1
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Bhate SH, Udgaonkar JB, Das R. Destabilization of polar interactions in the prion protein triggers misfolding and oligomerization. Protein Sci 2021; 30:2258-2271. [PMID: 34558139 DOI: 10.1002/pro.4188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/25/2022]
Abstract
The prion protein (PrP) misfolds and oligomerizes at pH 4 in the presence of physiological salt concentrations. Low pH and salt cause structural perturbations in the monomeric prion protein that lead to misfolding and oligomerization. However, the changes in stability within different regions of the PrP prior to oligomerization are poorly understood. In this study, we have characterized the local stability in PrP at high resolution using amide temperature coefficients (TC ) measured by nuclear magnetic resonance (NMR) spectroscopy. The local stability of PrP was investigated under native as well as oligomerizing conditions. We have also studied the rapidly oligomerizing PrP variant (Q216R) and the protective PrP variant (A6). We report that at low pH, salt destabilizes PrP at several polar residues, and the hydrogen bonds in helices α2 and α3 are weakened. In addition, salt changes the curvature of the α3 helix, which likely disrupts α2-α3 contacts and leads to oligomerization. These results are corroborated by the TC values of rapidly oligomerizing Q216R-PrP. The poly-alanine substitution in A6-PrP stabilizes α2, which prevents oligomerization. Altogether, these results highlight the importance of native polar interactions in determining the stability of PrP and reveal the structural disruptions in PrP that lead to misfolding and oligomerization.
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Affiliation(s)
- Suhas H Bhate
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, TIFR, Bangalore, India.,Indian Institute for Science Education and Research, Pune, India
| | - Ranabir Das
- National Centre for Biological Sciences, TIFR, Bangalore, India
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2
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Bettinger J, Ghaemmaghami S. Methionine oxidation within the prion protein. Prion 2020; 14:193-205. [PMID: 32744136 PMCID: PMC7518762 DOI: 10.1080/19336896.2020.1796898] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 11/01/2022] Open
Abstract
Prion diseases are characterized by the self-templated misfolding of the cellular prion protein (PrPC) into infectious aggregates (PrPSc). The detailed molecular basis of the misfolding and aggregation of PrPC remains incompletely understood. It is believed that the transient misfolding of PrPC into partially structured intermediates precedes the formation of insoluble protein aggregates and is a critical component of the prion misfolding pathway. A number of environmental factors have been shown to induce the destabilization of PrPC and promote its initial misfolding. Recently, oxidative stress and reactive oxygen species (ROS) have emerged as one possible mechanism by which the destabilization of PrPC can be induced under physiological conditions. Methionine residues are uniquely vulnerable to oxidation by ROS and the formation of methionine sulfoxides leads to the misfolding and subsequent aggregation of PrPC. Here, we provide a review of the evidence for the oxidation of methionine residues in PrPC and its potential role in the formation of pathogenic prion aggregates.
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Affiliation(s)
- John Bettinger
- Department of Biology, University of Rochester, Rochester, NY, USA
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3
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Lima AN, de Oliveira RJ, Braz ASK, de Souza Costa MG, Perahia D, Scott LPB. Effects of pH and aggregation in the human prion conversion into scrapie form: a study using molecular dynamics with excited normal modes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:583-590. [PMID: 29546436 DOI: 10.1007/s00249-018-1292-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 02/19/2018] [Accepted: 03/12/2018] [Indexed: 12/20/2022]
Abstract
There are two different prion conformations: (1) the cellular natural (PrPC) and (2) the scrapie (PrPSc), an infectious form that tends to aggregate under specific conditions. PrPC and PrPSc are widely different regarding secondary and tertiary structures. PrPSc contains more and longer β-strands compared to PrPC. The lack of solved PrPSc structures precludes a proper understanding of the mechanisms related to the transition between cellular and scrapie forms, as well as the aggregation process. In order to investigate the conformational transition between PrPC and PrPSc, we applied MDeNM (molecular dynamics with excited normal modes), an enhanced sampling simulation technique that has been recently developed to probe large structural changes. These simulations yielded new structural rearrangements of the cellular prion that would have been difficult to obtain with standard MD simulations. We observed an increase in β-sheet formation under low pH (≤ 4) and upon oligomerization, whose relevance was discussed on the basis of the energy landscape theory for protein folding. The characterization of intermediate structures corresponding to transition states allowed us to propose a conversion model from the cellular to the scrapie prion, which possibly ignites the fibril formation. This model can assist the design of new drugs to prevent neurological disorders related to the prion aggregation mechanism.
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Affiliation(s)
- Angelica Nakagawa Lima
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Antônio Sérgio Kimus Braz
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
| | | | - David Perahia
- Laboratorie de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Cachan, France
| | - Luis Paulo Barbour Scott
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil.
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4
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Moulick R, Udgaonkar JB. Identification and Structural Characterization of the Precursor Conformation of the Prion Protein which Directly Initiates Misfolding and Oligomerization. J Mol Biol 2017; 429:886-899. [DOI: 10.1016/j.jmb.2017.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/19/2017] [Accepted: 01/19/2017] [Indexed: 12/11/2022]
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5
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Modulation of prion polymerization and toxicity by rationally designed peptidomimetics. Biochem J 2016; 474:123-147. [DOI: 10.1042/bcj20160737] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 10/25/2016] [Accepted: 10/31/2016] [Indexed: 11/17/2022]
Abstract
Misfolding and aggregation of cellular prion protein is associated with a large array of neurological disorders commonly called the transmissible spongiform encephalopathies. Designing inhibitors against prions has remained a daunting task owing to limited information about mechanism(s) of their pathogenic self-assembly. Here, we explore the anti-prion properties of a combinatorial library of bispidine-based peptidomimetics (BPMs) that conjugate amino acids with hydrophobic and aromatic side chains. Keeping the bispidine unit unaltered, a series of structurally diverse BPMs were synthesized and tested for their prion-modulating properties. Administration of Leu- and Trp-BPMs delayed and completely inhibited the amyloidogenic conversion of human prion protein (HuPrP), respectively. We found that each BPM induced the HuPrP to form unique oligomeric nanostructures differing in their biophysical properties, cellular toxicities and response to conformation-specific antibodies. While Leu-BPMs were found to stabilize the oligomers, Trp-BPMs effected transient oligomerization, resulting in the formation of non-toxic, non-fibrillar aggregates. Yet another aromatic residue, Phe, however, accelerated the aggregation process in HuPrP. Molecular insights obtained through MD (molecular dynamics) simulations suggested that each BPM differently engages a conserved Tyr 169 residue at the α2–β2 loop of HuPrP and affects the stability of α2 and α3 helices. Our results demonstrate that this new class of molecules having chemical scaffolds conjugating hydrophobic/aromatic residues could effectively modulate prion aggregation and toxicity.
