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Silva CJ, Erickson-Beltran ML. General Method of Quantifying the Extent of Methionine Oxidation in the Prion Protein. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:255-263. [PMID: 36608322 DOI: 10.1021/jasms.2c00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The normal cellular prion protein (PrPC) and its infectious conformer, PrPSc, possess a disproportionately greater amount of methionines than would be expected for a typical mammalian protein. The thioether of methionine can be readily oxidized to the corresponding sulfoxide, which means that oxidation of methionine can be used to map the surface of the conformation of PrPC or PrPSc, as covalent changes are retained after denaturation. We identified a set of peptides (TNMK, MLGSAMSR, LLGSAMSR, PMIHFGNDWEDR, ENMNR, ENMYR, IMER, MMER, MIER, VVEQMCVTQYQK, and VVEQMCITQYQR) that contains every methionine in sheep, cervid, mouse, and bank vole PrP. Each is the product of a tryptic digestion and is suitable for a multiple reaction monitoring (MRM) based analysis. The peptides chromatograph well. The oxidized and unoxidized peptides containing one methionine readily separate. The unoxidized, two singly oxidized, and doubly oxidized forms of the MLGSAMSR and MMER peptides are also readily distinguishable. This approach can be used to determine the surface exposure of each methionine by measuring its oxidation after reaction with added hydrogen peroxide.
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Affiliation(s)
- Christopher J Silva
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, 800 Buchanan Street, Albany, California 94710, United States
| | - Melissa L Erickson-Beltran
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, 800 Buchanan Street, Albany, California 94710, United States
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2
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Silva CJ. Chronic Wasting Disease (CWD) in Cervids and the Consequences of a Mutable Protein Conformation. ACS OMEGA 2022; 7:12474-12492. [PMID: 35465121 PMCID: PMC9022204 DOI: 10.1021/acsomega.2c00155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/18/2022] [Indexed: 05/15/2023]
Abstract
Chronic wasting disease (CWD) is a prion disease of cervids (deer, elk, moose, etc.). It spreads readily from CWD-contaminated environments and among wild cervids. As of 2022, North American CWD has been found in 29 states, four Canadian provinces and South Korea. The Scandinavian form of CWD originated independently. Prions propagate their pathology by inducing a natively expressed prion protein (PrPC) to adopt the prion conformation (PrPSc). PrPC and PrPSc differ solely in their conformation. Like other prion diseases, transmissible CWD prions can arise spontaneously. The CWD prions can respond to selection pressures resulting in the emergence of new strain phenotypes. Annually, 11.5 million Americans hunt and harvest nearly 6 million deer, indicating that CWD is a potential threat to an important American food source. No tested CWD strain has been shown to be zoonotic. However, this may not be true for emerging strains. Should a zoonotic CWD strain emerge, it could adversely impact the hunting economy and game meat consumers.
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Affiliation(s)
- Christopher J. Silva
- Produce Safety & Microbiology
Research Unit, Western Regional Research Center, Agricultural Research
Service, United States Department of Agriculture, Albany, California 94710, United States of America
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3
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Silva CJ, Erickson-Beltran M. Detecting Differences in Prion Protein Conformation by Quantifying Methionine Oxidation. ACS OMEGA 2022; 7:2649-2660. [PMID: 35097263 PMCID: PMC8793083 DOI: 10.1021/acsomega.1c04989] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
A prion's pathogenic character is enciphered in its conformation, which also defines the chemical environments of its amino acids. Differences in chemical environments influence the reactivity of amino acid side chains, in a conformation-dependent manner. Chemical oxidation of susceptible methionines would identify those methionines on the surface of a prion, which would reveal conformation-dependent information. We identified a set of methionine-containing peptides derived from the tryptic, chymotryptic, or tryptic/chymotryptic digestion of recombinant prion protein and the Sc237 strain of hamster-adapted scrapie. We developed a multiple reaction monitoring-based method of quantifying the extent of the methionine oxidation in those peptides. This approach can be used to define a prion's conformation and to distinguish among prion strains, which is an important component of food safety.
