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Burato A, Legname G. Comparing Prion Proteins Across Species: Is Zebrafish a Useful Model? Mol Neurobiol 2024:10.1007/s12035-024-04324-z. [PMID: 38918277 DOI: 10.1007/s12035-024-04324-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Despite the considerable body of research dedicated to the field of neurodegeneration, the gap in knowledge on the prion protein and its intricate involvement in brain diseases remains substantial. However, in the past decades, many steps forward have been taken toward a better understanding of the molecular mechanisms underlying both the physiological role of the prion protein and the misfolding event converting it into its pathological counterpart, the prion. This review aims to provide an overview of the main findings regarding this protein, highlighting the advantages of many different animal models that share a conserved amino acid sequence and/or structure with the human prion protein. A particular focus will be given to the species Danio rerio, a compelling research organism for the investigation of prion biology, thanks to its conserved orthologs, ease of genetic manipulation, and cost-effectiveness of high-throughput experimentation. We will explore its potential in filling some of the gaps on physiological and pathological aspects of the prion protein, with the aim of directing the future development of therapeutic interventions.
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Affiliation(s)
- Anna Burato
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy.
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2
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Kamps J, Bader V, Winklhofer KF, Tatzelt J. Liquid-liquid phase separation of the prion protein is regulated by the octarepeat domain independently of histidines and copper. J Biol Chem 2024; 300:107310. [PMID: 38657863 PMCID: PMC11126799 DOI: 10.1016/j.jbc.2024.107310] [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: 12/27/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) of the mammalian prion protein is mainly driven by its intrinsically disordered N-terminal domain (N-PrP). However, the specific intermolecular interactions that promote LLPS remain largely unknown. Here, we used extensive mutagenesis and comparative analyses of evolutionarily distant PrP species to gain insight into the relationship between protein sequence and phase behavior. LLPS of mouse PrP is dependent on two polybasic motifs in N-PrP that are conserved in all tetrapods. A unique feature of mammalian N-PrP is the octarepeat domain with four histidines that mediate binding to copper ions. We now show that the octarepeat is critical for promoting LLPS and preventing the formation of PrP aggregates. Amphibian N-PrP, which contains the polybasic motifs but lacks a repeat domain and histidines, does not undergo LLPS and forms nondynamic protein assemblies indicative of aggregates. Insertion of the mouse octarepeat domain restored LLPS of amphibian N-PrP, supporting its essential role in regulating the phase transition of PrP. This activity of the octarepeat domain was neither dependent on the four highly conserved histidines nor on copper binding. Instead, the regularly spaced tryptophan residues were critical for regulating LLPS, presumably via cation-π interactions with the polybasic motifs. Our study reveals a novel role for the tryptophan residues in the octarepeat in controlling phase transition of PrP and indicates that the ability of mammalian PrP to undergo LLPS has evolved with the octarepeat in the intrinsically disordered domain but independently of the histidines.
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Affiliation(s)
- Janine Kamps
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany; Cluster of Excellence RESOLV, Bochum, Germany
| | - Verian Bader
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany; Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Cluster of Excellence RESOLV, Bochum, Germany; Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany; Cluster of Excellence RESOLV, Bochum, Germany.
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3
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Halder P, Mitra P. Human prion protein: exploring the thermodynamic stability and structural dynamics of its pathogenic mutants. J Biomol Struct Dyn 2022; 40:11274-11290. [PMID: 34338141 DOI: 10.1080/07391102.2021.1957715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Human familial prion diseases are known to be associated with different single-point mutants of the gene coding for prion protein with a primary focus at several locations of the globular domain. We have identified 12 different single-point pathogenic mutants of human prion protein (HuPrP) with the help of extensive perturbations/mutation technique at multiple locations of HuPrP sequence related to potentiality towards conformational disorders. Among these, some of the mutants include pathogenic variants that corroborate well with the literature reported proteins while majority include some unique single-point mutants that are either not explicitly studied early or studied for variants with different residues at the specific position. Primarily, our study sheds light on the unfolding mechanism of the above mentioned mutants in depth. Besides, we could identify some mutants under investigation that demonstrates not only unfolding of the helical structures but also extension and generation of the β-sheet structures and or simultaneously have highly exposed hydrophobic surface which is assumed to be linked with the production of aggregate/fibril structures of the prion protein. Among the identified mutants, Q212E needs special attention due to its maximum exposure of hydrophobic core towards solvent and E200Q is found to be important due to its maximum extent of β-content. We are also able to identify different respective structural conformations of the proteins according to their degree of structural unfolding and those conformations can be extracted and further studied in detail. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Puspita Halder
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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4
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Transport of Prions in the Peripheral Nervous System: Pathways, Cell Types, and Mechanisms. Viruses 2022; 14:v14030630. [PMID: 35337037 PMCID: PMC8954800 DOI: 10.3390/v14030630] [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: 02/28/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 01/27/2023] Open
Abstract
Prion diseases are transmissible protein misfolding disorders that occur in animals and humans where the endogenous prion protein, PrPC, undergoes a conformational change into self-templating aggregates termed PrPSc. Formation of PrPSc in the central nervous system (CNS) leads to gliosis, spongiosis, and cellular dysfunction that ultimately results in the death of the host. The spread of prions from peripheral inoculation sites to CNS structures occurs through neuroanatomical networks. While it has been established that endogenous PrPC is necessary for prion formation, and that the rate of prion spread is consistent with slow axonal transport, the mechanistic details of PrPSc transport remain elusive. Current research endeavors are primarily focused on the cellular mechanisms of prion transport associated with axons. This includes elucidating specific cell types involved, subcellular machinery, and potential cofactors present during this process.
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Intrinsic disorder and phase transitions: Pieces in the puzzling role of the prion protein in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:1-43. [PMID: 34656326 DOI: 10.1016/bs.pmbts.2021.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
After four decades of prion protein research, the pressing questions in the literature remain similar to the common existential dilemmas. Who am I? Some structural characteristics of the cellular prion protein (PrPC) and scrapie PrP (PrPSc) remain unknown: there are no high-resolution atomic structures for either full-length endogenous human PrPC or isolated infectious PrPSc particles. Why am I here? It is not known why PrPC and PrPSc are found in specific cellular compartments such as the nucleus; while the physiological functions of PrPC are still being uncovered, the misfolding site remains obscure. Where am I going? The subcellular distribution of PrPC and PrPSc is wide (reported in 10 different locations in the cell). This complexity is further exacerbated by the eight different PrP fragments yielded from conserved proteolytic cleavages and by reversible post-translational modifications, such as glycosylation, phosphorylation, and ubiquitination. Moreover, about 55 pathological mutations and 16 polymorphisms on the PrP gene (PRNP) have been described. Prion diseases also share unique, challenging features: strain phenomenon (associated with the heterogeneity of PrPSc conformations) and the possible transmissibility between species, factors which contribute to PrP undruggability. However, two recent concepts in biochemistry-intrinsically disordered proteins and phase transitions-may shed light on the molecular basis of PrP's role in physiology and disease.
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6
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Polido SA, Kamps J, Tatzelt J. Biological Functions of the Intrinsically Disordered N-Terminal Domain of the Prion Protein: A Possible Role of Liquid-Liquid Phase Separation. Biomolecules 2021; 11:1201. [PMID: 34439867 PMCID: PMC8391301 DOI: 10.3390/biom11081201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/26/2022] Open
Abstract
The mammalian prion protein (PrPC) is composed of a large intrinsically disordered N-terminal and a structured C-terminal domain, containing three alpha-helical regions and a short, two-stranded beta-sheet. Traditionally, the activity of a protein was linked to the ability of the polypeptide chain to adopt a stable secondary/tertiary structure. This concept has been extended when it became evident that intrinsically disordered domains (IDDs) can participate in a broad range of defined physiological activities and play a major functional role in several protein classes including transcription factors, scaffold proteins, and signaling molecules. This ability of IDDs to engage in a variety of supramolecular complexes may explain the large number of PrPC-interacting proteins described. Here, we summarize diverse physiological and pathophysiological activities that have been described for the unstructured N-terminal domain of PrPC. In particular, we focus on subdomains that have been conserved in evolution.
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Affiliation(s)
- Stella A. Polido
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (S.A.P.); (J.K.)
| | - Janine Kamps
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (S.A.P.); (J.K.)
- Cluster of Excellence RESOLV, Ruhr University Bochum, 44801 Bochum, Germany
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (S.A.P.); (J.K.)
- Cluster of Excellence RESOLV, Ruhr University Bochum, 44801 Bochum, Germany
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7
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The First Report of the Prion Protein Gene ( PRNP) Sequence in Pekin Ducks ( Anas platyrhynchos domestica): The Potential Prion Disease Susceptibility in Ducks. Genes (Basel) 2021; 12:genes12020193. [PMID: 33525657 PMCID: PMC7911840 DOI: 10.3390/genes12020193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 11/28/2022] Open
Abstract
Pathogenic prion protein (PrPSc), converted from normal prion protein (PrPC), causes prion disease. Although prion disease has been reported in several mammalian species, chickens are known to show strong resistance to prion diseases. In addition to chickens, the domestic duck occupies a large proportion in the poultry industry and may be regarded as a potential resistant host against prion disease. However, the DNA sequence of the prion protein gene (PRNP) has not been reported in domestic ducks. Here, we performed amplicon sequencing targeting the duck PRNP gene with the genomic DNA of Pekin ducks. In addition, we aligned the PrP sequence of the Pekin duck with that of various species using ClustalW2 and carried out phylogenetic analysis using Molecular Evolutionary Genetics Analysis X (MEGA X). We also constructed the structural modeling of the tertiary and secondary structures in avian PrP using SWISS-MODEL. Last, we investigated the aggregation propensity on Pekin duck PrP using AMYCO. We first reported the DNA sequence of the PRNP gene in Pekin ducks and found that the PrP sequence of Pekin ducks is more similar to that of geese than to that of chickens and mallards (wild ducks). Interestingly, Pekin duck PrP showed a high proportion of β-sheets compared to that of chicken PrP, and a high aggregation propensity compared to that of avian PrPs. However, Pekin duck PrP with substitutions of chicken-specific amino acids showed reduced aggregation propensities. To the best of our knowledge, this is the first report on the genetic characteristics of the PRNP sequence in Pekin ducks.
