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Li Q, Zhu Y, Meng X, Tong HHY, Liu H. Experiment and molecular dynamics simulations reveal proanthocyanidin B2 and B3 can inhibit prion aggregation by different mechanisms. J Biomol Struct Dyn 2024; 42:2424-2436. [PMID: 37144732 DOI: 10.1080/07391102.2023.2209663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
Prion diseases are a group of fatal neurodegenerative diseases caused by the misfolding and aggregation of prion protein (PrP), and the inhibition of PrP aggregation is one of the most effective therapeutic strategies. Proanthocyanidin B2 (PB2) and B3 (PB3), the effective natural antioxidants have been evaluated for the inhibition of amyloid-related protein aggregation. Since PrP has similar aggregation mechanism with other amyloid-related proteins, will PB2 and PB3 affect the aggregation of PrP? In this paper, experimental and molecular dynamics (MD) simulation methods were combined to investigate the influence of PB2 and PB3 on PrP aggregation. Thioflavin T assays showed PB2 and PB3 could inhibit PrP aggregation in a concentrate-dependent manner in vitro. To understand the underlying mechanism, we performed 400 ns all-atom MD simulations. The results suggested PB2 could stabilize the α2 C-terminus and the hydrophobic core of protein by stabilizing two important salt bridges R156-E196 and R156-D202, and consequently made global structure of protein more stable. Surprisingly, PB3 could not stabilize PrP, which may inhibit PrP aggregation through a different mechanism. Since dimerization is the first step of aggregation, will PB3 inhibit PrP aggregation by inhibiting the dimerization? To verify our assumption, we then explored the effect of PB3 on protein dimerization by performing 800 ns MD simulations. The results suggested PB3 could reduce the residue contacts and hydrogen bonds between two monomers, preventing dimerization process of PrP. The possible inhibition mechanism of PB2 and PB3 on PrP aggregation could provide useful information for drug development against prion diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Qin Li
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Yongchang Zhu
- College of Chemical Engineering, Shijiazhuang University, Shijiazhuang, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Henry H Y Tong
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
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2
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Gupta T, Arora L, Mukhopadhyay S, Pal SK. Ultrasensitive Detection of Lipid-Induced Misfolding of the Prion Protein at the Aqueous-Liquid Crystal Interface. J Phys Chem Lett 2024; 15:2117-2122. [PMID: 38363235 DOI: 10.1021/acs.jpclett.3c02770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The misfolding of the α-helical cellular prion protein into a self-propagating β-rich aggregated form is a key pathogenic event in fatal and transmissible neurodegenerative diseases collectively known as prion diseases. Herein, we utilize the interfacial properties of liquid crystals (LCs) to monitor the lipid-membrane-induced conformational switching of prion protein (PrP) into β-rich amyloid fibrils. The lipid-induced conformational switching resulting in aggregation occurs at the nanomolar protein concentration and is primarily mediated by electrostatic interactions between PrP and lipid headgroups. Our LC-based methodology offers a potent and sensitive tool to detect and delineate molecular mechanisms of PrP misfolding mediated by lipid-protein interactions at the aqueous interface under physiological conditions.
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Affiliation(s)
- Tarang Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Lisha Arora
- Department of Chemical Sciences, Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Samrat Mukhopadhyay
- Department of Chemical and Biological Sciences, Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Santanu Kumar Pal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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3
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Lauzon D, Vallée-Bélisle A. Functional advantages of building nanosystems using multiple molecular components. Nat Chem 2023; 15:458-467. [PMID: 36759713 DOI: 10.1038/s41557-022-01127-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/15/2022] [Indexed: 02/11/2023]
Abstract
Over half of all the natural nanomachines in living organisms are multimeric and likely exploit the self-assembly of their components to provide functional benefits. However, the advantages and disadvantages of building nanosystems using multiple molecular components remain relatively unexplored at the thermodynamic, kinetic and functional levels. In this study we used theory and a simple DNA-based model that forms the same nanostructures with different numbers of components to advance our knowledge in this area. Despite its lower assembly rate, we found that a system built with three components may undergo a more cooperative assembly transition from less preorganized components, which facilitates the emergence of functionalities. Using simple variations of its components, we also found that trimeric nanosystems display a much higher level of programmability than their dimeric counterparts because they can assemble with various levels of cooperativity, self-inhibition and time-dependent properties. We show here how two simple strategies (for example, cutting and adding components) can be employed to efficiently programme the regulatory function of a more complex, artificially selected, RNA-cleaving catalytic nanosystem.
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Affiliation(s)
- D Lauzon
- Laboratoire de Biosenseurs & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - A Vallée-Bélisle
- Laboratoire de Biosenseurs & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec, Canada.
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4
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Zhang T, Pan Y, Kandapal S, Sun X, Xu B. Following the Aggregation of Human Prion Protein on Heparin Functionalized Gold Surface in Real Time. ACS APPLIED BIO MATERIALS 2022; 5:5457-5464. [PMID: 36228282 DOI: 10.1021/acsabm.2c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The aggregation of the prion protein (PrP) plays a key role in the development of prion diseases and is believed to be an autocatalytic process with a very high kinetic barrier. Intensive studies have focused on overcoming the kinetic barriers under extremely nonphysiological in vitro conditions by altering the pH of PrP solution on solid surfaces, such as gold, mica, and a lipid bilayer. Importantly, sulfated glycosaminoglycans (GAGs), including heparin, were found to be associated with PrP misfolding and aggregation, suggesting GAGs have catalytic roles in PrP aggregation processes. However, the exact role and details of GAGs in the PrP aggregation are not clear and need a thorough perusal. Here, we investigate the PrP aggregation process on a heparin functionalized gold surface by in situ, real-time monitoring of the atomic scale details of the whole aggregation process by single molecule atomic force microscopy (AFM), combining simultaneous topographic and recognition (TREC) imaging and single molecule force spectroscopy (SMFS). We observed the whole aggregation process for full-length human recombinant PrP (23-231) aggregation on the heparin modified gold surface, from the formation of oligomers, to the assembly of protofibrils and short fibers, and the formation of elongated mature fibers. Heparin is found to promote the PrP aggregation by facilitating the formation of oligomers during the early nucleation stage.