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6
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Mukundan V, Maksoudian C, Vogel MC, Chehade I, Katsiotis MS, Alhassan SM, Magzoub M. Cytotoxicity of prion protein-derived cell-penetrating peptides is modulated by pH but independent of amyloid formation. Arch Biochem Biophys 2016; 613:31-42. [PMID: 27818203 DOI: 10.1016/j.abb.2016.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 10/30/2016] [Accepted: 11/02/2016] [Indexed: 11/25/2022]
Abstract
Prion diseases are associated with conversion of cellular prion protein (PrPC) into an abnormally folded and infectious scrapie isoform (PrPSc). We previously showed that peptides derived from the unprocessed N-termini of mouse and bovine prion proteins, mPrP1-28 and bPrP1-30, function as cell-penetrating peptides (CPPs), and destabilize model membrane systems, which could explain the infectivity and toxicity of prion diseases. However, subsequent studies revealed that treatment with mPrP1-28 or bPrP1-30 significantly reduce PrPSc levels in prion-infected cells. To explain these seemingly contradictory results, we correlated the aggregation, membrane perturbation and cytotoxicity of the peptides with their cellular uptake and intracellular localization. Although the peptides have a similar primary sequence, mPrP1-28 is amyloidogenic, whereas bPrP1-30 forms smaller oligomeric or non-fibrillar aggregates. Surprisingly, bPrP1-30 induces much higher cytotoxicity than mPrP1-28, indicating that amyloid formation and toxicity are independent. The toxicity is correlated with prolonged residence at the plasma membrane and membrane perturbation. Both ordered aggregation and toxicity of the peptides are inhibited by low pH. Under non-toxic conditions, the peptides are internalized by lipid-raft dependent macropinocytosis and localize to acidic lysosomal compartments. Our results shed light on the antiprion mechanism of the prion protein-derived CPPs and identify a potential site for PrPSc formation.
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Affiliation(s)
- Vineeth Mukundan
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Christy Maksoudian
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Maria C Vogel
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ibrahim Chehade
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Marios S Katsiotis
- Department of Chemical Engineering, The Petroleum Institute, Abu Dhabi, United Arab Emirates
| | - Saeed M Alhassan
- Department of Chemical Engineering, The Petroleum Institute, Abu Dhabi, United Arab Emirates
| | - Mazin Magzoub
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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7
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Yu Y, Yu Z, Zheng Z, Wang H, Wu X, Guo C, Lin D. Distinct effects of mutations on biophysical properties of human prion protein monomers and oligomers. Acta Biochim Biophys Sin (Shanghai) 2016; 48:1016-1025. [PMID: 27649893 DOI: 10.1093/abbs/gmw094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/15/2016] [Indexed: 02/05/2023] Open
Abstract
Prion diseases are a group of fatal neurodegenerative illnesses, resulting from the conformational conversion of the cellular prion protein (PrPC) into a misfolded form (PrPSc). The formation of neurotoxic soluble prion protein oligomer (PrPO) is regarded as a key step in the development of prion diseases. About 10%-15% of human prion diseases are caused by mutations in the prion protein gene; however, the underlying molecular mechanisms remain unclear. In the present work, we compared the biophysical properties of wild-type (WT) human prion protein 91-231 (WT HuPrP91-231) and its disease-associated variants (P105L, D178N, V203I, and Q212P) using several biophysical techniques. In comparison with WT HuPrPC, the Q212P and D178N variants possessed greatly increased conversion propensities of PrPC into PrPO, while the V203I variant had dramatically decreased conversion propensity. The P105L variant displayed a similar conversion propensity to WT HuPrPC Guanidine hydrochloride-induced unfolding experiments ranked the thermodynamic stabilities of these proteins as Q212P < D178N < WT ≈ P105L < V203I. It was thus suggested that the conversion propensities of the prion proteins are closely associated with their thermodynamic stabilities. Furthermore, structural comparison illustrated that Q212P, D178N, and V203I variants underwent larger structural changes compared with WT HuPrPC, while the P105L variant adopted a similar structure to the WT HuPrPC The mutation-induced structural perturbations might change the thermodynamic stabilities of the HuPrPC variants, and correspondingly alter the conversion propensities for these prion proteins. Our results extend the mechanistic understanding of prion pathogenesis, and lay the basis for the prevention and treatment of prion diseases.