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Hara H, Sakaguchi S. N-Terminal Regions of Prion Protein: Functions and Roles in Prion Diseases. Int J Mol Sci 2020; 21:ijms21176233. [PMID: 32872280 PMCID: PMC7504422 DOI: 10.3390/ijms21176233] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 01/30/2023] Open
Abstract
The normal cellular isoform of prion protein, designated PrPC, is constitutively converted to the abnormally folded, amyloidogenic isoform, PrPSc, in prion diseases, which include Creutzfeldt-Jakob disease in humans and scrapie and bovine spongiform encephalopathy in animals. PrPC is a membrane glycoprotein consisting of the non-structural N-terminal domain and the globular C-terminal domain. During conversion of PrPC to PrPSc, its 2/3 C-terminal region undergoes marked structural changes, forming a protease-resistant structure. In contrast, the N-terminal region remains protease-sensitive in PrPSc. Reverse genetic studies using reconstituted PrPC-knockout mice with various mutant PrP molecules have revealed that the N-terminal domain has an important role in the normal function of PrPC and the conversion of PrPC to PrPSc. The N-terminal domain includes various characteristic regions, such as the positively charged residue-rich polybasic region, the octapeptide repeat (OR) region consisting of five repeats of an octapeptide sequence, and the post-OR region with another positively charged residue-rich polybasic region followed by a stretch of hydrophobic residues. We discuss the normal functions of PrPC, the conversion of PrPC to PrPSc, and the neurotoxicity of PrPSc by focusing on the roles of the N-terminal regions in these topics.
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Zink RM. Genetic and evolutionary considerations of the Chronic Wasting Disease - Human species barrier. INFECTION GENETICS AND EVOLUTION 2020; 84:104484. [PMID: 32731042 DOI: 10.1016/j.meegid.2020.104484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 01/13/2023]
Abstract
Transmissible spongiform encephalopathies can jump species barriers. In relatively few cases is the possible route of transmission thought to be known, mostly involving humans, cattle and sheep. It is thought that sheep might be the cause of Bovine Spongiform Encephalopathy (BSE) and Chronic Wasting Disease (CWD) in cervids, and that humans might have gotten prion disease (e.g., vCJD) from eating meat from BSE+ cows. A looming societal question is whether humans will acquire a prion disease from ingesting prions from CWD+ deer. On an evolutionary tree of the PRNP gene in mammals, deer, sheep and cow are relatively closely related, whereas these three species are relatively distant from humans. If a prion disease jumped the species barrier from cow to humans, the phylogenetic gap from deer to humans is no greater, and sheer evolutionary distance alone cannot explain a CWD species barrier in humans. Aspects of the PRNP gene were compared among these species to search for genetic differences that might influence the permeability of the species barrier. Human prion disease has been associated with having more than four copies of the octarepeat unit (PHGGGWG), whereas deer, sheep and cow all have three copies. Two amino acid positions in the metal-binding region (96 and 97) have been implicated in species barriers (Breydo and Uversky, 2011), whereas no variation was detected in white-tailed deer and mule deer with and without CWD, or in black-tailed deer, Key deer or Coues deer. Four out of 10 differences between deer and human in the β2-α2 loop might preclude CWD prions from converting human PrPC to PrPSc because of disruption of a steric zipper. The reasons for a CWD species barrier between deer and humans, if there is one, is still unresolved.
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Affiliation(s)
- Robert M Zink
- School of Natural Resources, School of Biological Sciences, Nebraska State Museum, University of Nebraska-Lincoln, Lincoln, NE 68503, United States of America.
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10
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Güere ME, Våge J, Tharaldsen H, Benestad SL, Vikøren T, Madslien K, Hopp P, Rolandsen CM, Røed KH, Tranulis MA. Chronic wasting disease associated with prion protein gene ( PRNP) variation in Norwegian wild reindeer ( Rangifer tarandus). Prion 2019; 14:1-10. [PMID: 31852336 PMCID: PMC6959294 DOI: 10.1080/19336896.2019.1702446] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The emergence of CWD in Europe in 2016 and the first natural infection in wild reindeer warranted disease management. This led to the testing of 2424 hunted or culled reindeer during 2016–2018, from the infected subpopulation in the Nordfjella mountain range in Southern Norway. To identify any association between PRNP variation and CWD susceptibility, we characterized the open reading frame of the PRNP gene in 19 CWD positive reindeer and in 101 age category- and sex-matched CWD negative controls. Seven variant positions were identified: 6 single nucleotide variants (SNVs) and a 24 base pair (bp) deletion located between nucleotide position 238 and 272, encoding four instead of five octapeptide repeats. With a single exception, all variant positions but one were predicted to be non-synonymous. The synonymous SNV and the deletion are novel in reindeer. Various combinations of the non-synonymous variant positions resulted in the identification of five PRNP alleles (A-E) that structured into 14 genotypes. We identified an increased CWD risk in reindeer carrying two copies of the most common allele, A, coding for serine in position 225 (Ser225) and in those carrying allele A together with the 24 bp deletion.
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Affiliation(s)
- Mariella E Güere
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Jørn Våge
- Norwegian Veterinary Institute, Oslo, Norway
| | - Helene Tharaldsen
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | | | | | | | - Petter Hopp
- Norwegian Veterinary Institute, Oslo, Norway
| | | | - Knut H Røed
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Michael A Tranulis
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
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11
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Magrì A, Tabbì G, Cucci LM, Satriano C, Pietropaolo A, Malgieri G, Isernia C, La Mendola D. The curious case of opossum prion: a physicochemical study on copper(ii) binding to the bis-decarepeat fragment from the protein N-terminal domain. Dalton Trans 2019; 48:17533-17543. [PMID: 31748763 DOI: 10.1039/c9dt02510c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The opossum is a peculiar model of immunity to prion diseases. Here we scrutinised the bis-decarepeat peptide sequence of the opossum prion (Op_bis-deca) protein by a multitechnique approach, with a combined experimental (potentiometry, UV-visible, circular dichroism, NMR and EPR spectroscopy, quartz crystal microbalance with dissipation monitoring and confocal microscopy) and simulation (DFT calculations) approach. Results showed that the macrochelate structures formed upon the binding to Cu(ii) by the analogous bis-octarepeat peptide sequence of human prion (Hu_bis-octa) are not found in the case of Op_bis-deca. At physiological pH and equimolar amount of copper ions, the [CuLH-2] is the major species formed by Op_bis-deca. In this species one imidazole and two amide nitrogen atoms are involved in metal coordination and its stability constant value is lower than that of the analogous species formed by Hu_bis-octa, due to the presence of an extra proline residue. Moreover, the study on the interaction of the peptides or the peptide/Cu(ii) complexes with the model cell membranes made of supported lipid bilayers disclosed different levels of interaction, monitored by the viscoelastic changes of the membranes, which exhibited a similar viscoelastic response at the interface of the two complexes, while in the absence of Cu(ii), the Hu_bis-octa/SLB interface was more viscoelastic than the Op_bis-deca one.
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Affiliation(s)
- Antonio Magrì
- Institute of Crystallography, National Research Council (CNR), S.S. Catania, Via P. Gaifami 18, 95126 Catania, Italy
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12
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Hackl S, Becker CFW. Prion protein-Semisynthetic prion protein (PrP) variants with posttranslational modifications. J Pept Sci 2019; 25:e3216. [PMID: 31713950 PMCID: PMC6899880 DOI: 10.1002/psc.3216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 12/16/2022]
Abstract
Deciphering the pathophysiologic events in prion diseases is challenging, and the role of posttranslational modifications (PTMs) such as glypidation and glycosylation remains elusive due to the lack of homogeneous protein preparations. So far, experimental studies have been limited in directly analyzing the earliest events of the conformational change of cellular prion protein (PrPC ) into scrapie prion protein (PrPSc ) that further propagates PrPC misfolding and aggregation at the cellular membrane, the initial site of prion infection, and PrP misfolding, by a lack of suitably modified PrP variants. PTMs of PrP, especially attachment of the glycosylphosphatidylinositol (GPI) anchor, have been shown to be crucially involved in the PrPSc formation. To this end, semisynthesis offers a unique possibility to understand PrP behavior invitro and invivo as it provides access to defined site-selectively modified PrP variants. This approach relies on the production and chemoselective linkage of peptide segments, amenable to chemical modifications, with recombinantly produced protein segments. In this article, advances in understanding PrP conversion using semisynthesis as a tool to obtain homogeneous posttranslationally modified PrP will be discussed.
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Affiliation(s)
- Stefanie Hackl
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Vienna, Austria
| | - Christian F W Becker
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Vienna, Austria
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13
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Yamaguchi K, Kamatari YO, Ono F, Shibata H, Fuse T, Elhelaly AE, Fukuoka M, Kimura T, Hosokawa-Muto J, Ishikawa T, Tobiume M, Takeuchi Y, Matsuyama Y, Ishibashi D, Nishida N, Kuwata K. A designer molecular chaperone against transmissible spongiform encephalopathy slows disease progression in mice and macaques. Nat Biomed Eng 2019; 3:206-219. [PMID: 30948810 DOI: 10.1038/s41551-019-0349-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/07/2019] [Indexed: 01/10/2023]
Abstract
Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative diseases that lack therapeutic solutions. Here, we show that the molecular chaperone (N,N'-([cyclohexylmethylene]di-4,1-phenylene)bis(2-[1-pyrrolidinyl]acetamide)), designed via docking simulations, molecular dynamics simulations and quantum chemical calculations, slows down the progress of TSEs. In vitro, the designer molecular chaperone stabilizes the normal cellular prion protein, eradicates prions in infected cells, prevents the formation of drug-resistant strains and directly inhibits the interaction between prions and abnormal aggregates, as shown via real-time quaking-induced conversion and in vitro conversion NMR. Weekly intraperitoneal injection of the chaperone in prion-infected mice prolonged their survival, and weekly intravenous administration of the compound in macaques infected with bovine TSE slowed down the development of neurological and psychological symptoms and reduced the concentration of disease-associated biomarkers in the animals' cerebrospinal fluid. The de novo rational design of chaperone compounds could lead to therapeutics that can bind to different prion protein strains to ameliorate the pathology of TSEs.
