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Vugmeyster L, Ostrovsky D, Rodgers A, Gwin K, Smirnov SL, McKnight CJ, Fu R. Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR. Chemphyschem 2024; 25:e202300565. [PMID: 38175858 PMCID: PMC10922872 DOI: 10.1002/cphc.202300565] [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: 08/09/2023] [Revised: 12/01/2023] [Indexed: 01/06/2024]
Abstract
Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO USA 80204
| | - Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Kirsten Gwin
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Serge L. Smirnov
- Department of Chemistry, Western Washington University, Bellingham, WA 98225
| | - C. James McKnight
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL USA 32310
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2
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do Amaral MJ, Mohapatra S, Passos AR, Lopes da Silva TS, Carvalho RS, da Silva Almeida M, Pinheiro AS, Wegmann S, Cordeiro Y. Copper drives prion protein phase separation and modulates aggregation. SCIENCE ADVANCES 2023; 9:eadi7347. [PMID: 37922348 PMCID: PMC10624353 DOI: 10.1126/sciadv.adi7347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/03/2023] [Indexed: 11/05/2023]
Abstract
Prion diseases are characterized by prion protein (PrP) transmissible aggregation and neurodegeneration, which has been linked to oxidative stress. The physiological function of PrP seems related to sequestering of redox-active Cu2+, and Cu2+ dyshomeostasis is observed in prion disease brain. It is unclear whether Cu2+ contributes to PrP aggregation, recently shown to be mediated by PrP condensation. This study indicates that Cu2+ promotes PrP condensation in live cells at the cell surface and in vitro through copartitioning. Molecularly, Cu2+ inhibited PrP β-structure and hydrophobic residues exposure. Oxidation, induced by H2O2, triggered liquid-to-solid transition of PrP:Cu2+ condensates and promoted amyloid-like PrP aggregation. In cells, overexpression of PrPC initially protected against Cu2+ cytotoxicity but led to PrPC aggregation upon extended copper exposure. Our data suggest that PrP condensates function as a buffer for copper that prevents copper toxicity but can transition into PrP aggregation at prolonged oxidative stress.
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Affiliation(s)
- Mariana Juliani do Amaral
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | | | - Aline Ribeiro Passos
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | | | | | - Marcius da Silva Almeida
- Plataforma Avançada de Biomoléculas, Centro Nacional de Biologia Estrutural e Bioimagem, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anderson Sá Pinheiro
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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3
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Suh JM, Kim M, Yoo J, Han J, Paulina C, Lim MH. Intercommunication between metal ions and amyloidogenic peptides or proteins in protein misfolding disorders. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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Schepers J, Carter Z, Kritsiligkou P, Grant CM. Methionine Sulfoxide Reductases Suppress the Formation of the [ PSI+] Prion and Protein Aggregation in Yeast. Antioxidants (Basel) 2023; 12:antiox12020401. [PMID: 36829961 PMCID: PMC9952077 DOI: 10.3390/antiox12020401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Prions are self-propagating, misfolded forms of proteins associated with various neurodegenerative diseases in mammals and heritable traits in yeast. How prions form spontaneously into infectious amyloid-like structures without underlying genetic changes is poorly understood. Previous studies have suggested that methionine oxidation may underlie the switch from a soluble protein to the prion form. In this current study, we have examined the role of methionine sulfoxide reductases (MXRs) in protecting against de novo formation of the yeast [PSI+] prion, which is the amyloid form of the Sup35 translation termination factor. We show that [PSI+] formation is increased during normal and oxidative stress conditions in mutants lacking either one of the yeast MXRs (Mxr1, Mxr2), which protect against methionine oxidation by reducing the two epimers of methionine-S-sulfoxide. We have identified a methionine residue (Met124) in Sup35 that is important for prion formation, confirming that direct Sup35 oxidation causes [PSI+] prion formation. [PSI+] formation was less pronounced in mutants simultaneously lacking both MXR isoenzymes, and we show that the morphology and biophysical properties of protein aggregates are altered in this mutant. Taken together, our data indicate that methionine oxidation triggers spontaneous [PSI+] prion formation, which can be alleviated by methionine sulfoxide reductases.
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Affiliation(s)
- Jana Schepers
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Duesbergweg 6, 55099 Mainz, Germany
| | - Zorana Carter
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Paraskevi Kritsiligkou
- Division of Redox Regulation, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Chris M. Grant
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
- Correspondence:
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5
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Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues. J Biol Chem 2022; 298:101872. [PMID: 35346688 PMCID: PMC9062257 DOI: 10.1016/j.jbc.2022.101872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/20/2022] Open
Abstract
The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications, making it important to delineate factors that influence methionine oxidation rates within a given protein. This is especially important for biopharmaceuticals, where oxidation can lead to deactivation and degradation. Previously, neighboring residue effects and solvent accessibility have been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of proteins. We surveyed the Escherichia coli proteome using several proteomic methodologies and globally measured oxidation rates of methionine residues in the presence and absence of tertiary structure, as well as the folding stabilities of methionine-containing domains. These data indicated that buried methionines have a wide range of protection factors against oxidation that correlate strongly with folding stabilities. Consistent with this, we show that in comparison to E. coli, the proteome of the thermophile Thermus thermophilus is significantly more stable and thus more resistant to methionine oxidation. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and propose a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures. Overall, these results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability.
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6
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Demasi M, Augusto O, Bechara EJH, Bicev RN, Cerqueira FM, da Cunha FM, Denicola A, Gomes F, Miyamoto S, Netto LES, Randall LM, Stevani CV, Thomson L. Oxidative Modification of Proteins: From Damage to Catalysis, Signaling, and Beyond. Antioxid Redox Signal 2021; 35:1016-1080. [PMID: 33726509 DOI: 10.1089/ars.2020.8176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significance: The systematic investigation of oxidative modification of proteins by reactive oxygen species started in 1980. Later, it was shown that reactive nitrogen species could also modify proteins. Some protein oxidative modifications promote loss of protein function, cleavage or aggregation, and some result in proteo-toxicity and cellular homeostasis disruption. Recent Advances: Previously, protein oxidation was associated exclusively to damage. However, not all oxidative modifications are necessarily associated with damage, as with Met and Cys protein residue oxidation. In these cases, redox state changes can alter protein structure, catalytic function, and signaling processes in response to metabolic and/or environmental alterations. This review aims to integrate the present knowledge on redox modifications of proteins with their fate and role in redox signaling and human pathological conditions. Critical Issues: It is hypothesized that protein oxidation participates in the development and progression of many pathological conditions. However, no quantitative data have been correlated with specific oxidized proteins or the progression or severity of pathological conditions. Hence, the comprehension of the mechanisms underlying these modifications, their importance in human pathologies, and the fate of the modified proteins is of clinical relevance. Future Directions: We discuss new tools to cope with protein oxidation and suggest new approaches for integrating knowledge about protein oxidation and redox processes with human pathophysiological conditions. Antioxid. Redox Signal. 35, 1016-1080.