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Affiliation(s)
- Yuanhui Yu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ziyao Yu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhen Zheng
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Huilin Wang
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xueji Wu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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8
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Wang B, Lou Z, Zhang H, Xu B. Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level. J Chem Phys 2016; 144:114701. [DOI: 10.1063/1.4943878] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Bin Wang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605, USA
| | - Zhichao Lou
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605, USA
- College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, People’s Republic of China
| | - Haiqian Zhang
- College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, People’s Republic of China
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605, USA
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9
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Lou Z, Wang B, Guo C, Wang K, Zhang H, Xu B. Molecular-level insights of early-stage prion protein aggregation on mica and gold surface determined by AFM imaging and molecular simulation. Colloids Surf B Biointerfaces 2015; 135:371-378. [DOI: 10.1016/j.colsurfb.2015.07.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/17/2015] [Accepted: 07/21/2015] [Indexed: 10/23/2022]
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10
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Moulick R, Das R, Udgaonkar JB. Partially Unfolded Forms of the Prion Protein Populated under Misfolding-promoting Conditions: CHARACTERIZATION BY HYDROGEN EXCHANGE MASS SPECTROMETRY AND NMR. J Biol Chem 2015; 290:25227-40. [PMID: 26306043 DOI: 10.1074/jbc.m115.677575] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 12/16/2022] Open
Abstract
The susceptibility of the cellular prion protein (PrP(C)) to convert to an alternative misfolded conformation (PrP(Sc)), which is the key event in the pathogenesis of prion diseases, is indicative of a conformationally flexible native (N) state. In the present study, hydrogen-deuterium exchange (HDX) in conjunction with mass spectrometry and nuclear magnetic resonance spectroscopy were used for the structural and energetic characterization of the N state of the full-length mouse prion protein, moPrP(23-231), under conditions that favor misfolding. The kinetics of HDX of 34 backbone amide hydrogens in the N state were determined at pH 4. In contrast to the results of previous HDX studies on the human and Syrian hamster prion proteins at a higher pH, various segments of moPrP were found to undergo different extents of subglobal unfolding events at pH 4, a pH at which the protein is known to be primed to misfold to a β-rich conformation. No residual structure around the disulfide bond was observed for the unfolded state at pH 4. The N state of the prion protein was observed to be at equilibrium with at least two partially unfolded forms (PUFs). These PUFs, which are accessed by stochastic fluctuations of the N state, have altered surface area exposure relative to the N state. One of these PUFs resembles a conformation previously implicated to be an initial intermediate in the conversion of monomeric protein into misfolded oligomer at pH 4.
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Affiliation(s)
- Roumita Moulick
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Ranabir Das
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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11
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Söderberg KL, Guterstam P, Langel U, Gräslund A. Targeting prion propagation using peptide constructs with signal sequence motifs. Arch Biochem Biophys 2014; 564:254-61. [PMID: 25447819 DOI: 10.1016/j.abb.2014.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 12/25/2022]
Abstract
Synthetic peptides with sequences derived from the cellular prion protein (PrP(C)) unprocessed N-terminus are able to counteract the propagation of proteinase K resistant prions (PrP(Res), indicating the presence of the prion isoform of the prion protein) in cell cultures (Löfgren et al., 2008). The anti-prion peptides have characteristics like cell penetrating peptides (CPPs) and consist of the prion protein hydrophobic signal sequence followed by a polycationic motif (residues KKRPKP), in mouse PrP(C) corresponding to residues 1-28. Here we analyze the sequence elements required for the anti-prion effect of KKRPKP-conjugates. Neuronal GT1-1 cells were infected with either prion strain RML or 22L. Variable peptide constructs originating from the mPrP1-28 sequence were analyzed for anti-prion effects, measured as disappearance of proteinase K resistant prions (PrP(Res)) in the infected cell cultures. We find that even a 5 amino acid N-terminal shortening of the signal peptide abolishes the anti-prion effect. We show that the signal peptide from PrP(C) can be replaced with the signal peptide from the Neural cell adhesion molecule-1; NCAM11-19, with a retained capacity to reduce PrP(Res) levels. The anti-prion effect is lost if the polycationic N-terminal PrP(C)-motif is conjugated to any conventional CPP, such as TAT48-60, transportan-10 or penetratin. We propose a mechanism by which a signal peptide from a secretory or cell surface protein acts to promote the transport of a prion-binding polycationic PrP(C)-motif to a subcellular location where prion conversion occurs (most likely the Endosome Recycling Compartment), thereby targeting prion propagation.
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Affiliation(s)
- Kajsa Löfgren Söderberg
- The Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Peter Guterstam
- The Department of Neurochemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ulo Langel
- The Department of Neurochemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Astrid Gräslund
- The Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
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12
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Trevitt CR, Hosszu LLP, Batchelor M, Panico S, Terry C, Nicoll AJ, Risse E, Taylor WA, Sandberg MK, Al-Doujaily H, Linehan JM, Saibil HR, Scott DJ, Collinge J, Waltho JP, Clarke AR. N-terminal domain of prion protein directs its oligomeric association. J Biol Chem 2014; 289:25497-508. [PMID: 25074940 PMCID: PMC4162156 DOI: 10.1074/jbc.m114.566588] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The self-association of prion protein (PrP) is a critical step in the pathology of prion diseases. It is increasingly recognized that small non-fibrillar β-sheet-rich oligomers of PrP may be of crucial importance in the prion disease process. Here, we characterize the structure of a well defined β-sheet-rich oligomer, containing ∼12 PrP molecules, and often enclosing a central cavity, formed using full-length recombinant PrP. The N-terminal region of prion protein (residues 23-90) is required for the formation of this distinct oligomer; a truncated form comprising residues 91-231 forms a broad distribution of aggregated species. No infectivity or toxicity was found using cell and animal model systems. This study demonstrates that examination of the full repertoire of conformers and assembly states that can be accessed by PrP under specific experimental conditions should ideally be done using the full-length protein.
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Affiliation(s)
- Clare R Trevitt
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Laszlo L P Hosszu
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Mark Batchelor
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Silvia Panico
- the Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX
| | - Cassandra Terry
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Andrew J Nicoll
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Emmanuel Risse
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - William A Taylor
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Malin K Sandberg
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Huda Al-Doujaily
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Jacqueline M Linehan
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Helen R Saibil
- the Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX
| | - David J Scott
- the National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, the ISIS Spallation Neutron and Muon Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, and
| | - John Collinge
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Jonathan P Waltho
- the Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Anthony R Clarke
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG,
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13
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Cheng CJ, Daggett V. Molecular dynamics simulations capture the misfolding of the bovine prion protein at acidic pH. Biomolecules 2014; 4:181-201. [PMID: 24970211 PMCID: PMC4030982 DOI: 10.3390/biom4010181] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/07/2014] [Accepted: 02/09/2014] [Indexed: 12/24/2022] Open
Abstract
Bovine spongiform encephalopathy (BSE), or mad cow disease, is a fatal neurodegenerative disease that is transmissible to humans and that is currently incurable. BSE is caused by the prion protein (PrP), which adopts two conformers; PrPC is the native innocuous form, which is α-helix rich; and PrPSc is the β-sheet rich misfolded form, which is infectious and forms neurotoxic species. Acidic pH induces the conversion of PrPC to PrPSc. We have performed molecular dynamics simulations of bovine PrP at various pH regimes. An acidic pH environment induced conformational changes that were not observed in neutral pH simulations. Putative misfolded structures, with nonnative β-strands formed in the flexible N-terminal domain, were found in acidic pH simulations. Two distinct pathways were observed for the formation of nonnative β-strands: at low pH, hydrophobic contacts with M129 nucleated the nonnative β-strand; at mid-pH, polar contacts involving Q168 and D178 facilitated the formation of a hairpin at the flexible N-terminus. These mid- and low pH simulations capture the process of nonnative β-strand formation, thereby improving our understanding of how PrPC misfolds into the β-sheet rich PrPSc and how pH factors into the process.
