP(C) to PrP(Sc) in prion-infected neuroblastoma cells. J Virol 2012; 86:5626-36. [PMID: 22398286 DOI: 10.1128/jvi.06606-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prion diseases are characterized by the replicative propagation of disease-associated forms of prion protein (PrP(Sc); PrP refers to prion protein). The propagation is believed to proceed via two steps; the initial binding of the normal form of PrP (PrP(C)) to PrP(Sc) and the subsequent conversion of PrP(C) to PrP(Sc). We have explored the two-step model in prion-infected mouse neuroblastoma (ScN2a) cells by focusing on the mouse PrP (MoPrP) segment 92-GGTHNQWNKPSKPKTN-107, which is within a region previously suggested to be part of the binding interface or shown to differ in its accessibility to anti-PrP antibodies between PrP(C) and PrP(Sc). Exchanging the MoPrP segment with the corresponding chicken PrP segment (106-GGSYHNQKPWKPPKTN-121) revealed the necessity of MoPrP residues 99 to 104 for the chimeras to achieve the PrP(Sc) state, while segment 95 to 98 was replaceable with the chicken sequence. An alanine substitution at position 100, 102, 103, or 104 of MoPrP gave rise to nonconvertible mutants that associated with MoPrP(Sc) and interfered with the conversion of endogenous MoPrP(C). The interference was not evoked by a chimera (designated MCM2) in which MoPrP segment 95 to 104 was changed to the chicken sequence, though MCM2 associated with MoPrP(Sc). Incubation of the cells with a synthetic peptide composed of MoPrP residues 93 to 107 or alanine-substituted cognates did not inhibit the conversion, whereas an anti-P8 antibody recognizing the above sequence in PrP(C) reduced the accumulation of PrP(Sc) after 10 days of incubation of the cells. These results suggest the segment 100 to 104 of MoPrP(C) plays a key role in conversion after binding to MoPrP(Sc).
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31
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Sajnani G, Silva CJ, Ramos A, Pastrana MA, Onisko BC, Erickson ML, Antaki EM, Dynin I, Vázquez-Fernández E, Sigurdson CJ, Carter JM, Requena JR. PK-sensitive PrP is infectious and shares basic structural features with PK-resistant PrP. PLoS Pathog 2012; 8:e1002547. [PMID: 22396643 PMCID: PMC3291653 DOI: 10.1371/journal.ppat.1002547] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 01/10/2012] [Indexed: 11/25/2022] Open
Abstract
One of the main characteristics of the transmissible isoform of the prion protein (PrPSc) is its partial resistance to proteinase K (PK) digestion. Diagnosis of prion disease typically relies upon immunodetection of PK-digested PrPSc following Western blot or ELISA. More recently, researchers determined that there is a sizeable fraction of PrPSc that is sensitive to PK hydrolysis (sPrPSc). Our group has previously reported a method to isolate this fraction by centrifugation and showed that it has protein misfolding cyclic amplification (PMCA) converting activity. We compared the infectivity of the sPrPSc versus the PK-resistant (rPrPSc) fractions of PrPSc and analyzed the biochemical characteristics of these fractions under conditions of limited proteolysis. Our results show that sPrPSc and rPrPSc fractions have comparable degrees of infectivity and that although they contain different sized multimers, these multimers share similar structural properties. Furthermore, the PK-sensitive fractions of two hamster strains, 263K and Drowsy (Dy), showed strain-dependent differences in the ratios of the sPrPSc to the rPrPSc forms of PrPSc. Although the sPrPSc and rPrPSc fractions have different resistance to PK-digestion, and have previously been shown to sediment differently, and have a different distribution of multimers, they share a common structure and phenotype. Prion diseases are protein misfolding disorders. Different strains of prions are known to have variable resistance to proteinase K (PK) digestion. Furthermore, the same strain possesses both a PK sensitive (sPrPSc) and PK resistant (rPrPSc) aggregate of PrP. We developed methods to isolate the sPrPSc from rPrPSc fraction of the 263K strain of hamster-adapted scrapie. Both fractions were infectious, but have different physico-chemical properties. When we analyzed the lesion targets in the brain produced by each fraction they were essentially identical, suggesting that they were the same strain. The biochemical differences in the phenotypes of these two fractions are due to different sized multimers that share common structural properties. Furthermore, the comparison of the sensitive fractions of two hamster strains, 263K and Drowsy (Dy), showed strain-dependent differences in the ratios of the PK-sensitive to the PK-resistant forms of PrPSc.
