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Louka A, Zacco E, Temussi PA, Tartaglia GG, Pastore A. RNA as the stone guest of protein aggregation. Nucleic Acids Res 2020; 48:11880-11889. [PMID: 33068411 PMCID: PMC7708036 DOI: 10.1093/nar/gkaa822] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/12/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
The study of prions as infectious aggregates dates several decades. From its original formulation, the definition of a prion has progressively changed to the point that many aggregation-prone proteins are now considered bona fide prions. RNA molecules, not included in the original 'protein-only hypothesis', are also being recognized as important factors contributing to the 'prion behaviour', that implies the transmissibility of an aberrant fold. In particular, an association has recently emerged between aggregation and the assembly of prion-like proteins in RNA-rich complexes, associated with both physiological and pathological events. Here, we discuss the historical rising of the concept of prion-like domains, their relation to RNA and their role in protein aggregation. As a paradigmatic example, we present the case study of TDP-43, an RNA-binding prion-like protein associated with amyotrophic lateral sclerosis. Through this example, we demonstrate how the current definition of prions has incorporated quite different concepts making the meaning of the term richer and more stimulating. An important message that emerges from our analysis is the dual role of RNA in protein aggregation, making RNA, that has been considered for many years a 'silent presence' or the 'stone guest' of protein aggregation, an important component of the process.
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Affiliation(s)
- Alexandra Louka
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
| | - Elsa Zacco
- Center for Human Technologies, Central RNA laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
- University “Federico II’’ Napoli, via Cynthia, Napoli 80100, Italy
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Central RNA laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain and ICREA, 23 Passeig Lluıs Companys, Barcelona 08010, Spain
- Charles Darwin department of Biology and Biotechnology, Sapienza University of Rome, Piazzale A. Moro 5, Rome 00185, Italy
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
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Kovachev PS, Gomes MPB, Cordeiro Y, Ferreira NC, Valadão LPF, Ascari LM, Rangel LP, Silva JL, Sanyal S. RNA modulates aggregation of the recombinant mammalian prion protein by direct interaction. Sci Rep 2019; 9:12406. [PMID: 31455808 PMCID: PMC6712051 DOI: 10.1038/s41598-019-48883-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/12/2019] [Indexed: 12/22/2022] Open
Abstract
Recent studies have proposed that nucleic acids act as potential cofactors for protein aggregation and prionogenesis. By means of sedimentation, transmission electron microscopy, circular dichroism, static and dynamic light scattering, we have studied how RNA can influence the aggregation of the murine recombinant prion protein (rPrP). We find that RNA, independent of its sequence, source and size, modulates rPrP aggregation in a bimodal fashion, affecting both the extent and the rate of rPrP aggregation in a concentration dependent manner. Analogous to RNA-induced liquid-liquid phase transitions observed for other proteins implicated in neurodegenerative diseases, high protein to RNA ratios stimulate rPrP aggregation, while low ratios suppress it. However, the latter scenario also promotes formation of soluble oligomeric aggregates capable of seeding de novo rPrP aggregation. Furthermore, RNA co-aggregates with rPrP and thereby gains partial protection from RNase digestion. Our results also indicate that rPrP interacts with the RNAs with its N-terminus. In summary, this study elucidates the proposed adjuvant role of RNA in prion protein aggregation and propagation, and thus advocates an auxiliary role of the nucleic acids in protein aggregation in general.
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Affiliation(s)
- Petar Stefanov Kovachev
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden
| | - Mariana P B Gomes
- Instituto de Tecnologia em Imunobiológicos, Bio-Manguinhos, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Natália C Ferreira
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil.,Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Leticia P Felix Valadão
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Lucas M Ascari
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Luciana P Rangel
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Jerson L Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil.
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden.
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Gao Z, Shi J, Cai L, Luo M, Wong BS, Dong X, Sy MS, Li C. Prion dimer is heterogenous and is modulated by multiple negative and positive motifs. Biochem Biophys Res Commun 2018; 509:570-576. [PMID: 30600179 DOI: 10.1016/j.bbrc.2018.12.113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 12/15/2018] [Indexed: 01/16/2023]
Abstract
The conversion of the normal prion protein (PrP) into a scrapie prion (PrPSc) is incompletely understood. Theoretically, the smallest PrP aggregate is a dimer. Human PrP contains two cysteines at positions 179 (C179) and 214 (C214) enabling disulfide bonding. Here, we report that our recombinant human PrP (r-hPrP) preparations contain 0.2-0.8% dimer, which is linked by either one or two disulfide bonds, connected by C179-C179, C214-C214, or C179-C214. Furthermore, dimerization is regulated by multiple motifs. While residues 36-42 inhibit, residues 90-125, and 195-212 promote dimerization. Mutating individual residue between 36 and 42 enhances dimerization whereas mutating the positively charged residues within 95-115, or the negatively charged residues within 195-212 prevent dimerization. Although deletion of the entire octapeptide-repeat (5OR) region prevents dimerization, mutating the histidines within the 5OR enhances dimerization. In addition, we found that two out of three brain lysates from patients with inherited prion disease had more PrP dimers than controls. Thus, PrP dimerization may contribute to prion diseases.
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Affiliation(s)
- Zhenxing Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, State Key Laboratory of Virology, 44 Xiao Hong Shan Zhong Qu, Wuhan, 430071, China; Affiliated Cancer Hospital & Institute of Guangzhou Medical University, 78 Heng Zhi Gang Road, Guangzhou, 510095, China
| | - Jing Shi
- Xiangyang Center for Disease Control and Prevention, 172 Tan Xi Road, Xiangyang, Hubei, China
| | - Lili Cai
- Wuhan Institute of Virology, Chinese Academy of Sciences, State Key Laboratory of Virology, 44 Xiao Hong Shan Zhong Qu, Wuhan, 430071, China
| | - Minhua Luo
- Wuhan Institute of Virology, Chinese Academy of Sciences, State Key Laboratory of Virology, 44 Xiao Hong Shan Zhong Qu, Wuhan, 430071, China
| | - Boon-Seng Wong
- Health and Social Sciences Cluster, Singapore Institute of Technology, Singapore
| | - Xiaoping Dong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing, 102206, China
| | - Man-Sun Sy
- Department of Pathology, School of Medicine, Case Western Reserve University, 2103 Cornell Road, Cleveland, USA
| | - Chaoyang Li
- Wuhan Institute of Virology, Chinese Academy of Sciences, State Key Laboratory of Virology, 44 Xiao Hong Shan Zhong Qu, Wuhan, 430071, China; Affiliated Cancer Hospital & Institute of Guangzhou Medical University, 78 Heng Zhi Gang Road, Guangzhou, 510095, China.
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Unraveling Prion Protein Interactions with Aptamers and Other PrP-Binding Nucleic Acids. Int J Mol Sci 2017; 18:ijms18051023. [PMID: 28513534 PMCID: PMC5454936 DOI: 10.3390/ijms18051023] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/23/2017] [Accepted: 05/04/2017] [Indexed: 12/13/2022] Open
Abstract
Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative disorders that affect humans and other mammals. The etiologic agents common to these diseases are misfolded conformations of the prion protein (PrP). The molecular mechanisms that trigger the structural conversion of the normal cellular PrP (PrPC) into the pathogenic conformer (PrPSc) are still poorly understood. It is proposed that a molecular cofactor would act as a catalyst, lowering the activation energy of the conversion process, therefore favoring the transition of PrPC to PrPSc. Several in vitro studies have described physical interactions between PrP and different classes of molecules, which might play a role in either PrP physiology or pathology. Among these molecules, nucleic acids (NAs) are highlighted as potential PrP molecular partners. In this context, the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) methodology has proven extremely valuable to investigate PrP–NA interactions, due to its ability to select small nucleic acids, also termed aptamers, that bind PrP with high affinity and specificity. Aptamers are single-stranded DNA or RNA oligonucleotides that can be folded into a wide range of structures (from harpins to G-quadruplexes). They are selected from a nucleic acid pool containing a large number (1014–1016) of random sequences of the same size (~20–100 bases). Aptamers stand out because of their potential ability to bind with different affinities to distinct conformations of the same protein target. Therefore, the identification of high-affinity and selective PrP ligands may aid the development of new therapies and diagnostic tools for TSEs. This review will focus on the selection of aptamers targeted against either full-length or truncated forms of PrP, discussing the implications that result from interactions of PrP with NAs, and their potential advances in the studies of prions. We will also provide a critical evaluation, assuming the advantages and drawbacks of the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technique in the general field of amyloidogenic proteins.