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Affiliation(s)
- Keiichi Yamaguchi
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.,Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yuji O Kamatari
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,Life Science Research Center, Gifu University, Gifu, Japan
| | - Fumiko Ono
- Faculty of Animal Crisis Management, Chiba Institute of Science, Choshi, Japan.,Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
| | - Hiroaki Shibata
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba, Japan.,Center for Development of Advanced Medical Technology, Jichi Medical University, Shimotsuke, Japan
| | - Takayuki Fuse
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Abdelazim Elsayed Elhelaly
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.,Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Suez Canal University, Ismalia, Egypt
| | - Mayuko Fukuoka
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Tsutomu Kimura
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,Department of Chemistry, Faulty of Science Division II, Tokyo University of Science, Tokyo, Japan
| | - Junji Hosokawa-Muto
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,First Department of Forsenic Science, National Research Institute of Police Science, Kashiwa, Japan
| | - Takeshi Ishikawa
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Minoru Tobiume
- Department of Pathology, National Institute of Infectious Disease, Tokyo, Japan
| | - Yoshinori Takeuchi
- Department of Biostatistics, School of Public Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Matsuyama
- Department of Biostatistics, School of Public Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Ishibashi
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kazuo Kuwata
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan. .,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan. .,Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu, Japan.
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14
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Hecel A, Valensin D, Kozłowski H. How copper ions and membrane environment influence the structure of the human and chicken tandem repeats domain? J Inorg Biochem 2018; 191:143-153. [PMID: 30529722 DOI: 10.1016/j.jinorgbio.2018.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/14/2022]
Abstract
Prion proteins (PrPs) from different species have the enormous ability to anchor copper ions. The N-terminal domain of human prion protein (hPrP) contains four tandem repeats of the -PHGGGWGQ- octapeptide sequence. This octarepeat domain can bind up to four Cu2+ ions. Similarly to hPrP, chicken prion protein (chPrP) is able to interact with Cu2+ through the tandem hexapeptide -HNPGYP- region (residues 53-94). In this work, we focused on the human octapeptide repeat (human Octa4, hPrP60-91) (Ac-PHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQ-NH2) and chicken hexapeptide repeat (chicken Hexa4, chPrP54-77) (Ac-HNPGYPHNPGYPHNPGYPHNPGYP-NH2) prion protein fragments. Due to the fact that PrP is a membrane-anchored glycoprotein and its unstructured and flexible N-terminal domain may interact with the lipid bilayer, our studies were carried out in presence of the surfactant sodium dodecyl sulfate (SDS) mimicking the membrane environment in vitro. The main objective of this work was to understand the effects of copper ion on the structural rearrangements of the human and chicken N-terminal repeat domain. The obtained results provide a fundamental first step in describing the thermodynamic (potentiometric titrations) and structural properties of Cu(II) binding (UV-Vis, NMR, CD spectroscopy) to both human Octa4 and chicken Hexa4 repeats in both a DMSO/water and SDS micelle environment. Interestingly, in SDS environment, both ligands indicate different copper coordination modes, which results of the conformational changes in micelle environment. Our results strongly support that copper binding mode strongly depends on the protein backbone structure. Moreover, we focused on previously obtained results for amyloidogenic human and chicken fragments in membrane mimicking environment.
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Affiliation(s)
- Aleksandra Hecel
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50383 Wroclaw, Poland.
| | - Daniela Valensin
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Henryk Kozłowski
- Opole Medical School in Opole, Katowicka 68, 45060 Opole, Poland
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15
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Salvesen Ø, Tatzelt J, Tranulis MA. The prion protein in neuroimmune crosstalk. Neurochem Int 2018; 130:104335. [PMID: 30448564 DOI: 10.1016/j.neuint.2018.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/04/2018] [Accepted: 11/14/2018] [Indexed: 01/11/2023]
Abstract
The cellular prion protein (PrPC) is a medium-sized glycoprotein, attached to the cell surface by a glycosylphosphatidylinositol anchor. PrPC is encoded by a single-copy gene, PRNP, which is abundantly expressed in the central nervous system and at lower levels in non-neuronal cells, including those of the immune system. Evidence from experimental knockout of PRNP in rodents, goats, and cattle and the occurrence of a nonsense mutation in goat that prevents synthesis of PrPC, have shown that the molecule is non-essential for life. Indeed, no easily recognizable phenotypes are associate with a lack of PrPC, except the potentially advantageous trait that animals without PrPC cannot develop prion disease. This is because, in prion diseases, PrPC converts to a pathogenic "scrapie" conformer, PrPSc, which aggregates and eventually induces neurodegeneration. In addition, endogenous neuronal PrPC serves as a toxic receptor to mediate prion-induced neurotoxicity. Thus, PrPC is an interesting target for treatment of prion diseases. Although loss of PrPC has no discernable effect, alteration of its normal physiological function can have very harmful consequences. It is therefore important to understand cellular processes involving PrPC, and research of this topic has advanced considerably in the past decade. Here, we summarize data that indicate the role of PrPC in modulating immune signaling, with emphasis on neuroimmune crosstalk both under basal conditions and during inflammatory stress.
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Affiliation(s)
- Øyvind Salvesen
- Faculty of Veterinary Medicine, Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, Sandnes, Norway.
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Germany.
| | - Michael A Tranulis
- Faculty of Veterinary Medicine, Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway.
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16
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Abstract
The cellular prion protein, PrPC, is a small, cell surface glycoprotein with a function that is currently somewhat ill defined. It is also the key molecule involved in the family of neurodegenerative disorders called transmissible spongiform encephalopathies, which are also known as prion diseases. The misfolding of PrPC to a conformationally altered isoform, designated PrPTSE, is the main molecular process involved in pathogenesis and appears to precede many other pathologic and clinical manifestations of disease, including neuronal loss, astrogliosis, and cognitive loss. PrPTSE is also believed to be the major component of the infectious "prion," the agent responsible for disease transmission, and preparations of this protein can cause prion disease when inoculated into a naïve host. Thus, understanding the biochemical and biophysical properties of both PrPC and PrPTSE, and ultimately the mechanisms of their interconversion, is critical if we are to understand prion disease biology. Although entire books could be devoted to research pertaining to the protein, herein we briefly review the state of knowledge of prion biochemistry, including consideration of prion protein structure, function, misfolding, and dysfunction.
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Affiliation(s)
- Andrew C Gill
- School of Chemistry, Joseph Banks Laboratories, University of Lincoln, Lincoln, United Kingdom; Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, United Kingdom.
| | - Andrew R Castle
- Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, United Kingdom
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17
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Wang LJ, Gu XD, Yu GH, Shen L, Ji HF. Different effects of lipid on conformational conversion of chicken and murine prion proteins. Vet Microbiol 2018; 224:1-7. [PMID: 30269782 DOI: 10.1016/j.vetmic.2018.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 08/09/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
Prion diseases are characterized by the conformational conversion of the cellular prion protein (PrPC) to the pathogenic isoform (PrPSc). Lipids have been found to interact with PrPC and contribute to the efficient formation of PrPSc. Non-mammalian PrPs are not readily to undergo the conversion process into an infectious isoform, yet the effect of lipid on the conformational conversion of non-mammalian PrPC remains to be explored. Herein, the effects of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) on full-length recombinant chicken PrP (ChPrP) 24-249 and murine PrP (MoPrP) 23-230 were investigated. Firstly, it was found that in the presence of chemical denaturant, POPG remarkably inhibited MoPrP amyloid fibril growth, while had slight effect on that of ChPrP as estimated by amyloid fibril growth and transmissible electronic microscope assays. Secondly, under physiological condition, POPG induced conformation changes in both MoPrP and ChPrP using Thioflavin T (ThT) fluorescence, circular dichroism, proteinase K digestion and transmission electron microscopy assays. With a POPG:PrP molar ratio of 30:1, the ThT fluorescence of MoPrP was found to be lower than that of ChPrP, however, the POPG-induced MoPrP had higher β-sheet content and was more proteinase K-resistant than POPG-induced ChPrP. In summary, the present results suggested that the effects of POPG on conformational conversion of MoPrP and ChPrP were different under both denaturation and physiological conditions.
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Affiliation(s)
- Li-Juan Wang
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China
| | - Xiao-Dan Gu
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China
| | - Guo-Hua Yu
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, School of Life Sciences, Longyan University, Longyan 364012, China
| | - Liang Shen
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China.
| | - Hong-Fang Ji
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China.
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18
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Hecel A, Draghi S, Valensin D, Kozlowski H. The effect of a membrane-mimicking environment on the interactions of Cu 2+ with an amyloidogenic fragment of chicken prion protein. Dalton Trans 2018; 46:7758-7769. [PMID: 28589973 DOI: 10.1039/c7dt01069a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prion proteins (PrP) from different species have the ability to tightly bind Cu2+ ions. Copper coordination sites are located in the disordered and flexible N-terminal region which contains several His anchoring sites. Among them, two His residues are found in the so called amyloidogenic PrP region which is believed to play a key role in the process leading to oligomer and fibril formation. Both chicken and human amyloidogenic regions have a hydrophobic C-terminal region rich in Ala and Val amino acids. Recent findings revealed that this domain undergoes random coil to α-helix structuring upon interaction with membrane models. This interaction might strongly impact metal binding abilities either in terms of donor sets or affinity. In this study we investigated Cu2+ interaction with an amyloidogenic fragment, chPrP105-140, derived from chicken prion protein (chPrP), in different solution environments. The behavior of the peptide and its metal complexes was analyzed in water and in the presence of negative and positive charged membrane mimicking environments formed by sodium dodecyl sulfate (SDS) and dodecyl trimethyl ammonium chloride (DTAC) micelles. The metal coordination sphere, the metal binding affinity and stoichiometry were evaluated by combining spectroscopic and potentiometric methods. Finally we compare copper(ii) interactions with human and chicken amyloidogenic fragments. Our results indicate that the chicken amyloidogenic fragment is a stronger copper ligand than the human amyloidogenic fragment.