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Affiliation(s)
- Gustavo Sajnani
- Department of Medicine, School of Medicine, University of Santiago de Compostela, Santiago de Compostela, Galiza, Spain.
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32
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Fontana A, de Laureto PP, Spolaore B, Frare E. Identifying disordered regions in proteins by limited proteolysis. Methods Mol Biol 2012; 896:297-318. [PMID: 22821533 DOI: 10.1007/978-1-4614-3704-8_20] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Limited proteolysis experiments can be successfully used to detect sites of disorder in otherwise folded globular proteins. The approach relies on the fact that the proteolysis of a polypeptide substrate requires its binding in an extended conformation at the protease's active site and thus an enhanced backbone flexibility or local unfolding of the site of proteolytic attack. A striking correlation was found between sites of limited proteolysis and sites of enhanced chain flexibility of the polypeptide chain, this last evaluated by the crystallographically determined B-factor. In numerous cases, it has been shown that limited proteolysis occurs at chain regions characterized by missing electron density and thus being disordered. Therefore, limited proteolysis is a simple and reliable experimental technique that can detect sites of disorder in proteins, thus complementing the results that can be obtained by the use of other physicochemical and computational approaches.
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Affiliation(s)
- Angelo Fontana
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy.
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33
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Hu KN, McGlinchey RP, Wickner RB, Tycko R. Segmental polymorphism in a functional amyloid. Biophys J 2011; 101:2242-50. [PMID: 22067164 DOI: 10.1016/j.bpj.2011.09.051] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 09/22/2011] [Accepted: 09/29/2011] [Indexed: 11/25/2022] Open
Abstract
Although amyloid fibrils are generally considered to be causative or contributing agents in amyloid diseases, several amyloid fibrils are also believed to have biological functions. Among these are fibrils formed by Pmel17 within melanosomes, which act as a template for melanin deposition. We use solid-state NMR to show that the molecular structures of fibrils formed by the 130-residue pseudo-repeat domain Pmel17:RPT are polymorphic even within the biologically relevant pH range. Thus, biological function in amyloid fibrils does not necessarily imply a unique molecular structure. Solid-state NMR spectra of three Pmel17:RPT polymorphs show that in all cases, only a subset (~30%) of the full amino acid sequence contributes to the immobilized fibril core. Although the repetitive nature of the sequence and incomplete spectral resolution prevent the determination of unique chemical shift assignments from two- and three-dimensional solid-state NMR spectra, we use a Monte Carlo assignment algorithm to identify protein segments that are present in or absent from the fibril core. The results show that the identity of the core-forming segments varies from one polymorph to another, a phenomenon known as segmental polymorphism.
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Affiliation(s)
- Kan-Nian Hu
- Laboratory of Chemical Physics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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34
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Tycko R, Savtchenko R, Ostapchenko VG, Makarava N, Baskakov IV. The α-helical C-terminal domain of full-length recombinant PrP converts to an in-register parallel β-sheet structure in PrP fibrils: evidence from solid state nuclear magnetic resonance. Biochemistry 2011; 49:9488-97. [PMID: 20925423 DOI: 10.1021/bi1013134] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report the results of solid state nuclear magnetic resonance (NMR) measurements on amyloid fibrils formed by the full-length prion protein PrP (residues 23−231, Syrian hamster sequence). Measurements of intermolecular 13C−13C dipole−dipole couplings in selectively carbonyl-labeled samples indicate that β-sheets in these fibrils have an in-register parallel structure, as previously observed in amyloid fibrils associated with Alzheimer’s disease and type 2 diabetes and in yeast prion fibrils. Two-dimensional 13C−13C and 15N−13C solid state NMR spectra of a uniformly 15N- and 13C-labeled sample indicate that a relatively small fraction of the full sequence, localized to the C-terminal end, forms the structurally ordered, immobilized core. Although unique site-specific assignments of the solid state NMR signals cannot be obtained from these spectra, analysis with a Monte Carlo/simulated annealing algorithm suggests that the core is comprised primarily of residues in the 173−224 range. These results are consistent with earlier electron paramagnetic resonance studies of fibrils formed by residues 90−231 of the human PrP sequence, formed under somewhat different conditions [Cobb, N. J., Sonnichsen, F. D., McHaourab, H., and Surewicz, W. K. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 18946−18951], suggesting that an in-register parallel β-sheet structure formed by the C-terminal end may be a general feature of PrP fibrils prepared in vitro.