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Chamachi NG, Chakrabarty S. Temperature-Induced Misfolding in Prion Protein: Evidence of Multiple Partially Disordered States Stabilized by Non-Native Hydrogen Bonds. Biochemistry 2017; 56:833-844. [DOI: 10.1021/acs.biochem.6b01042] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Neharika G. Chamachi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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Lee KS, Parquette JR. A self-assembled nanotube for the direct aldol reaction in water. Chem Commun (Camb) 2016; 51:15653-6. [PMID: 26360936 DOI: 10.1039/c5cc06142c] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanotubes formed by the aqueous assembly of a proline-lysine dipeptide (1) were used to create the hydrophobic microenvironments required to catalyze the aldol reaction in water. The self-assembly process occurred most efficiently in the presence of the substrates, producing an array of homogeneous nanotubes under the reaction conditions. The nanotubes formed by dipeptide 1 served as an efficient catalyst for the aldol reaction that functioned at low loading levels and provided good to excellent conversions. The catalytic activity of 1 was minimal under conditions that dissociated the nanotube into soluble monomers.
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Affiliation(s)
- Kwang Soo Lee
- Department of Chemistry and Biochemistry, The Ohio State University, 151 W. Woodruff Ave., Columbus, OH 43210, USA.
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Mammalian prion protein (PrP) forms conformationally different amyloid intracellular aggregates in bacteria. Microb Cell Fact 2015; 14:174. [PMID: 26536866 PMCID: PMC4634817 DOI: 10.1186/s12934-015-0361-y] [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: 07/06/2015] [Accepted: 10/17/2015] [Indexed: 01/21/2023] Open
Abstract
Background An increasing number of proteins are being shown to assemble into amyloid structures that lead to pathological states. Among them, mammalian prions outstand due to their ability to transmit the pathogenic conformation, becoming thus infectious. The structural conversion of the cellular prion protein (PrPC), into its misfolded pathogenic form (PrPSc) is the central event of prion-driven pathologies. The study of the structural properties of intracellular amyloid aggregates in general and of prion-like ones in particular is a challenging task. In this context, the evidence that the inclusion bodies formed by amyloid proteins in bacteria display amyloid-like structural and functional properties make them a privileged system to model intracellular amyloid aggregation. Results Here we provide the first demonstration that recombinant murine PrP and its C-terminal domain (90–231) attain amyloid conformations inside bacteria. Moreover, the inclusions formed by these two PrP proteins display conformational diversity, since they differ in fibril morphology, binding affinity to amyloid dyes, stability, resistance to proteinase K digestion and neurotoxicity. Conclusions Overall, our results suggest that modelling PrP amyloid formation in microbial cell factories might open an avenue for a better understanding of the structural features modulating the pathogenic impact of this intriguing protein. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0361-y) contains supplementary material, which is available to authorized users.
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Martínez J, Sánchez R, Castellanos M, Makarava N, Aguzzi A, Baskakov IV, Gasset M. PrP charge structure encodes interdomain interactions. Sci Rep 2015; 5:13623. [PMID: 26323476 PMCID: PMC4555102 DOI: 10.1038/srep13623] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/31/2015] [Indexed: 11/19/2022] Open
Abstract
Almost all proteins contain charged residues, and their chain distribution is tailored to fulfill essential ionic interactions for folding, binding and catalysis. Among proteins, the hinged two-domain chain of the cellular prion protein (PrPC) exhibits a peculiar charge structure with unclear consequences in its structural malleability. To decipher the charge design role, we generated charge-reverted mutants for each domain and analyzed their effect on conformational and metabolic features. We found that charges contain the information for interdomain interactions. Use of dynamic light scattering and thermal denaturation experiments delineates the compaction of the α-fold by an electrostatic compensation between the polybasic 23–30 region and the α3 electronegative surface. This interaction increases stability and disfavors fibrillation. Independently of this structural effect, the N-terminal electropositive clusters regulate the α-cleavage efficiency. In the fibrillar state, use of circular dichroism, atomic-force and fluorescence microscopies reveal that the N-terminal positive clusters and the α3 electronegative surface dictate the secondary structure, the assembly hierarchy and the growth length of the fibril state. These findings show that the PrP charge structure functions as a code set up to ensure function and reduce pathogenic routes.
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Affiliation(s)
- Javier Martínez
- Instituto Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid 28006, Spain
| | - Rosa Sánchez
- Instituto Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid 28006, Spain
| | - Milagros Castellanos
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain; IMDEA-Nanociencia, Madrid 28049, Spain
| | - Natallia Makarava
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital of Zürich, Zürich 8091, Switzerland
| | - Ilia V Baskakov
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - María Gasset
- Instituto Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid 28006, Spain
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Abstract
Amino acid repeats (AARs) are abundant in protein sequences. They have particular roles in protein function and evolution. Simple repeat patterns generated by DNA slippage tend to introduce length variations and point mutations in repeat regions. Loss of normal and gain of abnormal function owing to their variable length are potential risks leading to diseases. Repeats with complex patterns mostly refer to the functional domain repeats, such as the well-known leucine-rich repeat and WD repeat, which are frequently involved in protein–protein interaction. They are mainly derived from internal gene duplication events and stabilized by ‘gate-keeper’ residues, which play crucial roles in preventing inter-domain aggregation. AARs are widely distributed in different proteomes across a variety of taxonomic ranges, and especially abundant in eukaryotic proteins. However, their specific evolutionary and functional scenarios are still poorly understood. Identifying AARs in protein sequences is the first step for the further investigation of their biological function and evolutionary mechanism. In principle, this is an NP-hard problem, as most of the repeat fragments are shaped by a series of sophisticated evolutionary events and become latent periodical patterns. It is not possible to define a uniform criterion for detecting and verifying various repeat patterns. Instead, different algorithms based on different strategies have been developed to cope with different repeat patterns. In this review, we attempt to describe the amino acid repeat-detection algorithms currently available and compare their strategies based on an in-depth analysis of the biological significance of protein repeats.
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Moulick R, Udgaonkar JB. Thermodynamic characterization of the unfolding of the prion protein. Biophys J 2014; 106:410-20. [PMID: 24461016 DOI: 10.1016/j.bpj.2013.11.4491] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 11/15/2013] [Accepted: 11/27/2013] [Indexed: 12/16/2022] Open
Abstract
The prion protein appears to be unusually susceptible to conformational change, and unlike nearly all other proteins, it can easily be made to convert to alternative misfolded conformations. To understand the basis of this structural plasticity, a detailed thermodynamic characterization of two variants of the mouse prion protein (moPrP), the full-length moPrP (23-231) and the structured C-terminal domain, moPrP (121-231), has been carried out. All thermodynamic parameters governing unfolding, including the changes in enthalpy, entropy, free energy, and heat capacity, were found to be identical for the two protein variants. The N-terminal domain remains unstructured and does not interact with the C-terminal domain in the full-length protein at pH 4. Moreover, the enthalpy and entropy of unfolding of moPrP (121-231) are similar in magnitude to values reported for other proteins of similar size. However, the protein has an unusually high native-state heat capacity, and consequently, the change in heat capacity upon unfolding is much lower than that expected for a protein of similar size. It appears, therefore, that the native state of the prion protein undergoes substantial fluctuations in enthalpy and hence, in structure.