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Affiliation(s)
- Tong Zhang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Yangang Pan
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Sneha Kandapal
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Xin Sun
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
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Ryabova N, Fakhranurova L, Balobanov V, Marchenkov V, Glukhov A, Ilyina N, Kochetov A, Suvorina M, Surin A, Katina N. Carbonic anhydrase amyloid fibrils composed of laterally associated protofilaments show reduced cytotoxicity. Biochem Biophys Res Commun 2022; 593:46-51. [DOI: 10.1016/j.bbrc.2022.01.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/10/2022] [Indexed: 11/26/2022]
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6
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Russo L, Salzano G, Corvino A, Bistaffa E, Moda F, Celauro L, D'Abrosca G, Isernia C, Milardi D, Giachin G, Malgieri G, Legname G, Fattorusso R. Structural and dynamical determinants of a β-sheet-enriched intermediate involved in amyloid fibrillar assembly of human prion protein. Chem Sci 2022; 13:10406-10427. [PMID: 36277622 PMCID: PMC9473526 DOI: 10.1039/d2sc00345g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/04/2022] [Indexed: 12/02/2022] Open
Abstract
The conformational conversion of the cellular prion protein (PrPC) into a misfolded, aggregated and infectious scrapie isoform is associated with prion disease pathology and neurodegeneration. Despite the significant number of experimental and theoretical studies the molecular mechanism regulating this structural transition is still poorly understood. Here, via Nuclear Magnetic Resonance (NMR) methodologies we investigate at the atomic level the mechanism of the human HuPrP(90–231) thermal unfolding and characterize the conformational equilibrium between its native structure and a β-enriched intermediate state, named β-PrPI. By comparing the folding mechanisms of metal-free and Cu2+-bound HuPrP(23–231) and HuPrP(90–231) we show that the coupling between the N- and C-terminal domains, through transient electrostatic interactions, is the key molecular process in tuning long-range correlated μs–ms dynamics that in turn modulate the folding process. Moreover, via thioflavin T (ThT)-fluorescence fibrillization assays we show that β-PrPI is involved in the initial stages of PrP fibrillation, overall providing a clear molecular description of the initial phases of prion misfolding. Finally, we show by using Real-Time Quaking-Induced Conversion (RT-QuIC) that the β-PrPI acts as a seed for the formation of amyloid aggregates with a seeding activity comparable to that of human infectious prions. The N-ter domain in HuPrP regulates the folding mechanism by tuning the long-range μs–ms dynamics. Removal of the N-ter domain triggers the formation of a stable β-enriched intermediate state inducing amyloid aggregates with HuPrPSc seeding activity.![]()
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Affiliation(s)
- Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Giulia Salzano
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Andrea Corvino
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Edoardo Bistaffa
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Division of Neurology 5 and Neuropathology, Milano, Italy
| | - Fabio Moda
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Division of Neurology 5 and Neuropathology, Milano, Italy
| | - Luigi Celauro
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Danilo Milardi
- Institute of Crystallography, National Research Council, Catania, Italy
| | - Gabriele Giachin
- Department of Chemical Sciences (DiSC), University of Padua, Padova, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- ELETTRA Laboratory, Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
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7
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Vodyanoy V. The Role of Endogenous Metal Nanoparticles in Biological Systems. Biomolecules 2021; 11:1574. [PMID: 34827572 PMCID: PMC8615972 DOI: 10.3390/biom11111574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/09/2021] [Accepted: 10/19/2021] [Indexed: 12/03/2022] Open
Abstract
The blood and tissues of vertebrate animals and mammals contain small endogenous metal nanoparticles. These nanoparticles were observed to be composed of individual atoms of iron, copper, zinc, silver, gold, platinum, and other metals. Metal nanoparticles can bind proteins and produce proteinaceous particles called proteons. A small fraction of the entire pool of nanoparticles is usually linked with proteins to form proteons. These endogenous metal nanoparticles, along with engineered zinc and copper nanoparticles at subnanomolar levels, were shown to be lethal to cultured cancer cells. These nanoparticles appear to be elemental crystalline metal nanoparticles. It was discovered that zinc nanoparticles produce no odor response but increase the odor reaction if mixed with an odorant. Some other metal nanoparticles, including copper, silver, gold, and platinum nanoparticles, do not affect the responses to odorants. The sources of metal nanoparticles in animal blood and tissues may include dietary plants and gut microorganisms. The solid physiological and biochemical properties of metal nanoparticles reflect their importance in cell homeostasis and disease.
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Affiliation(s)
- Vitaly Vodyanoy
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn, AL 36849, USA
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8
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Serpa JJ, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. Proteomics 2021; 21:e2000298. [PMID: 34482645 PMCID: PMC9285417 DOI: 10.1002/pmic.202000298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/10/2021] [Accepted: 08/27/2021] [Indexed: 11/08/2022]
Abstract
The conversion of the native monomeric cellular prion protein (PrPC ) into an aggregated pathological β-oligomeric form (PrPβ ) and an infectious form (PrPSc ) is the central element in the development of prion diseases. The structure of the aggregates and the molecular mechanisms of the conformational changes involved in the conversion are still unknown. We applied mass spectrometry combined with chemical crosslinking, hydrogen/deuterium exchange, limited proteolysis, and surface modification for the differential characterization of the native and the urea+acid-converted prion β-oligomer structures to obtain insights into the mechanisms of conversion and aggregation. For the determination of the structure of the monomer and the dimer unit of the β-oligomer, we applied a recently-developed approach for de novo protein structure determination which is based on the incorporation of zero-length and short-distance crosslinking data as intra- and inter-protein constraints in discrete molecular dynamics simulations (CL-DMD). Based on all of the structural-proteomics experimental data and the computationally predicted structures of the monomer units, we propose the potential mode of assembly of the β-oligomer. The proposed β-oligomer assembly provides a clue on the β-sheet nucleation site, and how template-based conversion of the native prion molecule occurs, growth of the prion aggregates, and maturation into fibrils may occur.
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Affiliation(s)
- Jason J Serpa
- University of Victoria -Genome British Columbia Proteomics Centre, Victoria, British Columbia, Canada
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Evgeniy V Petrotchenko
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
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9
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Louka A, Zacco E, Temussi PA, Tartaglia GG, Pastore A. RNA as the stone guest of protein aggregation. Nucleic Acids Res 2020; 48:11880-11889. [PMID: 33068411 PMCID: PMC7708036 DOI: 10.1093/nar/gkaa822] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/12/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
The study of prions as infectious aggregates dates several decades. From its original formulation, the definition of a prion has progressively changed to the point that many aggregation-prone proteins are now considered bona fide prions. RNA molecules, not included in the original 'protein-only hypothesis', are also being recognized as important factors contributing to the 'prion behaviour', that implies the transmissibility of an aberrant fold. In particular, an association has recently emerged between aggregation and the assembly of prion-like proteins in RNA-rich complexes, associated with both physiological and pathological events. Here, we discuss the historical rising of the concept of prion-like domains, their relation to RNA and their role in protein aggregation. As a paradigmatic example, we present the case study of TDP-43, an RNA-binding prion-like protein associated with amyotrophic lateral sclerosis. Through this example, we demonstrate how the current definition of prions has incorporated quite different concepts making the meaning of the term richer and more stimulating. An important message that emerges from our analysis is the dual role of RNA in protein aggregation, making RNA, that has been considered for many years a 'silent presence' or the 'stone guest' of protein aggregation, an important component of the process.
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Affiliation(s)
- Alexandra Louka
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
| | - Elsa Zacco
- Center for Human Technologies, Central RNA laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
- University “Federico II’’ Napoli, via Cynthia, Napoli 80100, Italy
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Central RNA laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain and ICREA, 23 Passeig Lluıs Companys, Barcelona 08010, Spain
- Charles Darwin department of Biology and Biotechnology, Sapienza University of Rome, Piazzale A. Moro 5, Rome 00185, Italy
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
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10
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Myers R, Cembran A, Fernandez-Funez P. Insight From Animals Resistant to Prion Diseases: Deciphering the Genotype - Morphotype - Phenotype Code for the Prion Protein. Front Cell Neurosci 2020; 14:254. [PMID: 33013324 PMCID: PMC7461849 DOI: 10.3389/fncel.2020.00254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/24/2020] [Indexed: 12/30/2022] Open
Abstract
Prion diseases are a group of neurodegenerative diseases endemic in humans and several ruminants caused by the misfolding of native prion protein (PrP) into pathological conformations. Experimental work and the mad-cow epidemic of the 1980s exposed a wide spectrum of animal susceptibility to prion diseases, including a few highly resistant animals: horses, rabbits, pigs, and dogs/canids. The variable susceptibility to disease offers a unique opportunity to uncover the mechanisms governing PrP misfolding, neurotoxicity, and transmission. Previous work indicates that PrP-intrinsic differences (sequence) are the main contributors to disease susceptibility. Several residues have been cited as critical for encoding PrP conformational stability in prion-resistant animals, including D/E159 in dog, S167 in horse, and S174 in rabbit and pig PrP (all according to human numbering). These amino acids alter PrP properties in a variety of assays, but we still do not clearly understand the structural correlates of PrP toxicity. Additional insight can be extracted from comparative structural studies, followed by molecular dynamics simulations of selected mutations, and testing in manipulable animal models. Our working hypothesis is that protective amino acids generate more compact and stable structures in a C-terminal subdomain of the PrP globular domain. We will explore this idea in this review and identify subdomains within the globular domain that may hold the key to unravel how conformational stability and disease susceptibility are encoded in PrP.
