1
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Gomez-Cardona E, Eskandari-Sedighi G, Fahlman R, Westaway D, Julien O. Application of N-Terminal Labeling Methods Provide Novel Insights into Endoproteolysis of the Prion Protein in Vivo. ACS Chem Neurosci 2024; 15:134-146. [PMID: 38095594 PMCID: PMC10768724 DOI: 10.1021/acschemneuro.3c00533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/04/2024] Open
Abstract
Alternative α- and β-cleavage events in the cellular prion protein (PrPC) central region generate fragments with distinct biochemical features that affect prion disease pathogenesis, but the assignment of precise cleavage positions has proven challenging. Exploiting mouse transgenic models expressing wild-type (WT) PrPC and an octarepeat region mutant allele (S3) with increased β-fragmentation, cleavage sites were defined using LC-MS/MS in conjunction with N-terminal enzymatic labeling and chemical in-gel acetylation. Our studies profile the net proteolytic repertoire of the adult brain, as deduced from defining hundreds of proteolytic events in other proteins, and position individual cleavage events in PrPC α- and β-target areas imputed from earlier, lower resolution methods; these latter analyses established site heterogeneity, with six cleavage sites positioned in the β-cleavage region of WT PrPC and nine positions for S3 PrPC. Regarding α-cleavage, aside from reported N-termini at His110 and Val111, we identified a total of five shorter fragments in the brain of both mice lines. We infer that aminopeptidase activity in the brain could contribute to the ragged N-termini observed around PrPC's α- and β-cleavage sites, with this work providing a point of departure for further in vivo studies of brain proteases.
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Affiliation(s)
- Erik Gomez-Cardona
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ghazaleh Eskandari-Sedighi
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Center
for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2M8, Canada
| | - Richard Fahlman
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - David Westaway
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Center
for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2M8, Canada
- Department
of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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2
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Gielnik M, Szymańska A, Dong X, Jarvet J, Svedružić ŽM, Gräslund A, Kozak M, Wärmländer SKTS. Prion Protein Octarepeat Domain Forms Transient β-Sheet Structures upon Residue-Specific Binding to Cu(II) and Zn(II) Ions. Biochemistry 2023. [PMID: 37163663 DOI: 10.1021/acs.biochem.3c00129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Misfolding of the cellular prion protein (PrPC) is associated with the development of fatal neurodegenerative diseases called transmissible spongiform encephalopathies (TSEs). Metal ions appear to play a crucial role in PrPC misfolding. PrPC is a combined Cu(II) and Zn(II) metal-binding protein, where the main metal-binding site is located in the octarepeat (OR) region. Thus, the biological function of PrPC may involve the transport of divalent metal ions across membranes or buffering concentrations of divalent metal ions in the synaptic cleft. Recent studies have shown that an excess of Cu(II) ions can result in PrPC instability, oligomerization, and/or neuroinflammation. Here, we have used biophysical methods to characterize Cu(II) and Zn(II) binding to the isolated OR region of PrPC. Circular dichroism (CD) spectroscopy data suggest that the OR domain binds up to four Cu(II) ions or two Zn(II) ions. Binding of the first metal ion results in a structural transition from the polyproline II helix to the β-turn structure, while the binding of additional metal ions induces the formation of β-sheet structures. Fluorescence spectroscopy data indicate that the OR region can bind both Cu(II) and Zn(II) ions at neutral pH, but under acidic conditions, it binds only Cu(II) ions. Molecular dynamics simulations suggest that binding of either metal ion to the OR region results in the formation of β-hairpin structures. As the formation of β-sheet structures can be a first step toward amyloid formation, we propose that high concentrations of either Cu(II) or Zn(II) ions may have a pro-amyloid effect in TSE diseases.