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Affiliation(s)
- Roumita Moulick
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
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Silva JL, Oliveira AC, Vieira TCRG, de Oliveira GAP, Suarez MC, Foguel D. High-Pressure Chemical Biology and Biotechnology. Chem Rev 2014; 114:7239-67. [DOI: 10.1021/cr400204z] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jerson L. Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Andrea C. Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Tuane C. R. G. Vieira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Guilherme A. P. de Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Marisa C. Suarez
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Debora Foguel
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
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Kuczius T, Kelsch R. Effects of metal binding on solubility and resistance of physiological prions depend on tissues and glycotypes. J Cell Biochem 2014; 114:2690-8. [PMID: 23794222 DOI: 10.1002/jcb.24616] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 06/14/2013] [Indexed: 12/13/2022]
Abstract
Prion diseases entail the conversion of a normal host-encoded prion protein (PrP(C)) into an infectious isoform (PrP(Sc)). Various PrP(C) types differing in banding profiles and detergent solubility are present in different tissues, but only few PrP(Sc) types have been generated although PrP(C) acts as substrate. We hypothesize that distinct PrP(C) subtypes may be converted more efficiently to PrP(Sc) than others. One prerequisite for the analysis is the identification of the PrP(C) subtypes present in the protein complexes. Metal binding to PrP(C) is one of the most prominent features of the protein which induces increased proteolysis resistance and structural changes which might play an important role in the conversion process. Here we analyzed the metal-induced structural PrP(C) transformation of two different Triton X-100 soluble PrP(C) types derived from human platelets and brains by changes in protein solubility. We found that zinc and copper rendered approximately half of total PrP(C) and mainly un- and low-glycosylated PrP(C) to the Triton insoluble fraction. Our results indicate the presence of at least two distinct PrP(C) subtypes by metal interactions. The differentiation of high and low soluble metal bound PrP(C) offers precious information about PrP(C) protein composition and provides approaches for analyzing the transformation efficiency to PrP(Sc).
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Affiliation(s)
- Thorsten Kuczius
- Institute for Hygiene, Westfälische Wilhelms-Universität and University Hospital Münster, Robert Koch-Strasse 41, 48149, Münster, Germany
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Malavasi N, Cordeiro Y, Rodrigues D, Chura-Chambi R, Lemke L, Morganti L. The effect of temperature on protein refolding at high pressure: Enhanced green fluorescent protein as a model. Process Biochem 2014. [DOI: 10.1016/j.procbio.2013.09.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Pressure–temperature folding landscape in proteins involved in neurodegenerative diseases and cancer. Biophys Chem 2013; 183:9-18. [DOI: 10.1016/j.bpc.2013.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 06/03/2013] [Accepted: 06/03/2013] [Indexed: 01/02/2023]
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Laferrière F, Tixador P, Moudjou M, Chapuis J, Sibille P, Herzog L, Reine F, Jaumain E, Laude H, Rezaei H, Béringue V. Quaternary structure of pathological prion protein as a determining factor of strain-specific prion replication dynamics. PLoS Pathog 2013; 9:e1003702. [PMID: 24130496 PMCID: PMC3795044 DOI: 10.1371/journal.ppat.1003702] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 08/27/2013] [Indexed: 11/18/2022] Open
Abstract
Prions are proteinaceous infectious agents responsible for fatal neurodegenerative diseases in animals and humans. They are essentially composed of PrP(Sc), an aggregated, misfolded conformer of the ubiquitously expressed host-encoded prion protein (PrP(C)). Stable variations in PrP(Sc) conformation are assumed to encode the phenotypically tangible prion strains diversity. However the direct contribution of PrP(Sc) quaternary structure to the strain biological information remains mostly unknown. Applying a sedimentation velocity fractionation technique to a panel of ovine prion strains, classified as fast and slow according to their incubation time in ovine PrP transgenic mice, has previously led to the observation that the relationship between prion infectivity and PrP(Sc) quaternary structure was not univocal. For the fast strains specifically, infectivity sedimented slowly and segregated from the bulk of proteinase-K resistant PrP(Sc). To carefully separate the respective contributions of size and density to this hydrodynamic behavior, we performed sedimentation at the equilibrium and varied the solubilization conditions. The density profile of prion infectivity and proteinase-K resistant PrP(Sc) tended to overlap whatever the strain, fast or slow, leaving only size as the main responsible factor for the specific velocity properties of the fast strain most infectious component. We further show that this velocity-isolable population of discrete assemblies perfectly resists limited proteolysis and that its templating activity, as assessed by protein misfolding cyclic amplification outcompetes by several orders of magnitude that of the bulk of larger size PrP(Sc) aggregates. Together, the tight correlation between small size, conversion efficiency and duration of disease establishes PrP(Sc) quaternary structure as a determining factor of prion replication dynamics. For certain strains, a subset of PrP assemblies appears to be the best template for prion replication. This has important implications for fundamental studies on prions.
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Affiliation(s)
- Florent Laferrière
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Philippe Tixador
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Mohammed Moudjou
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Jérôme Chapuis
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Pierre Sibille
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Laetitia Herzog
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Fabienne Reine
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Emilie Jaumain
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Hubert Laude
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Human Rezaei
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Vincent Béringue
- INRA (Institut National de la Recherche Agronomique), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
- * E-mail:
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17
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Li H, Ye S, Wei F, Ma S, Luo Y. In situ molecular-level insights into the interfacial structure changes of membrane-associated prion protein fragment [118-135] investigated by sum frequency generation vibrational spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:16979-16988. [PMID: 23116165 DOI: 10.1021/la302655p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Protein aggregation is associated with many "protein deposition diseases". A precise molecular detail of the conformational transitions of such a membrane-associated protein structure is critical to understand the disease mechanism and develop effective treatments. One potential model peptide for studying the mechanism of protein deposition diseases is prion protein fragment [118-135] (PrP118-135), which shares homology with the C-terminal domain of the Alzheimer's β-amyloid peptide. In this study, sum frequency generation vibrational spectroscopy (SFG-VS) has been applied to characterize interactions between PrP118-135 and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) lipid bilayer in situ. The conformation change and orientation of PrP118-135 in lipid bilayers have been determined using SFG spectra with different polarization combinations. It is found that low-concentration PrP118-135 predominantly adopts α-helical structure but with tiny β-sheet structure. With the PrP118-135 concentration increasing, the molecular number ratio of parallel β-sheet structure increases and reaches about 44% at a concentration of 0.10 mg/mL, indicating the formation of abnormally folded scrapie isoforms. The α-helical structure inserts into the lipid bilayer with a tilt angle of ~32° versus the surface normal, while the β-sheet structure lies down on the lipid bilayer with the tilt and twist angle both of 90°. The 3300 cm(-1) N-H stretching signal in psp spectra arises from α-helical structure at low PrP concentration and from the β-sheet structure at high PrP concentration. Results from this study will provide an in-depth insight into the early events in the aggregation of PrP in cell membrane.
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Affiliation(s)
- Hongchun Li
- Hefei National Laboratory for Physical Sciences at Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, People's Republic of China 230026
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18
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Abstract
The cellular prion protein (PrPC) is subjected to various processing under physiological and pathological conditions, of which the α-cleavage within the central hydrophobic domain not only disrupts a region critical for both PrP toxicity and PrPC to PrPSc conversion but also produces the N1 fragment that is neuroprotective and the C1 fragment that enhances the pro-apoptotic effect of staurosporine in one report and inhibits prion in another. The proteases responsible for the α-cleavage of PrPC are controversial. The effect of ADAM10, ADAM17, and ADAM9 on N1 secretion clearly indicates their involvement in the α-cleavage of PrPC, but there has been no report of direct PrPC α-cleavage activity with any of the three ADAMs in a purified protein form. We demonstrated that, in muscle cells, ADAM8 is the primary protease for the α-cleavage of PrPC, but another unidentified protease(s) must also play a minor role. We also found that PrPC regulates ADAM8 expression, suggesting that a close examination on the relationships between PrPC and its processing enzymes may reveal novel roles and underlying mechanisms for PrPC in non-prion diseases such as asthma and cancer.