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Affiliation(s)
- Marilene Demasi
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, Brazil
| | - Ohara Augusto
- Departamento de Bioquímica and Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Etelvino J H Bechara
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Renata N Bicev
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda M Cerqueira
- CENTD, Centre of Excellence in New Target Discovery, Instituto Butantan, São Paulo, Brazil
| | - Fernanda M da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Denicola
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
| | - Fernando Gomes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Sayuri Miyamoto
- Departamento de Bioquímica and Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Luis E S Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Lía M Randall
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
| | - Cassius V Stevani
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Leonor Thomson
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
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7
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Zhao Z, Shimon D, Metanis N. Chemoselective Copper-Mediated Modification of Selenocysteines in Peptides and Proteins. J Am Chem Soc 2021; 143:12817-12824. [PMID: 34346673 DOI: 10.1021/jacs.1c06101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Highly valuable bioconjugated molecules must be synthesized through efficient, chemoselective chemical modifications of peptides and proteins. Herein, we report the chemoselective modification of peptides and proteins via a reaction between selenocysteine residues and aryl/alkyl radicals. In situ radical generation from hydrazine substrates and copper ions proceeds rapidly in an aqueous buffer at near neutral pH (5-8), providing a variety of Se-modified linear and cyclic peptides and proteins conjugated to aryl and alkyl molecules, and to affinity label tag (biotin). This chemistry opens a new avenue for chemical protein modifications.
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Affiliation(s)
- Zhenguang Zhao
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem 91904, Israel
| | - Daphna Shimon
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem 91904, Israel
| | - Norman Metanis
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem 9190401, Israel
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8
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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: 10] [Impact Index Per Article: 2.5] [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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9
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Bohl J, Sicard C, Rezaei H, Van der Rest G, Halgand F. Evidence of conformational landscape alteration and macromolecular complex formation in the early stages of in vitro human prion protein oxidation. Arch Biochem Biophys 2020; 690:108432. [PMID: 32663474 DOI: 10.1016/j.abb.2020.108432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 10/23/2022]
Abstract
Oxidative stress is proposed to be one of the major causes of neurodegenerative diseases. Cellular prion protein (PrP) oxidation has been widely studied using chemical reagents such as hydrogen peroxide. However, the experimental conditions used do not faithfully reflect the physiological environment of the cell. With the goal to explore the conformational landscape of PrP under oxidative stress, we conducted a set of experiments combining the careful control of the nature and the amount of ROS produced by a60Co γ-irradiation source. Characterization of the resulting protein species was achieved using a set of analytical techniques. Under our experimental condition hydroxyl radical are the main reactive species produced. The most important findings are i) the formation of molecular assemblies under oxidative stress, ii) the detection of a majority of unmodified monomer mixed with oxidized monomers in these molecular assemblies at low hydroxyl radical concentration, iii) the absence of significant oxidation on the monomer fraction after irradiation. Molecular assemblies are produced in small amounts and were shown to be an octamer. These results suggest either i) an active recruitment of intact monomers by molecular assemblies' oxidized monomers then inducing a structural change of their intact counterparts or ii) an intrinsic capability of intact monomer conformers to spontaneously associate to form stable molecular assemblies when oxidized monomers are present. Finally, abundances of the intact monomer conformers after irradiation were modified. This suggests that monomers of the molecular assemblies exchange structural information with intact irradiated monomer. All these results shed a new light on structural exchange information between PrP monomers under oxidative stress.
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Affiliation(s)
- Jan Bohl
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France
| | - Cécile Sicard
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France
| | - Human Rezaei
- Institut National de la Recherche Agronomique, UR892, Virologie Immunologie Moléculaires, Domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Guillaume Van der Rest
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France
| | - Frédéric Halgand
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France.
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10
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Prasad KN, Bondy SC. Oxidative and Inflammatory Events in Prion Diseases: Can They Be Therapeutic Targets? Curr Aging Sci 2020; 11:216-225. [PMID: 30636622 PMCID: PMC6635421 DOI: 10.2174/1874609812666190111100205] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/17/2018] [Accepted: 12/10/2018] [Indexed: 01/15/2023]
Abstract
Prion diseases are a group of incurable infectious terminal neurodegenerative diseases caused by the aggregated misfolded PrPsc in selected mammals including humans. The complex physical interaction between normal prion protein PrPc and infectious PrPsc causes conformational change from the α- helix structure of PrPc to the β-sheet structure of PrPsc, and this process is repeated. Increased oxidative stress is one of the factors that facilitate the conversion of PrPc to PrPsc. This overview presents evidence to show that increased oxidative stress and inflammation are involved in the progression of this disease. Evidence is given for the participation of redoxsensitive metals Cu and Fe with PrPsc inducing oxidative stress by disturbing the homeostasis of these metals. The fact that some antioxidants block the toxicity of misfolded PrPc peptide supports the role of oxidative stress in prion disease. After exogenous infection in mice, PrPsc enters the follicular dendritic cells where PrPsc replicates before neuroinvasion where they continue to replicate and cause inflammation leading to neurodegeneration. Therefore, reducing levels of oxidative stress and inflammation may decrease the rate of the progression of this disease. It may be an important order to reduce oxidative stress and inflammation at the same time. This may be achieved by increasing the levels of antioxidant enzymes by activating the Nrf2 pathway together with simultaneous administration of dietary and endogenous antioxidants. It is proposed that a mixture of micronutrients could enable these concurrent events thereby reducing the progression of human prion disease.
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Affiliation(s)
- Kedar N Prasad
- Engage Global, 245 El Faison Drive, San Rafael, CA, United States
| | - Stephen C Bondy
- Center for Occupational and Environmental Health, Department of Medicine, University of California, Irvine, CA 92697, United States
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11
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Karri S, Singh S, Paripati AK, Marada A, Krishnamoorthy T, Guruprasad L, Balasubramanian D, Sepuri NBV. Adaptation of Mge1 to oxidative stress by local unfolding and altered Interaction with mitochondrial Hsp70 and Mxr2. Mitochondrion 2019; 46:140-148. [DOI: 10.1016/j.mito.2018.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/19/2018] [Accepted: 04/04/2018] [Indexed: 10/17/2022]
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12
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Walgenbach DG, Gregory AJ, Klein JC. Unique methionine-aromatic interactions govern the calmodulin redox sensor. Biochem Biophys Res Commun 2018; 505:236-241. [PMID: 30243720 DOI: 10.1016/j.bbrc.2018.09.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/08/2018] [Indexed: 10/28/2022]
Abstract
Calmodulin contains multiple redox sensitive methionines whose oxidation alters the regulation of numerous targets. Molecular dynamics simulations were used to define the molecular principles that govern how calmodulin is structurally poised to detect and respond to methionine oxidation. We found that calmodulin's open and closed states were preferentially stabilized by unique, redox sensitive, methionine-aromatic interactions. Key methionine-aromatic interactions were coupled to reorientation of EF hand helices. Methionine to glutamine substitutions designed to mimic methionine oxidation strongly altered conformational transitions by modulating the strength of methionine-aromatic interactions. Together, these results suggest a broadly applicable redox sensing mechanism though which methionine oxidation by cellular oxidants alters the strength of methionine-aromatic interactions critical for functional protein dynamics.
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Affiliation(s)
| | - Andrew J Gregory
- University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI, USA
| | - Jennifer C Klein
- University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI, USA.