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Cukierman DS, Bodnár N, Diniz R, Nagy L, Kállay C, Rey NA. Full Equilibrium Picture in Aqueous Binary and Ternary Systems Involving Copper(II), 1-Methylimidazole-Containing Hydrazonic Ligands, and the 103-112 Human Prion Protein Fragment. Inorg Chem 2022; 61:723-737. [PMID: 34918515 DOI: 10.1021/acs.inorgchem.1c03598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we describe two novel 1-methylimidazole N-acylhydyrazonic ligands and their interaction with copper(II) in solution. Binary systems constituted by each of these hydrazones and the metal ion were studied by potentiometric titrations. The magnitude of their affinities for zinc(II) was also determined for the sake of comparison. Additionally, a full evaluation of the copper(II) chelation profile of the new ligands in ternary systems containing a human prion protein fragment was performed. Mixed ligand complexes comprising the HuPrP103-112 fragment, copper(II) ions, and an N-acylhydrazone were characterized by potentiometry, ultraviolet-visible spectroscopy, and circular dichroism. Some of these species were also identified by electrospray ionization mass spectrometry and unequivocally assigned through their isotopic distribution pattern. To the best of our knowledge, this is the first report concerning the stability of ternary complexes involving a hydrazonic metal-protein interaction modulator, copper, and a peptide. The ability of N-acylhydrazones to prevent peptide oxidation was also examined. Both ligands can partially prevent the formation of the doubly oxidized product, a process mediated by copper(II) ions. Oxidative stress is considered an important hallmark of neurodegenerative diseases such as prion-related spongiform encephalopathies. In this context, active intervention with respect to the deleterious copper-catalyzed methionine oxidation could represent an interesting therapeutic approach.
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Affiliation(s)
- Daphne S Cukierman
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro 22451-900, Brazil
| | - Nikolett Bodnár
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen 4032, Hungary
| | - Renata Diniz
- Department of Chemistry, ICEx, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Lajos Nagy
- Department of Applied Chemistry, University of Debrecen, Debrecen 4032, Hungary
| | - Csilla Kállay
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen 4032, Hungary
| | - Nicolás A Rey
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro 22451-900, Brazil
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Silva CJ, Onisko BC, Dynin IC, Erickson-Beltran M, Requena JR. Time of Detection of Prions in the Brain by Nanoscale Liquid Chromatography Coupled to Tandem Mass Spectrometry Is Comparable to Animal Bioassay. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2279-2286. [PMID: 33586964 DOI: 10.1021/acs.jafc.0c06241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Prions cause transmissible and inevitably fatal neurological diseases in agriculturally important animals, including bovine spongiform encephalopathy in domestic cattle, scrapie in sheep and goats, and chronic wasting disease in cervids. Because animals are largely asymptomatic throughout the course of the disease, early detection of prion disease is important. Hamsters were peripherally (ip) inoculated with hamster-adapted (Sc237) prions. By week 13 of a 14-week disease course, clinical signs appeared. A multiple-reaction-monitoring-based method was used to quantitate the amount of proteinase-K-digested prions (PrP 27-30) and the extent of methionine 213 oxidation present in the brains of infected hamsters. Detectable amounts of PrP 27-30 were present in all animals after 4 weeks. The extent of methionine 213 oxidation decreased over time. When we compared our quantitation results to those from other researchers using bioassay, we observed that consistent detection of PrP 27-30 by mass spectrometry occurs at a time when prions are reliably detected by bioassay.