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Affiliation(s)
- Jingjing Liang
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
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19
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Antony H, Wiegmans AP, Wei MQ, Chernoff YO, Khanna KK, Munn AL. Potential roles for prions and protein-only inheritance in cancer. Cancer Metastasis Rev 2012; 31:1-19. [PMID: 22138778 DOI: 10.1007/s10555-011-9325-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inherited mutations are known to cause familial cancers. However, the cause of sporadic cancers, which likely represent the majority of cancers, is yet to be elucidated. Sporadic cancers contain somatic mutations (including oncogenic mutations); however, the origin of these mutations is unclear. An intriguing possibility is that a stable alteration occurs in somatic cells prior to oncogenic mutations and promotes the subsequent accumulation of oncogenic mutations. This review explores the possible role of prions and protein-only inheritance in cancer. Genetic studies using lower eukaryotes, primarily yeast, have identified a large number of proteins as prions that confer dominant phenotypes with cytoplasmic (non-Mendelian) inheritance. Many of these have mammalian functional homologs. The human prion protein (PrP) is known to cause neurodegenerative diseases and has now been found to be upregulated in multiple cancers. PrP expression in cancer cells contributes to cancer progression and resistance to various cancer therapies. Epigenetic changes in the gene expression and hyperactivation of MAP kinase signaling, processes that in lower eukaryotes are affected by prions, play important roles in oncogenesis in humans. Prion phenomena in yeast appear to be influenced by stresses, and there is considerable evidence of the association of some amyloids with biologically positive functions. This suggests that if protein-only somatic inheritance exists in mammalian cells, it might contribute to cancer phenotypes. Here, we highlight evidence in the literature for an involvement of prion or prion-like mechanisms in cancer and how they may in the future be viewed as diagnostic markers and potential therapeutic targets.
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Affiliation(s)
- H Antony
- Griffith Health Institute, Griffith University, Southport, Queensland, Australia.
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20
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Macedo B, Millen TA, Braga CACA, Gomes MPB, Ferreira PS, Kraineva J, Winter R, Silva JL, Cordeiro Y. Nonspecific Prion Protein–Nucleic Acid Interactions Lead to Different Aggregates and Cytotoxic Species. Biochemistry 2012; 51:5402-13. [DOI: 10.1021/bi300440e] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruno Macedo
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, RJ 21941-590,
Rio de Janeiro, Brazil
| | - Thiago A. Millen
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Carolina A. C. A. Braga
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Mariana P. B. Gomes
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, RJ 21941-590,
Rio de Janeiro, Brazil
| | - Priscila S. Ferreira
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Julia Kraineva
- Faculty of Chemistry,
Physical
Chemistry I, Dortmund University, Dortmund,
Germany
| | - Roland Winter
- Faculty of Chemistry,
Physical
Chemistry I, Dortmund University, Dortmund,
Germany
| | - Jerson L. Silva
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Yraima Cordeiro
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, RJ 21941-590,
Rio de Janeiro, Brazil
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21
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Ano Bom APD, Rangel LP, Costa DCF, de Oliveira GAP, Sanches D, Braga CA, Gava LM, Ramos CHI, Cepeda AOT, Stumbo AC, De Moura Gallo CV, Cordeiro Y, Silva JL. Mutant p53 aggregates into prion-like amyloid oligomers and fibrils: implications for cancer. J Biol Chem 2012; 287:28152-62. [PMID: 22715097 PMCID: PMC3431633 DOI: 10.1074/jbc.m112.340638] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Over 50% of all human cancers lose p53 function. To evaluate the role of aggregation in cancer, we asked whether wild-type (WT) p53 and the hot-spot mutant R248Q could aggregate as amyloids under physiological conditions and whether the mutant could seed aggregation of the wild-type form. The central domains (p53C) of both constructs aggregated into a mixture of oligomers and fibrils. R248Q had a greater tendency to aggregate than WT p53. Full-length p53 aggregated into amyloid-like species that bound thioflavin T. The amyloid nature of the aggregates was demonstrated using x-ray diffraction, electron microscopy, FTIR, dynamic light scattering, cell viabilility assay, and anti-amyloid immunoassay. The x-ray diffraction pattern of the fibrillar aggregates was consistent with the typical conformation of cross β-sheet amyloid fibers with reflexions of 4.7 Å and 10 Å. A seed of R248Q p53C amyloid oligomers and fibrils accelerated the aggregation of WT p53C, a behavior typical of a prion. The R248Q mutant co-localized with amyloid-like species in a breast cancer sample, which further supported its prion-like effect. A tumor cell line containing mutant p53 also revealed massive aggregation of p53 in the nucleus. We conclude that aggregation of p53 into a mixture of oligomers and fibrils sequestrates the native protein into an inactive conformation that is typical of a prionoid. This prion-like behavior of oncogenic p53 mutants provides an explanation for the negative dominance effect and may serve as a potential target for cancer therapy.
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Affiliation(s)
- Ana P D Ano Bom
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
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22
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Seeliger J, Weise K, Opitz N, Winter R. The effect of Aβ on IAPP aggregation in the presence of an isolated β-cell membrane. J Mol Biol 2012; 421:348-63. [PMID: 22321797 DOI: 10.1016/j.jmb.2012.01.048] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 01/10/2012] [Accepted: 01/26/2012] [Indexed: 01/21/2023]
Abstract
Fibrillar aggregates of the islet amyloid polypeptide (IAPP) and amyloid-β (Aβ) are known to deposit at pancreatic β-cells and neuronal cells and are associated with the cell degenerative diseases type-2 diabetes mellitus (T2DM) and Alzheimer's disease (AD), respectively. Since IAPP is secreted by β-cells and a membrane-damaging effect of IAPP has been discussed as a reason for β-cell dysfunction and the development of T2DM, studies of the interaction of IAPP with the β-cell membrane are of high relevance for gaining a molecular-level understanding of the underlying mechanism. Recently, it has also been shown that patients suffering from T2DM exhibit an increased risk to develop AD and vice versa, and a molecular link between AD and T2DM has been suggested. In this study, membrane lipids from the rat insulinoma-derived INS-1E β-cell line were isolated, and their interaction with the amyloidogenic peptides IAPP and Aβ and a mixture of both peptides has been studied. To yield insight into the associated peptides' conformational changes and their effect on the membrane integrity during aggregation, we have carried out attenuated total reflection Fourier transform infrared spectroscopy, fluorescence microscopy, and atomic force microscopy experiments. The IAPP-Aβ heterocomplexes formed were shown to adsorb, aggregate, and permeabilize the isolated β-cell membrane significantly slower than pure IAPP, however, at a rate that is much faster than that of pure Aβ. In addition, it could be shown that isolated β-cell membranes cause similar effects on the kinetics of IAPP and IAPP-Aβ fibril formation as anionic heterogeneous model membranes.
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Affiliation(s)
- Janine Seeliger
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry, TU Dortmund University, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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23
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Liu C, Zhang Y. Nucleic acid-mediated protein aggregation and assembly. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2011; 84:1-40. [DOI: 10.1016/b978-0-12-386483-3.00005-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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24
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Silva JL, Vieira TCRG, Gomes MPB, Rangel LP, Scapin SMN, Cordeiro Y. Experimental approaches to the interaction of the prion protein with nucleic acids and glycosaminoglycans: Modulators of the pathogenic conversion. Methods 2010; 53:306-17. [PMID: 21145399 DOI: 10.1016/j.ymeth.2010.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 12/02/2010] [Indexed: 11/17/2022] Open
Abstract
The concept that transmissible spongiform encephalopathies (TSEs) are caused only by proteins has changed the traditional paradigm that disease transmission is due solely to an agent that carries genetic information. The central hypothesis for prion diseases proposes that the conversion of a cellular prion protein (PrP(C)) into a misfolded, β-sheet-rich isoform (PrP(Sc)) accounts for the development of (TSE). There is substantial evidence that the infectious material consists chiefly of a protein, PrP(Sc), with no genomic coding material, unlike a virus particle, which has both. However, prions seem to have other partners that chaperone their activities in converting the PrP(C) into the disease-causing isoform. Nucleic acids (NAs) and glycosaminoglycans (GAGs) are the most probable accomplices of prion conversion. Here, we review the recent experimental approaches that have been employed to characterize the interaction of prion proteins with nucleic acids and glycosaminoglycans. A PrP recognizes many nucleic acids and GAGs with high affinities, and this seems to be related to a pathophysiological role for this interaction. A PrP binds nucleic acids and GAGs with structural selectivity, and some PrP:NA complexes can become proteinase K-resistant, undergoing amyloid oligomerization and conversion to a β-sheet-rich structure. These results are consistent with the hypothesis that endogenous polyanions (such as NAs and GAGs) may accelerate the rate of prion disease progression by acting as scaffolds or lattices that mediate the interaction between PrP(C) and PrP(Sc) molecules. In addition to a still-possible hypothesis that nucleic acids and GAGs, especially those from the host, may modulate the conversion, the recent structural characterization of the complexes has raised the possibility of developing new diagnostic and therapeutic strategies.