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Affiliation(s)
- Aleksandra Hecel
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14., 50-383 Wroclaw, Poland
| | - Sara Draghi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Daniela Valensin
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Henryk Kozlowski
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland
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19
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The function of the cellular prion protein in health and disease. Acta Neuropathol 2018; 135:159-178. [PMID: 29151170 DOI: 10.1007/s00401-017-1790-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/11/2022]
Abstract
The essential role of the cellular prion protein (PrPC) in prion disorders such as Creutzfeldt-Jakob disease is well documented. Moreover, evidence is accumulating that PrPC may act as a receptor for protein aggregates and transduce neurotoxic signals in more common neurodegenerative disorders, such as Alzheimer's disease. Although the pathological roles of PrPC have been thoroughly characterized, a general consensus on its physiological function within the brain has not yet been established. Knockout studies in various organisms, ranging from zebrafish to mice, have implicated PrPC in a diverse range of nervous system-related activities that include a key role in the maintenance of peripheral nerve myelination as well as a general ability to protect against neurotoxic stimuli. Thus, the function of PrPC may be multifaceted, with different cell types taking advantage of unique aspects of its biology. Deciphering the cellular function(s) of PrPC and the consequences of its absence is not simply an academic curiosity, since lowering PrPC levels in the brain is predicted to be a powerful therapeutic strategy for the treatment of prion disease. In this review, we outline the various approaches that have been employed in an effort to uncover the physiological and pathological functions of PrPC. While these studies have revealed important clues about the biology of the prion protein, the precise reason for PrPC's existence remains enigmatic.
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20
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21
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Abskharon R, Dang J, Elfarash A, Wang Z, Shen P, Zou LS, Hassan S, Wang F, Fujioka H, Steyaert J, Mulaj M, Surewicz WK, Castilla J, Wohlkonig A, Zou WQ. Soluble polymorphic bank vole prion proteins induced by co-expression of quiescin sulfhydryl oxidase in E. coli and their aggregation behaviors. Microb Cell Fact 2017; 16:170. [PMID: 28978309 PMCID: PMC5628483 DOI: 10.1186/s12934-017-0782-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/21/2017] [Indexed: 12/17/2022] Open
Abstract
Background The infectious prion protein (PrPSc or prion) is derived from its cellular form (PrPC) through a conformational transition in animal and human prion diseases. Studies have shown that the interspecies conversion of PrPC to PrPSc is largely swayed by species barriers, which is mainly deciphered by the sequence and conformation of the proteins among species. However, the bank vole PrPC (BVPrP) is highly susceptible to PrPSc from different species. Transgenic mice expressing BVPrP with the polymorphic isoleucine (109I) but methionine (109M) at residue 109 spontaneously develop prion disease. Results To explore the mechanism underlying the unique susceptibility and convertibility, we generated soluble BVPrP by co-expression of BVPrP with Quiescin sulfhydryl oxidase (QSOX) in Escherichia coli. Interestingly, rBVPrP-109M and rBVPrP-109I exhibited distinct seeded aggregation pathways and aggregate morphologies upon seeding of mouse recombinant PrP fibrils, as monitored by thioflavin T fluorescence and electron microscopy. Moreover, they displayed different aggregation behaviors induced by seeding of hamster and mouse prion strains under real-time quaking-induced conversion. Conclusions Our results suggest that QSOX facilitates the formation of soluble prion protein and provide further evidence that the polymorphism at residue 109 of QSOX-induced BVPrP may be a determinant in mediating its distinct convertibility and susceptibility.
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Affiliation(s)
- Romany Abskharon
- VIB Center for Structural Biology, VIB, 1050, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050, Brussels, Belgium.,National Institute of Oceanography and Fisheries (NIFO), Cairo, 11516, Egypt.,Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Johnny Dang
- Departments of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ameer Elfarash
- Genetic Department, Faculty of Agriculture, Assiut University, Assuit, 71516, Egypt
| | - Zerui Wang
- Departments of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,The First Hospital of Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Pingping Shen
- Departments of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,The First Hospital of Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Lewis S Zou
- Departments of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sedky Hassan
- Botany Department, Faculty of Science, Assiut University, New Valley Branch, El-Kharja, 72511, Egypt
| | - Fei Wang
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Hisashi Fujioka
- Electron Microscopy Core Facility, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jan Steyaert
- VIB Center for Structural Biology, VIB, 1050, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050, Brussels, Belgium
| | - Mentor Mulaj
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Joaquín Castilla
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Bizkaia, Spain
| | - Alexandre Wohlkonig
- VIB Center for Structural Biology, VIB, 1050, Brussels, Belgium. .,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050, Brussels, Belgium.
| | - Wen-Quan Zou
- Departments of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA. .,Departments of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, USA. .,National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA. .,National Center for Regenerative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA. .,The First Hospital of Jilin University, Changchun, Jilin Province, People's Republic of China. .,State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
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22
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Malevanets A, Chong PA, Hansen DF, Rizk P, Sun Y, Lin H, Muhandiram R, Chakrabartty A, Kay LE, Forman-Kay JD, Wodak SJ. Interplay of buried histidine protonation and protein stability in prion misfolding. Sci Rep 2017; 7:882. [PMID: 28408762 PMCID: PMC5429843 DOI: 10.1038/s41598-017-00954-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/20/2017] [Indexed: 12/03/2022] Open
Abstract
Misofolding of mammalian prion proteins (PrP) is believed to be the cause of a group of rare and fatal neurodegenerative diseases. Despite intense scrutiny however, the mechanism of the misfolding reaction remains unclear. We perform nuclear Magnetic Resonance and thermodynamic stability measurements on the C-terminal domains (residues 90–231) of two PrP variants exhibiting different pH-induced susceptibilities to aggregation: the susceptible hamster prion (GHaPrP) and its less susceptible rabbit homolog (RaPrP). The pKa of histidines in these domains are determined from titration experiments, and proton-exchange rates are measured at pH 5 and pH 7. A single buried highly conserved histidine, H187/H186 in GHaPrP/RaPrP, exhibited a markedly down shifted pKa ~5 for both proteins. However, noticeably larger pH-induced shifts in exchange rates occur for GHaPrP versus RaPrP. Analysis of the data indicates that protonation of the buried histidine destabilizes both PrP variants, but produces a more drastic effect in the less stable GHaPrP. This interpretation is supported by urea denaturation experiments performed on both PrP variants at neutral and low pH, and correlates with the difference in disease susceptibility of the two species, as expected from the documented linkage between destabilization of the folded state and formation of misfolded and aggregated species.
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Affiliation(s)
- Anatoly Malevanets
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada
| | - P Andrew Chong
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - D Flemming Hansen
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,University College London, Division of Biosciences, London, WC1E 6BT, UK
| | - Paul Rizk
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Yulong Sun
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Hong Lin
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada
| | - Ranjith Muhandiram
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Avi Chakrabartty
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Lewis E Kay
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Julie D Forman-Kay
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Shoshana J Wodak
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,VIB Structural Biology Research Center, VUB, Pleinlaan 2, 1050, Brussels, Belgium.
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23
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The role of the unusual threonine string in the conversion of prion protein. Sci Rep 2016; 6:38877. [PMID: 27982059 PMCID: PMC5159806 DOI: 10.1038/srep38877] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/15/2016] [Indexed: 01/24/2023] Open
Abstract
The conversion of normal prion protein (PrP) into pathogenic PrP conformers is central to prion disease, but the mechanism remains unclear. The α-helix 2 of PrP contains a string of four threonines, which is unusual due to the high propensity of threonine to form β-sheets. This structural feature was proposed as the basis for initiating PrP conversion, but experimental results have been conflicting. We studied the role of the threonine string on PrP conversion by analyzing mouse Prnpa and Prnpb polymorphism that contains a polymorphic residue at the beginning of the threonine string, and PrP mutants in which threonine 191 was replaced by valine, alanine, or proline. The PMCA (protein misfolding cyclic amplification) assay was able to recapitulate the in vivo transmission barrier between PrPa and PrPb. Relative to PMCA, the amyloid fibril growth assay is less restrictive, but it did reflect certain properties of in vivo prion transmission. Our results suggest a plausible theory explaining the apparently contradictory results in the role of the threonine string in PrP conversion and provide novel insights into the complicated relationship among PrP stability, seeded conformational change, and prion structure, which is critical for understanding the molecular basis of prion infectivity.
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24
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Do prion protein gene polymorphisms induce apoptosis in non-mammals? J Biosci 2016; 41:97-107. [PMID: 26949092 DOI: 10.1007/s12038-015-9584-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Genetic variations such as single nucleotide polymorphisms (SNPs) in prion protein coding gene, Prnp, greatly affect susceptibility to prion diseases in mammals. Here, the coding region of Prnp was screened for polymorphisms in redeared turtle, Trachemys scripta. Four polymorphisms, L203V, N205I, V225A and M237V, were common in 15 out of 30 turtles; in one sample, three SNPs, L203V, N205I and M237V, and in the remaining 14 samples, only L203V and N205I polymorphisms, were investigated. Besides, C658T, C664T, C670A and C823A SNPs were silent mutations. To elucidate the relationship between the SNPs and apoptosis, TUNEL assays and active caspase-3 immunodetection techniques in brain sections of the polymorphic samples were performed. The results revealed that TUNEL-positive cells and active caspase-3-positive cells in the turtles with four polymorphisms were significantly increased compared with those of the turtles with two polymorphisms (P less than 0.01 and P less than 0.05, respectively). In conclusion, this study provides preliminary information about the possible relationship between SNPs within the Prnp locus and apoptosis in a non-mammalian species, Trachemys scripta, in which prion disease has never been reported.