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Affiliation(s)
- Christopher J Silva
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan Street, Albany, California 94710, United States
| | - Bruce C Onisko
- OniPro Biosciences, Kensington, California 94707, United States
| | - Irina C Dynin
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan Street, Albany, California 94710, United States
| | - Melissa Erickson-Beltran
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan Street, Albany, California 94710, United States
| | - Jesús R Requena
- CIMUS Biomedical Research Institute & Department of Medical Sciences, University of Santiago de Compostela-IDIS, 15782 Santiago de Compostela, Spain
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Bettinger J, Ghaemmaghami S. Methionine oxidation within the prion protein. Prion 2020; 14:193-205. [PMID: 32744136 PMCID: PMC7518762 DOI: 10.1080/19336896.2020.1796898] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 11/01/2022] Open
Abstract
Prion diseases are characterized by the self-templated misfolding of the cellular prion protein (PrPC) into infectious aggregates (PrPSc). The detailed molecular basis of the misfolding and aggregation of PrPC remains incompletely understood. It is believed that the transient misfolding of PrPC into partially structured intermediates precedes the formation of insoluble protein aggregates and is a critical component of the prion misfolding pathway. A number of environmental factors have been shown to induce the destabilization of PrPC and promote its initial misfolding. Recently, oxidative stress and reactive oxygen species (ROS) have emerged as one possible mechanism by which the destabilization of PrPC can be induced under physiological conditions. Methionine residues are uniquely vulnerable to oxidation by ROS and the formation of methionine sulfoxides leads to the misfolding and subsequent aggregation of PrPC. Here, we provide a review of the evidence for the oxidation of methionine residues in PrPC and its potential role in the formation of pathogenic prion aggregates.
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Affiliation(s)
- John Bettinger
- Department of Biology, University of Rochester, Rochester, NY, USA
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Silva CJ, Erickson-Beltran ML, Dynin IC. Quantifying the Role of Lysine in Prion Replication by Nano-LC Mass Spectrometry and Bioassay. Front Bioeng Biotechnol 2020; 8:562953. [PMID: 33072723 PMCID: PMC7542330 DOI: 10.3389/fbioe.2020.562953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/24/2020] [Indexed: 11/26/2022] Open
Abstract
Prions propagate by a template driven process, inducing the normal cellular isoform (PrPC) to adopt the prion (PrPSc) conformation. In PrPC, the positions of lysines are highly conserved and strongly influence prion propagation. In this study, covalent modification was used to quantitate the role of lysines in the PrPSc template that drives prion replication. The ε-amino group of lysines in the PrPSc (hamster-adapted scrapie Sc237) template was acetylated by either acetic anhydride (Ac2O) or the N-hydroxysuccinimide ester of acetic acid (Ac-NHS). The extent of lysine acetylation in PrPSc was quantitated by mass spectrometry or Western blot-based analysis. Identical samples were bioassayed to quantitate the loss of infectivity associated with lysine acetylation. The reduction of infectivity at the highest reagent concentration was approximately 90% (∼10-fold). Ten of the eleven prion lysines were acetylated to a greater extent (25−400-fold) than the observed loss of infectivity. Only one lysine, at position 220 (K220), had a reactivity that is consistent with the loss of infectivity. Although lysines are highly conserved and play a crucial role in converting PrPC into the PrPSc conformation, once that conformation is adopted, the lysines present in the PrPSc template play only a limited role in prion replication. In principle, this approach could be used to clarify the role of other amino acids in the replication of prions and other prion-like protein misfolding diseases.
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Affiliation(s)
- Christopher J Silva
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, CA, United States
| | - Melissa L Erickson-Beltran
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, CA, United States
| | - Irina C Dynin
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, CA, United States
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Silva CJ. Food Forensics: Using Mass Spectrometry To Detect Foodborne Protein Contaminants, as Exemplified by Shiga Toxin Variants and Prion Strains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:8435-8450. [PMID: 29860833 DOI: 10.1021/acs.jafc.8b01517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Food forensicists need a variety of tools to detect the many possible food contaminants. As a result of its analytical flexibility, mass spectrometry is one of those tools. Use of the multiple reaction monitoring (MRM) method expands its use to quantitation as well as detection of infectious proteins (prions) and protein toxins, such as Shiga toxins. The sample processing steps inactivate prions and Shiga toxins; the proteins are digested with proteases to yield peptides suitable for MRM-based analysis. Prions are detected by their distinct physicochemical properties and differential covalent modification. Shiga toxin analysis is based on detecting peptides derived from the five identical binding B subunits comprising the toxin. 15N-labeled internal standards are prepared from cloned proteins. These examples illustrate the power of MRM, in that the same instrument can be used to safely detect and quantitate protein toxins, prions, and small molecules that might contaminate our food.