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Affiliation(s)
- Jerson L Silva
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil.
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25
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Silva JL, Vieira TCRG, Gomes MPB, Bom APA, Lima LMTR, Freitas MS, Ishimaru D, Cordeiro Y, Foguel D. Ligand binding and hydration in protein misfolding: insights from studies of prion and p53 tumor suppressor proteins. Acc Chem Res 2010; 43:271-9. [PMID: 19817406 PMCID: PMC2825094 DOI: 10.1021/ar900179t] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Protein misfolding has been implicated in a large number of diseases termed protein- folding disorders (PFDs), which include Alzheimer's disease, Parkinson's disease, transmissible spongiform encephalopathies, familial amyloid polyneuropathy, Huntington's disease, and type II diabetes. In these diseases, large quantities of incorrectly folded proteins undergo aggregation, destroying brain cells and other tissues. The interplay between ligand binding and hydration is an important component of the formation of misfolded protein species. Hydration drives various biological processes, including protein folding, ligand binding, macromolecular assembly, enzyme kinetics, and signal transduction. The changes in hydration and packing, both when proteins fold correctly or when folding goes wrong, leading to PFDs, are examined through several biochemical, biophysical, and structural approaches. Although in many cases the binding of a ligand such as a nucleic acid helps to prevent misfolding and aggregation, there are several examples in which ligands induce misfolding and assembly into amyloids. This occurs simply because the formation of structured aggregates (such as protofibrillar and fibrillar amyloids) involves decreases in hydration, formation of a hydrogen-bond network in the secondary structure, and burying of nonpolar amino acid residues, processes that also occur in the normal folding landscape. In this Account, we describe the present knowledge of the folding and misfolding of different proteins, with a detailed emphasis on mammalian prion protein (PrP) and tumoral suppressor protein p53; we also explore how ligand binding and hydration together influence the fate of the proteins. Anfinsen's paradigm that the structure of a protein is determined by its amino acid sequence is to some extent contradicted by the observation that there are two isoforms of the prion protein with the same sequence: the cellular and the misfolded isoform. The cellular isoform of PrP has a disordered N-terminal domain and a highly flexible, not-well-packed C-terminal domain, which might account for its significant hydration. When PrP binds to biological molecules, such as glycosaminoglycans and nucleic acids, the disordered segments appear to fold and become less hydrated. Formation of the PrP-nucleic acid complex seems to accelerate the conversion of the cellular form of the protein into the disease-causing isoform. For p53, binding to some ligands, including nucleic acids, would prevent misfolding of the protein. Recently, several groups have begun to analyze the folding-misfolding of the individual domains of p53, but several questions remain unanswered. We discuss the implications of these findings for understanding the productive and incorrect folding pathways of these proteins in normal physiological states and in human disease, such as prion disorders and cancer. These studies are shown to lay the groundwork for the development of new drugs.
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Affiliation(s)
- Jerson L. Silva
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem
| | - Tuane C. R. G. Vieira
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem
| | - Mariana P. B. Gomes
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem
| | - Ana Paula Ano Bom
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem
| | | | - Monica S. Freitas
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem
| | - Daniella Ishimaru
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem
| | | | - Debora Foguel
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem
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26
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Shao H, Parquette JR. A π-conjugated hydrogel based on an Fmoc-dipeptide naphthalene diimide semiconductor. Chem Commun (Camb) 2010; 46:4285-7. [DOI: 10.1039/c0cc00701c] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Taubner LM, Bienkiewicz EA, Copié V, Caughey B. Structure of the flexible amino-terminal domain of prion protein bound to a sulfated glycan. J Mol Biol 2009; 395:475-90. [PMID: 19913031 DOI: 10.1016/j.jmb.2009.10.075] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 09/24/2009] [Accepted: 10/28/2009] [Indexed: 11/29/2022]
Abstract
The intrinsically disordered amino-proximal domain of hamster prion protein (PrP) contains four copies of a highly conserved octapeptide sequence, PHGGGWGQ, that is flanked by two polycationic residue clusters. This N-terminal domain mediates the binding of sulfated glycans, which can profoundly influence the conversion of PrP to pathological forms and the progression of prion disease. To investigate the structural consequences of sulfated glycan binding, we performed multidimensional heteronuclear ((1)H, (13)C, (15)N) NMR (nuclear magnetic resonance), circular dichroism (CD), and fluorescence studies on hamster PrP residues 23-106 (PrP 23-106) and fragments thereof when bound to pentosan polysulfate (PPS). While the majority of PrP 23-106 remain disordered upon PPS binding, the octarepeat region adopts a repeating loop-turn structure that we have determined by NMR. The beta-like turns within the repeats are corroborated by CD data demonstrating that these turns are also present, although less pronounced, without PPS. Binding to PPS exposes a hydrophobic surface composed of aligned tryptophan side chains, the spacing and orientation of which are consistent with a self-association or ligand binding site. The unique tryptophan motif was probed by intrinsic tryptophan fluorescence, which displayed enhanced fluorescence of PrP 23-106 when bound to PPS, consistent with the alignment of tryptophan side chains. Chemical-shift mapping identified binding sites on PrP 23-106 for PPS, which include the octarepeat histidine and an N-terminal basic cluster previously linked to sulfated glycan binding. These data may in part explain how sulfated glycans modulate PrP conformational conversions and oligomerizations.
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Affiliation(s)
- Lara M Taubner
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA.
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28
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Shao H, Nguyen T, Romano NC, Modarelli DA, Parquette JR. Self-Assembly of 1-D n-Type Nanostructures Based on Naphthalene Diimide-Appended Dipeptides. J Am Chem Soc 2009; 131:16374-6. [DOI: 10.1021/ja906377q] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hui Shao
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, and Department of Chemistry and The Center for Laser and Optical Spectroscopy, Knight Chemical Laboratory, The University of Akron, Akron, Ohio 44325-3601
| | - Tuan Nguyen
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, and Department of Chemistry and The Center for Laser and Optical Spectroscopy, Knight Chemical Laboratory, The University of Akron, Akron, Ohio 44325-3601
| | - Natalie C. Romano
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, and Department of Chemistry and The Center for Laser and Optical Spectroscopy, Knight Chemical Laboratory, The University of Akron, Akron, Ohio 44325-3601
| | - David A. Modarelli
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, and Department of Chemistry and The Center for Laser and Optical Spectroscopy, Knight Chemical Laboratory, The University of Akron, Akron, Ohio 44325-3601
| | - Jon R. Parquette
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, and Department of Chemistry and The Center for Laser and Optical Spectroscopy, Knight Chemical Laboratory, The University of Akron, Akron, Ohio 44325-3601
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29
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Characterization of ordered aggregates of cerato-platanin and their involvement in fungus–host interactions. Biochim Biophys Acta Gen Subj 2009; 1790:1334-44. [DOI: 10.1016/j.bbagen.2009.07.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 06/25/2009] [Accepted: 07/10/2009] [Indexed: 11/19/2022]
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30
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Roostaee A, Côté S, Roucou X. Aggregation and amyloid fibril formation induced by chemical dimerization of recombinant prion protein in physiological-like conditions. J Biol Chem 2009; 284:30907-16. [PMID: 19710507 DOI: 10.1074/jbc.m109.057950] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prion diseases are caused by the conversion of a cellular protein (PrP(C)) into a misfolded, aggregated isoform (PrP(Res)). Misfolding of recombinant PrP(C) in the absence of PrP(Res) template, cellular factors, denaturing agents, or at neutral pH has not been achieved. A number of studies indicate that dimerization of PrP(C) may be a key step in the aggregation process. In an effort to understand the molecular event that may activate misfolding of PrP(C) in more relevant physiological conditions, we tested if enforced dimerization of PrP(C) may induce a conformational change reminiscent of the conversion of PrP(C) to PrP(Res). We used a well described inducible dimerization strategy whereby a chimeric PrP(C) composed of a modified FK506-binding protein (Fv) fused with PrP(C) and termed Fv-PrP is incubated in the presence of a monomeric FK506 or dimerizing AP20187 ligand. Addition of AP20187 but not FK506 to recombinant Fv-PrP (rFv-PrP) in physiological-like conditions resulted in a rapid conformational change characterized by an increase in beta-sheet structure and simultaneous aggregation of the protein. Aggregates were partially resistant to proteinase K and induced the conversion of soluble rFv-PrP in serial seeding experiments. As judged from thioflavin T binding and electron microscopy, aggregates converted to amyloid fibers. Aggregates were toxic to cultured cells, whereas soluble rFv-PrP and amyloid fibers were harmless. This study strongly supports the proposition that dimerization of PrP(C) is a key pathological primary event in the conversion of PrP(C) and may initiate the pathogenesis of prion diseases.