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Affiliation(s)
- Maciej Gielnik
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, PL 61-614 Poznań, Poland
| | - Aneta Szymańska
- Department of Biomedical Chemistry, Faculty of Chemistry, Gdańsk University, PL 80-308 Gdańsk, Poland
| | - Xiaolin Dong
- Chemistry Section, Stockholm University, 10691 Stockholm, Sweden
| | - Jüri Jarvet
- Chemistry Section, Stockholm University, 10691 Stockholm, Sweden
- The National Institute of Chemical Physics and Biophysics, 12618 Tallinn, Estonia
| | - Željko M Svedružić
- Department of Biotechnology, University of Rijeka, HR 51000 Rijeka, Croatia
| | - Astrid Gräslund
- Chemistry Section, Stockholm University, 10691 Stockholm, Sweden
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, PL 61-614 Poznań, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, PL 30-392 Kraków, Poland
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3
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Vanni I, Iacobone F, D’Agostino C, Giovannelli M, Pirisinu L, Altmeppen HC, Castilla J, Torres JM, Agrimi U, Nonno R. An optimized Western blot assay provides a comprehensive assessment of the physiological endoproteolytic processing of the prion protein. J Biol Chem 2022; 299:102823. [PMID: 36565989 PMCID: PMC9867980 DOI: 10.1016/j.jbc.2022.102823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022] Open
Abstract
The prion protein (PrPC) is subjected to several conserved endoproteolytic events producing bioactive fragments that are of increasing interest for their physiological functions and their implication in the pathogenesis of prion diseases and other neurodegenerative diseases. However, systematic and comprehensive investigations on the full spectrum of PrPC proteoforms have been hampered by the lack of methods able to identify all PrPC-derived proteoforms. Building on previous knowledge of PrPC endoproteolytic processing, we thus developed an optimized Western blot assay able to obtain the maximum information about PrPC constitutive processing and the relative abundance of PrPC proteoforms in a complex biological sample. This approach led to the concurrent identification of the whole spectrum of known endoproteolytic-derived PrPC proteoforms in brain homogenates, including C-terminal, N-terminal and, most importantly, shed PrPC-derived fragments. Endoproteolytic processing of PrPC was remarkably similar in the brain of widely used wild type and transgenic rodent models, with α-cleavage-derived C1 representing the most abundant proteoform and ADAM10-mediated shedding being an unexpectedly prominent proteolytic event. Interestingly, the relative amount of shed PrPC was higher in WT mice than in most other models. Our results indicate that constitutive endoproteolytic processing of PrPC is not affected by PrPC overexpression or host factors other than PrPC but can be impacted by PrPC primary structure. Finally, this method represents a crucial step in gaining insight into pathophysiological roles, biomarker suitability, and therapeutic potential of shed PrPC and for a comprehensive appraisal of PrPC proteoforms in therapies, drug screening, or in the progression of neurodegenerative diseases.
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Affiliation(s)
- Ilaria Vanni
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy.
| | - Floriana Iacobone
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Claudia D’Agostino
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Matteo Giovannelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Laura Pirisinu
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Joaquin Castilla
- Basque Research and Technology Alliance (BRTA) - CIC BioGUNE & IKERBasque, Bizkaia, Spain,Centro de Investigación Biomédica en Red de Enfermedades infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Maria Torres
- Centro de Investigación en Sanidad Animal (CISA-INIA-CSIC), Valdeolmos, Madrid, Spain
| | - Umberto Agrimi
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Romolo Nonno
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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4
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Rahman A, Saikia B, Gogoi CR, Baruah A. Advances in the understanding of protein misfolding and aggregation through molecular dynamics simulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:31-48. [PMID: 36044970 DOI: 10.1016/j.pbiomolbio.2022.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Aberrant protein folding known as protein misfolding is counted as one of the striking factors of neurodegenerative diseases. The extensive range of pathologies caused by protein misfolding, aggregation and subsequent accumulation are mainly classified into either gain of function diseases or loss of function diseases. In order to seek for novel strategies for treatment and diagnosis of neurodegenerative diseases, insights into the mechanism of misfolding and aggregation is essential. A comprehensive knowledge on the factors influencing misfolding and aggregation is required as well. An extensive experimental study on protein aggregation is somewhat challenging due to the insoluble and noncrystalline nature of amyloid fibrils. Thus there has been a growing use of computational approaches including Monte Carlo simulation, docking simulation, molecular dynamics simulation in the study of protein misfolding and aggregation. The review presents a discussion on molecular dynamics simulation alone as to how it has emerged as a promising tool in the understanding of protein misfolding and aggregation in general, detailing upon three different aspects considering four misfold prone proteins in particular. It is noticeable that all four proteins considered in this review i.e prion, superoxide dismutase1, huntingtin and amyloid β are linked to chronic neurodegenerative diseases with debilitating effects. Initially the review elaborates on the factors influencing the misfolding and aggregation. Next, it addresses our current understanding of the amyloid structures and the associated aggregation mechanisms, finally, summarizing the contribution of this computational tool in the search for therapeutic strategies against the respective protein-deposition diseases.