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Affiliation(s)
- Christopher J Silva
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service , United States Department of Agriculture , Albany , California 94710 , United States
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9
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Silva CJ, Erickson-Beltran ML, Martín-Burriel I, Badiola JJ, Requena JR, Bolea R. Determining the Relative Susceptibility of Four Prion Protein Genotypes to Atypical Scrapie. Anal Chem 2018; 90:1255-1262. [PMID: 29240410 DOI: 10.1021/acs.analchem.7b03985] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Atypical scrapie is a sheep prion (PrPSc) disease whose epidemiology is consistent with a sporadic origin and is associated with specific polymorphisms of the normal cellular prion protein (PrPC). To determine the relative amounts of PrP polymorphisms present in atypical scrapie, total PrP was digested with chymotrypsin to generate characteristic peptides spanning relevant polymorphisms at positions 136, 141, 154, 171, and 172 of sheep PrPC. A multiple reaction monitoring method (MRM), employing 15N-labeled internal standards, was used to detect and quantify these polymorphisms present in both the PrPSc and PrPC from heterozygous (ALRRY and ALHQY or ALRQD or AFRQY) atypical scrapie-infected or uninfected control sheep. Both polymorphisms of the full length and truncated (C1) natively expressed PrPC are produced in equal amounts. The overall amount of PrPC present in the infected or uninfected animals was similar. PrPSc isolated from heterozygotes was composed of significant amounts of both PrP polymorphisms, including the ALRRY polymorphism which is highly resistant to classical scrapie. Thus, an atypical scrapie infection does not result from an overexpression of sheep PrPC. The replication of all atypical scrapie prions occurs at comparable rates, despite polymorphisms at positions 141, 154, 171, or 172.
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Affiliation(s)
- Christopher J Silva
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States of America
| | - Melissa L Erickson-Beltran
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States of America
| | - Inmaculada Martín-Burriel
- LAGENBIO, Laboratorio de Genética Bioquímica, Facultad de Veterinaria, IA2 Universidad de Zaragoza , 50013, Zaragoza, Spain.,Veterinary Faculty, Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes (CIEETE), Universidad de Zaragoza , 50013, Zaragoza, Spain
| | - Juan José Badiola
- Veterinary Faculty, Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes (CIEETE), Universidad de Zaragoza , 50013, Zaragoza, Spain
| | - Jesús R Requena
- CIMUS Biomedical Research Institute & Department of Medical Sciences, University of Santiago de Compostela-IDIS , Santiago de Compostela, Spain
| | - Rosa Bolea
- Veterinary Faculty, Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes (CIEETE), Universidad de Zaragoza , 50013, Zaragoza, Spain
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10
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Silva CJ, Erickson-Beltran ML, Hui C, Badiola JJ, Nicholson EM, Requena JR, Bolea R. Quantitating PrP Polymorphisms Present in Prions from Heterozygous Scrapie-Infected Sheep. Anal Chem 2016; 89:854-861. [PMID: 27936597 DOI: 10.1021/acs.analchem.6b03822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Scrapie is a prion (PrPSc) disease of sheep. The incubation period of sheep scrapie is strongly influenced by polymorphisms at positions 136, 154, and 171 of a sheep's normal cellular prion protein (PrPC). Chymotrypsin was used to digest sheep recombinant PrP to identify a set of characteristic peptides [M132LGSXMSRPL141 (X = A or V), Y153XENMY158 (X,= H or R), and Y166RPVDXY172 (X = H, K, Q, or R)] that could be used to detect and quantitate polymorphisms at positions 136, 154, and 171 of sheep PrPC or PrPSc. These peptides were used to develop a multiple reaction monitoring method (MRM) to detect the amounts of a particular polymorphism in a sample of PrPSc isolated from sheep heterozygous for their PrPC proteins. The limit of detection for these peptides was less than 50 attomole. Spinal cord tissue from heterozygous (ARQ/VRQ or ARH/ARQ) scrapie-infected Rasa Aragonesa sheep was analyzed using this MRM method. Both sets of heterozygotes show the presence of both polymorphisms in PrPSc. This was true for samples containing both proteinase K (PK)-sensitive and PK-resistant PrPSc and samples containing only the PK-resistant PrPSc. These results show that heterozygous animals contain PrPSc that is composed of significant amounts of both PrP polymorphisms.