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Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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35
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Gong B, Ramos A, Vázquez-Fernández E, Silva CJ, Alonso J, Liu Z, Requena JR. Probing structural differences between PrP(C) and PrP(Sc) by surface nitration and acetylation: evidence of conformational change in the C-terminus. Biochemistry 2011; 50:4963-72. [PMID: 21526750 DOI: 10.1021/bi102073j] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We used two chemical modifiers, tetranitromethane (TNM) and acetic anhydride (Ac(2)O), which specifically target accessible tyrosine and lysine residues, respectively, to modify recombinant Syrian hamster PrP(90-231) [rSHaPrP(90-231)] and SHaPrP 27-30, the proteinase K-resistant core of PrP(Sc) isolated from brain of scrapie-infected Syrian hamsters. Our aim was to find locations of conformational change. Modified proteins were subjected to in-gel proteolytic digestion with trypsin or chymotrypsin and subsequent analysis by mass spectrometry (MALDI-TOF). Several differences in chemical reactivity were observed. With TNM, the most conspicuous reactivity difference seen involves peptide E(221)-R(229) (containing Y(225) and Y(226)), which in rSHaPrP(90-231) was much more extensively modified than in SHaPrP 27-30; peptide H(111)-R(136), containing Y(128), was also more modified in rSHaPrP(90-231). Conversely, peptides Y(149)-R(151), Y(157)-R(164), and R(151)-Y(162) suffered more extensive modification in SHaPrP 27-30. Acetic anhydride modified very extensively peptide G(90)-K(106), containing K(101), K(104), K(106), and the amino terminus, in both rSHaPrP(90-231) and SHaPrP 27-30. These results suggest that (1) SHaPrP 27-30 exhibits important conformational differences in the C-terminal region with respect to rSHaPrP(90-231), resulting in the loss of solvent accessibility of Y(225) and Y(226), very solvent-exposed in the latter conformation; because other results suggest preservation of the two C-terminal helices, this might mean that these are tightly packed in SHaPrP 27-30. (2) On the other hand, tyrosines contained in the stretch spanning approximately Y(149)-R(164) are more accessible in SHaPrP 27-30, suggesting rearrangements in α-helix H1 and the short β-sheet of rSHaPrP(90-231). (3) The amino-terminal region of SHaPrP 27-30 is very accessible. These data should help in the validation and construction of structural models of PrP(Sc).
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Affiliation(s)
- Binbin Gong
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
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Foo CK, Ohhashi Y, Kelly MJS, Tanaka M, Weissman JS. Radically different amyloid conformations dictate the seeding specificity of a chimeric Sup35 prion. J Mol Biol 2011; 408:1-8. [PMID: 21333653 DOI: 10.1016/j.jmb.2011.02.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/09/2011] [Accepted: 02/10/2011] [Indexed: 11/30/2022]
Abstract
A remarkable feature of prion biology is that the same prion protein can misfold into more than one infectious conformation, and these conformations in turn lead to distinct heritable prion strains with different phenotypes. The yeast prion [PSI(+)] is a powerful system for studying how changes in strain conformation affect cross-species transmission. We have previously established that a chimera of the Saccharomyces cerevisiae (SC) and Candida albicans (CA) Sup35 prion domains can cross the SC/CA species barrier in a strain-dependent manner. In vitro, the conversion of the monomeric chimera into the prion (amyloid) form can be seeded by either SC or CA Sup35 amyloid fibers, resulting in two strains: Chim[SC] and Chim[CA]. These strains have a "molecular memory" of their originating species in that Chim[SC] preferentially seeds the conversion of SC Sup35, and vice versa. To investigate how this species specificity is conformationally encoded, we used amide exchange and limited proteolysis to probe the structures of these two strains. We found that the amyloid cores of Chim[SC] and Chim[CA] are predominantly confined to the SC-derived and CA-derived residues, respectively. In addition, the chimera is able to propagate the Chim[CA] conformation even when the SC residues comprising the Chim[SC] core were deleted. Thus, the two strains have non-overlapping and modular amyloid cores that determine whether SC or CA residues are presented on the growing face of the prion seed. These observations establish how conformations determine the specificity of prion transmission and demonstrate a remarkable plasticity to amyloid misfolding.