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Affiliation(s)
- Chin Jung Cheng
- Department of Bioengineering, University of Washington, Seattle WA 98195-5013, USA.
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle WA 98195-5013, USA.
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14
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Baillod P, Garrec J, Tavernelli I, Rothlisberger U. Prion versus Doppel Protein Misfolding: New Insights from Replica-Exchange Molecular Dynamics Simulations. Biochemistry 2013; 52:8518-26. [DOI: 10.1021/bi400884e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Pascal Baillod
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Julian Garrec
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- CNRS,
UMR 7565 Structure et Réactivité des Systèmes
Moléculaires Complexes, Nancy Université, Nancy, France
| | - Ivano Tavernelli
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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15
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Molecular dynamics studies on the NMR and X-ray structures of rabbit prion proteins. J Theor Biol 2013; 342:70-82. [PMID: 24184221 DOI: 10.1016/j.jtbi.2013.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/25/2013] [Accepted: 10/09/2013] [Indexed: 12/27/2022]
Abstract
Prion diseases, traditionally referred to as transmissible spongiform encephalopathies (TSEs), are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species, manifesting as scrapie in sheep and goats, bovine spongiform encephalopathy (BSE or mad-cow disease) in cattle, chronic wasting disease in deer and elk, and Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, and kulu in humans, etc. These neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrP(C)) into insoluble abnormally folded infectious prions (PrP(Sc)), and the conversion of PrP(C) to PrP(Sc) is believed to involve conformational change from a predominantly α-helical protein to one rich in β-sheet structure. Such a conformational change may be amenable to study by molecular dynamics (MD) techniques. For rabbits, classical studies show that they have a low susceptibility to be infected by PrP(Sc), but recently it was reported that rabbit prions can be generated through saPMCA (serial automated Protein Misfolding Cyclic Amplification) in vitro and the rabbit prion is infectious and transmissible. In this paper, we first do a detailed survey on the research advances of rabbit prion protein (RaPrP) and then we perform MD simulations on the NMR and X-ray molecular structures of rabbit prion protein wild-type and mutants. The survey shows to us that rabbits were not challenged directly in vivo with other known prion strains and the saPMCA result did not pass the test of the known BSE strain of cattle. Thus, we might still look rabbits as a prion resistant species. MD results indicate that the three α-helices of the wild-type are stable under the neutral pH environment (but under low pH environment the three α-helices have been unfolded into β-sheets), and the three α-helices of the mutants (I214V and S173N) are unfolded into rich β-sheet structures under the same pH environment. In addition, we found an interesting result that the salt bridges such as ASP201-ARG155, ASP177-ARG163 contribute greatly to the structural stability of RaPrP.
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16
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Yamaguchi KI, Kamatari YO, Fukuoka M, Miyaji R, Kuwata K. Nearly Reversible Conformational Change of Amyloid Fibrils as Revealed by pH-Jump Experiments. Biochemistry 2013; 52:6797-806. [DOI: 10.1021/bi400698u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kei-ichi Yamaguchi
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Yuji O. Kamatari
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Reiji Miyaji
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
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17
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Garrec J, Tavernelli I, Rothlisberger U. Two misfolding routes for the prion protein around pH 4.5. PLoS Comput Biol 2013; 9:e1003057. [PMID: 23696721 PMCID: PMC3656106 DOI: 10.1371/journal.pcbi.1003057] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 03/27/2013] [Indexed: 11/18/2022] Open
Abstract
Using molecular dynamics simulations, we show that the prion protein (PrP) exhibits a dual behavior, with two possible transition routes, upon protonation of H187 around pH 4.5, which mimics specific conditions encountered in endosomes. Our results suggest a picture in which the protonated imidazole ring of H187 experiences an electrostatic repulsion with the nearby guanidinium group of R136, to which the system responds by pushing either H187 or R136 sidechains away from their native cavities. The regions to which H187 and R136 are linked, namely the C-terminal part of H2 and the loop connecting S1 to H1, respectively, are affected in a different manner depending on which pathway is taken. Specific in vivo or in vitro conditions, such as the presence of molecular chaperones or a particular experimental setup, may favor one transition pathway over the other, which can result in very different [Formula: see text] monomers. This has some possible connections with the observation of various fibril morphologies and the outcome of prion strains. In addition, the finding that the interaction of H187 with R136 is a weak point in mammalian PrP is supported by the absence of the [Formula: see text] residue pair in non-mammalian species that are known to be resistant to prion diseases.