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13
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Yadahalli S, Li J, Lane DP, Gosavi S, Verma CS. Characterizing the conformational landscape of MDM2-binding p53 peptides using Molecular Dynamics simulations. Sci Rep 2017; 7:15600. [PMID: 29142290 PMCID: PMC5688104 DOI: 10.1038/s41598-017-15930-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/03/2017] [Indexed: 11/09/2022] Open
Abstract
The conformational landscapes of p53 peptide variants and phage derived peptide (12/1) variants, all known to bind to MDM2, are studied using hamiltonian replica exchange molecular dynamics simulations. Complementing earlier observations, the current study suggests that the p53 peptides largely follow the ‘conformational selection’ paradigm in their recognition of and complexation by MDM2 while the 12/1 peptides likely undergo some element of conformational selection but are mostly driven by ‘binding induced folding’. This hypothesis is further supported by pulling simulations that pull the peptides away from their bound states with MDM2. This data extends the earlier mechanisms proposed to rationalize the entropically driven binding of the p53 set and the enthalpically driven binding of the 12/1 set. Using our hypothesis, we suggest mutations to the 12/1 peptide that increase its helicity in simulations and may, in turn, shift the binding towards conformational selection. In summary, understanding the conformational landscapes of the MDM2-binding peptides may suggest new peptide designs with bespoke binding mechanisms.
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Affiliation(s)
- Shilpa Yadahalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, 560065, India.,Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Manipal University, Madhav Nagar, Manipal, 576104, India.,p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648, Singapore
| | - Jianguo Li
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Singapore Eye Research Institute, 11 Third Hospital Avenue, #06-00, Singapore, 168751, Singapore
| | - David P Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648, Singapore
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, 560065, India
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore. .,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 11758, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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14
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Disrupting the cortical actin cytoskeleton points to two distinct mechanisms of yeast [PSI+] prion formation. PLoS Genet 2017; 13:e1006708. [PMID: 28369054 PMCID: PMC5393896 DOI: 10.1371/journal.pgen.1006708] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 04/17/2017] [Accepted: 03/20/2017] [Indexed: 02/04/2023] Open
Abstract
Mammalian and fungal prions arise de novo; however, the mechanism is poorly understood in molecular terms. One strong possibility is that oxidative damage to the non-prion form of a protein may be an important trigger influencing the formation of its heritable prion conformation. We have examined the oxidative stress-induced formation of the yeast [PSI+] prion, which is the altered conformation of the Sup35 translation termination factor. We used tandem affinity purification (TAP) and mass spectrometry to identify the proteins which associate with Sup35 in a tsa1 tsa2 antioxidant mutant to address the mechanism by which Sup35 forms the [PSI+] prion during oxidative stress conditions. This analysis identified several components of the cortical actin cytoskeleton including the Abp1 actin nucleation promoting factor, and we show that deletion of the ABP1 gene abrogates oxidant-induced [PSI+] prion formation. The frequency of spontaneous [PSI+] prion formation can be increased by overexpression of Sup35 since the excess Sup35 increases the probability of forming prion seeds. In contrast to oxidant-induced [PSI+] prion formation, overexpression-induced [PSI+] prion formation was only modestly affected in an abp1 mutant. Furthermore, treating yeast cells with latrunculin A to disrupt the formation of actin cables and patches abrogated oxidant-induced, but not overexpression-induced [PSI+] prion formation, suggesting a mechanistic difference in prion formation. [PIN+], the prion form of Rnq1, localizes to the IPOD (insoluble protein deposit) and is thought to influence the aggregation of other proteins. We show Sup35 becomes oxidized and aggregates during oxidative stress conditions, but does not co-localize with Rnq1 in an abp1 mutant which may account for the reduced frequency of [PSI+] prion formation. Prions are infectious agents which are composed of misfolded proteins and have been implicated in progressive neurodegenerative diseases such as Creutzfeldt Jakob Disease (CJD). Most prion diseases occur sporadically and are then propagated in a protein-only mechanism via induced protein misfolding. Little is currently known regarding how normally soluble proteins spontaneously form their prion forms. Previous studies have implicated oxidative damage of the non-prion form of some proteins as an important trigger for the formation of their heritable prion conformation. Using a yeast prion model we found that the cortical actin cytoskeleton is required for the transition of an oxidized protein to its heritable infectious conformation. In mutants which disrupt the cortical actin cytoskeleton, the oxidized protein aggregates, but does not localize to its normal amyloid deposition site, termed the IPOD. The IPOD serves as a site where prion proteins undergo fragmentation and seeding and we show that preventing actin-mediated localization to this site prevents both spontaneous and oxidant-induced prion formation.
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15
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Kadumuri RV, Gullipalli J, Subramanian S, Jaipuria G, Atreya HS, Vadrevu R. Crowding interactions perturb structure and stability by destabilizing the stable core of the α-subunit of tryptophan synthase. FEBS Lett 2016; 590:2096-105. [PMID: 27311646 DOI: 10.1002/1873-3468.12259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/06/2016] [Accepted: 06/13/2016] [Indexed: 11/12/2022]
Abstract
The consequences of crowding derived from relatively small and intrinsically disordered proteins are not clear yet. We report the effect of ficoll-70 on the structure and stability of native and partially folded states of the 29 kDa alpha subunit of tryptophan synthase (αTS). Overall, combining the changes in the circular dichroism and fluorescence spectra, in conjunction with the gradual loss of cooperativity under urea denaturation in the presence of increasing amounts of ficoll, it may be concluded that the crowding agent perturbs not only the native state but also the partially folded state of αTS. Importantly, NMR data indicate that ficoll interacts with the residues that constitute the stable core of the protein thus shedding light on the origin of the observed perturbation.
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Affiliation(s)
- Rajashekar Varma Kadumuri
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Jagadeesh Gullipalli
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - SriVidya Subramanian
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Garima Jaipuria
- NMR Research Centre, Indian Institute of Science, Bangalore, India
| | | | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
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16
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Guitart K, Loers G, Buck F, Bork U, Schachner M, Kleene R. Improvement of neuronal cell survival by astrocyte-derived exosomes under hypoxic and ischemic conditions depends on prion protein. Glia 2016; 64:896-910. [PMID: 26992135 DOI: 10.1002/glia.22963] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 12/18/2015] [Indexed: 02/05/2023]
Abstract
Prion protein (PrP) protects neural cells against oxidative stress, hypoxia, ischemia, and hypoglycemia. In the present study we confirm that cultured PrP-deficient neurons are more sensitive to oxidative stress than wild-type neurons and present the novel findings that wild-type, but not PrP-deficient astrocytes protect wild-type cerebellar neurons against oxidative stress and that exosomes released from stressed wild-type, but not from stressed PrP-deficient astrocytes reduce neuronal cell death induced by oxidative stress. We show that neuroprotection by exosomes of stressed astrocytes depends on exosomal PrP but not on neuronal PrP and that astrocyte-derived exosomal PrP enters into neurons, suggesting neuronal uptake of astrocyte-derived exosomes. Upon exposure of wild-type astrocytes to hypoxic or ischemic conditions PrP levels in exosomes were increased. By mass spectrometry and Western blot analysis, we detected increased levels of 37/67 kDa laminin receptor, apolipoprotein E and the ribosomal proteins S3 and P0, and decreased levels of clusterin/apolipoprotein J in exosomes from wild-type astrocytes exposed to oxygen/glucose deprivation relative to exosomes from astrocytes maintained under normoxic conditions. The levels of these proteins were not altered in exosomes from stressed PrP-deficient astrocytes relative to unstressed PrP-deficient astrocytes. These results indicate that PrP in astrocytes is a sensor for oxidative stress and mediates beneficial cellular responses, e.g. release of exosomes carrying PrP and other molecules, resulting in improved survival of neurons under hypoxic and ischemic conditions.