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Affiliation(s)
- Ryan Myers
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, United States
| | - Alessandro Cembran
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Pedro Fernandez-Funez
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, United States
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11
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Pal S, Maity S, Sardar S, Begum S, Dalui R, Parvej H, Bera K, Pradhan A, Sepay N, Paul S, Halder UC. Antioxidant ferulic acid prevents the aggregation of bovine β-lactoglobulin in vitro. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-01796-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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Varela AE, England KA, Cavagnero S. Kinetic trapping in protein folding. Protein Eng Des Sel 2020; 32:103-108. [PMID: 31390019 DOI: 10.1093/protein/gzz018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/03/2019] [Indexed: 12/31/2022] Open
Abstract
The founding principles of protein folding introduced by Christian Anfinsen, together with the numerous mechanistic investigations that followed, assume that protein folding is a thermodynamically controlled process. On the other hand, this review underscores the fact that thermodynamic control is far from being the norm in protein folding, as long as one considers an extended chemical-potential landscape encompassing aggregates, in addition to native, unfolded and intermediate states. Here, we highlight the key role of kinetic trapping of the protein native state relative to unfolded, intermediate and, most importantly, aggregated states. We propose that kinetic trapping serves an important role in biology by protecting the bioactive states of a large number of proteins from deleterious aggregation. In the event that undesired aggregates were somehow formed, specialized intracellular disaggregation machines have evolved to convert any aberrant populations back to the native state, thus restoring a fully bioactive and aggregation-protected protein cohort.
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Affiliation(s)
- Angela E Varela
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kevin A England
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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13
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Scialò C, De Cecco E, Manganotti P, Legname G. Prion and Prion-Like Protein Strains: Deciphering the Molecular Basis of Heterogeneity in Neurodegeneration. Viruses 2019; 11:E261. [PMID: 30875755 PMCID: PMC6466326 DOI: 10.3390/v11030261] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 12/12/2022] Open
Abstract
Increasing evidence suggests that neurodegenerative disorders share a common pathogenic feature: the presence of deposits of misfolded proteins with altered physicochemical properties in the Central Nervous System. Despite a lack of infectivity, experimental data show that the replication and propagation of neurodegenerative disease-related proteins including amyloid-β (Aβ), tau, α-synuclein and the transactive response DNA-binding protein of 43 kDa (TDP-43) share a similar pathological mechanism with prions. These observations have led to the terminology of "prion-like" to distinguish between conditions with noninfectious characteristics but similarities with the prion replication and propagation process. Prions are considered to adapt their conformation to changes in the context of the environment of replication. This process is known as either prion selection or adaptation, where a distinct conformer present in the initial prion population with higher propensity to propagate in the new environment is able to prevail over the others during the replication process. In the last years, many studies have shown that prion-like proteins share not only the prion replication paradigm but also the specific ability to aggregate in different conformations, i.e., strains, with relevant clinical, diagnostic and therapeutic implications. This review focuses on the molecular basis of the strain phenomenon in prion and prion-like proteins.
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Affiliation(s)
- Carlo Scialò
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy.
| | - Elena De Cecco
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy.
| | - Paolo Manganotti
- Clinical Unit of Neurology, Department of Medicine, Surgery and Health Sciences, University Hospital and Health Services of Trieste, University of Trieste, 34149 Trieste, Italy.
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy.
- ELETTRA Sincrotrone Trieste S.C.p.A, Basovizza, 34149 Trieste, Italy.
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14
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Structural Determinants of the Prion Protein N-Terminus and Its Adducts with Copper Ions. Int J Mol Sci 2018; 20:ijms20010018. [PMID: 30577569 PMCID: PMC6337743 DOI: 10.3390/ijms20010018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/24/2022] Open
Abstract
The N-terminus of the prion protein is a large intrinsically disordered region encompassing approximately 125 amino acids. In this paper, we review its structural and functional properties, with a particular emphasis on its binding to copper ions. The latter is exploited by the region’s conformational flexibility to yield a variety of biological functions. Disease-linked mutations and proteolytic processing of the protein can impact its copper-binding properties, with important structural and functional implications, both in health and disease progression.
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15
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Makarava N, Savtchenko R, Lasch P, Beekes M, Baskakov IV. Preserving prion strain identity upon replication of prions in vitro using recombinant prion protein. Acta Neuropathol Commun 2018; 6:92. [PMID: 30208966 PMCID: PMC6134792 DOI: 10.1186/s40478-018-0597-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 11/24/2022] Open
Abstract
Last decade witnessed an enormous progress in generating authentic infectious prions or PrPSc in vitro using recombinant prion protein (rPrP). Previous work established that rPrP that lacks posttranslational modification is able to support replication of highly infectious PrPSc with assistance of cofactors of polyanionic nature and/or lipids. Unexpectedly, previous studies also revealed that seeding of rPrP by brain-derived PrPSc gave rise to new prion strains with new disease phenotypes documenting loss of a strain identity upon replication in rPrP substrate. Up to now, it remains unclear whether prion strain identity can be preserved upon replication in rPrP. The current study reports that faithful replication of hamster strain SSLOW could be achieved in vitro using rPrP as a substrate. We found that a mixture of phosphatidylethanolamine (PE) and synthetic nucleic acid polyA was sufficient for stable replication of hamster brain-derived SSLOW PrPSc in serial Protein Misfolding Cyclic Amplification (sPMCA) that uses hamster rPrP as a substrate. The disease phenotype generated in hamsters upon transmission of recombinant PrPSc produced in vitro was strikingly similar to the original SSLOW diseases phenotype with respect to the incubation time to disease, as well as clinical, neuropathological and biochemical features. Infrared microspectroscopy (IR-MSP) indicated that PrPSc produced in animals upon transmission of recombinant PrPSc is structurally similar if not identical to the original SSLOW PrPSc. The current study is the first to demonstrate that rPrP can support replication of brain-derived PrPSc while preserving its strain identity. In addition, the current work is the first to document that successful propagation of a hamster strain could be achieved in vitro using hamster rPrP.
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Sengupta I, Udgaonkar JB. Structural mechanisms of oligomer and amyloid fibril formation by the prion protein. Chem Commun (Camb) 2018; 54:6230-6242. [PMID: 29789820 DOI: 10.1039/c8cc03053g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Misfolding and aggregation of the prion protein is responsible for multiple neurodegenerative diseases. Works from several laboratories on folding of both the WT and multiple pathogenic mutant variants of the prion protein have identified several structurally dissimilar intermediates, which might be potential precursors to misfolding and aggregation. The misfolded aggregates themselves are morphologically distinct, critically dependent on the solution conditions under which they are prepared, but always β-sheet rich. Despite the lack of an atomic resolution structure of the infectious pathogenic agent in prion diseases, several low resolution models have identified the β-sheet rich core of the aggregates formed in vitro, to lie in the α2-α3 subdomain of the prion protein, albeit with local stabilities that vary with the type of aggregate. This feature article describes recent advances in the investigation of in vitro prion protein aggregation using multiple spectroscopic probes, with particular focus on (1) identifying aggregation-prone conformations of the monomeric protein, (2) conditions which trigger misfolding and oligomerization, (3) the mechanism of misfolding and aggregation, and (4) the structure of the misfolded intermediates and final aggregates.