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25
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Bakkebø MK, Mouillet-Richard S, Espenes A, Goldmann W, Tatzelt J, Tranulis MA. The Cellular Prion Protein: A Player in Immunological Quiescence. Front Immunol 2015; 6:450. [PMID: 26388873 PMCID: PMC4557099 DOI: 10.3389/fimmu.2015.00450] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/19/2015] [Indexed: 01/09/2023] Open
Abstract
Despite intensive studies since the 1990s, the physiological role of the cellular prion protein (PrP(C)) remains elusive. Here, we present a novel concept suggesting that PrP(C) contributes to immunological quiescence in addition to cell protection. PrP(C) is highly expressed in diverse organs that by multiple means are particularly protected from inflammation, such as the brain, eye, placenta, pregnant uterus, and testes, while at the same time it is expressed in most cells of the lymphoreticular system. In this paradigm, PrP(C) serves two principal roles: to modulate the inflammatory potential of immune cells and to protect vulnerable parenchymal cells against noxious insults generated through inflammation. Here, we review studies of PrP(C) physiology in view of this concept.
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Affiliation(s)
- Maren K. Bakkebø
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway
| | | | - Arild Espenes
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Wilfred Goldmann
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Jörg Tatzelt
- Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Michael A. Tranulis
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway,*Correspondence: Michael A. Tranulis, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Campus Adamstuen, Oslo 0033, Norway,
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26
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Generic amyloidogenicity of mammalian prion proteins from species susceptible and resistant to prions. Sci Rep 2015; 5:10101. [PMID: 25960067 PMCID: PMC4650755 DOI: 10.1038/srep10101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/30/2015] [Indexed: 11/30/2022] Open
Abstract
Prion diseases are lethal, infectious diseases associated with prion protein (PrP) misfolding. A large number of mammals are susceptible to both sporadic and acquired prion diseases. Although PrP is highly conserved and ubiquitously expressed in all mammals, not all species exhibit prion disease. By employing full length recombinant PrP from five known prion susceptible species (human, cattle, cat, mouse and hamster) and two species considered to be prion resistant (pig and dog) the amyloidogenicity of these PrPs has been delineated. All the mammalian PrPs, even from resistant species, were swiftly converted from the native state to amyloid-like structure when subjected to a native condition conversion assay. The PrPs displayed amyloidotypic tinctorial and ultrastructural hallmarks. Self-seeded conversion of the PrPs displayed significantly decreased lag phases demonstrating that nucleation dependent polymerization is a dominating mechanism in the fibrillation process. Fibrils from Aβ1-40, Aβ1-42, Lysozyme, Insulin and Transthyretin did not accelerate conversion of HuPrP whereas fibrils from HuPrP90-231 and HuPrP121-231 as well as full length PrPs of all PrPs efficiently seeded conversion showing specificity of the assay requiring the C-terminal PrP sequence. Our findings have implications for PrP misfolding and could have ramifications in the context of prion resistant species and silent carriers.
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Buchner L, Güntert P. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA. JOURNAL OF BIOMOLECULAR NMR 2015; 62:81-95. [PMID: 25796507 DOI: 10.1007/s10858-015-9921-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/16/2015] [Indexed: 05/07/2023]
Abstract
The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but a systematic evaluation of its performance has not yet been reported. In this paper we systematically analyze the reliability of combined automated NOESY assignment and structure calculation with CYANA under a variety of conditions on the basis of the experimental NMR data sets of ten proteins. To evaluate the robustness of the algorithm, the original high-quality experimental data sets were modified in different ways to simulate the effect of data imperfections, i.e. incomplete or erroneous chemical shift assignments, missing NOESY cross peaks, inaccurate peak positions, inaccurate peak intensities, lower dimensionality NOESY spectra, and higher tolerances for the matching of chemical shifts and peak positions. The results show that the algorithm is remarkably robust with regard to imperfections of the NOESY peak lists and the chemical shift tolerances but susceptible to lacking or erroneous resonance assignments, in particular for nuclei that are involved in many NOESY cross peaks.
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Affiliation(s)
- Lena Buchner
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
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Nyström S, Hammarström P. Is the prevalent human prion protein 129M/V mutation a living fossil from a Paleolithic panzootic superprion pandemic? Prion 2015; 8:2-10. [PMID: 24398570 PMCID: PMC7030913 DOI: 10.4161/pri.27601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Prion diseases are consistently associated with prion protein (PrP(C)) misfolding rendering a cascade of auto-catalytic self-perpetuation of misfolded PrP in an afflicted individual. The molecular process is intriguingly similar to all known amyloid diseases both local and systemic. The prion disease is also infectious by the transfer of misfolded PrP from one individual to the next. Transmissibility is surprisingly efficient in prion diseases and given the rapid disease progression following initial symptoms the prionoses stand out from other amyloidoses, which all may be transmissible under certain circumstances. The nature of the infectious prion as well as the genotype of the host is important for transmissibility. For hitherto unexplained reasons the majority of Europeans carry a missense mutation on one or both alleles of the PrP gene (PRNP), and hence express a variant of PrP with a substitution for valine (V) instead of methionine (M) in position 129. In fact the 129M/V variant is very common in all populations except for the Japanese. Sporadic Creutzfeldt-Jakob disease is a disease rarely striking people below the age of 60, where homozygosity especially 129MM is a very strong risk factor. Paradoxically, the 129M/V polymorphism suggestive of heterozygote advantage is one of the most clear cut disease associated traits of the human population, yet prion disease is extraordinarily rare. The genetic basis for how this trait spread with such prevalence within human populations is still target to investigations and deserves attention. This short essay represents a somewhat provocative hypothetical notion of a possible ancient significance of this polymorphism.
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Buchner L, Güntert P. Increased reliability of nuclear magnetic resonance protein structures by consensus structure bundles. Structure 2015; 23:425-34. [PMID: 25579816 DOI: 10.1016/j.str.2014.11.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/17/2014] [Accepted: 11/17/2014] [Indexed: 11/17/2022]
Abstract
Nuclear magnetic resonance (NMR) structures are represented by bundles of conformers calculated from different randomized initial structures using identical experimental input data. The spread among these conformers indicates the precision of the atomic coordinates. However, there is as yet no reliable measure of structural accuracy, i.e., how close NMR conformers are to the "true" structure. Instead, the precision of structure bundles is widely (mis)interpreted as a measure of structural quality. Attempts to increase precision often overestimate accuracy by tight bundles of high precision but much lower accuracy. To overcome this problem, we introduce a protocol for NMR structure determination with the software package CYANA, which produces, like the traditional method, bundles of conformers in agreement with a common set of conformational restraints but with a realistic precision that is, throughout a variety of proteins and NMR data sets, a much better estimate of structural accuracy than the precision of conventional structure bundles.
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Affiliation(s)
- Lena Buchner
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany; Frankfurt Institute of Advanced Studies, Goethe University Frankfurt, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany; Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo 192-0397, Japan.
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Structural and dynamic properties of the human prion protein. Biophys J 2014; 106:1152-63. [PMID: 24606939 DOI: 10.1016/j.bpj.2013.12.053] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 12/11/2013] [Accepted: 12/26/2013] [Indexed: 11/23/2022] Open
Abstract
Prion diseases involve the conformational conversion of the cellular prion protein (PrP(C)) to its misfolded pathogenic form (PrP(Sc)). To better understand the structural mechanism of this conversion, we performed extensive all-atom, explicit-solvent molecular-dynamics simulations for three structures of the wild-type human PrP (huPrP) at different pH values and temperatures. Residue 129 is polymorphic, being either Met or Val. Two of the three structures have Met in position 129 and the other has Val. Lowering the pH or raising the temperature induced large conformational changes of the C-terminal globular domain and increased exposure of its hydrophobic core. In some simulations, HA and its preceding S1-HA loop underwent large displacements. The C-terminus of HB was unstable and sometimes partially unfolded. Two hydrophobic residues, Phe-198 and Met-134, frequently became exposed to solvent. These conformational changes became more dramatic at lower pH or higher temperature. Furthermore, Tyr-169 and the S2-HB loop, or the X-loop, were different in the starting structures but converged to common conformations in the simulations for the Met-129, but not the Val-129, protein. α-Strands and β-strands formed in the initially unstructured N-terminus. α-Strand propensity in the N-terminus was different between the Met-129 and Val129 proteins, but β-strand propensity was similar. This study reveals detailed structural and dynamic properties of huPrP, providing insight into the mechanism of the conversion of PrP(C) to PrP(Sc).
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Evolutionary implications of metal binding features in different species' prion protein: an inorganic point of view. Biomolecules 2014; 4:546-65. [PMID: 24970230 PMCID: PMC4101497 DOI: 10.3390/biom4020546] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/29/2014] [Accepted: 05/06/2014] [Indexed: 12/21/2022] Open
Abstract
Prion disorders are a group of fatal neurodegenerative conditions of mammals. The key molecular event in the pathogenesis of such diseases is the conformational conversion of prion protein, PrPC, into a misfolded form rich in β-sheet structure, PrPSc, but the detailed mechanistic aspects of prion protein conversion remain enigmatic. There is uncertainty on the precise physiological function of PrPC in healthy individuals. Several evidences support the notion of its role in copper homeostasis. PrPC binds Cu2+ mainly through a domain composed by four to five repeats of eight amino acids. In addition to mammals, PrP homologues have also been identified in birds, reptiles, amphibians and fish. The globular domain of protein is retained in the different species, suggesting that the protein carries out an essential common function. However, the comparison of amino acid sequences indicates that prion protein has evolved differently in each vertebrate class. The primary sequences are strongly conserved in each group, but these exhibit a low similarity with those of mammals. The N-terminal domain of different prions shows tandem amino acid repeats with an increasing amount of histidine residues going from amphibians to mammals. The difference in the sequence affects the number of copper binding sites, the affinity and the coordination environment of metal ions, suggesting that the involvement of prion in metal homeostasis may be a specific characteristic of mammalian prion protein. In this review, we describe the similarities and the differences in the metal binding of different species' prion protein, as revealed by studies carried out on the entire protein and related peptide fragments.