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Affiliation(s)
- Kathrin Guitart
- Zentrum Für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Loers
- Zentrum Für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Buck
- Institut Für Klinische Chemie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Ute Bork
- Zentrum Für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Melitta Schachner
- Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey
- Center for Neuroscience, Shantou University Medical College, Shantou, Guangdong, China
| | - Ralf Kleene
- Zentrum Für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
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17
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Abstract
The molecular basis by which fungal and mammalian prions arise spontaneously is poorly understood. A number of different environmental stress conditions are known to increase the frequency of yeast [PSI(+)] prion formation in agreement with the idea that conditions which cause protein misfolding may promote the conversion of normally soluble proteins to their amyloid forms. A recent study from our laboratory has shown that the de novo formation of the [PSI(+)] prion is significantly increased in yeast mutants lacking key antioxidants suggesting that endogenous reactive oxygen species are sufficient to promote prion formation. Our findings strongly implicate oxidative damage of Sup35 as an important trigger for the formation of the heritable [PSI(+)] prion in yeast. This review discusses the mechanisms by which the direct oxidation of Sup35 might lead to structural transitions favoring conversion to the transmissible amyloid-like form. This is analogous to various environmental factors which have been proposed to trigger misfolding of the mammalian prion protein (PrP(C)) into the aggregated scrapie form (PrP(Sc)).
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Affiliation(s)
- Chris M Grant
- a Faculty of Life Sciences; University of Manchester ; Manchester , UK
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18
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Virrueta A, O'Hern CS, Regan L. Understanding the physical basis for the side‐chain conformational preferences of methionine. Proteins 2016; 84:900-11. [DOI: 10.1002/prot.25026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/17/2016] [Accepted: 02/03/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Alejandro Virrueta
- Department of Mechanical Engineering & Materials ScienceYale UniversityNew Haven Connecticut
- Integrated Graduate Program in Physical & Engineering BiologyYale UniversityNew Haven Connecticut
| | - Corey S. O'Hern
- Department of Mechanical Engineering & Materials ScienceYale UniversityNew Haven Connecticut
- Integrated Graduate Program in Physical & Engineering BiologyYale UniversityNew Haven Connecticut
- Department of PhysicsYale UniversityNew Haven Connecticut
- Department of Applied PhysicsYale UniversityNew Haven Connecticut
| | - Lynne Regan
- Integrated Graduate Program in Physical & Engineering BiologyYale UniversityNew Haven Connecticut
- Department of Molecular Biophysics & BiochemistryYale UniversityNew Haven Connecticut
- Department of ChemistryYale UniversityNew Haven Connecticut
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19
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Roles of methionine oxidation in E200K prion protein misfolding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:346-58. [DOI: 10.1016/j.bbapap.2016.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 01/05/2016] [Accepted: 01/05/2016] [Indexed: 01/20/2023]
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20
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Arcos-López T, Qayyum M, Rivillas-Acevedo L, Miotto MC, Grande-Aztatzi R, Fernández CO, Hedman B, Hodgson KO, Vela A, Solomon EI, Quintanar L. Spectroscopic and Theoretical Study of Cu(I) Binding to His111 in the Human Prion Protein Fragment 106-115. Inorg Chem 2016; 55:2909-22. [PMID: 26930130 PMCID: PMC4804749 DOI: 10.1021/acs.inorgchem.5b02794] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
The ability of the cellular prion
protein (PrPC) to bind copper in vivo points to a physiological
role for PrPC in copper transport. Six copper binding sites
have been identified in the nonstructured N-terminal region of human
PrPC. Among these sites, the His111 site is unique in that
it contains a MKHM motif that would confer interesting CuI and CuII binding properties. We have evaluated CuI coordination to the PrP(106–115) fragment of the human
PrP protein, using NMR and X-ray absorption spectroscopies and electronic
structure calculations. We find that Met109 and Met112 play an important
role in anchoring this metal ion. CuI coordination to His111
is pH-dependent: at pH >8, 2N1O1S species are formed with one Met
ligand; in the range of pH 5–8, both methionine (Met) residues
bind to CuI, forming a 1N1O2S species, where N is from
His111 and O is from a backbone carbonyl or a water molecule; at pH
<5, only the two Met residues remain coordinated. Thus, even upon
drastic changes in the chemical environment, such as those occurring
during endocytosis of PrPC (decreased pH and a reducing
potential), the two Met residues in the MKHM motif enable PrPC to maintain the bound CuI ions, consistent with
a copper transport function for this protein. We also find that the
physiologically relevant CuI-1N1O2S species activates dioxygen
via an inner-sphere mechanism, likely involving the formation of a
copper(II) superoxide complex. In this process, the Met residues are
partially oxidized to sulfoxide; this ability to scavenge superoxide
may play a role in the proposed antioxidant properties of PrPC. This study provides further insight into the CuI coordination properties of His111 in human PrPC and the
molecular mechanism of oxygen activation by this site. CuI coordination to the His111 site in the HuPrP protein
is highly dependent on the pH: at pH <5, two methionine (Met) residues
bind CuI; in the range of pH 5−8, both Met residues
remain coordinated, forming a 1N1O2S species, with N from His111 and
O from a backbone carbonyl or a water molecule; at pH >8, 2N1O1S
species are formed with only a Met ligand. The CuI-1N1O2S
species activates dioxygen, and in this process, the Met residues
are partially oxidized to sulfoxide.
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Affiliation(s)
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University , Stanford, California 94395, United States
| | | | - Marco C Miotto
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and Instituto de Investigaciones para el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda , S2002LRK Rosario, Argentina
| | | | - Claudio O Fernández
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and Instituto de Investigaciones para el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda , S2002LRK Rosario, Argentina
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC, Stanford University , Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University , Stanford, California 94395, United States.,Stanford Synchrotron Radiation Lightsource (SSRL), SLAC, Stanford University , Menlo Park, California 94025, United States
| | - Alberto Vela
- Departamento de Química, Cinvestav , Gustavo A. Madero, 07360 México
| | - Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94395, United States.,Stanford Synchrotron Radiation Lightsource (SSRL), SLAC, Stanford University , Menlo Park, California 94025, United States
| | - Liliana Quintanar
- Departamento de Química, Cinvestav , Gustavo A. Madero, 07360 México
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Singh J, Udgaonkar JB. The Pathogenic Mutation T182A Converts the Prion Protein into a Molten Globule-like Conformation Whose Misfolding to Oligomers but Not to Fibrils Is Drastically Accelerated. Biochemistry 2016; 55:459-69. [DOI: 10.1021/acs.biochem.5b01266] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jogender Singh
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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22
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Milisav I, Šuput D, Ribarič S. Unfolded Protein Response and Macroautophagy in Alzheimer's, Parkinson's and Prion Diseases. Molecules 2015; 20:22718-56. [PMID: 26694349 PMCID: PMC6332363 DOI: 10.3390/molecules201219865] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/30/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022] Open
Abstract
Proteostasis are integrated biological pathways within cells that control synthesis, folding, trafficking and degradation of proteins. The absence of cell division makes brain proteostasis susceptible to age-related changes and neurodegeneration. Two key processes involved in sustaining normal brain proteostasis are the unfolded protein response and autophagy. Alzheimer’s disease (AD), Parkinson’s disease (PD) and prion diseases (PrDs) have different clinical manifestations of neurodegeneration, however, all share an accumulation of misfolded pathological proteins associated with perturbations in unfolded protein response and macroautophagy. While both the unfolded protein response and macroautophagy play an important role in the prevention and attenuation of AD and PD progression, only macroautophagy seems to play an important role in the development of PrDs. Macroautophagy and unfolded protein response can be modulated by pharmacological interventions. However, further research is necessary to better understand the regulatory pathways of both processes in health and neurodegeneration to be able to develop new therapeutic interventions.