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Affiliation(s)
- Ishita Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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17
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Varela AE, Lang JF, Wu Y, Dalphin MD, Stangl AJ, Okuno Y, Cavagnero S. Kinetic Trapping of Folded Proteins Relative to Aggregates under Physiologically Relevant Conditions. J Phys Chem B 2018; 122:7682-7698. [DOI: 10.1021/acs.jpcb.8b05360] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Angela E. Varela
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jonathan F. Lang
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yufan Wu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Matthew D. Dalphin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew J. Stangl
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yusuke Okuno
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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18
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Liu D, Wang X. Hierarchical Self-Assembly Induced by Dilution-Enhanced Hydrophobic Hydration. Chemistry 2018; 24:6737-6741. [DOI: 10.1002/chem.201801213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Dapeng Liu
- Department of Chemistry; Waterloo Institute for Nanotechnology; 200 Uni Ave. Waterloo ON N2L 3G1 Canada
| | - Xiaosong Wang
- Department of Chemistry; Waterloo Institute for Nanotechnology; 200 Uni Ave. Waterloo ON N2L 3G1 Canada
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Katina NS, Balobanov VA, Ilyina NB, Vasiliev VD, Marchenkov VV, Glukhov AS, Nikulin AD, Bychkova VE. sw ApoMb Amyloid Aggregation under Nondenaturing Conditions: The Role of Native Structure Stability. Biophys J 2017; 113:991-1001. [PMID: 28877500 DOI: 10.1016/j.bpj.2017.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/17/2022] Open
Abstract
Investigation of the molecular mechanisms underlying amyloid-related human diseases attracts close attention. These diseases, the number of which currently is above 40, are characterized by formation of peptide or protein aggregates containing a cross-β structure. Most of the amyloidogenesis mechanisms described so far are based on experimental studies of aggregation of short peptides, intrinsically disordered proteins, or proteins under denaturing conditions, and studies of amyloid aggregate formations by structured globular proteins under conditions close to physiological ones are still in the initial stage. We investigated the effect of amino acid substitutions on propensity of the completely helical protein sperm whale apomyoglobin (sw ApoMb) for amyloid formation from its structured state in the absence of denaturing agents. Stability and aggregation of mutated sw ApoMb were studied using circular dichroism, Fourier transform infrared spectroscopy, x-ray diffraction, native electrophoresis, and electron microscopy techniques. Here, we demonstrate that stability of the protein native state determines both protein aggregation propensity and structural peculiarities of formed aggregates. Specifically, structurally stable mutants show low aggregation propensity and moderately destabilized sw ApoMb variants form amyloids, whereas their strongly destabilized mutants form both amyloids and nonamyloid aggregates.
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Affiliation(s)
- Natalya S Katina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Vitalii A Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Nelly B Ilyina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Victor D Vasiliev
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Victor V Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Anatoly S Glukhov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Valentina E Bychkova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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20
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Abstract
Protein sequences are evolved to encode generally one folded structure, out of a nearly infinite array of possible folds. Underlying this code is a funneled free energy landscape that guides folding to the native conformation. Protein misfolding and aggregation are also a manifestation of free-energy landscapes. The detailed mechanisms of these processes are poorly understood, but often involve rare, transient species and a variety of different pathways. The inherent complexity of misfolding has hampered efforts to measure aggregation pathways and the underlying energy landscape, especially using traditional methods where ensemble averaging obscures important rare and transient events. We recently studied the misfolding and aggregation of prion protein by examining 2 monomers tethered in close proximity as a dimer, showing how the steps leading to the formation of a stable aggregated state can be resolved in the single-molecule limit and the underlying energy landscape thereby reconstructed. This approach allows a more quantitative comparison of native folding versus misfolding, including fundamental differences in the dynamics for misfolding. By identifying key steps and interactions leading to misfolding, it should help to identify potential drug targets. Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates.
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Affiliation(s)
- Derek R Dee
- a Department of Physics , University of Alberta , Edmonton , AB , Canada
| | - Michael T Woodside
- a Department of Physics , University of Alberta , Edmonton , AB , Canada;,b National Institute for Nanotechnology, National Research Council , Edmonton , AB , Canada
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21
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Method for Folding of Recombinant Prion Protein to Soluble β-Sheet Secondary Structure. Methods Mol Biol 2017. [PMID: 28861779 DOI: 10.1007/978-1-4939-7244-9_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
A key event in the pathogenesis of prion diseases is the change in structure of the normal cellular form of the prion protein from a predominantly α-helix form to the β-sheet-rich prion protein found in disease-associated tissue. To allow more detailed structural research into PrP misfolding, it is necessary to have techniques which enable enrichment of the β-sheet content in recombinant PrP.This method describes the procedure for inducing β-folding of recombinant PrP to resemble a disease-associated structure and ultimately produce soluble β-folded recombinant PrP.
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22
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Xia H, Fu H, Zhang Y, Shih KC, Ren Y, Anuganti M, Nieh MP, Cheng J, Lin Y. Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ. J Am Chem Soc 2017; 139:11106-11116. [DOI: 10.1021/jacs.7b04986] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Yanfeng Zhang
- Department
of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | | | | | | | | | - Jianjun Cheng
- Department
of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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23
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Requena JR, Wille H. The Structure of the Infectious Prion Protein and Its Propagation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 150:341-359. [PMID: 28838667 DOI: 10.1016/bs.pmbts.2017.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The prion diseases, which include Creutzfeldt-Jakob disease in humans, chronic wasting disease in cervids (i.e., deer, elk, moose, and reindeer), bovine spongiform encephalopathy in cattle, as well as sheep and goat scrapie, are caused by the conversion of the cellular prion protein (PrPC) into a disease-causing conformer (PrPSc). PrPC is a regular, GPI-anchored protein that is expressed on the cell surface of neurons and many other cell types. The structure of PrPC is well studied, based on analyses of recombinant PrP, which is thought to mimic the structure of native PrPC. The mature protein contains an N-terminal, unfolded domain and a C-terminal, globular domain that consists of three α-helices and only a small, two-stranded β-sheet. In contrast, PrPSc was found to contain predominantly β-structure and to aggregate into a variety of quaternary structures, such as oligomers, amorphous aggregates, amyloid fibrils, and two-dimensional crystals. The tendency of PrPSc to aggregate into these diverse forms is also responsible for our incomplete knowledge about its molecular structure. Nevertheless, the repeating nature of the more regular PrPSc aggregates has provided informative insights into the structure of the infectious conformer, albeit at limited resolution. These data established a four-rung β-solenoid architecture as the main element of its structure. Moreover, the four-rung β-solenoid architecture provides a molecular framework for an autocatalytic propagation mechanism, which could explain the conversion of PrPC into PrPSc.
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Affiliation(s)
- Jesús R Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Holger Wille
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada.
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24
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Legname G, Moda F. The Prion Concept and Synthetic Prions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 150:147-156. [PMID: 28838659 DOI: 10.1016/bs.pmbts.2017.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Transmissible spongiform encephalopathies or prion diseases are a group of fatal neurodegenerative diseases caused by unconventional infectious agents, known as prions (PrPSc). Prions derive from a conformational conversion of the normally folded prion protein (PrPC), which acquires pathological and infectious features. Moreover, PrPSc is able to transmit the pathological conformation to PrPC through a mechanism that is still not well understood. The generation of synthetic prions, which behave like natural prions, is of fundamental importance to study the process of PrPC conversion and to assess the efficacy of therapeutic strategies to interfere with this process. Moreover, the ability of synthetic prions to induce pathology in animals confirms that the pathological properties of the prion strains are all enciphered in abnormal conformations, characterizing these infectious agents.
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Affiliation(s)
- Giuseppe Legname
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
| | - Fabio Moda
- IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy.
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25
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Abstract
Prion diseases, like Alzheimer's disease and Parkinson disease, are rapidly progressive neurodegenerative disorders caused by misfolding followed by aggregation and accumulation of protein deposits in neuronal cells. Here we measure intramolecular polypeptide backbone reconfiguration as a way to understand the molecular basis of prion aggregation. Our hypothesis is that when reconfiguration is either much faster or much slower than bimolecular diffusion, biomolecular association is not stable, but as the reconfiguration rate becomes similar to the rate of biomolecular diffusion, the association is more stable and subsequent aggregation is faster. Using the technique of Trp-Cys contact quenching, we investigate the effects of various conditions on reconfiguration dynamics of the Syrian hamster and rabbit prion proteins. This protein exhibits behavior in all three reconfiguration regimes. We conclude that the hamster prion is prone to aggregation at pH 4.4 because its reconfiguration rate is slow enough to expose hydrophobic residues on the same time scale that bimolecular association occurs, whereas the rabbit sequence avoids aggregation by reconfiguring 10 times faster than the hamster sequence.