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Affiliation(s)
- Christopher J Silva
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States
| | - Melissa L Erickson-Beltran
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States
| | - Colleen Hui
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States
| | - Juan José Badiola
- Veterinary Faculty, Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes (CIEETE), Universidad de Zaragoza , 50013, Zaragoza Spain
| | - Eric M Nicholson
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service , Ames, Iowa 50010, United States
| | - Jesús R Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS , Santiago de Compostela, 15782 Spain
| | - Rosa Bolea
- Veterinary Faculty, Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes (CIEETE), Universidad de Zaragoza , 50013, Zaragoza Spain
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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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Silva CJ, Erickson-Beltran ML, Dynin IC. Covalent Surface Modification of Prions: A Mass Spectrometry-Based Means of Detecting Distinctive Structural Features of Prion Strains. Biochemistry 2016; 55:894-902. [PMID: 26786805 DOI: 10.1021/acs.biochem.5b01068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prions (PrP(Sc)) are molecular pathogens that are able to convert the isosequential normal cellular prion protein (PrP(C)) into a prion. The only demonstrated difference between PrP(C) and PrP(Sc) is conformational: they are isoforms. A given host can be infected by more than one kind or strain of prion. Five strains of hamster-adapted scrapie [Sc237 (=263K), drowsy, 139H, 22AH, and 22CH] and recombinant PrP were reacted with five different concentrations (0, 1, 5, 10, and 20 mM) of reagent (N-hydroxysuccinimide ester of acetic acid) that acetylates lysines. The extent of lysine acetylation was quantitated by mass spectrometry. The lysines in rPrP react similarly. The lysines in the strains react differently from one another in a given strain and react differently when strains are compared. Lysines in the C-terminal region of prions have different strain-dependent reactivity. The results are consistent with a recently proposed model for the structure of a prion. This model proposes that prions are composed of a four-rung β-solenoid structure comprised of four β-sheets that are joined by loops and turns of amino acids. Variation in the amino acid composition of the loops and β-sheet structures is thought to result in different strains of prions.
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Affiliation(s)
- Christopher J Silva
- Western Regional Research Center, United States Department of Agriculture , Albany, California 94710, United States
| | - Melissa L Erickson-Beltran
- Western Regional Research Center, United States Department of Agriculture , Albany, California 94710, United States
| | - Irina C Dynin
- Western Regional Research Center, United States Department of Agriculture , Albany, California 94710, United States
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13
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Abstract
Prion diseases are a heterogeneous class of fatal neurodegenerative disorders associated with misfolding of host cellular prion protein (PrP(C)) into a pathological isoform, termed PrP(Sc). Prion diseases affect various mammals, including humans, and effective treatments are not available. Prion diseases are distinguished from other protein misfolding disorders - such as Alzheimer's or Parkinson's disease - in that they are infectious. Prion diseases occur sporadically without any known exposure to infected material, and hereditary cases resulting from rare mutations in the prion protein have also been documented. The mechanistic underpinnings of prion and other neurodegenerative disorders remain poorly understood. Various proteomics techniques have been instrumental in early PrP(Sc) detection, biomarker discovery, elucidation of PrP(Sc) structure and mapping of biochemical pathways affected by pathogenesis. Moving forward, proteomics approaches will likely become more integrated into the clinical and research settings for the rapid diagnosis and characterization of prion pathogenesis.
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Affiliation(s)
- Roger A Moore
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIH,NIAID, Hamilton, MT 59840, USA
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Proteinase K and the structure of PrPSc: The good, the bad and the ugly. Virus Res 2015; 207:120-6. [PMID: 25816779 DOI: 10.1016/j.virusres.2015.03.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/14/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022]
Abstract
Infectious proteins (prions) are, ironically, defined by their resistance to proteolytic digestion. A defining characteristic of the transmissible isoform of the prion protein (PrP(Sc)) is its partial resistance to proteinase K (PK) digestion. Diagnosis of prion disease typically relies upon immunodetection of PK-digested PrP(Sc) by Western blot, ELISA or immunohistochemical detection. PK digestion has also been used to detect differences in prion strains. Thus, PK has been a crucial tool to detect and, thereby, control the spread of prions. PK has also been used as a tool to probe the structure of PrP(Sc). Mass spectrometry and antibodies have been used to identify PK cleavage sites in PrP(Sc). These results have been used to identify the more accessible, flexible stretches connecting the β-strand components in PrP(Sc). These data, combined with physical constraints imposed by spectroscopic results, were used to propose a qualitative model for the structure of PrP(Sc). Assuming that PrP(Sc) is a four rung β-solenoid, we have threaded the PrP sequence to satisfy the PK proteolysis data and other experimental constraints.