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Mercer RCC, Ma L, Watts JC, Strome R, Wohlgemuth S, Yang J, Cashman NR, Coulthart MB, Schmitt-Ulms G, Jhamandas JH, Westaway D. The prion protein modulates A-type K+ currents mediated by Kv4.2 complexes through dipeptidyl aminopeptidase-like protein 6. J Biol Chem 2013; 288:37241-55. [PMID: 24225951 DOI: 10.1074/jbc.m113.488650] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Widely expressed in the adult central nervous system, the cellular prion protein (PrP(C)) is implicated in a variety of processes, including neuronal excitability. Dipeptidyl aminopeptidase-like protein 6 (DPP6) was first identified as a PrP(C) interactor using in vivo formaldehyde cross-linking of wild type (WT) mouse brain. This finding was confirmed in three cell lines and, because DPP6 directs the functional assembly of K(+) channels, we assessed the impact of WT and mutant PrP(C) upon Kv4.2-based cell surface macromolecular complexes. Whereas a Gerstmann-Sträussler-Scheinker disease version of PrP with eight extra octarepeats was a loss of function both for complex formation and for modulation of Kv4.2 channels, WT PrP(C), in a DPP6-dependent manner, modulated Kv4.2 channel properties, causing an increase in peak amplitude, a rightward shift of the voltage-dependent steady-state inactivation curve, a slower inactivation, and a faster recovery from steady-state inactivation. Thus, the net impact of wt PrP(C) was one of enhancement, which plays a critical role in the down-regulation of neuronal membrane excitability and is associated with a decreased susceptibility to seizures. Insofar as previous work has established a requirement for WT PrP(C) in the Aβ-dependent modulation of excitability in cholinergic basal forebrain neurons, our findings implicate PrP(C) regulation of Kv4.2 channels as a mechanism contributing to the effects of oligomeric Aβ upon neuronal excitability and viability.
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Kretzschmar H, Tatzelt J. Prion disease: a tale of folds and strains. Brain Pathol 2013; 23:321-32. [PMID: 23587138 DOI: 10.1111/bpa.12045] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 02/04/2013] [Indexed: 12/31/2022] Open
Abstract
Research on prions, the infectious agents of devastating neurological diseases in humans and animals, has been in the forefront of developing the concept of protein aggregation diseases. Prion diseases are distinguished from other neurodegenerative diseases by three peculiarities. First, prion diseases, in addition to being sporadic or genetic like all other neurodegenerative diseases, are infectious diseases. Animal models were developed early on (a long time before the advent of transgenic technology), and this has made possible the discovery of the prion protein as the infectious agent. Second, human prion diseases have true equivalents in animals, such as scrapie, which has been the subject of experimental research for many years. Variant Creutzfeldt-Jakob disease (vCJD) is a zoonosis caused by bovine spongiform encephalopathy (BSE) prions. Third, they show a wide variety of phenotypes in humans and animals, much wider than the variants of any other sporadic or genetic neurodegenerative disease. It has now become firmly established that particular PrP(Sc) isoforms are closely related to specific human prion strains. The variety of human prion diseases, still an enigma in its own right, is a focus of this article. Recently, a series of experiments has shown that the concept of aberrant protein folding and templating, first developed for prions, may apply to a variety of neurodegenerative diseases. In the wake of these discoveries, the term prion has come to be used for Aβ, α-synuclein, tau and possibly others. The self-propagation of alternative conformations seems to be the common denominator of these "prions," which in future, in order to avoid confusion, may have to be specified either as "neurodegenerative prions" or "infectious prions."
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Russo L, Raiola L, Campitiello MA, Magrì A, Fattorusso R, Malgieri G, Pappalardo G, La Mendola D, Isernia C. Probing the residual structure in avian prion hexarepeats by CD, NMR and MD techniques. Molecules 2013; 18:11467-84. [PMID: 24043142 PMCID: PMC6270093 DOI: 10.3390/molecules180911467] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 02/06/2023] Open
Abstract
Many proteins perform essential biological functions by means of regions that lacking specific organized structure exist as an ensemble of interconverting transient conformers. The characterization of such regions, including the description of their structural propensities, number of conformations and relative populations can provide useful insights. Prion diseases result from the conversion of a normal glycoprotein into a misfolded pathogenic isoform. The structures of mammal and chicken prion proteins show a similar fold with a globular domain and a flexible N-terminal portion that contains different repeated regions: octarepeats (PHGGGWGQ) in mammals and hexarepeats (PHNPGY) in chickens. The higher number of prolines in the hexarepeat region suggests that this region may retain a significant amount of residual secondary structure. Here, we report the CD, NMR and MD characterization of a peptide (2-HexaPY) composed of two hexarepeats. We combine experimental NMR data and MD to investigate at atomic level its ensemble-averaged structural properties, demonstrating how each residue of both repeats has a different quantified PPII propensity that shows a periodicity along the sequence. This feature explains the absence of cooperativity to stabilize a PPII conformation. Nonetheless, such residual structure can play a role in nucleating local structural transitions as well as modulating intra-molecular or inter-molecular interactions.
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Affiliation(s)
- Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Luca Raiola
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Maria Anna Campitiello
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Antonio Magrì
- CNR-Istituto di Biostrutture e Bioimmagini, viale Doria 6, 95125 Catania, Italy; E-Mails: (A.M.); (G.P.)
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, Università di Napoli “Federico II”, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Gaetano Malgieri
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Giuseppe Pappalardo
- CNR-Istituto di Biostrutture e Bioimmagini, viale Doria 6, 95125 Catania, Italy; E-Mails: (A.M.); (G.P.)
| | - Diego La Mendola
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy; E-Mail:
| | - Carla Isernia
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, Università di Napoli “Federico II”, Via Mezzocannone 16, 80134 Napoli, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-0823-274-636; Fax: +39-0823-274-605
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Pocanschi CL, Ehsani S, Mehrabian M, Wille H, Reginold W, Trimble WS, Wang H, Yee A, Arrowsmith CH, Bozóky Z, Kay LE, Forman-Kay JD, Rini JM, Schmitt-Ulms G. The ZIP5 ectodomain co-localizes with PrP and may acquire a PrP-like fold that assembles into a dimer. PLoS One 2013; 8:e72446. [PMID: 24039764 PMCID: PMC3765157 DOI: 10.1371/journal.pone.0072446] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 07/18/2013] [Indexed: 01/11/2023] Open
Abstract
The cellular prion protein (PrP(C)) was recently observed to co-purify with members of the LIV-1 subfamily of ZIP zinc transporters (LZTs), precipitating the surprising discovery that the prion gene family descended from an ancestral LZT gene. Here, we compared the subcellular distribution and biophysical characteristics of LZTs and their PrP-like ectodomains. When expressed in neuroblastoma cells, the ZIP5 member of the LZT subfamily was observed to be largely directed to the same subcellular locations as PrP(C) and both proteins were seen to be endocytosed through vesicles decorated with the Rab5 marker protein. When recombinantly expressed, the PrP-like domain of ZIP5 could be obtained with yields and levels of purity sufficient for structural analyses but it tended to aggregate, thereby precluding attempts to study its structure. These obstacles were overcome by moving to a mammalian cell expression system. The subsequent biophysical characterization of a homogeneous preparation of the ZIP5 PrP-like ectodomain shows that this protein acquires a dimeric, largely globular fold with an α-helical content similar to that of mammalian PrP(C). The use of a mammalian cell expression system also allowed for the expression and purification of stable preparations of Takifugu rubripes PrP-1, thereby overcoming a key hindrance to high-resolution work on a fish PrP(C).
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Affiliation(s)
- Cosmin L. Pocanschi
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Sepehr Ehsani
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mohadeseh Mehrabian
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Holger Wille
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - William Reginold
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - William S. Trimble
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hansen Wang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Adelinda Yee
- Structural Genomics Consortium, Toronto, Ontario, Canada
| | | | - Zoltán Bozóky
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lewis E. Kay
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julie D. Forman-Kay
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - James M. Rini
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Molecular dynamics simulation of temperature induced unfolding of animal prion protein. J Mol Model 2013; 19:4433-41. [DOI: 10.1007/s00894-013-1955-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/22/2013] [Indexed: 01/22/2023]
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Richmond K, Masterson P, Ortiz JF, Siltberg-Liberles J. Did the prion protein become vulnerable to misfolding after an evolutionary divide and conquer event? J Biomol Struct Dyn 2013; 32:1074-84. [PMID: 23859022 DOI: 10.1080/07391102.2013.809022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite high sequence identity among mammalian prion proteins (PrPs), mammals have varying rates of susceptibility to prion disease resulting in a so-called species barrier. The species barrier follows no clear pattern, with closely related species or similar sequences being no more likely to infect each other, and remains an unresolved enigma. Variation of the conformationally flexible regions may alter the thermodynamics of the conformational change, commonly referred to as the conformational conversion, which occurs in the pathogenic process of the mammalian prion protein. A conformational ensemble scenario is supported by the species barrier in prion disease and evidence that there are strains of pathogenic prion with different conformations within species. To study how conformational flexibility has evolved in the prion protein, an investigation was undertaken on the evolutionary dynamics of structurally disordered regions in the mammalian prion protein, non-mammalian prion protein that is not vulnerable to prion disease, and remote homologs Doppel and Shadoo. Structural disorder prediction analyzed in an evolutionary context revealed that the occurrence of increased or altered conformational flexibility in mammalian PrPs coincides with key events among PrP, Doppel, and Shadoo. Comparatively rapid evolutionary dynamics of conformational flexibility in the prion protein suggest that the species barrier is not a static phenomenon. A small number of amino acid substitutions can repopulate the conformational ensemble and have a disproportionately large effect on pathogenesis.