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Affiliation(s)
- Aziza Rahman
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Bondeepa Saikia
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Chimi Rekha Gogoi
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Anupaul Baruah
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India.
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5
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Kovač V, Čurin Šerbec V. Prion Protein: The Molecule of Many Forms and Faces. Int J Mol Sci 2022; 23:ijms23031232. [PMID: 35163156 PMCID: PMC8835406 DOI: 10.3390/ijms23031232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023] Open
Abstract
Cellular prion protein (PrPC) is a glycosylphosphatidylinositol (GPI)-anchored protein most abundantly found in the outer membrane of neurons. Due to structural characteristics (a flexible tail and structured core), PrPC interacts with a wide range of partners. Although PrPC has been proposed to be involved in many physiological functions, only peripheral nerve myelination homeostasis has been confirmed as a bona fide function thus far. PrPC misfolding causes prion diseases and PrPC has been shown to mediate β-rich oligomer-induced neurotoxicity in Alzheimer’s and Parkinson’s disease as well as neuroprotection in ischemia. Upon proteolytic cleavage, PrPC is transformed into released and attached forms of PrP that can, depending on the contained structural characteristics of PrPC, display protective or toxic properties. In this review, we will outline prion protein and prion protein fragment properties as well as overview their involvement with interacting partners and signal pathways in myelination, neuroprotection and neurodegenerative diseases.
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6
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Schilling KM, Tao L, Wu B, Kiblen JTM, Ubilla-Rodriguez NC, Pushie MJ, Britt RD, Roseman GP, Harris DA, Millhauser GL. Both N-Terminal and C-Terminal Histidine Residues of the Prion Protein Are Essential for Copper Coordination and Neuroprotective Self-Regulation. J Mol Biol 2020; 432:4408-4425. [PMID: 32473880 PMCID: PMC7387163 DOI: 10.1016/j.jmb.2020.05.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 01/19/2023]
Abstract
The cellular prion protein (PrPC) comprises two domains: a globular C-terminal domain and an unstructured N-terminal domain. Recently, copper has been observed to drive tertiary contact in PrPC, inducing a neuroprotective cis interaction that structurally links the protein's two domains. The location of this interaction on the C terminus overlaps with the sites of human pathogenic mutations and toxic antibody docking. Combined with recent evidence that the N terminus is a toxic effector regulated by the C terminus, there is an emerging consensus that this cis interaction serves a protective role, and that the disruption of this interaction by misfolded PrP oligomers may be a cause of toxicity in prion disease. We demonstrate here that two highly conserved histidines in the C-terminal domain of PrPC are essential for the protein's cis interaction, which helps to protect against neurotoxicity carried out by its N terminus. We show that simultaneous mutation of these histidines drastically weakens the cis interaction and enhances spontaneous cationic currents in cultured cells, the first C-terminal mutant to do so. Whereas previous studies suggested that Cu2+ coordination was localized solely to the protein's N-terminal domain, we find that both domains contribute equatorially coordinated histidine residue side-chains, resulting in a novel bridging interaction. We also find that extra N-terminal histidines in pathological familial mutations involving octarepeat expansions inhibit this interaction by sequestering copper from the C terminus. Our findings further establish a structural basis for PrPC's C-terminal regulation of its otherwise toxic N terminus.
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Affiliation(s)
- Kevin M Schilling
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Lizhi Tao
- Department of Chemistry, University of California, 1 Shields Ave., Davis, CA 95616, USA
| | - Bei Wu
- Department of Biochemistry, Boston University School of Medicine, 72 E. Concord St Silvio Conte., Boston, MA 02118, USA
| | - Joseph T M Kiblen
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Natalia C Ubilla-Rodriguez
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - M Jake Pushie
- Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd B419, Saskatoon, SK S7N 5E5, Canada
| | - R David Britt
- Department of Chemistry, University of California, 1 Shields Ave., Davis, CA 95616, USA
| | - Graham P Roseman
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - David A Harris
- Department of Biochemistry, Boston University School of Medicine, 72 E. Concord St Silvio Conte., Boston, MA 02118, USA.
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA 95064, USA.