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Affiliation(s)
- Alireza Roostaee
- Department of Biochemistry, Faculty of Medicine, University of Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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31
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Jenkins DC, Pearson DS, Harvey A, Sylvester ID, Geeves MA, Pinheiro TJT. Rapid folding of the prion protein captured by pressure-jump. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2009; 38:625-635. [PMID: 19255752 PMCID: PMC4509520 DOI: 10.1007/s00249-009-0420-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 01/16/2009] [Accepted: 01/29/2009] [Indexed: 12/23/2022]
Abstract
The conversion of the cellular form of the prion protein (PrP(C)) to an altered disease state, generally denoted as scrapie isoform (PrP(Sc)), appears to be a crucial molecular event in prion diseases. The details of this conformational transition are not fully understood, but it is perceived that they are associated with misfolding of PrP or its incapacity to maintain the native fold during its cell cycle. Here we present a tryptophan mutant of PrP (F198W), which has enhanced fluorescence sensitivity to unfolding/refolding transitions. Equilibrium folding was studied by circular dichroism and fluorescence. Pressure-jump experiments were successfully applied to reveal rapid submillisecond folding events of PrP at temperatures not accessed before.
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Affiliation(s)
- David C Jenkins
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - David S Pearson
- Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Andrew Harvey
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Ian D Sylvester
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Michael A Geeves
- Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Teresa J T Pinheiro
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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32
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Cold destabilization and temperature jump of the murine prion protein mPrP(23–231). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:669-73. [DOI: 10.1016/j.bbapap.2009.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 01/14/2009] [Accepted: 01/15/2009] [Indexed: 11/23/2022]
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33
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Palladino P, Ronga L, Benedetti E, Rossi F, Ragone R. Peptide Fragment Approach to Prion Misfolding: The Alpha-2 Domain. Int J Pept Res Ther 2009. [DOI: 10.1007/s10989-009-9171-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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34
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Silva JL, Foguel D. Hydration, cavities and volume in protein folding, aggregation and amyloid assembly. Phys Biol 2009; 6:015002. [DOI: 10.1088/1478-3975/6/1/015002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Can copper binding to the prion protein generate a misfolded form of the protein? Biometals 2009; 22:159-75. [PMID: 19140013 DOI: 10.1007/s10534-008-9196-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 12/07/2008] [Indexed: 10/21/2022]
Abstract
The native prion protein (PrP) has a two domain structure, with a globular folded alpha-helical C-terminal domain and a flexible extended N-terminal region. The latter can selectively bind Cu(2+) via four His residues in the octarepeat (OR) region, as well as two sites (His96 and His111) outside this region. In the disease state, the folded C-terminal domain of PrP undergoes a conformational change, forming amorphous aggregates high in beta-sheet content. Cu(2+) bound to the ORs can be redox active and has been shown to induce cleavage within the OR region, a process requiring conserved Trp residues. Using computational modeling, we have observed that electron transfer from Trp residues to copper can be favorable. These models also reveal that an indole-based radical cation or Cu(+) can initiate reactions leading to protein backbone cleavage. We have also demonstrated, by molecular dynamics simulations, that Cu(2+) binding to the His96 and His111 residues in the remaining PrP N-terminal fragment can induce localized beta-sheet structure, allowing us to suggest a potential mechanism for the initiation of beta-sheet misfolding in the C-terminal domain by Cu(2+).
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36
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Pushie MJ, Vogel HJ. A potential mechanism for Cu2+ reduction, beta-cleavage, and beta-sheet initiation within the N-terminal domain of the prion protein: insights from density functional theory and molecular dynamics calculations. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2009; 72:1040-1059. [PMID: 19697239 DOI: 10.1080/15287390903084389] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The N-terminal region of the native human prion protein encompasses four highly conserved octarepeats that each contain a single His, Pro, Gln, and Trp residue as well as several Gly residues. At neutral pH these repeats are capable of individually binding copper (Cu(2+)) ions, involving the His side chain and the backbone amide of the Gly residues. In addition, the two His residues at positions 96 and 111 are also capable of binding Cu(2+). At low concentrations of the metal ion or at low pH, one Cu(2+) may be bound by multiple His residues of the four octarepeats. This complex is known to be redox active, while none of the other Cu(2+)-bound complexes are. Using density functional theory and molecular dynamics calculations data demonstrated how this form of the protein could reduce Cu(2+), through a process involving electron transfer from the Trp side chain. The reduced Cu gives rise to reactive oxygen species (ROS), which can lead to beta-cleavage of the prion protein chain at any of the Gly residues around position 90. Protein fragments of lengths similar to those arising from beta-cleavage are predominantly found in both healthy and Creutzfeldt-Jakob disease (CJD)-affected brains. Models of Cu binding to the His96 and His111 residues also indicate that different modes of Cu(2+) binding result in formation of stable beta-hairpin structures in this region of the protein. It is postulated that through interactions with the C-terminal part of the protein these hairpins may initiate misfolding and yield more stable beta-sheet structures that might associate in the same fashion with additional prion proteins.
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Affiliation(s)
- M Jake Pushie
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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37
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Chang B, Miller MW, Bulgin MS, Sorenson-Melson S, Balachandran A, Chiu A, Rubenstein R. PrP antibody binding-induced epitope modulation evokes immunocooperativity. J Neuroimmunol 2008; 205:94-100. [PMID: 18977037 DOI: 10.1016/j.jneuroim.2008.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 09/17/2008] [Accepted: 09/17/2008] [Indexed: 11/28/2022]
Abstract
We have characterized the antibody-antigen binding events of the prion protein (PrP) utilizing three new PrP-specific monoclonal antibodies (Mabs). The degree of immunoreactivity was dependent on the denaturation treatment with the combination of heat and SDS resulting in the highest levels of epitope accessibility and antibody binding. Interestingly however, this harsh denaturation treatment was not sufficient to completely and irreversibly abolish protein conformation. The Mabs differed in their PrP epitopes with Mab 08-1/11F12 binding in the region of PrP(93-122), Mab 08-1/8E9 reacting to PrP(155-200) and Mab 08-1/5D6 directed to an undefined conformational epitope. Using normal and infected brains from hamsters, sheep and deer, we demonstrate that the binding of PrP to one Mab triggers PrP epitope unmasking, which enhances the binding of a second Mab. This phenomenon, termed positive immunocooperativity, is specific regarding epitope and the sequence of binding events. Positive immunocooperativity will likely increase immunoassay sensitivity since assay conditions for PrP(Sc) detection does not require protease digestion.