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Affiliation(s)
- Irina Milisav
- Institute of Pathophysiology, Faculty of Medicine, Zaloška 4, Ljubljana SI-1000, Slovenia.
- Faculty of Health Sciences, Zdravstvena pot 5, SI-1000 Ljubljana, Slovenija.
| | - Dušan Šuput
- Institute of Pathophysiology, Faculty of Medicine, Zaloška 4, Ljubljana SI-1000, Slovenia.
| | - Samo Ribarič
- Institute of Pathophysiology, Faculty of Medicine, Zaloška 4, Ljubljana SI-1000, Slovenia.
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23
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Abstract
Intracellular proteolysis is critical to maintain timely degradation of altered proteins including oxidized proteins. This review attempts to summarize the most relevant findings about oxidant protein modification, as well as the impact of reactive oxygen species on the proteolytic systems that regulate cell response to an oxidant environment: the ubiquitin-proteasome system (UPS), autophagy and the unfolded protein response (UPR). In the presence of an oxidant environment, these systems are critical to ensure proteostasis and cell survival. An example of altered degradation of oxidized proteins in pathology is provided for neurodegenerative diseases. Future work will determine if protein oxidation is a valid target to combat proteinopathies. Proteins undergo reversible and irreversible redox modifications. Oxidized proteins are cleared mainly through the 20S proteasome and autophagy. The proteolytic systems exhibit a dynamic crosstalk to adapt to redox alterations. Protein oxidation together with impaired degradation are linked to neurodegeneration.
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24
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Haigh CL, Drew SC. Cavitation during the protein misfolding cyclic amplification (PMCA) method – The trigger for de novo prion generation? Biochem Biophys Res Commun 2015; 461:494-500. [DOI: 10.1016/j.bbrc.2015.04.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/07/2015] [Indexed: 12/14/2022]
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25
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Silva CJ. Applying the tools of chemistry (mass spectrometry and covalent modification by small molecule reagents) to the detection of prions and the study of their structure. Prion 2015; 8:42-50. [PMID: 24509645 DOI: 10.4161/pri.27891] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Prions are molecular pathogens, able to convert a normal cellular prion protein (PrP(C)) into a prion (PrP(Sc)). The information necessary for this conversion is contained in the conformation of PrP(Sc). Mass spectrometry (MS) and small-molecule covalent reactions have been used to study prions. Mass spectrometry has been used to detect and quantitate prions in the attomole range (10⁻¹⁸ mole). MS-based analysis showed that both possess identical amino acid sequences, one disulfide bond, a GPI anchor, asparagine-linked sugar antennae, and unoxidized methionines. Mass spectrometry has been used to define elements of the secondary and tertiary structure of wild-type PrP(Sc) and GPI-anchorless PrP(Sc). It has also been used to study the quaternary structure of the PrP(Sc) multimer. Small molecule reagents react differently with the same lysine in the PrP(C) conformation than in the PrP(Sc) conformation. Such differences can be detected by Western blot using mAbs with lysine-containing epitopes, such as 3F4 and 6D11. This permits the detection of PrP(Sc) without the need for proteinase K pretreatment and can be used to distinguish among prion strains. These results illustrate how two important chemical tools, mass spectrometry and covalent modification by small molecules, are being applied to the detection and structural study of prions. Furthermore these tools are or can be applied to the study of the other protein misfolding diseases such as Alzheimer Disease, Parkinson Disease, or ALS.
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26
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Doronina VA, Staniforth GL, Speldewinde SH, Tuite MF, Grant CM. Oxidative stress conditions increase the frequency of de novo formation of the yeast [PSI+] prion. Mol Microbiol 2015; 96:163-74. [PMID: 25601439 PMCID: PMC4407919 DOI: 10.1111/mmi.12930] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2015] [Indexed: 01/09/2023]
Abstract
Prions are self‐perpetuating amyloid protein aggregates which underlie various neurodegenerative diseases in mammals and heritable traits in yeast. The molecular basis of how yeast and mammalian prions form spontaneously into infectious amyloid‐like structures is poorly understood. We have explored the hypothesis that oxidative stress is a general trigger for prion formation using the yeast [PSI+] prion, which is the altered conformation of the Sup35 translation termination factor. We show that the frequency of [PSI+] prion formation is elevated under conditions of oxidative stress and in mutants lacking key antioxidants. We detect increased oxidation of Sup35 methionine residues in antioxidant mutants and show that overexpression of methionine sulphoxide reductase abrogates both the oxidation of Sup35 and its conversion to the [PSI+] prion. [PSI+] prion formation is particularly elevated in a mutant lacking the Sod1 Cu,Zn‐superoxide dismutase. We have used fluorescence microscopy to show that the de novo appearance of [PSI+] is both rapid and increased in frequency in this mutant. Finally, electron microscopy analysis of native Sup35 reveals that similar fibrillar structures are formed in both the wild‐type and antioxidant mutants. Together, our data indicate that oxidative stress is a general trigger of [PSI+] formation, which can be alleviated by antioxidant defenses.
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Affiliation(s)
- Victoria A Doronina
- Faculty of Life Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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27
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McCarthy MR, Thompson AR, Nitu F, Moen RJ, Olenek MJ, Klein JC, Thomas DD. Impact of methionine oxidation on calmodulin structural dynamics. Biochem Biophys Res Commun 2014; 456:567-72. [PMID: 25478640 DOI: 10.1016/j.bbrc.2014.11.091] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 12/22/2022]
Abstract
We have used electron paramagnetic resonance (EPR) to examine the structural impact of oxidizing specific methionine (M) side chains in calmodulin (CaM). It has been shown that oxidation of either M109 or M124 in CaM diminishes CaM regulation of the muscle calcium release channel, the ryanodine receptor (RyR), and that mutation of M to Q (glutamine) in either case produces functional effects identical to those of oxidation. Here we have used site-directed spin labeling and double electron-electron resonance (DEER), a pulsed EPR technique that measures distances between spin labels, to characterize the structural changes resulting from these mutations. Spin labels were attached to a pair of introduced cysteine residues, one in the C-lobe (T117C) and one in the N-lobe (T34C) of CaM, and DEER was used to determine the distribution of interspin distances. Ca binding induced a large increase in the mean distance, in concert with previous X-ray crystallography and NMR data, showing a closed structure in the absence of Ca and an open structure in the presence of Ca. DEER revealed additional information about CaM's structural heterogeneity in solution: in both the presence and absence of Ca, CaM populates both structural states, one with probes separated by ∼4nm (closed) and another at ∼6nm (open). Ca shifts the structural equilibrium constant toward the open state by a factor of 13. DEER reveals the distribution of interprobe distances, showing that each of these states is itself partially disordered, with the width of each population ranging from 1 to 3nm. Both mutations (M109Q and M124Q) decrease the effect of Ca on the structure of CaM, primarily by decreasing the closed-to-open equilibrium constant in the presence of Ca. We propose that Met oxidation alters CaM's functional interaction with its target proteins by perturbing this Ca-dependent structural shift.