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Affiliation(s)
- Catherine K Foo
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biomedical Science, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
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37
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Hafner-Bratkovic I, Bester R, Pristovsek P, Gaedtke L, Veranic P, Gaspersic J, Mancek-Keber M, Avbelj M, Polymenidou M, Julius C, Aguzzi A, Vorberg I, Jerala R. Globular domain of the prion protein needs to be unlocked by domain swapping to support prion protein conversion. J Biol Chem 2011; 286:12149-56. [PMID: 21324909 DOI: 10.1074/jbc.m110.213926] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Prion diseases are fatal transmissible neurodegenerative diseases affecting many mammalian species. The normal prion protein (PrP) converts into a pathological aggregated form, PrPSc, which is enriched in the β-sheet structure. Although the high resolution structure of the normal PrP was determined, the structure of the converted form of PrP remains inaccessible to high resolution techniques. To map the PrP conversion process we introduced disulfide bridges into different positions within the globular domain of PrP, tethering selected secondary structure elements. The majority of tethered PrP mutants exhibited increased thermodynamic stability, nevertheless, they converted efficiently. Only the disulfides that tether subdomain B1-H1-B2 to subdomain H2-H3 prevented PrP conversion in vitro and in prion-infected cell cultures. Reduction of disulfides recovered the ability of these mutants to convert, demonstrating that the separation of subdomains is an essential step in conversion. Formation of disulfide-linked proteinase K-resistant dimers in fibrils composed of a pair of single cysteine mutants supports the model based on domain-swapped dimers as the building blocks of prion fibrils. In contrast to previously proposed structural models of PrPSc suggesting conversion of large secondary structural segments, we provide evidence for the conservation of secondary structural elements of the globular domain upon PrP conversion. Previous studies already showed that dimerization is the rate-limiting step in PrP conversion. We show that separation and swapping of subdomains of the globular domain is necessary for conversion. Therefore, we propose that the domain-swapped dimer of PrP precedes amyloid formation and represents a potential target for therapeutic intervention.
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Affiliation(s)
- Iva Hafner-Bratkovic
- Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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38
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Ostapchenko VG, Sawaya MR, Makarava N, Savtchenko R, Nilsson KPR, Eisenberg D, Baskakov IV. Two amyloid States of the prion protein display significantly different folding patterns. J Mol Biol 2010; 400:908-21. [PMID: 20553730 DOI: 10.1016/j.jmb.2010.05.051] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/27/2010] [Accepted: 05/21/2010] [Indexed: 12/16/2022]
Abstract
It has been well established that a single amino acid sequence can give rise to several conformationally distinct amyloid states. The extent to which amyloid structures formed within the same sequence are different, however, remains unclear. To address this question, we studied two amyloid states (referred to as R- and S-fibrils) produced in vitro from highly purified full-length recombinant prion protein. Several biophysical techniques including X-ray diffraction, CD, Fourier transform infrared spectroscopy (FTIR), hydrogen-deuterium exchange, proteinase K digestion, and binding of a conformation-sensitive fluorescence dye revealed that R- and S-fibrils have substantially different secondary, tertiary, and quaternary structures. While both states displayed a 4. 8-A meridional X-ray diffraction typical for amyloid cross-beta-spines, they showed markedly different equatorial profiles, suggesting different folding pattern of beta-strands. The experiments on hydrogen-deuterium exchange monitored by FTIR revealed that only small fractions of amide protons were protected in R- or S-fibrils, an argument for the dynamic nature of their cross-beta-structure. Despite this fact, both amyloid states were found to be very stable conformationally as judged from temperature-induced denaturation monitored by FTIR and the conformation-sensitive dye. Upon heating to 80 degrees C, only local unfolding was revealed, while individual state-specific cross-beta features were preserved. The current studies demonstrated that the two amyloid states formed by the same amino acid sequence exhibited significantly different folding patterns that presumably reflect two different architectures of cross-beta-structure. Both S- and R-fibrils, however, shared high conformational stability, arguing that the energy landscape for protein folding and aggregation can contain several deep free-energy minima.