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Affiliation(s)
- Kacy Richmond
- a Department of Molecular Biology , University of Wyoming , 1000 E. University Ave., Laramie , WY 82071 , USA
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Chuang CC, Liao TY, Chen EHL, Chen RPY. How do amino acid substitutions affect the amyloidogenic properties and seeding efficiency of prion peptides. Amino Acids 2013; 45:785-96. [PMID: 23736988 PMCID: PMC3776267 DOI: 10.1007/s00726-013-1522-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 05/22/2013] [Indexed: 11/28/2022]
Abstract
The amino acid sequences in the amyloidogenic region (amino acids 108–144) of several mammalian prion proteins were compared and variations were found to occur at residues 109 (M or L), 112 (M or V), 129 (M, V, or L), 135 (N or S), 138 (M, L, or I), 139 (M or I), and 143 (N or S). Using the bovine PrP peptide (residues 108–144 based on the numbering of the human prion protein sequence) as a control peptide, several peptides with one amino acid differing from that of the bovine PrP peptide at residues 109, 112, 135, 138, 139, or 143 and several mammalian PrP peptides were synthesized, and the effects of these amino acid substitutions on the amyloidogenic properties of these peptides were compared and discussed on the basis of the chemical and structural properties of amino acids. Our results showed that the V112M substitution accelerated nucleation of amyloidogenesis, while the N143S and I139M substitutions retarded nucleation. These effects tended to cancel each other out when two substitutions with opposite effects were present on the same peptide. Moreover, acceleration or inhibition of nucleation was not necessarily correlated with effect on seeding efficiency. Using amyloid fibrils prepared from the bovine PrP peptide as seeds, the seeding efficiency for the monomer peptides with the M129L, S135N, N143S, or I139M substitution was decreased compared to that for bPrP peptide. Of all the mammalian peptides used in this study, the dog, mule deer, and pig PrP peptides had the lowest seeding efficiencies.
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Affiliation(s)
- Chi-Chen Chuang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 106, Taiwan, ROC
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Hefke F, Schmucki R, Güntert P. Prediction of peak overlap in NMR spectra. JOURNAL OF BIOMOLECULAR NMR 2013; 56:113-123. [PMID: 23585271 DOI: 10.1007/s10858-013-9727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 04/04/2013] [Indexed: 06/02/2023]
Abstract
Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.
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Affiliation(s)
- Frederik Hefke
- Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Frankfurt am Main, Germany
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Garrec J, Tavernelli I, Rothlisberger U. Two misfolding routes for the prion protein around pH 4.5. PLoS Comput Biol 2013; 9:e1003057. [PMID: 23696721 PMCID: PMC3656106 DOI: 10.1371/journal.pcbi.1003057] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 03/27/2013] [Indexed: 11/18/2022] Open
Abstract
Using molecular dynamics simulations, we show that the prion protein (PrP) exhibits a dual behavior, with two possible transition routes, upon protonation of H187 around pH 4.5, which mimics specific conditions encountered in endosomes. Our results suggest a picture in which the protonated imidazole ring of H187 experiences an electrostatic repulsion with the nearby guanidinium group of R136, to which the system responds by pushing either H187 or R136 sidechains away from their native cavities. The regions to which H187 and R136 are linked, namely the C-terminal part of H2 and the loop connecting S1 to H1, respectively, are affected in a different manner depending on which pathway is taken. Specific in vivo or in vitro conditions, such as the presence of molecular chaperones or a particular experimental setup, may favor one transition pathway over the other, which can result in very different [Formula: see text] monomers. This has some possible connections with the observation of various fibril morphologies and the outcome of prion strains. In addition, the finding that the interaction of H187 with R136 is a weak point in mammalian PrP is supported by the absence of the [Formula: see text] residue pair in non-mammalian species that are known to be resistant to prion diseases.
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Affiliation(s)
- Julian Garrec
- Laboratory of Computational Chemistry and Biochemistry - Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry - Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry - Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail:
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41
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Hagiwara K, Hara H, Hanada K. Species-barrier phenomenon in prion transmissibility from a viewpoint of protein science. J Biochem 2013; 153:139-45. [PMID: 23284000 DOI: 10.1093/jb/mvs148] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transmissible spongiform encephalopathies (TSEs), or prion diseases, are fatal infectious neurodegenerative disorders. Their causative agents are prions, which are composed of disease-associated forms of prion protein (PrP(Sc)). Naturally occurring cases of TSEs are found in several mammalian species including humans, sheep, goats, minks, cattle and deer. Prions are also experimentally transmissible to other mammals such as mice, hamsters and monkeys, but interspecies transmission is often inefficient due to the 'species-barrier'. Studies have suggested that the barrier is not only simply determined by differences in amino acid sequences of cellular PrP (PrP(C)) among animal species, but also by prion strains which are closely associated with conformational properties of PrP(Sc) aggregates. Although the conformational properties of PrP(Sc) remain largely unknown, recent investigation of local structures of PrP(C) and, in particular, structural modelling of PrP(Sc) aggregates have provided molecular insight into this field. In this review, we discuss the species-barrier phenomenon in terms of the protein science.
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Affiliation(s)
- Ken'ichi Hagiwara
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan.
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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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43
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Prion Protein mPrP[F175A](121–231): Structure and Stability in Solution. J Mol Biol 2012; 423:496-502. [DOI: 10.1016/j.jmb.2012.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/15/2012] [Accepted: 08/16/2012] [Indexed: 11/24/2022]
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Arena G, La Mendola D, Pappalardo G, Sóvágó I, Rizzarelli E. Interactions of Cu2+ with prion family peptide fragments: Considerations on affinity, speciation and coordination. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.03.038] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Pimenta J, Domingos A, Santos P, Marques CC, Cantante C, Santos A, Barbas JP, Baptista MC, Horta AEM, Viegas A, Mesquita P, Gonçalves J, Fontes CA, Prates JAM, Pereira RMLN. Is prnt a pseudogene? Identification of ram Prt in testis and ejaculated spermatozoa. PLoS One 2012; 7:e42957. [PMID: 22937002 PMCID: PMC3427297 DOI: 10.1371/journal.pone.0042957] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 07/16/2012] [Indexed: 11/18/2022] Open
Abstract
A hallmark of prion diseases or transmissible spongiform encephalopaties is the conversion of the cellular prion protein (PrP(C)), expressed by the prion gene (prnp), into an abnormally folded isoform (PrP(Sc)) with amyloid-like features that causes scrapie in sheep among other diseases. prnp together with prnd (which encodes a prion-like protein designated as Doppel), and prnt (that encodes the prion protein testis specific--Prt) with sprn (shadow of prion protein gene, that encodes Shadoo or Sho) genes, constitute the "prion gene complex". Whereas a role for prnd in the proper functioning of male reproductive system has been confirmed, the function of prnt, a recently discovered prion family gene, comprises a conundrum leading to the assumption that ruminant prnt is a pseudogene with no protein expression. The main objective of the present study was to identify Prt localization in the ram reproductive system and simultaneously to elucidate if ovine prnt gene is transcribed into protein-coding RNA. Moreover, as Prt is a prnp-related protein, the amyloid propensity was also tested for ovine and caprine Prt. Recombinant Prt was used to immunize BALB/c mice, and the anti-Prt polyclonal antibody (APPA) immune response was evaluated by ELISA and Western Blot. When tested by indirect immunofluorescence, APPA showed high avidity to the ram sperm head apical ridge subdomain, before and after induced capacitation, but did not show the same behavior against goat spermatozoa, suggesting high antibody specificity against ovine-Prt. Prt was also found in the testis when assayed by immunohistochemistry during ram spermatogenesis, where spermatogonia, spermatocytes, spermatids and spermatozoa, stained positive. These observations strongly suggest ovine prnt to be a translated protein-coding gene, pointing to a role for Prt protein in the ram reproductive physiology. Besides, caprine Prt appears to exhibit a higher amyloid propensity than ovine Prt, mostly associated with its phenylalanine residue.