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Affiliation(s)
- Julian Garrec
- Laboratory of Computational Chemistry and Biochemistry - Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry - Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry - Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail:
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18
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Glaves JP, Gorski PA, Alier K, Ma L, Renault L, Primeau JO, Jhamandas JH, Young HS. Distinct morphological and electrophysiological properties of an elk prion peptide. Peptides 2013; 40:49-56. [PMID: 23262353 DOI: 10.1016/j.peptides.2012.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/08/2012] [Accepted: 12/10/2012] [Indexed: 12/20/2022]
Abstract
A key event in prion diseases is the conversion of the prion protein (PrP) from its native α-helical conformation to a misfolded, β-sheet rich conformation. Thus, preventing or reversing PrP misfolding could provide a means to disrupt prion disease progression and transmission. However, determining the structure of misfolded PrP has been notoriously difficult due to its inherent heterogeneity and aggregation behavior. For these reasons, simplified peptide fragments have been used as models that recapitulate characteristics of full-length PrP, such as amyloid-like aggregation and fibril formation, and in vitro toxicity. We provide a biochemical and structural comparison of PrP(127-147) peptides from elk, bovine and hamster using electrophysiology, electron microscopy and fluorescence. Our results demonstrate that the PrP(127-147) peptides adopt distinct populations of fibril structures. In addition, the elk PrP(127-147) peptide is unique in its ability to enhance Thioflavin T fluorescence and its ability to modulate neuronal ion channel conductances.
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Affiliation(s)
- John Paul Glaves
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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19
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Abstract
The structural conversion of the prion protein PrP into a transmissible, misfolded form is the central element of prion disease, yet there is little consensus as to how it occurs. Key aspects of conversion into the diseased state remain unsettled, from details about the earliest stages of misfolding such as the involvement of partially- or fully-unfolded intermediates to the structure of the infectious state. Part of the difficulty in understanding the structural conversion arises from the complexity of the underlying energy landscapes. Single molecule methods provide a powerful tool for probing complex folding pathways as in prion misfolding, because they allow rare and transient events to be observed directly. We discuss recent work applying single-molecule probes to study misfolding in prion proteins, and what it has revealed about the folding dynamics of PrP that may underlie its unique behavior. We also discuss single-molecule studies probing the interactions that stabilize non-native structures within aggregates, pointing the way to future work that may help identify the microscopic events triggering pathogenic conversion. Although single-molecule approaches to misfolding are relatively young, they have a promising future in prion science.
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Affiliation(s)
- Hao Yu
- Department of Physics, University of Alberta, Edmonton, AB Canada
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20
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Baillod P, Garrec J, Colombo MC, Tavernelli I, Rothlisberger U. Enhanced Sampling Molecular Dynamics Identifies PrPSc Structures Harboring a C-Terminal β-Core. Biochemistry 2012; 51:9891-9. [DOI: 10.1021/bi301091x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pascal Baillod
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Julian Garrec
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Maria-Carola Colombo
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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21
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Khanna R, Wilson SM, Brittain JM, Weimer J, Sultana R, Butterfield A, Hensley K. Opening Pandora's jar: a primer on the putative roles of CRMP2 in a panoply of neurodegenerative, sensory and motor neuron, and central disorders. FUTURE NEUROLOGY 2012; 7:749-771. [PMID: 23308041 DOI: 10.2217/fnl.12.68] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
CRMP2, also known as DPYSL2/DRP2, Unc-33, Ulip or TUC2, is a cytosolic phosphoprotein that mediates axon/dendrite specification and axonal growth. Mapping the CRMP2 interactome has revealed previously unappreciated functions subserved by this protein. Together with its canonical roles in neurite growth and retraction and kinesin-dependent axonal transport, it is now known that CRMP2 interacts with numerous binding partners to affect microtubule dynamics; protein endocytosis and vesicular cycling, synaptic assembly, calcium channel regulation and neurotransmitter release. CRMP2 signaling is regulated by post-translational modifications, including glycosylation, oxidation, proteolysis and phosphorylation; the latter being a fulcrum of CRMP2 functions. Here, the putative roles of CRMP2 in a panoply of neurodegenerative, sensory and motor neuron, and central disorders are discussed and evidence is presented for therapeutic strategies targeting CRMP2 functions.
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Affiliation(s)
- Rajesh Khanna
- Program in Medical Neurosciences, Paul & Carole Stark Neurosciences Research Institute Indianapolis, IN 46202, USA ; Departments of Pharmacology & Toxicology, Indianapolis, IN 46202, USA ; Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA ; Sophia Therapeutics LLC, Indianapolis, IN 46202, USA
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22
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Vila-Viçosa D, Campos SRR, Baptista AM, Machuqueiro M. Reversibility of prion misfolding: insights from constant-pH molecular dynamics simulations. J Phys Chem B 2012; 116:8812-21. [PMID: 22803931 DOI: 10.1021/jp3034837] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The prion protein (PrP) is the cause of a group of diseases known as transmissible spongiform encephalopathies (TSEs). Creutzfeldt-Jakob disease and bovine spongiform encephalopathy are examples of TSEs. Although the normal form of PrP (PrP(C)) is monomeric and soluble, it can misfold into a pathogenic form (PrP(Sc)) that has a high content of β-structure and can aggregate forming amyloid fibrils. The mechanism of conversion of PrP(C) into PrP(Sc) is not known but different triggers have been proposed. It can be catalyzed by a PrP(Sc) sample, or it can be induced by an external factor, such as low pH. The pH effect on the structure of PrP was recently studied by computational methods [Campos et al. J. Phys. Chem. B 2010, 114, 12692-12700], and an evident trend of loss of helical structure was observed with pH decrease, together with a gain of β-structures. In particular, one simulation at pH 2 showed an evident misfolding transition. The main goal of the present work was to study the effects of a change in pH to 7 in several transient conformations of this simulation, in order to draw some conclusions about the reversibility of PrP misfolding. Although the most significant effect caused by the change of pH to 7 was a global stabilization of the protein structure, we could also observe that some conformational transitions induced by pH 2 were reversible in many of our simulations, namely those started from the early moments of the misfolding transition. This observation is in good agreement with experiments showing that, even at pH as low as 1.7, it is possible to revert the misfolding process [Bjorndahl et al. Biochemistry 2011, 50, 1162-1173].