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Affiliation(s)
- Binggong Chang
- Department of Biochemistry, SUNY Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY 11203, USA
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38
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Jain S, Udgaonkar JB. Evidence for Stepwise Formation of Amyloid Fibrils by the Mouse Prion Protein. J Mol Biol 2008; 382:1228-41. [DOI: 10.1016/j.jmb.2008.07.052] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 06/28/2008] [Accepted: 07/21/2008] [Indexed: 11/16/2022]
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39
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Mor A, Ziv G, Levy Y. Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats. J Comput Chem 2008; 29:1992-8. [PMID: 18366022 DOI: 10.1002/jcc.20951] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Proteins with a long flexible polymeric tail attached at their N- or C-terminus are studied using molecular dynamics (MD) simulations of a coarse-grained model for protein folding where the temperature is regulated by either the Berendsen or the Langevin thermostat. These thermostats show different abilities to regulate the temperature of these systems that include flexible and more rigid regions. In the simulations with the Berendsen thermostat, the flexible tail is significantly hotter than the protein, both in its folded and unfolded states. Upon weakening the strength of the Berendsen thermostat, the temperature gradient between the fast and the slow degrees of freedom is significantly decreased, yet linkage between the temperatures of the flexible tail and the protein remains. The Langevin thermostat is proven to regulate the temperature of these inhomogenous systems reliably, without discriminating between the slow and fast degrees of freedom. The Langevin thermostat is less sensitive than is the Berendsen thermostat to the strength of the coupling between the protein system and the thermal bath. Our study calls for special care in choosing the thermostat for MD simulations of systems with inhomogenous degrees of freedom. Using the Berendsen thermostat with strong coupling would result in mistaken thermodynamic descriptions of such systems.
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Affiliation(s)
- Amit Mor
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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40
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Gomes MPB, Millen TA, Ferreira PS, e Silva NLC, Vieira TCRG, Almeida MS, Silva JL, Cordeiro Y. Prion protein complexed to N2a cellular RNAs through its N-terminal domain forms aggregates and is toxic to murine neuroblastoma cells. J Biol Chem 2008; 283:19616-25. [PMID: 18456654 PMCID: PMC2443653 DOI: 10.1074/jbc.m802102200] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Conversion of the cellular prion protein (PrPC) into its altered conformation, PrPSc, is believed to be the major cause of prion diseases. Although PrP is the only identified agent for these diseases, there is increasing evidence that other molecules can modulate the conversion. We have found that interaction of PrP with double-stranded DNA leads to a protein with higher β-sheet content and characteristics similar to those of PrPSc. RNA molecules can also interact with PrP and potentially modulate PrPC to PrPSc conversion or even bind differentially to both PrP isoforms. Here, we investigated the interaction of recombinant murine PrP with synthetic RNA sequences and with total RNA extracted from cultured neuroblastoma cells (N2aRNA). We found that PrP interacts with N2aRNA with nanomolar affinity, aggregates upon this interaction, and forms species partially resistant to proteolysis. RNA does not bind to N-terminal deletion mutants of PrP, indicating that the N-terminal region is important for this process. Cell viability assays showed that only the N2aRNA extract induces PrP-RNA aggregates that can alter the homeostasis of cultured cells. Small RNAs bound to PrP give rise to nontoxic small oligomers. Nuclear magnetic resonance measurements of the PrP-RNA complex revealed structural changes in PrP, but most of its native fold is maintained. These results indicate that there is selectivity in the species generated by interaction with different molecules of RNA. The catalytic effect of RNA on the PrPC→PrPSc conversion depends on the RNA sequence, and small RNA molecules may exert a protective effect.
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Affiliation(s)
- Mariana P B Gomes
- Programa de Biologia Estrutural, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, 21491-590 Rio de Janeiro, Brazil
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41
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Gomes MPB, Cordeiro Y, Silva JL. The peculiar interaction between mammalian prion protein and RNA. Prion 2008; 2:64-6. [PMID: 19098437 DOI: 10.4161/pri.2.2.6988] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In the past decade, the interaction between prions and nucleic acids has garnered significant attention from the scientific community. for many years, the participation of RNA and/or DNA in prion pathology has been largely ruled out by the "protein-only" hypothesis, but this is now being reconsidered. Experimental data now indicate that nucleic acids (particularly RNA), besides being carriers of genetic information, function as important key components during development, physiological responsiveness and cellular signaling. This revelation has brought a new perspective to prion pathology. Here we discuss the role of RNA molecules in prion protein aggregation and the resulting cellular toxicity. We combine our most recent findings with existing literature to shed new light on this exciting field of research.
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Affiliation(s)
- Mariana P B Gomes
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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42
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El Moustaine D, Perrier V, Smeller L, Lange R, Torrent J. Full-length prion protein aggregates to amyloid fibrils and spherical particles by distinct pathways. FEBS J 2008; 275:2021-31. [DOI: 10.1111/j.1742-4658.2008.06356.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Intriguing nucleic-acid-binding features of mammalian prion protein. Trends Biochem Sci 2008; 33:132-40. [DOI: 10.1016/j.tibs.2007.11.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Revised: 11/14/2007] [Accepted: 11/26/2007] [Indexed: 11/19/2022]
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44
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Smeller L, Meersman F, Heremans K. Stable misfolded states of human serum albumin revealed by high-pressure infrared spectroscopic studies. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:1127-32. [DOI: 10.1007/s00249-008-0277-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 01/17/2008] [Accepted: 01/22/2008] [Indexed: 10/22/2022]
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45
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Dumestre-Pérard C, Osmundson J, Lemaire-Vieille C, Thielens N, Grives A, Favier B, Csopaki F, Jamin M, Gagnon J, Cesbron JY. Activation of classical pathway of complement cascade by soluble oligomers of prion. Cell Microbiol 2008; 9:2870-9. [PMID: 17991046 DOI: 10.1111/j.1462-5822.2007.01002.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mice defective for C1q complement factor show enhanced resistance to peripheral prion inoculation, and previous work demonstrated a direct interaction between C1q and conformationally modified PrP. However, the nature and physiological consequences of this interaction remain uncharacterized. PrP amino acids 141-159 has been identified as a potential C1q binding site; we show, by both surface plasmon resonance (SPR) spectroscopy and ELISA, that C1q and its globular region bind to PrP mutagenized in the region of interest with comparable efficiency to that of wild-type protein. To test PrP's ability to activate complement, soluble oligomers of the PrP constructs were made. Only PrP and mutagenized PrP oligomers activate the classical complement cascade while PrP monomer and the C-terminal domain, both in oligomeric and in monomeric form, failed to induce activation. This suggests that a conformational change in PrP, which occurs both when PrP is bound to an SPR sensor chip and when it undergoes oligomerization, is requisite for PrP/C1q interaction and activation of the complement cascade. We propose that C1q may act as a natural sensor for prions, leading to activation of the classical complement cascade, which could result in local inflammation and subsequent recruitment of the immune cells that prions initially infect.
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Affiliation(s)
- Chantal Dumestre-Pérard
- Laboratoire d'Adaptation et Pathogenèse des Microorganismes, UMR5163 CNRS-UJF, Institut Jean Roget, BP170, 38042 Grenoble cedex 9, France
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46
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Revealing different aggregation pathways of amyloidogenic proteins by ultrasound velocimetry. Biophys J 2008; 94:3241-6. [PMID: 18192359 DOI: 10.1529/biophysj.107.123133] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this work, we performed a detailed thermodynamic study, including ultrasound velocimetry, densimetry, calorimetry, and FTIR spectroscopy, of an aggregation-prone protein (insulin) under different salt-screening conditions to gain a deeper insight into the scenario of physicochemical events during its temperature-induced unfolding and aggregation reactions. Differences in aggregation and fibrillization pathways are reflected in changes of the partial molar volume, the coefficients of thermal expansion and compressibility, and the infrared spectral properties of the protein. Combining all experimental data allows setting up a scheme for the temperature-dependent insulin aggregation reaction in the presence and absence of NaCl. As revealed by complementary atomic force microscopy studies, under charge-screening conditions, a process involving structural reorganization, ripening, and formation of more compact nuclei from amorphous oligomers is involved in the formation of mature fibrillar morphologies. In this work, our focus was to put forward a comprehensive discussion of the use of ultrasound velocimetry in disentangling different aggregation pathways. In fact, ultrasound velocimetry proved to be very sensitive to changes in aggregation pathway, highlighting the importance of density and compressibility changes in the different aggregation and fibrillization reactions of the protein.