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Affiliation(s)
- Jorge Pimenta
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
- CIISA, Faculdade de Medicina Veterinária (FMV), Universidade Técnica de Lisboa, Lisboa, Portugal
| | - Ana Domingos
- IHMT-CMDT – Instituto de Higiene e Medicina Tropical, Centro de Malária e Doenças Tropicais, Lisboa, Portugal
| | - Pedro Santos
- Hospital Universitário de Coimbra, Coimbra, Portugal
| | - Carla C. Marques
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
| | - Cátia Cantante
- Unidade de Retrovírus e Infecções Associadas (URIA), ADEIM-Centro de Patogénese Molecular/Instituto de Medicina Molecular (IMM), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Santos
- Unidade de Retrovírus e Infecções Associadas (URIA), ADEIM-Centro de Patogénese Molecular/Instituto de Medicina Molecular (IMM), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - João P. Barbas
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
| | - Maria C. Baptista
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
| | - António E. M. Horta
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
| | - Aldino Viegas
- REQUIMTE/CQFB Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Patrícia Mesquita
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
| | - João Gonçalves
- Unidade de Retrovírus e Infecções Associadas (URIA), ADEIM-Centro de Patogénese Molecular/Instituto de Medicina Molecular (IMM), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos A. Fontes
- CIISA, Faculdade de Medicina Veterinária (FMV), Universidade Técnica de Lisboa, Lisboa, Portugal
| | - José A. M. Prates
- CIISA, Faculdade de Medicina Veterinária (FMV), Universidade Técnica de Lisboa, Lisboa, Portugal
| | - Rosa M. L. N. Pereira
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
- Escola Universitária Vasco da Gama, Coimbra, Portugal
- * E-mail:
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Gendoo DMA, Harrison PM. The landscape of the prion protein's structural response to mutation revealed by principal component analysis of multiple NMR ensembles. PLoS Comput Biol 2012; 8:e1002646. [PMID: 22912570 PMCID: PMC3415401 DOI: 10.1371/journal.pcbi.1002646] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 07/04/2012] [Indexed: 11/18/2022] Open
Abstract
Prion Proteins (PrP) are among a small number of proteins for which large numbers of NMR ensembles have been resolved for sequence mutants and diverse species. Here, we perform a comprehensive principle components analysis (PCA) on the tertiary structures of PrP globular proteins to discern PrP subdomains that exhibit conformational change in response to point mutations and clade-specific evolutionary sequence mutation trends. This is to our knowledge the first such large-scale analysis of multiple NMR ensembles of protein structures, and the first study of its kind for PrPs. We conducted PCA on human (n = 11), mouse (n = 14), and wildtype (n = 21) sets of PrP globular structures, from which we identified five conformationally variable subdomains within PrP. PCA shows that different non-local patterns and rankings of variable subdomains arise for different pathogenic mutants. These subdomains may thus be key areas for initiating PrP conversion during disease. Furthermore, we have observed the conformational clustering of divergent TSE-non-susceptible species pairs; these non-phylogenetic clusterings indicate structural solutions towards TSE resistance that do not necessarily coincide with evolutionary divergence. We discuss the novelty of our approach and the importance of PrP subdomains in structural conversion during disease. Prion Proteins (PrP) cause a variety of incurable TSE diseases, and are among a small number of proteins for which large numbers of NMR ensembles have been resolved for sequence mutants and diverse species. Here, we perform a comprehensive PCA study to assess conformational variation and discern the landscape of the PrP structural response to sequence mutation. This is to our knowledge the first large-scale analysis of multiple NMR ensembles for a specific protein, and the first study to perform a multivariate PCA on the native globular structures of PrP. We conducted exhaustive PCA on three PrP subsets: human and mouse subsets that include structures of sequence mutants, and the set of wild-type PrP (16 PrP species). PCA shows that different non-local patterns of variable subdomains arise for different pathogenic mutants. These subdomains may thus be key areas for initiating PrP conversion during disease. Furthermore, we observed that some evolutionarily divergent species that are non-susceptible to TSEs have surprising structural similarities in their PrPs. We discuss the novelty of our approach with respect to prions, and the advantage of this analysis as a fast, reliable starting point to identify interesting domains that may warrant further experimental and computational analysis.
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Affiliation(s)
- Deena M. A. Gendoo
- Department of Biology, McGill University, Montreal, Quebec, Canada
- McGill Center for Bioinformatics, McGill University, Montreal, Quebec, Canada
| | - Paul M. Harrison
- Department of Biology, McGill University, Montreal, Quebec, Canada
- McGill Center for Bioinformatics, McGill University, Montreal, Quebec, Canada
- * E-mail:
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Issack BB, Berjanskii M, Wishart DS, Stepanova M. Exploring the essential collective dynamics of interacting proteins: application to prion protein dimers. Proteins 2012; 80:1847-65. [PMID: 22488640 DOI: 10.1002/prot.24082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Revised: 03/07/2012] [Accepted: 03/18/2012] [Indexed: 11/11/2022]
Abstract
Essential collective dynamics is a promising and robust approach for analysing the slow motions of macromolecules from short molecular dynamics trajectories. In this study, an extension of the method to treat a collection of interacting protein molecules is presented. The extension is applied to investigate the effects of dimerization on the collective dynamics of ovine prion protein molecules in two different arrangements. Examination of the structural plasticity shows that aggregation has a restricting effect on the local mobility of the prion protein molecules in the interfacial regions. Domain motions of the two dimeric ovine prion protein conformations are distinctly different and can be related to interatomic correlations at the interface. Correlated motions are among the slow collective modes extensively analysed by considering both main-chain and side-chain atoms. Correlation maps reveal the existence of a vast network of dynamically correlated side groups, which extends beyond individual subunits via interfacial interconnections. The network is formed by a core of hydrophobic side chains surrounded by hydrophilic groups at the periphery. The relevance of these findings are discussed in the context of mutations associated with prion diseases. The binding free energy of the dimeric conformations is evaluated to probe their thermodynamic stability. The descriptions afforded by the analysis of the essential collective dynamics of the prion dimers are consistent with their binding free energies. The agreement validates the extension of the methodology and provides a means of interpreting the collective dynamics in terms of the thermodynamic stability of ovine prion proteins.
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Affiliation(s)
- Bilkiss B Issack
- National Institute for Nanotechnology, National research Council, Edmonton, AB, Canada
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48
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Gottstein D, Kirchner DK, Güntert P. Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space. JOURNAL OF BIOMOLECULAR NMR 2012; 52:351-64. [PMID: 22351031 DOI: 10.1007/s10858-012-9615-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/03/2012] [Indexed: 05/18/2023]
Abstract
A method is introduced to represent an ensemble of conformers of a protein by a single structure in torsion angle space that lies closest to the averaged Cartesian coordinates while maintaining perfect covalent geometry and on average equal steric quality and an equally good fit to the experimental (e.g. NMR) data as the individual conformers of the ensemble. The single representative 'regmean structure' is obtained by simulated annealing in torsion angle space with the program CYANA using as input data the experimental restraints, restraints for the atom positions relative to the average Cartesian coordinates, and restraints for the torsion angles relative to the corresponding principal cluster average values of the ensemble. The method was applied to 11 proteins for which NMR structure ensembles are available, and compared to alternative, commonly used simple approaches for selecting a single representative structure, e.g. the structure from the ensemble that best fulfills the experimental and steric restraints, or the structure from the ensemble that has the lowest RMSD value to the average Cartesian coordinates. In all cases our method found a structure in torsion angle space that is significantly closer to the mean coordinates than the alternatives while maintaining the same quality as individual conformers. The method is thus suitable to generate representative single structure representations of protein structure ensembles in torsion angle space. Since in the case of NMR structure calculations with CYANA the single structure is calculated in the same way as the individual conformers except that weak positional and torsion angle restraints are added, we propose to represent new NMR structures by a 'regmean bundle' consisting of the single representative structure as the first conformer and all but one original individual conformers (the original conformer with the highest target function value is discarded in order to keep the number of conformers in the bundle constant). In this way, analyses that require a single structure can be carried out in the most meaningful way using the first model, while at the same time the additional information contained in the ensemble remains available.
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Affiliation(s)
- Daniel Gottstein
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
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49
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Linden R, Cordeiro Y, Lima LMTR. Allosteric function and dysfunction of the prion protein. Cell Mol Life Sci 2012; 69:1105-24. [PMID: 21984610 PMCID: PMC11114699 DOI: 10.1007/s00018-011-0847-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 09/16/2011] [Accepted: 09/20/2011] [Indexed: 12/30/2022]
Abstract
Transmissible spongiform encephalopathies (TSEs) are neurodegenerative diseases associated with progressive oligo- and multimerization of the prion protein (PrP(C)), its conformational conversion, aggregation and precipitation. We recently proposed that PrP(C) serves as a cell surface scaffold protein for a variety of signaling modules, the effects of which translate into wide-range functional consequences. Here we review evidence for allosteric functions of PrP(C), which constitute a common property of scaffold proteins. The available data suggest that allosteric effects among PrP(C) and its partners are involved in the assembly of multi-component signaling modules at the cell surface, impose upon both physiological and pathological conformational responses of PrP(C), and that allosteric dysfunction of PrP(C) has the potential to entail progressive signal corruption. These properties may be germane both to physiological roles of PrP(C), as well as to the pathogenesis of the TSEs and other degenerative/non-communicable diseases.
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Affiliation(s)
- Rafael Linden
- Instituto de Biofísica Carlos Chagas Filho, UFRJ, CCS, Cidade Universitária, Rio de Janeiro, Brazil.
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50
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Mouse prion protein (PrP) segment 100 to 104 regulates conversion of PrP(C) to PrP(Sc) in prion-infected neuroblastoma cells. J Virol 2012; 86:5626-36. [PMID: 22398286 DOI: 10.1128/jvi.06606-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prion diseases are characterized by the replicative propagation of disease-associated forms of prion protein (PrP(Sc); PrP refers to prion protein). The propagation is believed to proceed via two steps; the initial binding of the normal form of PrP (PrP(C)) to PrP(Sc) and the subsequent conversion of PrP(C) to PrP(Sc). We have explored the two-step model in prion-infected mouse neuroblastoma (ScN2a) cells by focusing on the mouse PrP (MoPrP) segment 92-GGTHNQWNKPSKPKTN-107, which is within a region previously suggested to be part of the binding interface or shown to differ in its accessibility to anti-PrP antibodies between PrP(C) and PrP(Sc). Exchanging the MoPrP segment with the corresponding chicken PrP segment (106-GGSYHNQKPWKPPKTN-121) revealed the necessity of MoPrP residues 99 to 104 for the chimeras to achieve the PrP(Sc) state, while segment 95 to 98 was replaceable with the chicken sequence. An alanine substitution at position 100, 102, 103, or 104 of MoPrP gave rise to nonconvertible mutants that associated with MoPrP(Sc) and interfered with the conversion of endogenous MoPrP(C). The interference was not evoked by a chimera (designated MCM2) in which MoPrP segment 95 to 104 was changed to the chicken sequence, though MCM2 associated with MoPrP(Sc). Incubation of the cells with a synthetic peptide composed of MoPrP residues 93 to 107 or alanine-substituted cognates did not inhibit the conversion, whereas an anti-P8 antibody recognizing the above sequence in PrP(C) reduced the accumulation of PrP(Sc) after 10 days of incubation of the cells. These results suggest the segment 100 to 104 of MoPrP(C) plays a key role in conversion after binding to MoPrP(Sc).
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