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26
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Moulick R, Udgaonkar JB. Identification and Structural Characterization of the Precursor Conformation of the Prion Protein which Directly Initiates Misfolding and Oligomerization. J Mol Biol 2017; 429:886-899. [DOI: 10.1016/j.jmb.2017.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/19/2017] [Accepted: 01/19/2017] [Indexed: 12/11/2022]
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27
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Chamachi NG, Chakrabarty S. Temperature-Induced Misfolding in Prion Protein: Evidence of Multiple Partially Disordered States Stabilized by Non-Native Hydrogen Bonds. Biochemistry 2017; 56:833-844. [DOI: 10.1021/acs.biochem.6b01042] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Neharika G. Chamachi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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28
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Singh RK, Chamachi NG, Chakrabarty S, Mukherjee A. Mechanism of Unfolding of Human Prion Protein. J Phys Chem B 2017; 121:550-564. [PMID: 28030950 DOI: 10.1021/acs.jpcb.6b11416] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Misfolding and aggregation of prion proteins are associated with several neurodegenerative diseases. Therefore, understanding the mechanism of the misfolding process is of enormous interest in the scientific community. It has been speculated and widely discussed that the native cellular prion protein (PrPC) form needs to undergo substantial unfolding to a more stable PrPC* state, which may further oligomerize into the toxic scrapie (PrPSc) form. Here, we have studied the mechanism of the unfolding of the human prion protein (huPrP) using a set of extensive well-tempered metadynamics simulations. Through multiple microsecond-long metadynamics simulations, we find several possible unfolding pathways. We show that each pathway leads to an unfolded state of lower free energy than the native state. Thus, our study may point to the signature of a PrPC* form that corresponds to a global minimum on the conformational free-energy landscape. Moreover, we find that these global minima states do not involve an increased β-sheet content, as was assumed to be a signature of PrPSc formation in previous simulation studies. We have further analyzed the origin of metastability of the PrPC form through free-energy surfaces of the chopped helical segments to show that the helices, particularly H2 and H3 of the prion protein, have the tendency to form either a random coil or a β-structure. Therefore, the secondary structural elements of the prion protein are only weakly stabilized by tertiary contacts and solvation forces so that relatively weak perturbations induced by temperature, pressure, pH, and so forth can lead to substantial unfolding with characteristics of intrinsically disordered proteins.
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Affiliation(s)
- Reman K Singh
- Department of Chemistry, Indian Institute of Science Education and Research , Pune 411008, Maharashtra, India
| | - Neharika G Chamachi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research , Pune 411008, Maharashtra, India
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29
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Ellett LJ, Johanssen VA. Analysis of Prion Protein Conformation Using Circular Dichroism Spectroscopy. Methods Mol Biol 2017; 1658:27-34. [PMID: 28861780 DOI: 10.1007/978-1-4939-7244-9_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
According to the protein-only hypothesis of prion propagation, the pathogenesis of prion disease is due to the misfolding of cellular PrP (PrPC) which gives rise to disease-associated PrPSc. This misfolding results in the predominantly α-helix secondary structure of PrP becoming increasingly β-sheet. Prion protein researchers often employ circular dichroism (CD) spectroscopy to rapidly analyze and identify the degree of α-helix and β-sheet content in their recombinant protein and peptide samples. CD is a nondestructive method of determining protein secondary structure and can be used to monitor the protein structural changes in various environments, e.g., pH and temperature. CD can also be used to investigate kinetic and thermodynamic characteristics of proteins and peptides.
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Affiliation(s)
- Laura J Ellett
- Department of Pathology, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Vanessa A Johanssen
- Department of Medicine, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia.
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30
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The Structure of Mammalian Prions and Their Aggregates. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:277-301. [PMID: 28109330 DOI: 10.1016/bs.ircmb.2016.08.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Prion diseases, such as Creutzfeldt-Jakob disease in humans, bovine spongiform encephalopathy in cattle, chronic wasting disease in cervids (i.e., deer, elk, moose, and reindeer), and sheep scrapie, are caused by the misfolding of the cellular prion protein (PrPC) into a disease-causing conformer (PrPSc). PrPC is a normal, GPI-anchored protein that is expressed on the surface of neurons and other cell types. The structure of PrPC is well understood, based on studies of recombinant PrP, which closely mimics the structure of native PrPC. In contrast, PrPSc is prone to aggregate into a variety of quaternary structures, such as oligomers, amorphous aggregates, and amyloid fibrils. The propensity of PrPSc to assemble into these diverse forms of aggregates is also responsible for our limited knowledge about its structure. Then again, the repeating nature of certain regular PrPSc aggregates has allowed (lower resolution) insights into the structure of the infectious conformer, establishing a four-rung β-solenoid structure as a key element of its architecture.
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31
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Yu Z, Huang P, Yu Y, Zheng Z, Huang Z, Guo C, Lin D. Unique Properties of the Rabbit Prion Protein Oligomer. PLoS One 2016; 11:e0160874. [PMID: 27529173 PMCID: PMC4987043 DOI: 10.1371/journal.pone.0160874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 07/26/2016] [Indexed: 11/26/2022] Open
Abstract
Prion diseases, also known as transmissible spongiform encephalopathies (TSEs), are a group of fatal neurodegenerative disorders infecting both humans and animals. Recent works have demonstrated that the soluble prion protein oligomer (PrPO), the intermediate of the conformational transformation from the host-derived cellular form (PrPC) to the disease-associated Scrapie form (PrPSc), exerts the major neurotoxicity in vitro and in vivo. Rabbits show strong resistance to TSEs, the underlying mechanism is unclear to date. It is expected that the relative TSEs-resistance of rabbits is closely associated with the unique properties of rabbit prion protein oligomer which remain to be addressed in detail. In the present work, we prepared rabbit prion protein oligomer (recRaPrPO) and human prion protein oligomer (recHuPrPO) under varied conditions, analyzed the effects of pH, NaCl concentration and incubation temperature on the oligomerization, and compared the properties of recRaPrPO and recHuPrPO. We found that several factors facilitated the formation of prion protein oligomers, including low pH, high NaCl concentration, high incubation temperature and low conformational stability of monomeric prion protein. RecRaPrPO was formed more slowly than recHuPrPO at physiological-like conditions (< 57°C, < 150 mM NaCl). Furthermore, recRaPrPO possessed higher susceptibility to proteinase K and lower cytotoxicity in vitro than recHuPrPO. These unique properties of recRaPrPO might substantially contribute to the TSEs-resistance of rabbits. Our work sheds light on the oligomerization of prion proteins and is of benefit to mechanistic understanding of TSEs-resistance of rabbits.
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Affiliation(s)
- Ziyao Yu
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Pei Huang
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuanhui Yu
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhen Zheng
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zicheng Huang
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- * E-mail:
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32
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Baskakov IV, Katorcha E. Multifaceted Role of Sialylation in Prion Diseases. Front Neurosci 2016; 10:358. [PMID: 27551257 PMCID: PMC4976111 DOI: 10.3389/fnins.2016.00358] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/18/2016] [Indexed: 11/13/2022] Open
Abstract
Mammalian prion or PrP(Sc) is a proteinaceous infectious agent that consists of a misfolded, self-replicating state of a sialoglycoprotein called the prion protein, or PrP(C). Sialylation of the prion protein N-linked glycans was discovered more than 30 years ago, yet the role of sialylation in prion pathogenesis remains poorly understood. Recent years have witnessed extraordinary growth in interest in sialylation and established a critical role for sialic acids in host invasion and host-pathogen interactions. This review article summarizes current knowledge on the role of sialylation of the prion protein in prion diseases. First, we discuss the correlation between sialylation of PrP(Sc) glycans and prion infectivity and describe the factors that control sialylation of PrP(Sc). Second, we explain how glycan sialylation contributes to the prion replication barrier, defines strain-specific glycoform ratios, and imposes constraints for PrP(Sc) structure. Third, several topics, including a possible role for sialylation in animal-to-human prion transmission, prion lymphotropism, toxicity, strain interference, and normal function of PrP(C), are critically reviewed. Finally, a metabolic hypothesis on the role of sialylation in the etiology of sporadic prion diseases is proposed.