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47
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Yu S, Yin S, Li C, Wong P, Chang B, Xiao F, Kang SC, Yan H, Xiao G, Tien P, Sy MS. Aggregation of prion protein with insertion mutations is proportional to the number of inserts. Biochem J 2007; 403:343-51. [PMID: 17187581 PMCID: PMC1874237 DOI: 10.1042/bj20061592] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mutation in the prion gene, PRNP, accounts for approx. 10-15% of human prion diseases. However, little is known about the mechanisms by which a mutant prion protein (PrP) causes disease. We compared the biochemical properties of a wild-type human prion protein, rPrP(C) (recombinant wild-type PrP), which has five octapeptide-repeats, with two recombinant human prion proteins with insertion mutations, one with three more octapeptide repeats, rPrP(8OR), and the other with five more octapeptide repeats, rPrP(10OR). We found that the insertion mutant proteins are more prone to aggregate, and the degree and kinetics of aggregation are proportional to the number of inserts. The octapeptide-repeat and alpha-helix 1 regions are important in aggregate formation, because aggregation is inhibited with monoclonal antibodies that are specific for epitopes in these regions. We also showed that a small amount of mutant protein could enhance the formation of mixed aggregates that are composed of mutant protein and wild-type rPrP(C). Accordingly, rPrP(10OR) is also more efficient in promoting the aggregation of rPrP(C) than rPrP(8OR). These findings provide a biochemical explanation for the clinical observations that the severity of the disease in patients with insertion mutations is proportional to the number of inserts, and thus have implications for the pathogenesis of inherited human prion disease.
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Affiliation(s)
- Shuiliang Yu
- *Department of Pathology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44120, U.S.A
| | - Shaoman Yin
- *Department of Pathology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44120, U.S.A
| | - Chaoyang Li
- *Department of Pathology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44120, U.S.A
| | - Poki Wong
- *Department of Pathology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44120, U.S.A
| | - Binggong Chang
- *Department of Pathology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44120, U.S.A
| | - Fan Xiao
- *Department of Pathology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44120, U.S.A
| | - Shin-Chung Kang
- *Department of Pathology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44120, U.S.A
| | - Huimin Yan
- *Department of Pathology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44120, U.S.A
- †Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Gengfu Xiao
- †Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Po Tien
- †Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
- ‡Institute of Microbiology, Chinese Academy of Science, Beijing 100080, People's Republic of China
| | - Man-Sun Sy
- *Department of Pathology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44120, U.S.A
- To whom correspondence should be addressed (email )
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48
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Ronga L, Tizzano B, Palladino P, Ragone R, Urso E, Maffia M, Ruvo M, Benedetti E, Rossi F. The prion protein: Structural features and related toxic peptides. Chem Biol Drug Des 2007; 68:139-47. [PMID: 17062011 DOI: 10.1111/j.1747-0285.2006.00427.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Prion diseases are characterized by the conversion of the physiological cellular form of the prion protein (PrP(C)) into an insoluble, partially protease-resistant abnormal scrapie form (PrP(Sc)). PrP(C) is normally expressed in mammalian cell and is highly conserved among species, although its role in cellular function remains elusive. The conversion of PrP(C) to PrP(Sc) parallels a conformational change of the polypeptide from a predominantly alpha-helical to a highly beta-sheet secondary structure. The pathogenesis and molecular basis of the consequent nerve cell loss are not understood. Limited structural information is available on aggregate formation by this protein as the possible cause of these diseases and on its toxicity. This brief overview focuses on the large amount of structure-activity studies based on the prion fragment approach, hinging on peptides derived from the unstructured N-terminal and globular C-terminal domains. It is well documented that most of the fragments with regular secondary structure, with the exception of helices 1 and 3, possess a high beta-sheet propensity and tendency to form beta-sheet-like aggregates. In this context, helix 2 plays a crucial role because it is able to adopt both misfolded and partially helical conformation. However, only a few mutants are able to display its intrinsic neurotoxicity.
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Affiliation(s)
- Luisa Ronga
- Dipartimento delle Scienze Biologiche, C I R Pe B, Università Federico II di Napoli and Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
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49
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Lima LMTR, Cordeiro Y, Tinoco LW, Marques AF, Oliveira CLP, Sampath S, Kodali R, Choi G, Foguel D, Torriani I, Caughey B, Silva JL. Structural insights into the interaction between prion protein and nucleic acid. Biochemistry 2006; 45:9180-7. [PMID: 16866364 DOI: 10.1021/bi060532d] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The infectious agent of transmissible spongiform encephalopathies (TSE) is believed to comprise, at least in part, the prion protein (PrP). Other molecules can modulate the conversion of the normal PrP(C) into the pathological conformer (PrP(Sc)), but the identity and mechanisms of action of the key physiological factors remain unclear. PrP can bind to nucleic acids with relatively high affinity. Here, we report small-angle X-ray scattering (SAXS) and nuclear magnetic resonance spectroscopy measurements of the tight complex of PrP with an 18 bp DNA sequence. This double-stranded DNA sequence (E2DBS) binds with nanomolar affinity to the full-length recombinant mouse PrP. The SAXS data show that formation of the rPrP-DNA complex leads to larger values of the maximum dimension and radius of gyration. In addition, the SAXS studies reveal that the globular domain of PrP participates importantly in the formation of the complex. The changes in NMR HSQC spectra were clustered in two major regions: one in the disordered portion of the PrP and the other in the globular domain. Although interaction is mediated mainly through the PrP globular domain, the unstructured region is also recruited to the complex. This visualization of the complex provides insight into how oligonucleotides bind to PrP and opens new avenues to the design of compounds against prion diseases.
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Affiliation(s)
- Luis Maurício T R Lima
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, 21941-590 Rio de Janeiro, RJ Brazil
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50
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Silva JL, Cordeiro Y, Foguel D. Protein folding and aggregation: Two sides of the same coin in the condensation of proteins revealed by pressure studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:443-51. [PMID: 16480935 DOI: 10.1016/j.bbapap.2005.11.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Accepted: 11/14/2005] [Indexed: 11/12/2022]
Abstract
Hydrostatic pressure can be considered as "thermodynamic tweezers" to approach the protein folding problem and to study the cases when folding goes wrong leading to the protein folding disorders. The main outcome of the use of high pressure in this field is the stabilization of folding intermediates such as partially folded conformations, thus allowing us to characterize their structural properties. Because partially folded intermediates are usually at the intersection between productive and off-pathway folding, they may give rise to misfolded proteins, aggregates and amyloids that are involved in many neurodegenerative diseases, such as transmissible spongiform encephalopathies, Alzheimer's disease, Parkinson's disease and Huntington's disease. Of particular interest is the use of hydrostatic pressure to unveil the structural transitions in prion conversion and to populate possible intermediates in the folding/unfolding pathway of the prion protein. The main hypothesis for prion diseases proposes that the cellular protein (PrP(C)) can be altered into a misfolded, beta-sheet-rich isoform, the PrP(Sc) (from scrapie). It has been demonstrated that hydrostatic pressure affects the balance between the different prion species. The last findings on the application of high pressure on amyloidogenic proteins will be discussed here as regards to their energetic and volumetric properties. The use of high pressure promises to contribute to the identification of the underlying mechanisms of these neurodegenerative diseases and to develop new therapeutic approaches.
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Affiliation(s)
- Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, and Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Universidade Federal do Rio de Janeiro, 21941-590 Rio de Janeiro, RJ, Brazil.
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