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Affiliation(s)
- Diogo Vila-Viçosa
- Centro de Química e Bioquímica e Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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23
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Younan ND, Nadal RC, Davies P, Brown DR, Viles JH. Methionine oxidation perturbs the structural core of the prion protein and suggests a generic misfolding pathway. J Biol Chem 2012; 287:28263-75. [PMID: 22654104 PMCID: PMC3436581 DOI: 10.1074/jbc.m112.354779] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxidative stress and misfolding of the prion protein (PrPC) are fundamental to prion diseases. We have therefore probed the effect of oxidation on the structure and stability of PrPC. Urea unfolding studies indicate that H2O2 oxidation reduces the thermodynamic stability of PrPC by as much as 9 kJ/mol. 1H-15N NMR studies indicate methionine oxidation perturbs key hydrophobic residues on one face of helix-C as follows: Met-205, Val-209, and Met-212 together with residues Val-160 and Tyr-156. These hydrophobic residues pack together and form the structured core of the protein, stabilizing its ternary structure. Copper-catalyzed oxidation of PrPC causes a more significant alteration of the structure, generating a monomeric molten globule species that retains its native helical content. Further copper-catalyzed oxidation promotes extended β-strand structures that lack a cooperative fold. This transition from the helical molten globule to β-conformation has striking similarities to a misfolding intermediate generated at low pH. PrP may therefore share a generic misfolding pathway to amyloid fibers, irrespective of the conditions promoting misfolding. Our observations support the hypothesis that oxidation of PrP destabilizes the native fold of PrPC, facilitating the transition to PrPSc. This study gives a structural and thermodynamic explanation for the high levels of oxidized methionine in scrapie isolates.
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Affiliation(s)
- Nadine D Younan
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom
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24
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Scouras AD, Daggett V. Disruption of the X-loop turn of the prion protein linked to scrapie resistance. Protein Eng Des Sel 2012; 25:243-9. [PMID: 22447804 DOI: 10.1093/protein/gzs009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The prion diseases are a class of neurodegenerative diseases caused by the misfolding and aggregation of the prion protein (PrP(C)) into toxic and infectious oligomers (PrP(Sc)). These oligomers are critical to understanding and combating these diseases. Differences in the sequence of PrP affect disease susceptibility, likely by shifting the tolerance of the protein for adaptation to PrP(Sc) conformations and/or the recognition event between PrP(Sc) and PrP(C) prior to conversion of the PrP(C). We selected two sets of PrP(Sc)-resistant mutant sequences for solvated atomistic molecular dynamics simulation to investigate the structural basis of resistance. The first group involved mutation in the X-loop (residues 164-171) resulting from selective breeding of sheep. The second group included eight mutants in mice identified by random mutagenesis targeting helix C followed by screening in cell cultures. Multiple simulations were performed of 14 different mutant and control constructs under different pH conditions for a total of 3.6 μs of simulation time. The X-loop formed a stable turn at neutral pH in wild-type PrP from both species. PrP(Sc)-resistant mutations disrupted this turn even though only one of the mutants is in the X-loop. The X-loop is compact and buried in our previously described spiral models of PrP(Sc)-like oligomers. On the basis of the findings presented here and in the context of the spiral oligomer model, we propose that expansion of the X-loop disrupts protofibril packing, providing a structural basis for resistance.
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Affiliation(s)
- Alexander D Scouras
- Department of Biochemistry, University of Washington, Seattle, WA 98195-5013, USA
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25
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Murciano-Calles J, Cobos ES, Mateo PL, Camara-Artigas A, Martinez JC. A comparative analysis of the folding and misfolding pathways of the third PDZ domain of PSD95 investigated under different pH conditions. Biophys Chem 2011; 158:104-10. [PMID: 21665351 DOI: 10.1016/j.bpc.2011.05.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 05/20/2011] [Accepted: 05/21/2011] [Indexed: 11/16/2022]
Abstract
Equilibrium unfolding at neutral pH of the third PDZ domain of PSD95 is well described by the presence of a partly unfolded intermediate that presents association phenomena. After some days' incubation annular and fibrillar structures form from the oligomers. At pH values below 3, however, differential scanning calorimetry shows that PDZ3 seems to unfold under a two-state scheme. Kinetic measurements followed by dynamic light scattering, ThT and ANS fluorescence reveal that the misfolding pathway still exists despite the absence of any populated intermediates and shows an irreversible assembling of the supramacromolecular structures as well as an appreciable lag-phase, contrary to what is found in similar experiments at neutral pH. Moreover, as shown by transmission-electron-microscopy images, the annular structures seen at neutral pH completely disappear from incubated solutions. According to the structural information, this titration behavior appears to be the consequence of a conformational equilibrium that depends on the protonation of some Glu residues located at the C-terminal α3 helix and at the hairpin formed by strands β2 and β3. Our calculations suggest that the enthalpic contribution of these interactions may well be as much as 40kJ·mol(-1). The possible regulatory role of this equilibrium upon PDZ3 functionality and amyloid formation is briefly discussed.
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Affiliation(s)
- Javier Murciano-Calles
- Department of Physical Chemistry and Institute of Biotechnology, University of Granada, Spain
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26
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Bjorndahl TC, Zhou GP, Liu X, Perez-Pineiro R, Semenchenko V, Saleem F, Acharya S, Bujold A, Sobsey CA, Wishart DS. Detailed biophysical characterization of the acid-induced PrP(c) to PrP(β) conversion process. Biochemistry 2011; 50:1162-73. [PMID: 21189021 DOI: 10.1021/bi101435c] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Prions are believed to spontaneously convert from a native, monomeric highly helical form (called PrP(c)) to a largely β-sheet-rich, multimeric and insoluble aggregate (called PrP(sc)). Because of its large size and insolubility, biophysical characterization of PrP(sc) has been difficult, and there are several contradictory or incomplete models of the PrP(sc) structure. A β-sheet-rich, soluble intermediate, called PrP(β), exhibits many of the same features as PrP(sc) and can be generated using a combination of low pH and/or mild denaturing conditions. Studies of the PrP(c) to PrP(β) conversion process and of PrP(β) folding intermediates may provide insights into the structure of PrP(sc). Using a truncated, recombinant version of Syrian hamster PrP(β) (shPrP(90-232)), we used NMR spectroscopy, in combination with other biophysical techniques (circular dichroism, dynamic light scattering, electron microscopy, fluorescence spectroscopy, mass spectrometry, and proteinase K digestion), to characterize the pH-driven PrP(c) to PrP(β) conversion process in detail. Our results show that below pH 2.8 the protein oligomerizes and conversion to the β-rich structure is initiated. At pH 1.7 and above, the oligomeric protein can recover its native monomeric state through dialysis to pH 5.2. However, when conversion is completed at pH 1.0, the large oligomer "locks down" irreversibly into a stable, β-rich form. At pH values above 3.0, the protein is amenable to NMR investigation. Chemical shift perturbations, NOE, amide line width, and T(2) measurements implicate the putative "amylome motif" region, "NNQNNF" as the region most involved in the initial helix-to-β conversion phase. We also found that acid-induced PrP(β) oligomers could be converted to fibrils without the use of chaotropic denaturants. The latter finding represents one of the first examples wherein physiologically accessible conditions (i.e., only low pH) were used to achieve PrP conversion and fibril formation.