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Affiliation(s)
- Megan R McCarthy
- Biochemistry, Molecular Biology and Biophysics Department, University of Minnesota, Minneapolis, MN 55455, USA
| | - Andrew R Thompson
- Biochemistry, Molecular Biology and Biophysics Department, University of Minnesota, Minneapolis, MN 55455, USA
| | - Florentin Nitu
- Biochemistry, Molecular Biology and Biophysics Department, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rebecca J Moen
- Chemistry and Geology Department, Minnesota State University, Mankato, MN 56001, USA
| | - Michael J Olenek
- Biology Department, University of Wisconsin, La Crosse, WI 54601, USA
| | - Jennifer C Klein
- Biology Department, University of Wisconsin, La Crosse, WI 54601, USA.
| | - David D Thomas
- Biochemistry, Molecular Biology and Biophysics Department, University of Minnesota, Minneapolis, MN 55455, USA.
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28
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Doolan KM, Colby DW. Conformation-dependent epitopes recognized by prion protein antibodies probed using mutational scanning and deep sequencing. J Mol Biol 2014; 427:328-40. [PMID: 25451031 DOI: 10.1016/j.jmb.2014.10.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 11/24/2022]
Abstract
Prion diseases are caused by a structural rearrangement of the cellular prion protein, PrP(C), into a disease-associated conformation, PrP(Sc), which may be distinguished from one another using conformation-specific antibodies. We used mutational scanning by cell-surface display to screen 1341 PrP single point mutants for attenuated interaction with four anti-PrP antibodies, including several with conformational specificity. Single-molecule real-time gene sequencing was used to quantify enrichment of mutants, returning 26,000 high-quality full-length reads for each screened population on average. Relative enrichment of mutants correlated to the magnitude of the change in binding affinity. Mutations that diminished binding of the antibody ICSM18 represented the core of contact residues in the published crystal structure of its complex. A similarly located binding site was identified for D18, comprising discontinuous residues in helix 1 of PrP, brought into close proximity to one another only when the alpha helix is intact. The specificity of these antibodies for the normal form of PrP likely arises from loss of this conformational feature after conversion to the disease-associated form. Intriguingly, 6H4 binding was found to depend on interaction with the same residues, among others, suggesting that its ability to recognize both forms of PrP depends on a structural rearrangement of the antigen. The application of mutational scanning and deep sequencing provides residue-level resolution of positions in the protein-protein interaction interface that are critical for binding, as well as a quantitative measure of the impact of mutations on binding affinity.
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Affiliation(s)
- Kyle M Doolan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - David W Colby
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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29
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Moen RJ, Cornea S, Oseid DE, Binder BP, Klein JC, Thomas DD. Redox-sensitive residue in the actin-binding interface of myosin. Biochem Biophys Res Commun 2014; 453:345-9. [PMID: 25264102 PMCID: PMC4272649 DOI: 10.1016/j.bbrc.2014.09.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 09/18/2014] [Indexed: 12/22/2022]
Abstract
We have examined the chemical and functional reversibility of oxidative modification in myosin. Redox regulation has emerged as a crucial modulator of protein function, with particular relevance to aging. We previously identified a single methionine residue in Dictyostelium discoideum (Dicty) myosin II (M394, near the myosin cardiomyopathy loop in the actin-binding interface) that is functionally sensitive to oxidation. We now show that oxidation of M394 is reversible by methionine sulfoxide reductase (Msr), restoring actin-activated ATPase activity. Sequence alignment reveals that M394 of Dicty myosin II is a cysteine residue in all human isoforms of skeletal and cardiac myosin. Using Dicty myosin II as a model for site-specific redox sensitivity of this Cys residue, the M394C mutant can be glutathionylated in vitro, resulting in reversible inhibition of actin-activated ATPase activity, with effects similar to those of methionine oxidation at this site. This work illustrates the potential for myosin to function as a redox sensor in both non-muscle and muscle cells, modulating motility/contractility in response to oxidative stress.
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Affiliation(s)
- Rebecca J Moen
- Department of Chemistry and Geology, Minnesota State University, Mankato, MN 56001, United States
| | - Sinziana Cornea
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Daniel E Oseid
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Benjamin P Binder
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Jennifer C Klein
- Department of Biology, University of Wisconsin, Lacrosse, Lacrosse, MN 54601, United States
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States.
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Feng B, Wang Z, Liu T, Jin R, Wang S, Wang W, Xiao G, Zhou Z. Methionine oxidation accelerates the aggregation and enhances the neurotoxicity of the D178N variant of the human prion protein. Biochim Biophys Acta Mol Basis Dis 2014; 1842:2345-56. [PMID: 25281825 DOI: 10.1016/j.bbadis.2014.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/27/2014] [Accepted: 09/24/2014] [Indexed: 12/30/2022]
Abstract
The D178N mutation of the prion protein (PrP) results in the hereditary prion disease fatal familial insomnia (FFI). Little is known regarding the effects of methionine oxidation on the pathogenesis of D178N-associated FFI. In the present study, we found that the D178N variant was more susceptible to oxidation than wild-type PrP, as indicated by reverse-phase high performance liquid chromatography (RP-HPLC) and mass spectrometry (MS) analysis. Circular dichroism (CD), differential scanning calorimetry (DSC), thioflavin T (ThT) binding assay studies demonstrated that methionine oxidation decreased the structural stability of the D178N variant, and the oxidized D178N variant exhibited a greater propensity to form β-sheet-rich oligomers and aggregates. Moreover, these aggregates of oxidized D178N PrP were more resistant to proteinase K (PK) digestion. Additionally, using fluorescence confocal microscopy, we detected a high degree of aggregation in D178N-transfected Neuro-2a (N2a) cells after treatment with hydrogen peroxide (H2O2). Furthermore, the oxidation and consequent aggregation of the D178N variant induced greater apoptosis of N2a cells, as monitored using flow cytometry. Collectively, these observations suggest that methionine oxidation accelerates the aggregation and enhances the neurotoxicity of the D178N variant, possibly providing direct evidence to link the pathogenesis of D178N-associated FFI with methionine oxidation.