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7
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McDonald AJ, Leon DR, Markham KA, Wu B, Heckendorf CF, Schilling K, Showalter HD, Andrews PC, McComb ME, Pushie MJ, Costello CE, Millhauser GL, Harris DA. Altered Domain Structure of the Prion Protein Caused by Cu 2+ Binding and Functionally Relevant Mutations: Analysis by Cross-Linking, MS/MS, and NMR. Structure 2019; 27:907-922.e5. [PMID: 30956132 DOI: 10.1016/j.str.2019.03.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/17/2019] [Accepted: 03/14/2019] [Indexed: 12/24/2022]
Abstract
The cellular isoform of the prion protein (PrPC) serves as precursor to the infectious isoform (PrPSc), and as a cell-surface receptor, which binds misfolded protein oligomers as well as physiological ligands such as Cu2+ ions. PrPC consists of two domains: a flexible N-terminal domain and a structured C-terminal domain. Both the physiological and pathological functions of PrP depend on intramolecular interactions between these two domains, but the specific amino acid residues involved have proven challenging to define. Here, we employ a combination of chemical cross-linking, mass spectrometry, NMR, molecular dynamics simulations, and functional assays to identify residue-level contacts between the N- and C-terminal domains of PrPC. We also determine how these interdomain contacts are altered by binding of Cu2+ ions and by functionally relevant mutations. Our results provide a structural basis for interpreting both the normal and toxic activities of PrP.
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Affiliation(s)
- Alex J McDonald
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Deborah R Leon
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kathleen A Markham
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bei Wu
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Christian F Heckendorf
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kevin Schilling
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hollis D Showalter
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Philip C Andrews
- Department of Biological Chemistry, Department of Chemistry, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark E McComb
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA
| | - M Jake Pushie
- Department of Surgery, Division of Neurosurgery, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Catherine E Costello
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
| | - David A Harris
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA.
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8
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Eigenbrod S, Frick P, Bertsch U, Mitteregger-Kretzschmar G, Mielke J, Maringer M, Piening N, Hepp A, Daude N, Windl O, Levin J, Giese A, Sakthivelu V, Tatzelt J, Kretzschmar H, Westaway D. Substitutions of PrP N-terminal histidine residues modulate scrapie disease pathogenesis and incubation time in transgenic mice. PLoS One 2017; 12:e0188989. [PMID: 29220360 PMCID: PMC5722314 DOI: 10.1371/journal.pone.0188989] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
Prion diseases have been linked to impaired copper homeostasis and copper induced-oxidative damage to the brain. Divalent metal ions, such as Cu2+ and Zn2+, bind to cellular prion protein (PrPC) at octapeptide repeat (OR) and non-OR sites within the N-terminal half of the protein but information on the impact of such binding on conversion to the misfolded isoform often derives from studies using either OR and non-OR peptides or bacterially-expressed recombinant PrP. Here we created new transgenic mouse lines expressing PrP with disrupted copper binding sites within all four histidine-containing OR's (sites 1-4, H60G, H68G, H76G, H84G, "TetraH>G" allele) or at site 5 (composed of residues His-95 and His-110; "H95G" allele) and monitored the formation of misfolded PrP in vivo. Novel transgenic mice expressing PrP(TetraH>G) at levels comparable to wild-type (wt) controls were susceptible to mouse-adapted scrapie strain RML but showed significantly prolonged incubation times. In contrast, amino acid replacement at residue 95 accelerated disease progression in corresponding PrP(H95G) mice. Neuropathological lesions in terminally ill transgenic mice were similar to scrapie-infected wt controls, but less severe. The pattern of PrPSc deposition, however, was not synaptic as seen in wt animals, but instead dense globular plaque-like accumulations of PrPSc in TgPrP(TetraH>G) mice and diffuse PrPSc deposition in (TgPrP(H95G) mice), were observed throughout all brain sections. We conclude that OR and site 5 histidine substitutions have divergent phenotypic impacts and that cis interactions between the OR region and the site 5 region modulate pathogenic outcomes by affecting the PrP globular domain.
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Affiliation(s)
- Sabina Eigenbrod
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - Petra Frick
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - Uwe Bertsch
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | | | - Janina Mielke
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - Marko Maringer
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - Niklas Piening
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - Alexander Hepp
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - Nathalie Daude
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Otto Windl
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - Johannes Levin
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - Vignesh Sakthivelu
- Department of Metabolic Biochemistry/Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Jörg Tatzelt
- Department of Metabolic Biochemistry/Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Hans Kretzschmar
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
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9
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Linsenmeier L, Altmeppen HC, Wetzel S, Mohammadi B, Saftig P, Glatzel M. Diverse functions of the prion protein - Does proteolytic processing hold the key? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2128-2137. [PMID: 28693923 DOI: 10.1016/j.bbamcr.2017.06.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 02/07/2023]
Abstract
Proteolytic processing of the cellular and disease-associated form of the prion protein leads to generation of bioactive soluble prion protein fragments and modifies the structure and function of its cell-bound form. The nature of proteases responsible for shedding, α-, β-, and γ-cleavage of the prion protein are only partially identified and their regulation is largely unknown. Here, we provide an overview of the increasingly multifaceted picture of prion protein proteolysis and shed light on physiological and pathological roles associated with these cleavages. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John.