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Affiliation(s)
- Trent C Bjorndahl
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E8
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27
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van der Kamp MW, Daggett V. Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations. Top Curr Chem (Cham) 2011; 305:169-97. [PMID: 21526434 DOI: 10.1007/128_2011_158] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Computer simulation of protein dynamics offers unique high-resolution information that complements experiment. Using experimentally derived structures of the natively folded prion protein (PrP), physically realistic dynamics and conformational changes can be simulated, including the initial steps of misfolding. By introducing mutations in silico, the effect of pathogenic mutations on PrP conformation and dynamics can be assessed. Here, we briefly introduce molecular dynamics methods and review the application of molecular dynamics simulations to obtain insight into various aspects of the PrP, including the mechanism of misfolding, the response to changes in the environment, and the influence of disease-related mutations.
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Affiliation(s)
- Marc W van der Kamp
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
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28
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Prion disease susceptibility is affected by beta-structure folding propensity and local side-chain interactions in PrP. Proc Natl Acad Sci U S A 2010; 107:19808-13. [PMID: 21041683 DOI: 10.1073/pnas.1005267107] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Prion diseases occur when the normally α-helical prion protein (PrP) converts to a pathological β-structured state with prion infectivity (PrP(Sc)). Exposure to PrP(Sc) from other mammals can catalyze this conversion. Evidence from experimental and accidental transmission of prions suggests that mammals vary in their prion disease susceptibility: Hamsters and mice show relatively high susceptibility, whereas rabbits, horses, and dogs show low susceptibility. Using a novel approach to quantify conformational states of PrP by circular dichroism (CD), we find that prion susceptibility tracks with the intrinsic propensity of mammalian PrP to convert from the native, α-helical state to a cytotoxic β-structured state, which exists in a monomer-octamer equilibrium. It has been controversial whether β-structured monomers exist at acidic pH; sedimentation equilibrium and dual-wavelength CD evidence is presented for an equilibrium between a β-structured monomer and octamer in some acidic pH conditions. Our X-ray crystallographic structure of rabbit PrP has identified a key helix-capping motif implicated in the low prion disease susceptibility of rabbits. Removal of this capping motif increases the β-structure folding propensity of rabbit PrP to match that of PrP from mouse, a species more susceptible to prion disease.
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29
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Hosszu LLP, Tattum MH, Jones S, Trevitt CR, Wells MA, Waltho JP, Collinge J, Jackson GS, Clarke AR. The H187R mutation of the human prion protein induces conversion of recombinant prion protein to the PrP(Sc)-like form. Biochemistry 2010; 49:8729-38. [PMID: 20718410 DOI: 10.1021/bi100572j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prion diseases are associated with a conformational switch in the prion protein (PrP) from its normal cellular form (denoted PrP(C)) to a disease-associated "scrapie" form (PrP(Sc)). A number of PrP(Sc)-like conformations can be generated by incubating recombinant PrP(C) at low pH, indicating that protonation of key residues is likely to destabilize PrP(C), facilitating its conversion to PrP(Sc). Here, we examine the stability of human PrP(C) with pH and find that PrP(C) fold stability is significantly reduced by the protonation of two histidine residues, His187 and His155. Mutation of His187 to an arginine, which imposes a permanently positively charged residue in this region of the protein, has a dramatic effect on the folding of PrP(C), resulting in a molecule that displays a markedly increased propensity to oligomerize. The oligomeric form is characterized by an increased β-sheet content, loss of fixed side chain interactions, and partial proteinase resistance. Hence, the protonation state of H187 appears to be crucial in determining the conformation of PrP; the unprotonated form favors native PrP(C), while the protonated form favors PrP(Sc)-like conformations. These results are relevant to the pathogenic H187R mutation found in humans, which is associated with an inherited prion disease [also termed Gerstmann-Sträussler-Scheinker (GSS) syndrome] with unusual features such as childhood neuropsychiatric illness. Our data imply that the intrinsic instability of the PrP(C) conformation in this variant is caused by a positive charge at this site in the protein. This mutation is distinct from all those associated with GSS, which have much more subtle physical consequences. The degree of instability might be the cause of the unusually early onset of mental disturbance in affected individuals.
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Affiliation(s)
- Laszlo L P Hosszu
- MRC Prion Unit, UCL Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG, UK
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30
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Campos SRR, Machuqueiro M, Baptista AM. Constant-pH Molecular Dynamics Simulations Reveal a β-Rich Form of the Human Prion Protein. J Phys Chem B 2010; 114:12692-700. [DOI: 10.1021/jp104753t] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sara R. R. Campos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - António M. Baptista
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
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31
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Wu D, Zhang W, Luo Q, Luo K, Huang L, Wang W, Huang T, Chen R, Lin Y, Pang D, Xiao G. Copper (II) promotes the formation of soluble neurotoxic PrP oligomers in acidic environment. J Cell Biochem 2010; 111:627-33. [DOI: 10.1002/jcb.22743] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Varshney A, Ahmad B, Rabbani G, Kumar V, Yadav S, Khan RH. Acid-induced unfolding of didecameric keyhole limpet hemocyanin: detection and characterizations of decameric and tetrameric intermediate states. Amino Acids 2010; 39:899-910. [DOI: 10.1007/s00726-010-0524-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 02/10/2010] [Indexed: 10/19/2022]
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Gerum C, Silvers R, Wirmer-Bartoschek J, Schwalbe H. Unfolded-state structure and dynamics influence the fibril formation of human prion protein. Angew Chem Int Ed Engl 2010; 48:9452-6. [PMID: 19882604 DOI: 10.1002/anie.200903771] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christian Gerum
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-Universität, 60438 Frankfurt, Germany
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Gerum C, Silvers R, Wirmer-Bartoschek J, Schwalbe H. Unfolded-State Structure and Dynamics Influence the Fibril Formation of Human Prion Protein. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903771] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Hosszu LLP, Trevitt CR, Jones S, Batchelor M, Scott DJ, Jackson GS, Collinge J, Waltho JP, Clarke AR. Conformational properties of beta-PrP. J Biol Chem 2009; 284:21981-21990. [PMID: 19369250 PMCID: PMC2755922 DOI: 10.1074/jbc.m809173200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 03/19/2009] [Indexed: 11/06/2022] Open
Abstract
Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly alpha-helical conformation to one dominated by beta-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91-231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant beta-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a beta-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126-227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state.