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Affiliation(s)
- Ilia V. Baskakov
- Department of Anatomy and Neurobiology, Center for Biomedical Engineering and Technology, University of Maryland School of MedicineBaltimore, MD, USA
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Lin K, Yu Z, Yu Y, Liao X, Huang P, Guo C, Lin D. Distinct effects of Cu2+-binding on oligomerization of human and rabbit prion proteins. Acta Biochim Biophys Sin (Shanghai) 2015; 47:842-50. [PMID: 26350098 DOI: 10.1093/abbs/gmv081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/12/2015] [Indexed: 11/13/2022] Open
Abstract
The cellular prion protein (PrP(C)) is a kind of cell-surface Cu(2+)-binding glycoprotein. The oligomerization of PrP(C) is highly related to transmissible spongiform encephalopathies (TSEs). Cu(2+) plays a vital role in the oligomerization of PrP(C), and participates in the pathogenic process of TSE diseases. It is expected that Cu(2+)-binding has different effects on the oligomerization of TSE-sensitive human PrP(C) (HuPrP(C)) and TSE-resistant rabbit PrP(C) (RaPrP(C)). However, the details of the distinct effects remain unclear. In the present study, we measured the interactions of Cu(2+) with HuPrP(C) (91-230) and RaPrP(C) (91-228) by isothermal titration calorimetry, and compared the effects of Cu(2+)-binding on the oligomerization of both PrPs. The measured dissociation constants (Kd) of Cu(2+) were 11.1 ± 2.1 μM for HuPrP(C) and 21.1 ± 3.1 μM for RaPrP(C). Cu(2+)-binding promoted the oligomerization of HuPrP(C) more significantly than that of RaPrP(C). The far-ultraviolet circular dichroism spectroscopy experiments showed that Cu(2+)-binding induced more significant secondary structure change and increased more β-sheet content for HuPrP(C) compared with RaPrP(C). Moreover, the urea-induced unfolding transition experiments indicated that Cu(2+)-binding decreased the conformational stability of HuPrP(C) more distinctly than that of RaPrP(C). These results suggest that RaPrP(C) possesses a low susceptibility to Cu(2+), potentially weakening the risk of Cu(2+)-induced TSE diseases. Our work sheds light on the Cu(2+)-promoted oligomerization of PrP(C), and may be helpful for further understanding the TSE-resistance of rabbits.
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Affiliation(s)
- Kejiang Lin
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China
| | - Ziyao Yu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China
| | - Yuanhui Yu
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xinli Liao
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Pei Huang
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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Moulick R, Das R, Udgaonkar JB. Partially Unfolded Forms of the Prion Protein Populated under Misfolding-promoting Conditions: CHARACTERIZATION BY HYDROGEN EXCHANGE MASS SPECTROMETRY AND NMR. J Biol Chem 2015; 290:25227-40. [PMID: 26306043 DOI: 10.1074/jbc.m115.677575] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 12/16/2022] Open
Abstract
The susceptibility of the cellular prion protein (PrP(C)) to convert to an alternative misfolded conformation (PrP(Sc)), which is the key event in the pathogenesis of prion diseases, is indicative of a conformationally flexible native (N) state. In the present study, hydrogen-deuterium exchange (HDX) in conjunction with mass spectrometry and nuclear magnetic resonance spectroscopy were used for the structural and energetic characterization of the N state of the full-length mouse prion protein, moPrP(23-231), under conditions that favor misfolding. The kinetics of HDX of 34 backbone amide hydrogens in the N state were determined at pH 4. In contrast to the results of previous HDX studies on the human and Syrian hamster prion proteins at a higher pH, various segments of moPrP were found to undergo different extents of subglobal unfolding events at pH 4, a pH at which the protein is known to be primed to misfold to a β-rich conformation. No residual structure around the disulfide bond was observed for the unfolded state at pH 4. The N state of the prion protein was observed to be at equilibrium with at least two partially unfolded forms (PUFs). These PUFs, which are accessed by stochastic fluctuations of the N state, have altered surface area exposure relative to the N state. One of these PUFs resembles a conformation previously implicated to be an initial intermediate in the conversion of monomeric protein into misfolded oligomer at pH 4.
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Affiliation(s)
- Roumita Moulick
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Ranabir Das
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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Contrasting Effects of Two Lipid Cofactors of Prion Replication on the Conformation of the Prion Protein. PLoS One 2015; 10:e0130283. [PMID: 26090881 PMCID: PMC4474664 DOI: 10.1371/journal.pone.0130283] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 05/18/2015] [Indexed: 01/03/2023] Open
Abstract
Recent studies introduced two experimental protocols for converting full-length recombinant prion protein (rPrP) purified from E.coli into the infectious prion state (PrPSc) with high infectivity titers. Both protocols employed protein misfolding cyclic amplification (PMCA) for generating PrPScde novo, but used two different lipids, 1-palmitoyl-2-oleolyl-sn-glycero-3-phospho(1’-rac-glycerol) (POPG) or phosphatidylethanolamine (PE), as conversion cofactors. The current study compares the effect of POPG and PE on the physical properties of native, α-helical full-length mouse rPrP under the solvent conditions used for converting rPrP into PrPSc. Surprisingly, the effects of POPG and PE on rPrP physical properties, including its conformation, thermodynamic stability, aggregation state and interaction with a lipid, were found to be remarkably different. PE was shown to have minimal, if any, effects on rPrP thermodynamic stability, cooperativity of unfolding, immediate solvent environment or aggregation state. In fact, little evidence indicates that PE interacts with rPrP directly. In contrast, POPG was found to bind to and induce dramatic changes in rPrP structure, including a loss of α-helical conformation and formation of large lipid-protein aggregates that were resistant to partially denaturing conditions. These results suggest that the mechanisms by which lipids assist conversion of rPrP into PrPSc might be fundamentally different for POPG and PE.
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36
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Sikosek T, Chan HS. Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface 2015; 11:20140419. [PMID: 25165599 DOI: 10.1098/rsif.2014.0419] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence-structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by 'hidden' conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution.
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Affiliation(s)
- Tobias Sikosek
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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Abstract
Concepts rooted in physics are becoming increasingly important in biology as we transition to an era in which quantitative descriptions of all processes from molecular to cellular level are needed. In this perspective I discuss two unexpected findings of universal behavior, uncommon in biology, in the self-assembly of proteins and RNA. These findings, which are surprising, reveal that physics ideas applied to biological problems, ranging from folding to gene expression to cellular movement and communication between cells, might lead to discovery of universal principles operating in adoptable living systems.
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Affiliation(s)
- D Thirumalai
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
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38
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Benetti F, Biarnés X, Attanasio F, Giachin G, Rizzarelli E, Legname G. Structural determinants in prion protein folding and stability. J Mol Biol 2014; 426:3796-3810. [PMID: 25280897 DOI: 10.1016/j.jmb.2014.09.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 07/30/2014] [Accepted: 09/15/2014] [Indexed: 01/21/2023]
Abstract
Prions are responsible for a heterogeneous group of fatal neurodegenerative diseases, involving post-translational modifications of the cellular prion protein. Epidemiological studies on Creutzfeldt-Jakob disease, a prototype prion disorder, show a majority of cases being sporadic, while the remaining occurrences are either genetic or iatrogenic. The molecular mechanisms by which PrP(C) is converted into its pathological isoform have not yet been established. While point mutations and seeds trigger the protein to cross the energy barriers, thus causing genetic and infectious transmissible spongiform encephalopathies, respectively, the mechanism responsible for sporadic forms remains unclear. Since prion diseases are protein-misfolding disorders, we investigated prion protein folding and stability as functions of different milieus. Using spectroscopic techniques and atomistic simulations, we dissected the contribution of major structural determinants, also defining the energy landscape of prion protein. In particular, we elucidated (i) the essential role of the octapeptide region in prion protein folding and stability, (ii) the presence of a very enthalpically stable intermediate in prion-susceptible species, and (iii) the role of the disulfide bridge in prion protein folding.