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Affiliation(s)
- Boya Feng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Zonglin Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Ting Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Rui Jin
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Shaobo Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Wei Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
| | - Zheng Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
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31
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Stanyon HF, Patel K, Begum N, Viles JH. Copper(II) sequentially loads onto the N-terminal amino group of the cellular prion protein before the individual octarepeats. Biochemistry 2014; 53:3934-99. [PMID: 24878028 DOI: 10.1021/bi500643b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cellular prion protein (PrPC) binds to Cu2+ ions in vivo, and a misfolded form of PrPC is responsible for a range of transmissible spongiform encephalopathies. Recently, disruption of Cu2+ homeostasis in mice has been shown to impart resistance to scrapie infection. Using full-length PrPC and model peptide fragments, we monitor the sequential loading of Cu2+ ions onto PrPC using visible circular dichroism. We show the N-terminal amino group of PrPC is not the principal binding site for Cu2+; however, surprisingly, it has an affinity for Cu2+ tighter than that of the individual octarepeat binding sites present within PrPC. We re-evaluate what is understood about the sequential loading of Cu2+ onto the full-length protein and show for the first time that Cu2+ loads onto the N-terminal amino group before the single octarepeat binding sites.
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32
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Moen RJ, Klein JC, Thomas DD. Electron paramagnetic resonance resolves effects of oxidative stress on muscle proteins. Exerc Sport Sci Rev 2014; 42:30-6. [PMID: 24188980 DOI: 10.1249/jes.0000000000000004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have used site-directed spin labeling and electron paramagnetic resonance (EPR) to explore the effects of oxidation on muscle function, with particular focus on the actin-myosin interaction. EPR measurements show that aging or oxidative modification causes a decrease in the fraction of myosins in the strong-binding state, which can be traced to the actin-binding cleft of the myosin catalytic domain.
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Affiliation(s)
- Rebecca J Moen
- 1Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN; 2Department of Chemistry and Geology, Minnesota State University, Mankato, Mankato, MN; and 3Department of Biology, University of Wisconsin, Lacrosse, Lacrosse, WI
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Serpa JJ, Makepeace KAT, Borchers TH, Wishart DS, Petrotchenko EV, Borchers CH. Using isotopically-coded hydrogen peroxide as a surface modification reagent for the structural characterization of prion protein aggregates. J Proteomics 2013; 100:160-6. [PMID: 24316355 DOI: 10.1016/j.jprot.2013.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 10/29/2013] [Accepted: 11/25/2013] [Indexed: 12/20/2022]
Abstract
UNLABELLED The conversion of the cellular prion protein (PrP(C)) into aggregated ß-oligomeric (PrP(ß)) and fibril (PrP(Sc)) forms is the central element in the development of prion diseases. Here we report the first use of isotopically-coded hydrogen peroxide surface modification combined with mass spectrometry (MS) for the differential characterization of PrP(C) and PrP(β). (16)O and (18)O hydrogen peroxide were used to oxidize methionine and tryptophan residues in PrP(C) and PrP(β), allowing for the relative quantitation of the extent of modification of each form of the prion protein. After modification with either light or heavy forms of hydrogen peroxide (H2(16)O2 and H2(18)O2), the PrP(C) and PrP(β) forms of the protein were then combined, digested with trypsin, and analysed by LC-MS. The (18)O/(16)O signal intensity ratios were used to determine the relative levels of oxidation of specific amino acids in the PrP(C) and PrP(β) forms. Using this approach we have detected several residues that are differentially-oxidized between the native and β-oligomeric prion forms, allowing determination of the regions of PrP(C) involved in the formation of PrP(β) aggregates. Modification of these residues in the β-oligomeric form is compatible with a flip of the β1-H1-β2 loop away from amphipathic helices 2 and 3 during conversion. BIOLOGICAL SIGNIFICANCE Surface modification using isotopically-coded hydrogen peroxide has allowed quantitative comparison of the exposure of methionine and tryptophan residues in PrP(C) and PrP(ß) forms of prion protein. Detected changes in surface exposure of a number of residues have indicated portions of the PrP structure which undergo conformational transition upon conversion. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- Jason J Serpa
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Karl A T Makepeace
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Tristan H Borchers
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - David S Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada
| | - Evgeniy V Petrotchenko
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Christoph H Borchers
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada; University of Victoria, Department of Biochemistry & Microbiology, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.
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Elmallah MIY, Borgmeyer U, Betzel C, Redecke L. Impact of methionine oxidation as an initial event on the pathway of human prion protein conversion. Prion 2013; 7:404-11. [PMID: 24121542 DOI: 10.4161/pri.26745] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Prion diseases comprise a group of fatal neurodegenerative disorders characterized by the autocatalytic conversion of the cellular prion protein PrP(C) into the infectious misfolded isoform PrP(Sc). Increasing evidence supports a specific role of oxidative stress in the onset of pathogenesis. Although the associated molecular mechanisms remain to be elucidated in detail, several studies currently suggest that methionine oxidation already detected in misfolded PrP(Sc) destabilizes the native PrP fold as an early event in the conversion pathway. To obtain more insights about the specific impact of surface-exposed methionine residues on the oxidative-induced conversion of human PrP we designed, produced, and comparatively investigated two new pseudosulfoxidation mutants of human PrP 121-231 that comprises the well-folded C-terminal domain. Applying circular dichroism spectroscopy and dynamic light scattering techniques we showed that pseudosulfoxidation of all surface exposed Met residues formed a monomeric molten globule-like species with striking similarities to misfolding intermediates recently reported by other groups. However, individual pseudosulfoxidation at the polymorphic M129 site did not significantly contribute to the structural destabilization. Further metal-induced oxidation of the partly unfolded pseudosulfoxidation mutant resulted in the formation of an oligomeric state that shares a comparable size and stability with PrP oligomers detected after the application of different other triggers for structural conversion, indicating a generic misfolding pathway of PrP. The obtained results highlight the specific importance of methionine oxidation at surface exposed residues for PrP misfolding, strongly supporting the hypothesis that increased oxidative stress could be one causative event for sporadic prion diseases and other neurodegenerative disorders.
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Affiliation(s)
- Mohammed I Y Elmallah
- Institute of Biochemistry and Molecular Biology; Department of Chemistry; University of Hamburg, c/o DESY; Hamburg, Germany
| | - Uwe Borgmeyer
- Institute for Molecular and Cellular Cognition; Center for Molecular Neurobiology (ZMNH); University Medical Center Eppendorf; Hamburg, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology; Department of Chemistry; University of Hamburg, c/o DESY; Hamburg, Germany
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation; Institute of Biochemistry and Molecular Biology; University of Hamburg; and Institute of Biochemistry; University of Lübeck, c/o DESY; Hamburg, Germany
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Timmes AG, Moore RA, Fischer ER, Priola SA. Recombinant prion protein refolded with lipid and RNA has the biochemical hallmarks of a prion but lacks in vivo infectivity. PLoS One 2013; 8:e71081. [PMID: 23936256 PMCID: PMC3728029 DOI: 10.1371/journal.pone.0071081] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/24/2013] [Indexed: 11/21/2022] Open
Abstract
During prion infection, the normal, protease-sensitive conformation of prion protein (PrPC) is converted via seeded polymerization to an abnormal, infectious conformation with greatly increased protease-resistance (PrPSc). In vitro, protein misfolding cyclic amplification (PMCA) uses PrPSc in prion-infected brain homogenates as an initiating seed to convert PrPC and trigger the self-propagation of PrPSc over many cycles of amplification. While PMCA reactions produce high levels of protease-resistant PrP, the infectious titer is often lower than that of brain-derived PrPSc. More recently, PMCA techniques using bacterially derived recombinant PrP (rPrP) in the presence of lipid and RNA but in the absence of any starting PrPSc seed have been used to generate infectious prions that cause disease in wild-type mice with relatively short incubation times. These data suggest that lipid and/or RNA act as cofactors to facilitate the de novo formation of high levels of prion infectivity. Using rPrP purified by two different techniques, we generated a self-propagating protease-resistant rPrP molecule that, regardless of the amount of RNA and lipid used, had a molecular mass, protease resistance and insolubility similar to that of PrPSc. However, we were unable to detect prion infectivity in any of our reactions using either cell-culture or animal bioassays. These results demonstrate that the ability to self-propagate into a protease-resistant insoluble conformer is not unique to infectious PrP molecules. They suggest that the presence of RNA and lipid cofactors may facilitate the spontaneous refolding of PrP into an infectious form while also allowing the de novo formation of self-propagating, but non-infectious, rPrP-res.