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Affiliation(s)
- Luise Linsenmeier
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hermann C Altmeppen
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sebastian Wetzel
- Institute of Biochemistry, Christian Albrechts University Kiel, Kiel, Germany
| | - Behnam Mohammadi
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paul Saftig
- Institute of Biochemistry, Christian Albrechts University Kiel, Kiel, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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10
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Evans EGB, Pushie MJ, Markham KA, Lee HW, Millhauser GL. Interaction between Prion Protein's Copper-Bound Octarepeat Domain and a Charged C-Terminal Pocket Suggests a Mechanism for N-Terminal Regulation. Structure 2016; 24:1057-67. [PMID: 27265848 DOI: 10.1016/j.str.2016.04.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 11/29/2022]
Abstract
Copper plays a critical role in prion protein (PrP) physiology. Cu(2+) binds with high affinity to the PrP N-terminal octarepeat (OR) domain, and intracellular copper promotes PrP expression. The molecular details of copper coordination within the OR are now well characterized. Here we examine how Cu(2+) influences the interaction between the PrP N-terminal domain and the C-terminal globular domain. Using nuclear magnetic resonance and copper-nitroxide pulsed double electron-electron resonance, with molecular dynamics refinement, we localize the position of Cu(2+) in its high-affinity OR-bound state. Our results reveal an interdomain cis interaction that is stabilized by a conserved, negatively charged pocket of the globular domain. Interestingly, this interaction surface overlaps an epitope recognized by the POM1 antibody, the binding of which drives rapid cerebellar degeneration mediated by the PrP N terminus. The resulting structure suggests that the globular domain regulates the N-terminal domain by binding the Cu(2+)-occupied OR within a complementary pocket.
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Affiliation(s)
- Eric G B Evans
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - M Jake Pushie
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Kate A Markham
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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11
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Lau A, McDonald A, Daude N, Mays CE, Walter ED, Aglietti R, Mercer RCC, Wohlgemuth S, van der Merwe J, Yang J, Gapeshina H, Kim C, Grams J, Shi B, Wille H, Balachandran A, Schmitt-Ulms G, Safar JG, Millhauser GL, Westaway D. Octarepeat region flexibility impacts prion function, endoproteolysis and disease manifestation. EMBO Mol Med 2015; 7:339-56. [PMID: 25661904 PMCID: PMC4364950 DOI: 10.15252/emmm.201404588] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/31/2014] [Accepted: 01/08/2015] [Indexed: 12/21/2022] Open
Abstract
The cellular prion protein (PrP(C)) comprises a natively unstructured N-terminal domain, including a metal-binding octarepeat region (OR) and a linker, followed by a C-terminal domain that misfolds to form PrP(S) (c) in Creutzfeldt-Jakob disease. PrP(C) β-endoproteolysis to the C2 fragment allows PrP(S) (c) formation, while α-endoproteolysis blocks production. To examine the OR, we used structure-directed design to make novel alleles, 'S1' and 'S3', locking this region in extended or compact conformations, respectively. S1 and S3 PrP resembled WT PrP in supporting peripheral nerve myelination. Prion-infected S1 and S3 transgenic mice both accumulated similar low levels of PrP(S) (c) and infectious prion particles, but differed in their clinical presentation. Unexpectedly, S3 PrP overproduced C2 fragment in the brain by a mechanism distinct from metal-catalysed hydrolysis reported previously. OR flexibility is concluded to impact diverse biological endpoints; it is a salient variable in infectious disease paradigms and modulates how the levels of PrP(S) (c) and infectivity can either uncouple or engage to drive the onset of clinical disease.