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Affiliation(s)
- Federico Benetti
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, I-34136 Trieste, Italy; Italian Institute of Technology, Scuola Internazionale Superiore di Studi Avanzati Unit, Via Bonomea 265, I-34136 Trieste, Italy
| | - Xevi Biarnés
- Department of Physics, Scuola Internazionale Superiore di Studi Avanzati, I-34136 Trieste, Italy
| | - Francesco Attanasio
- National Research Council, Institute of Biostructures and Bioimaging, Viale Andrea Doria 6, I-95125 Catania, Italy
| | - Gabriele Giachin
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, I-34136 Trieste, Italy
| | - Enrico Rizzarelli
- National Research Council, Institute of Biostructures and Bioimaging, Viale Andrea Doria 6, I-95125 Catania, Italy
| | - Giuseppe Legname
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, I-34136 Trieste, Italy; Italian Institute of Technology, Scuola Internazionale Superiore di Studi Avanzati Unit, Via Bonomea 265, I-34136 Trieste, Italy; Elettra - Sincrotrone Trieste S.C.p.A., AREA Science Park, I-34149 Basovizza Trieste, Italy.
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39
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WU XUE, FU TING, XIU ZHILONG, YIN LIU, WANG JINGUANG, LI GUOHUI. COMPARING FOLDING MECHANISMS OF DIFFERENT PRION PROTEINS BY Gō MODEL. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Prions are associated with neurodegenerative diseases induced by transmissible spongiform encephalopathies. The infectious scrapie form is referred to as PrP Sc , which has conformational change from normal prion with predominant α-helical conformation to the abnormal PrP Sc that is rich in β-sheet content. Neurodegenerative diseases have been found from both human and bovine sources, but there are no reports about infected by transmissible spongiform encephalopathies from rabbit, canine and horse sources. Here we used coarse-grained Gō model to compare the difference among human, bovine, rabbit, canine, and horse normal (cellular) prion proteins. The denatured state of normal prion has relation with the conversion from normal to abnormal prion protein, so we used all-atom Gō model to investigate the folding pathway and energy landscape for human prion protein. Through using coarse-grained Gō model, the cooperativity of the five prion proteins was characterized in terms of calorimetric criterion, sigmoidal transition, and free-energy profile. The rabbit and horse prion proteins have higher folding free-energy barrier and cooperativity, and canine prion protein has slightly higher folding free-energy barrier comparing with human and bovine prion proteins. The results from all-atom Gō model confirmed the validity of C α-Gō model. The correlations of our results with previous experimental and theoretical researches were discussed.
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Affiliation(s)
- XUE WU
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian 116024, P. R. China
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science 457, Zhongshan Road, Dalian, Liaoning, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - TING FU
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian 116024, P. R. China
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science 457, Zhongshan Road, Dalian, Liaoning, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - ZHI-LONG XIU
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian 116024, P. R. China
| | - LIU YIN
- Oncology Department in the 1st Affiliated Hospital of Dalian, Medical University, 222 Zhongshan Road, Liaoning Province, Dalian 116011, P. R. China
| | - JIN-GUANG WANG
- Thoracic Surgery Department in the 1st Affiliated Hospital of Dalian, Medical University, 222 Zhongshan Road, Liaoning Province, Dalian 116011, P. R. China
| | - GUO-HUI LI
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science 457, Zhongshan Road, Dalian, Liaoning, P. R. China
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40
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Baillod P, Garrec J, Tavernelli I, Rothlisberger U. Prion versus Doppel Protein Misfolding: New Insights from Replica-Exchange Molecular Dynamics Simulations. Biochemistry 2013; 52:8518-26. [DOI: 10.1021/bi400884e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Pascal Baillod
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Julian Garrec
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- CNRS,
UMR 7565 Structure et Réactivité des Systèmes
Moléculaires Complexes, Nancy Université, Nancy, France
| | - Ivano Tavernelli
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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41
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From prion diseases to prion-like propagation mechanisms of neurodegenerative diseases. Int J Cell Biol 2013; 2013:975832. [PMID: 24222767 PMCID: PMC3810426 DOI: 10.1155/2013/975832] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 11/17/2022] Open
Abstract
Prion diseases are fatal neurodegenerative sporadic, inherited, or acquired disorders. In humans, Creutzfeldt-Jakob disease is the most studied prion disease. In animals, the most frequent prion diseases are scrapie in sheep and goat, bovine spongiform encephalopathy in cattle, and the emerging chronic wasting disease in wild and captive deer in North America. The hallmark of prion diseases is the deposition in the brain of PrP(Sc), an abnormal β -sheet-rich form of the cellular prion protein (PrP(C)) (Prusiner 1982). According to the prion hypothesis, PrP(Sc) can trigger the autocatalytic conversion of PrP(C) into PrP(Sc), presumably in the presence of cofactors (lipids and small RNAs) that have been recently identified. In this review, we will come back to the original works that led to the discovery of prions and to the protein-only hypothesis proposed by Dr. Prusiner. We will then describe the recent reports on mammalian synthetic prions and recombinant prions that strongly support the protein-only hypothesis. The new concept of "deformed templating" regarding a new mechanism of PrP(Sc) formation and replication will be exposed. The review will end with a chapter on the prion-like propagation of other neurodegenerative disorders, such as Alzheimer's and Parkinson's disease and tauopathies.
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42
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Paul S, Mahanta S. Association of heat-shock proteins in various neurodegenerative disorders: is it a master key to open the therapeutic door? Mol Cell Biochem 2013; 386:45-61. [PMID: 24096700 DOI: 10.1007/s11010-013-1844-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 09/26/2013] [Indexed: 12/20/2022]
Abstract
A number of acute and chronic neurodegenerative disorders are caused due to misfolding and aggregation of many intra- and extracellular proteins. Protein misfolding and aggregation processes in cells are strongly regulated by cellular molecular chaperones known as heat-shock proteins (Hsps) that include Hsp60, Hsp70, Hsp40, and Hsp90. Recent studies have shown the evidences that Hsps are colocalized in protein aggregates in Alzheimer's disease (AD), Parkinson's disease (PD), Polyglutamine disease (PGD), Prion disease, and other neurodegenerative disorders. This fact indicates that Hsps might have attempted to prevent aggregate formation in cells and thus to suppress disease conditions. Experimental findings have already established in many cases that selective overexpression of Hsps like Hsp70 and Hsp40 prevented the disease progression in various animal models and cellular models. However, recently, various Hsp modulators like geldanamycin, 17-(dimethylaminoethylamino)-17-demethoxygeldanamycin, and celastrol have shown to up-regulate the expression level of Hsp70 and Hsp40, which in turn triggers the solubilization of diseased protein aggregates. Hsps are, therefore, if appropriately selected, an attractive choice for therapeutic targeting in various kinds of neurodegeneration and hence are expected to have strong potential as therapeutic agents in suppressing or curing AD, PD, PGD, and other devastative neurodegenerative disorders. In the present review, we report the experimental findings that describe the implication of Hsps in the development of neurodegeneration and explore the possibility of how Hsps can be used directly or as a target by other agents to prevent various neurodegeneration through preventing aggregation process and thus reducing the toxicity of the oligomers based on the previous reports.
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Affiliation(s)
- Subhankar Paul
- Structural Biology and Nanomedicine Laboratory, Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India,
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43
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Schlepckow K, Schwalbe H. Molecular mechanism of prion protein oligomerization at atomic resolution. Angew Chem Int Ed Engl 2013; 52:10002-5. [PMID: 23934741 DOI: 10.1002/anie.201305184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Indexed: 11/08/2022]
Abstract
Prion protein oligomerization: Despite the crucial role of oligomers during prion protein (PrP) pathogenesis the molecular mechanism of their formation has remained largely elusive. A 2D time-resolved NMR study which made it possible to characterize the oligomerization kinetics with unprecedented site-specificity is reported.