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Affiliation(s)
- Andrew G. Timmes
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Roger A. Moore
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Elizabeth R. Fischer
- Electron Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Suzette A. Priola
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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Sanchez-Garcia J, Arbelaez D, Jensen K, Rincon-Limas DE, Fernandez-Funez P. Polar substitutions in helix 3 of the prion protein produce transmembrane isoforms that disturb vesicle trafficking. Hum Mol Genet 2013; 22:4253-66. [PMID: 23771030 DOI: 10.1093/hmg/ddt276] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Prion diseases encompass a diverse group of neurodegenerative conditions characterized by the accumulation of misfolded prion protein (PrP) isoforms. Other conformational variants of PrP have also been proposed to contribute to neurotoxicity in prion diseases, including misfolded intermediates as well as cytosolic and transmembrane isoforms. To better understand PrP neurotoxicity, we analyzed the role of two highly conserved methionines in helix 3 on PrP biogenesis, folding and pathogenesis. Expression of the PrP-M205S and -M205,212S mutants in Drosophila led to hyperglycosylation, intracellular accumulation and widespread conformational changes due to failure of oxidative folding. Surprisingly, PrP-M205S and -M205,212S acquired a transmembrane topology (Ctm) previously linked to mutations in the signal peptide (SP) and the transmembrane domain (TMD). PrP-M205,212S also disrupted the accumulation of key neurodevelopmental proteins in lipid rafts, resulting in shortened axonal projections. These results uncover a new role for the hydrophobic domain in promoting oxidative folding and preventing the formation of neurotoxic Ctm PrP, mechanisms that may be relevant in the pathogenesis of both inherited and sporadic prion diseases.
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37
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Zhou Z, Xiao G. Conformational conversion of prion protein in prion diseases. Acta Biochim Biophys Sin (Shanghai) 2013; 45:465-76. [PMID: 23580591 DOI: 10.1093/abbs/gmt027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Prion diseases are a group of infectious fatal neurodegenerative diseases. The conformational conversion of a cellular prion protein (PrP(C)) into an abnormal misfolded isoform (PrP(Sc)) is the key event in prion diseases pathology. Under normal conditions, the high-energy barrier separates PrP(C) from PrP(Sc) isoform. However, pathogenic mutations, modifications as well as some cofactors, such as glycosaminoglycans, nucleic acids, and lipids, could modulate the conformational conversion process. Understanding the mechanism of conformational conversion of prion protein is essential for the biomedical research and the treatment of prion diseases. Particularly, the characterization of cofactors interacting with prion protein might provide new diagnostic and therapeutic strategies.
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Affiliation(s)
- Zheng Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Silva CJ, Dynin I, Erickson ML, Requena JR, Balachandran A, Hui C, Onisko BC, Carter JM. Oxidation of methionine 216 in sheep and elk prion protein is highly dependent upon the amino acid at position 218 but is not important for prion propagation. Biochemistry 2013; 52:2139-47. [PMID: 23458153 DOI: 10.1021/bi3016795] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We employed a sensitive mass spectrometry-based method to deconstruct, confirm, and quantitate the prions present in elk naturally infected with chronic wasting disease and sheep naturally infected with scrapie. We used this approach to study the oxidation of a methionine at position 216 (Met216), because this oxidation (MetSO216) has been implicated in prion formation. Three polymorphisms (Ile218, Val218, and Thr218) of sheep recombinant prion protein were prepared. Our analysis showed the novel result that the proportion of MetSO216 was highly dependent upon the amino acid residue at position 218 (I > V > T), indicating that Ile218 in sheep and elk prion protein (PrP) renders the Met216 intrinsically more susceptible to oxidation than the Val218 or Thr218 analogue. We were able to quantitate the prions in the attomole range. The presence of prions was verified by the detection of two confirmatory peptides: GENFTETDIK (sheep and elk) and ESQAYYQR (sheep) or ESEAYYQR (elk). This approach required much smaller amounts of tissue (600 μg) than traditional methods of detection (enzyme-linked immunosorbent assay, Western blot, and immunohistochemical analysis) (60 mg). In sheep and elk, a normal cellular prion protein containing MetSO216 is not actively recruited and converted to prions, although we observed that this Met216 is intrinsically more susceptible to oxidation.
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Affiliation(s)
- Christopher J Silva
- Western Regional Research Center, United States Department of Agriculture , Albany, California 94710, United States
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Huang X, Barnard J, Spitznagel TM, Krishnamurthy R. Protein Covalent Dimer Formation Induced by Reversed-Phase HPLC Conditions. J Pharm Sci 2013; 102:842-51. [DOI: 10.1002/jps.23431] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 11/15/2012] [Accepted: 12/05/2012] [Indexed: 11/12/2022]
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40
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Di Natale G, Ősz K, Kállay C, Pappalardo G, Sanna D, Impellizzeri G, Sóvágó I, Rizzarelli E. Affinity, speciation, and molecular features of copper(II) complexes with a prion tetraoctarepeat domain in aqueous solution: insights into old and new results. Chemistry 2013; 19:3751-61. [PMID: 23355367 DOI: 10.1002/chem.201202912] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/29/2012] [Indexed: 11/08/2022]
Abstract
Characterization of the copper(II) complexes formed with the tetraoctarepeat peptide at low and high metal-to-ligand ratios and in a large pH range, would provide a breakthrough in the interpretation of biological relevance of the different metal complexes of copper(II)-tetraoctarepeat system. In the present work, the potentiometric, UV/Vis, circular dichroism (CD), and electron paramagnetic resonance (EPR) studies were carried out on copper(II) complexes with a PEG-ylated derivative of the tetraoctarepeats peptide sequence (Ac-PEG27 -(PHGGGWGQ)4 -NH2 ) and the peptide Ac-(PHGGGWGQ)2 -NH2 . Conjugation of tetraoctarepeat peptide sequence with polyethyleneglycol improved the solubility of the copper(II) complexes. The results enable a straightforward explanation of the conflicting results originated from the underestimation of all metal-ligand equilibria and the ensuing speciation. A complete and reliable speciation is therefore obtained with the released affinity and binding details of the main complexes species formed in aqueous solution. The results contribute to clarify the discrepancies of several studies in which the authors ascribe the redox activity of copper(II)-tetraoctarepeat system considering only the average effects of several coexisting species with very different stoichiometries and binding modes.
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Affiliation(s)
- Giuseppe Di Natale
- CNR Institute of Biostructures and Bioimaging, V.le A. Doria 6, 95125 Catania, Italy
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