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Affiliation(s)
- Agnes Lau
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Alex McDonald
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Nathalie Daude
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada
| | - Charles E Mays
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada
| | - Eric D Walter
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Robin Aglietti
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Robert C C Mercer
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada
| | - Serene Wohlgemuth
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada
| | - Jacques van der Merwe
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada
| | - Jing Yang
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada
| | - Hristina Gapeshina
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada
| | - Chae Kim
- National Prion Disease Surveillance Center, Departments of Pathology and Neurology, School of Medicine Case Western Reserve University, Cleveland, OH, USA
| | - Jennifer Grams
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada
| | - Beipei Shi
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada
| | - Holger Wille
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | | | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jiri G Safar
- National Prion Disease Surveillance Center, Departments of Pathology and Neurology, School of Medicine Case Western Reserve University, Cleveland, OH, USA
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, Canada Department of Medicine, University of Alberta, Edmonton, AB, Canada Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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Pushie MJ, Nienaber KH, McDonald A, Millhauser GL, George GN. Combined EXAFS and DFT structure calculations provide structural insights into the 1:1 multi-histidine complexes of Cu(II) , Cu(I) , and Zn(II) with the tandem octarepeats of the mammalian prion protein. Chemistry 2014; 20:9770-83. [PMID: 25042361 DOI: 10.1002/chem.201304201] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 04/06/2014] [Indexed: 02/01/2023]
Abstract
The metal-coordinating properties of the prion protein (PrP) have been the subject of intense focus and debate since the first reports of its interaction with copper just before the turn of the century. The picture of metal coordination to PrP has been improved and refined over the past decade, but structural details of the various metal coordination modes have not been fully elucidated in some cases. In the present study, we have employed X-ray absorption near-edge spectroscopy as well as extended X-ray absorption fine structure (EXAFS) spectroscopy to structurally characterize the dominant 1:1 coordination modes for Cu(II) , Cu(I) , and Zn(II) with an N-terminal fragment of PrP. The PrP fragment corresponds to four tandem repeats representative of the mammalian octarepeat domain, designated as OR4 , which is also the most studied PrP fragment for metal interactions, making our findings applicable to a large body of previous work. Density functional theory (DFT) calculations have provided additional structural and thermodynamic data, and candidate structures have been used to inform EXAFS data analysis. The optimized geometries from DFT calculations have been used to identify potential coordination complexes for multi-histidine coordination of Cu(II) , Cu(I) , and Zn(II) in an aqueous medium, modelled using 4-methylimidazole to represent the histidine side chain. Through a combination of in silico coordination chemistry as well as rigorous EXAFS curve-fitting, using full multiple scattering on candidate structures derived from DFT calculations, we have characterized the predominant coordination modes for the 1:1 complexes of Cu(II) , Cu(I) , and Zn(II) with the OR4 peptide at pH 7.4 at atomic resolution, which are best represented as square-planar [Cu(II) (His)4 ](2+) , digonal [Cu(I) (His)2 ](+) , and tetrahedral [Zn(II) (His)3 (OH2 )](2+) , respectively.
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Affiliation(s)
- M Jake Pushie
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK, S7N 5E2 (Canada), Fax: (+1) 306-966-8593.
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13
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Copper-induced structural propensities of the amyloidogenic region of human prion protein. J Biol Inorg Chem 2014; 19:635-45. [DOI: 10.1007/s00775-014-1132-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 04/02/2014] [Indexed: 12/15/2022]
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14
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McDonald A, Pushie MJ, Millhauser GL, George GN. New insights into metal interactions with the prion protein: EXAFS analysis and structure calculations of copper binding to a single octarepeat from the prion protein. J Phys Chem B 2013; 117:13822-41. [PMID: 24102071 PMCID: PMC3890359 DOI: 10.1021/jp408239h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Copper coordination to the prion protein (PrP) has garnered considerable interest for almost 20 years, due in part to the possibility that this interaction may be part of the normal function of PrP. The most characterized form of copper binding to PrP has been Cu(2+) interaction with the conserved tandem repeats in the N-terminal domain of PrP, termed the octarepeats, with many studies focusing on single and multiple repeats of PHGGGWGQ. Extended X-ray absorption fine structure (EXAFS) spectroscopy has been used in several previous instances to characterize the solution structure of Cu(2+) binding into the peptide backbone in the HGGG portion of the octarepeats. All previous EXAFS studies, however, have benefitted from crystallographic structure information for [Cu(II) (Ac-HGGGW-NH2)(-2H)] but have not conclusively demonstrated that the complex EXAFS spectrum represents the same coordination environment for Cu(2+) bound to the peptide backbone. Density functional structure calculations as well as full multiple scattering EXAFS curve fitting analysis are brought to bear on the predominant coordination mode for Cu(2+) with the Ac-PHGGGWGQ-NH2 peptide at physiological pH, under high Cu(2+) occupancy conditions. In addition to the structure calculations, which provide a thermodynamic link to structural information, methods are also presented for extensive deconvolution of the EXAFS spectrum. We demonstrate how the EXAFS data can be analyzed to extract the maximum structural information and arrive at a structural model that is significantly improved over previous EXAFS characterizations. The EXAFS spectrum for the chemically reduced form of copper binding to the Ac-PHGGGWGQ-NH2 peptide is presented, which is best modeled as a linear two-coordinate species with a single His imidazole ligand and a water molecule. The extent of in situ photoreduction of the copper center during standard data collection is also presented, and EXAFS curve fitting of the photoreduced species reveals an intermediate structure that is similar to the Cu(2+) form with reduced coordination number.