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Affiliation(s)
- Laszlo L. P. Hosszu
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
- the Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, and
| | - Clare R. Trevitt
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Samantha Jones
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Mark Batchelor
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - David J. Scott
- the National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Graham S. Jackson
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - John Collinge
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Jonathan P. Waltho
- the Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, and
| | - Anthony R. Clarke
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
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Redecke L, Binder S, Elmallah MIY, Broadbent R, Tilkorn C, Schulz B, May P, Goos A, Eich A, Rübhausen M, Betzel C. UV-light-induced conversion and aggregation of prion proteins. Free Radic Biol Med 2009; 46:1353-61. [PMID: 19249347 DOI: 10.1016/j.freeradbiomed.2009.02.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 01/15/2009] [Accepted: 02/13/2009] [Indexed: 11/21/2022]
Abstract
Increasing evidence suggests a central role for oxidative stress in the pathology of prion diseases, a group of fatal neurodegenerative disorders associated with structural conversion of the prion protein (PrP). Because UV-light-induced protein damage is mediated by direct photo-oxidation and radical reactions, we investigated the structural consequences of UVB radiation on recombinant murine and human prion proteins at pH 7.4 and pH 5.0. As revealed by circular dichroism and dynamic light scattering measurements, the observed PrP aggregation follows two independent pathways: (i) complete unfolding of the protein structure associated with rapid precipitation or (ii) specific structural conversion into distinct soluble beta-oligomers. The choice of pathway was directly attributed to the chromophoric properties of the PrP species and the susceptibility to oxidation. Regarding size, the oligomers characterized in this study share a high degree of identity with oligomeric species formed after structural destabilization induced by other triggers, which significantly strengthens the theory that partly unfolded intermediates represent initial precursor molecules directing the pathway of PrP aggregation. Moreover, we identified the first suitable photo-trigger capable of inducing refolding of PrP, which has an important biotechnological impact in terms of analyzing the conversion process on small time scales.
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Affiliation(s)
- Lars Redecke
- Institute of Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Germany
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Julien O, Graether SP, Sykes BD. Monitoring prion protein stability by NMR. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2009; 72:1069-1074. [PMID: 19697241 DOI: 10.1080/15287390903084504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Prion diseases, or transmissible spongiform encephalopathies (TSE), are a group of fatal neurological diseases that affect both humans and animals. At the end of the 20th century, bovine spongiform encephalopathy (BSE), better known as mad cow disease, was shown to be transmissible to humans. This resulted in considerable concern for public health and a number of questions for scientists. The first question answered was the possible source of the disease, which appears to be the prion protein (PrP). There are two major forms of this protein: the native, noninfectious form (PrP(C)), and the misfolded infectious form (PrP(Sc)). PrP(C) is mainly alpha-helical in structure, whereas PrP(Sc) aggregates into an assembly of beta-sheets, forming amyloid fibrils. Since the first solution structure of the noninfectious form of the mouse prion protein, about 30 structures of the globular portion of PrP(C) have been characterized from different organisms. However, only a few minor differences are observed when comparing one PrP(C) structure to another. The key to understanding prion formation may then be not in the structure of PrP(C), but in the mechanism underlying PrP(C) unfolding and then conversion into a misfolded fibril state. To identify the possible region(s) of PrP(C) responsible for initiating the conversion into the amyloid fibril formation, nuclear magnetic resonance (NMR) was applied to characterize the stability and structure of PrP(C) and intermediate states during the conversion from PrP(C) to PrP(Sc). Subsequently urea was used to induce unfolding, and data analysis revealed region-specific structural stabilities that may bring insights into the mechanisms underlying conversion of protein into an infectious prion.
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Affiliation(s)
- Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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Deriziotis P, Tabrizi SJ. Prions and the proteasome. Biochim Biophys Acta Mol Basis Dis 2008; 1782:713-22. [PMID: 18644436 DOI: 10.1016/j.bbadis.2008.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Revised: 06/23/2008] [Accepted: 06/24/2008] [Indexed: 10/21/2022]
Abstract
Prion diseases are fatal neurodegenerative disorders that include Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy in animals. They are unique in terms of their biology because they are caused by the conformational re-arrangement of a normal host-encoded prion protein, PrPC, to an abnormal infectious isoform, PrPSc. Currently the precise mechanism behind prion-mediated neurodegeneration remains unclear. It is hypothesised than an unknown toxic gain of function of PrPSc, or an intermediate oligomeric form, underlies neuronal death. Increasing evidence suggests a role for the ubiquitin proteasome system (UPS) in prion disease. Both wild-type PrPC and disease-associated PrP isoforms accumulate in cells after proteasome inhibition leading to increased cell death, and abnormal beta-sheet-rich PrP isoforms have been shown to inhibit the catalytic activity of the proteasome. Here we review potential interactions between prions and the proteasome outlining how the UPS may be implicated in prion-mediated neurodegeneration.
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Affiliation(s)
- Pelagia Deriziotis
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, WC1N 3BG, UK
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