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Affiliation(s)
- Kai Schlepckow
- Institut für Organische Chemie und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany) http://schwalbe.org.chemie.uni-frankfurt.de
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44
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Schlepckow K, Schwalbe H. Molecular Mechanism of Prion Protein Oligomerization at Atomic Resolution. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Larda ST, Simonetti K, Al-Abdul-Wahid MS, Sharpe S, Prosser RS. Dynamic Equilibria between Monomeric and Oligomeric Misfolded States of the Mammalian Prion Protein Measured by 19F NMR. J Am Chem Soc 2013; 135:10533-41. [DOI: 10.1021/ja404584s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sacha Thierry Larda
- Department of Chemistry, University of Toronto, Toronto, Ontario,
Canada M5S 3H6
| | - Karen Simonetti
- Molecular
Structure and Function
Program, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | | | - Simon Sharpe
- Molecular
Structure and Function
Program, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
- Department of Biochemistry, University of Toronto, Toronto, Ontario,
Canada M5S 1A8
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, Toronto, Ontario,
Canada M5S 3H6
- Department of Biochemistry, University of Toronto, Toronto, Ontario,
Canada M5S 1A8
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46
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Sweeting B, Brown E, Khan MQ, Chakrabartty A, Pai EF. N-terminal helix-cap in α-helix 2 modulates β-state misfolding in rabbit and hamster prion proteins. PLoS One 2013; 8:e63047. [PMID: 23675452 PMCID: PMC3651167 DOI: 10.1371/journal.pone.0063047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/27/2013] [Indexed: 02/06/2023] Open
Abstract
Susceptibility of a particular species to prion disease is affected by small differences in the sequence of PrP and correlates with the propensity of its PrP to assume the β-state. A helix-cap motif in the β2-α2-loop of native α-helical rabbit PrP, a resistant species, contains sequence differences that influence intra- and interspecies transmission. To determine the effect the helix-cap motif on β-state refolding propensity, we mutated S170N, S174N, and S170N/S174N of the rabbit PrP helix-cap to resemble that of hamster PrP and conversely, N170S, N174S, and N170S/N174S of hamster PrP to resemble the helix-cap of rabbit PrP. High-resolution crystal structures (1.45-1.6 Å) revealed that these mutations ablate hydrogen-bonding interactions within the helix-cap motif in rabbit PrP(C). They also alter the β-state-misfolding propensity of PrP; the serine mutations in hamster PrP decrease the propensity up to 35%, whereas the asparagine mutations in rabbit PrP increase it up to 42%. Rapid dilution of rabbit and hamster into β-state buffer conditions causes quick conversion to β-state monomers. Kinetic monitoring using size-exclusion chromatography showed that the monomer population decreases exponentially mirrored by an increase in an octameric species. The monomer-octamer transition rates are faster for hamster than for rabbit PrP. The N170S/N174S mutant of hamster PrP has a smaller octamer component at the endpoint compared to the wild-type, whereas the kinetics of octamer formation in mutant and wild-type rabbit PrP are comparable. These findings demonstrate that the sequence of the β2-α2 helix-cap affects refolding to the β-state and subsequently, may influence susceptibility to prion disease.
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Affiliation(s)
- Braden Sweeting
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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47
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Chen J, Thirumalai D. Helices 2 and 3 are the initiation sites in the PrP(C) → PrP(SC) transition. Biochemistry 2012; 52:310-9. [PMID: 23256626 DOI: 10.1021/bi3005472] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
It is established that prion protein is the sole causative agent in a number of diseases in humans and animals. However, the nature of conformational changes that the normal cellular form, PrP(C), undergoes in its conversion to a self-replicating state is still not fully understood. The ordered C-terminus of PrP(C) proteins has three helices (H1-H3). Here, we use statistical coupling analysis (SCA) to infer covariations at various locations using a family of evolutionarily related sequences and the response of mouse and human PrP(C)s to mechanical force to decipher the initiation sites for the transition from PrP(C) to an aggregation-prone PrP* state. Sequence-based SCA predicts that the clustered residues in nonmammals are localized in the stable core (near H1) of PrP(C), whereas in mammalian PrP(C), they are localized in frustrated helices H2 and H3 where most of the pathogenic mutations are found. Force-extension curves and free energy profiles as a function of extension of mouse and human PrP(C) in the absence of a disulfide (SS) bond between residues Cys179 and Cys214, generated by applying mechanical force to the ends of the molecule, show a sequence of unfolding events starting first with rupture of H2 and H3. This is followed by disruption of structure in two strands. Helix H1, stabilized by three salt bridges, resists substantial force before unfolding. Force extension profiles and the dynamics of rupture of tertiary contacts also show that even in the presence of an SS bond the instabilities in most of H3 and parts of H2 still determine the propensity to form the PrP* state. In mouse PrP(C) with an SS bond, there are ∼10 residues that retain their order even at high forces. Both SCA and single-molecule force simulations show that in the conversion from PrP(C) to PrP(SC) major conformational changes occur (at least initially) in H2 and H3, which because of their sequence compositions are frustrated in the helical state. Implications of our findings for the structural model for the scrapie form of PrP(C) are discussed.
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Affiliation(s)
- Jie Chen
- Biophysics Program, Institute for Physical Science and Technology, and ‡Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, USA
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48
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Baillod P, Garrec J, Colombo MC, Tavernelli I, Rothlisberger U. Enhanced Sampling Molecular Dynamics Identifies PrPSc Structures Harboring a C-Terminal β-Core. Biochemistry 2012; 51:9891-9. [DOI: 10.1021/bi301091x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pascal Baillod
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Julian Garrec
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Maria-Carola Colombo
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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49
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Role of prion protein aggregation in neurotoxicity. Int J Mol Sci 2012; 13:8648-8669. [PMID: 22942726 PMCID: PMC3430257 DOI: 10.3390/ijms13078648] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 06/29/2012] [Accepted: 07/02/2012] [Indexed: 11/17/2022] Open
Abstract
In several neurodegenerative diseases, such as Parkinson, Alzheimer’s, Huntington, and prion diseases, the deposition of aggregated misfolded proteins is believed to be responsible for the neurotoxicity that characterizes these diseases. Prion protein (PrP), the protein responsible of prion diseases, has been deeply studied for the peculiar feature of its misfolded oligomers that are able to propagate within affected brains, inducing the conversion of the natively folded PrP into the pathological conformation. In this review, we summarize the available experimental evidence concerning the relationship between aggregation status of misfolded PrP and neuronal death in the course of prion diseases. In particular, we describe the main findings resulting from the use of different synthetic (mainly PrP106-126) and recombinant PrP-derived peptides, as far as mechanisms of aggregation and amyloid formation, and how these different spatial conformations can affect neuronal death. In particular, most data support the involvement of non-fibrillar oligomers rather than actual amyloid fibers as the determinant of neuronal death.
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50
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Younan ND, Nadal RC, Davies P, Brown DR, Viles JH. Methionine oxidation perturbs the structural core of the prion protein and suggests a generic misfolding pathway. J Biol Chem 2012; 287:28263-75. [PMID: 22654104 PMCID: PMC3436581 DOI: 10.1074/jbc.m112.354779] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxidative stress and misfolding of the prion protein (PrPC) are fundamental to prion diseases. We have therefore probed the effect of oxidation on the structure and stability of PrPC. Urea unfolding studies indicate that H2O2 oxidation reduces the thermodynamic stability of PrPC by as much as 9 kJ/mol. 1H-15N NMR studies indicate methionine oxidation perturbs key hydrophobic residues on one face of helix-C as follows: Met-205, Val-209, and Met-212 together with residues Val-160 and Tyr-156. These hydrophobic residues pack together and form the structured core of the protein, stabilizing its ternary structure. Copper-catalyzed oxidation of PrPC causes a more significant alteration of the structure, generating a monomeric molten globule species that retains its native helical content. Further copper-catalyzed oxidation promotes extended β-strand structures that lack a cooperative fold. This transition from the helical molten globule to β-conformation has striking similarities to a misfolding intermediate generated at low pH. PrP may therefore share a generic misfolding pathway to amyloid fibers, irrespective of the conditions promoting misfolding. Our observations support the hypothesis that oxidation of PrP destabilizes the native fold of PrPC, facilitating the transition to PrPSc. This study gives a structural and thermodynamic explanation for the high levels of oxidized methionine in scrapie isolates.
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Affiliation(s)
- Nadine D Younan
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom
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