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Affiliation(s)
- Alex McDonald
- Department of Geological Sciences, University of Saskatchewan , Saskatoon, Saskatchewan S7N 5E2, Canada
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15
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16
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Altmeppen HC, Puig B, Dohler F, Thurm DK, Falker C, Krasemann S, Glatzel M. Proteolytic processing of the prion protein in health and disease. AMERICAN JOURNAL OF NEURODEGENERATIVE DISEASE 2012; 1:15-31. [PMID: 23383379 PMCID: PMC3560451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 05/11/2012] [Indexed: 06/01/2023]
Abstract
A variety of physiological functions, not only restricted to the nervous system, are discussed for the cellular prion protein (PrP(C)). A prominent, non-physiological property of PrPC is the conversion into its pathogenic isoform (PrP(Sc)) during fatal, transmissible, and neurodegenerative prion diseases. The prion protein is subject to posttranslational proteolytic processing and these cleavage events have been shown i) to regulate its physiological functions, ii) to produce biologically active fragments, and iii) to potentially influence the course of prion disease. Here, we give an overview on the proteolytic processing under physiological and pathological conditions and critically review what is currently known about the three main cleavage events of the prion protein, namely α-cleavage, β-cleavage, and ectodomain shedding. The biological relevance of resulting fragments as well as controversies regarding candidate proteases, with special emphasis on members of the A-disintegrin-and-metalloproteinase (ADAM) family, will be discussed. In addition, we make suggestions aimed at facilitating clarity and progress in this important research field. The better understanding of this issue will not only answer basic questions in prion biology but will likely impact research on other neurodegenerative diseases as well.
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Affiliation(s)
- Hermann C Altmeppen
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf Hamburg, Germany
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17
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Structural characterization of Cu2+, Ni2+ and Zn2+ binding sites of model peptides associated with neurodegenerative diseases. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.07.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Pivetta T, Cannas MD, Demartin F, Castellano C, Vascellari S, Verani G, Isaia F. Synthesis, structural characterization, formation constants and in vitro cytotoxicity of phenanthroline and imidazolidine-2-thione copper(II) complexes. J Inorg Biochem 2011; 105:329-38. [DOI: 10.1016/j.jinorgbio.2010.11.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 11/23/2010] [Accepted: 11/23/2010] [Indexed: 01/23/2023]
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Pushie MJ, George GN. Active-site dynamics and large-scale domain motions of sulfite oxidase: a molecular dynamics study. J Phys Chem B 2010; 114:3266-75. [PMID: 20158265 DOI: 10.1021/jp908731f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physiologically vital enzyme sulfite oxidase employs rapid intramolecular electron transfer between a molybdenum ion in the C-terminal domain (the site of sulfite oxidation) and a heme moeity in the N-terminal domain to complete its catalytic cycle. Crystal structures of the enzyme show C- and N-terminal domain orientations that are not consistent with rapid intramolecular electron transfer. Domain motion has been postulated to explain this discrepancy. In the present work we employ molecular dynamics simulations to understand the large-scale domain motions of the enzyme. We observe motion of the N-terminal domain into an orientation similar to that postulated for rapid electron transfer. Our simulations also probe the dynamics of the active site and surrounding residues, adding a further level of structural and thermodynamic detail in understanding sulfite oxidase function.
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Affiliation(s)
- M Jake Pushie
- Molecular and Environmental Science Research Group, Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan, S7N 5E2, Canada
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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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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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