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Affiliation(s)
- Valeriy G Ostapchenko
- Center for Biomedical Engineering and Technology, University of Maryland, Baltimore, MD 21201, USA
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39
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Abstract
The mammalian prion PrPSc causes fatal neurodegenerative ailments in humans and farm animals. The molecular mechanisms of its propagation and transmissibility between species will not be understood until sufficient knowledge of its structure is gathered. This task has been hampered by the insoluble nature of PrPSc, which renders classic techniques, such as nuclear magnetic resonance or x-ray crystallography, unusable. However, a number of alternative approaches, such as limited proteolysis, electron microscopy and Fourier transform infrared spectroscopy, have yielded valuable low-resolution structural information. Pieced together, these data present PrPSc as a stackable molecule whose core is probably a β-solenoid formed by two or three rungs of short β-strands interspersed with numerous loops and turns. A reasonable understanding of its architecture might soon be achieved.
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Affiliation(s)
- Jesús R Requena
- Prion Research Unit, Department of Medicine, University of Santiago de Compostela, Rua de San Francisco s/n 15782, Santiago de Compostela, Galiza, Spain
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40
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Stubbs CJ, Loenarz C, Mecinović J, Yeoh KK, Hindley N, Liénard BM, Sobott F, Schofield CJ, Flashman E. Application of a Proteolysis/Mass Spectrometry Method for Investigating the Effects of Inhibitors on Hydroxylase Structure. J Med Chem 2009; 52:2799-805. [DOI: 10.1021/jm900285r] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Stubbs
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Christoph Loenarz
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Jasmin Mecinović
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Kar Kheng Yeoh
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Nicola Hindley
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Benoît M. Liénard
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Frank Sobott
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Emily Flashman
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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41
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Gielbert A, Davis LA, Sayers AR, Hope J, Gill AC, Sauer MJ. High-resolution differentiation of transmissible spongiform encephalopathy strains by quantitative N-terminal amino acid profiling (N-TAAP) of PK-digested abnormal prion protein. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:384-396. [PMID: 19053160 DOI: 10.1002/jms.1516] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
New forms of transmissible spongiform encephalopathy (TSE) continue to be identified, and consequently sensitive differential diagnosis is increasingly important both for the management of disease in humans and livestock and in providing confidence in the safety of the food chain. TSE diseases are associated with accumulation of protease-resistant prion protein (PrP(Sc)) and detection of this marker protein is central to diagnosis. Proteolysis by proteinase K (PK) generates protease-resistant products (PrP(res)) with partially variable N-termini. The conformation(s) of PrP(Sc) and thus the points of PK cleavage are thought to be dependent on the strain of prion disease. Western blot (WB) analysis of PrP(res) gives characteristic migration patterns that can be used to diagnose TSEs, but the relatively low resolution of this technique limits its ability to differentiate certain disease strains. Mass spectrometry (MS) has the capability to resolve these various PK cleavage sites to the level of individual amino acid residues. In the present study multiple selected reaction monitoring (mSRM) was used to detect and quantify PrP(res) N-terminal tryptic peptides by MS and thus to define the N-terminal amino acid profiles (N-TAAPs) of PrP(res) characteristic for various TSEs in sheep. The fragmentation behaviour of the N-terminal tryptic peptides was studied to allow selection of the transitions specific for each peptide. Different PrP(res) preparation methods were evaluated and the most effective approach applied to differentiate the N-TAAPs corresponding to various sheep TSE isolates. Marked differences were identified between the N-TAAPs of bovine spongiform encephalopathy (BSE) and classical scrapie, and between classical scrapie and the experimental strains SSBP/1 and CH1641, thereby validating this approach as a means of TSE-strain specific diagnosis.
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Affiliation(s)
- Adriana Gielbert
- Department of Molecular Pathogenesis and Genetics, Veterinary Laboratories Agency-Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, UK
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