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15
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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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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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Goto T, Murata K, Lee SH, Oe T. Complete amino acid sequencing and immunoaffinity clean-up can facilitate screening of various chemical modifications on human serum albumin. Anal Bioanal Chem 2013; 405:7383-95. [DOI: 10.1007/s00216-013-7146-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/10/2013] [Accepted: 06/13/2013] [Indexed: 01/07/2023]
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18
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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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Sturm R, Kreitinger G, Booth C, Smith L, Pedersen J, Li L. Absolute quantification of prion protein (90-231) using stable isotope-labeled chymotryptic peptide standards in a LC-MRM AQUA workflow. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1522-33. [PMID: 22714949 PMCID: PMC3579656 DOI: 10.1007/s13361-012-0411-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 05/08/2012] [Accepted: 05/10/2012] [Indexed: 05/12/2023]
Abstract
Substantial evidence indicates that the disease-associated conformer of the prion protein (PrP(TSE)) constitutes the etiologic agent in prion diseases. These diseases affect multiple mammalian species. PrP(TSE) has the ability to convert the conformation of the normal prion protein (PrP(C)) into a β-sheet rich form resistant to proteinase K digestion. Common immunological techniques lack the sensitivity to detect PrP(TSE) at subfemtomole levels, whereas animal bioassays, cell culture, and in vitro conversion assays offer higher sensitivity but lack the high-throughput the immunological assays offer. Mass spectrometry is an attractive alternative to the above assays as it offers high-throughput, direct measurement of a protein's signature peptide, often with subfemtomole sensitivities. Although a liquid chromatography-multiple reaction monitoring (LC-MRM) method has been reported for PrP(TSE), the chemical composition and lack of amino acid sequence conservation of the signature peptide may compromise its accuracy and make it difficult to apply to multiple species. Here, we demonstrate that an alternative protease (chymotrypsin) can produce signature peptides suitable for a LC-MRM absolute quantification (AQUA) experiment. The new method offers several advantages, including: (1) a chymotryptic signature peptide lacking chemically active residues (Cys, Met) that can confound assay accuracy; (2) low attomole limits of detection and quantitation (LOD and LOQ); and (3) a signature peptide retaining the same amino acid sequence across most mammals naturally susceptible to prion infection as well as important laboratory models. To the authors' knowledge, this is the first report on the use of a non-tryptic peptide in a LC-MRM AQUA workflow.
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Affiliation(s)
- Robert Sturm
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison
| | - Gloria Kreitinger
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison
| | - Clarissa Booth
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison
| | - Lloyd Smith
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison
| | - Joel Pedersen
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison
- Department of Soil Science, University of Wisconsin-Madison
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison
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20
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Cui ZJ, Han ZQ, Li ZY. Modulating protein activity and cellular function by methionine residue oxidation. Amino Acids 2012; 43:505-17. [PMID: 22146868 DOI: 10.1007/s00726-011-1175-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 11/21/2011] [Indexed: 02/07/2023]
Abstract
The sulfur-containing amino acid residue methionine (Met) in a peptide/protein is readily oxidized to methionine sulfoxide [Met(O)] by reactive oxygen species both in vitro and in vivo. Methionine residue oxidation by oxidants is found in an accumulating number of important proteins. Met sulfoxidation activates calcium/calmodulin-dependent protein kinase II and the large conductance calcium-activated potassium channels, delays inactivation of the Shaker potassium channel ShC/B and L-type voltage-dependent calcium channels. Sulfoxidation at critical Met residues inhibits fibrillation of atherosclerosis-related apolipoproteins and multiple neurodegenerative disease-related proteins, such as amyloid beta, α-synuclein, prion, and others. Methionine residue oxidation is also correlated with marked changes in cellular activities. Controlled key methionine residue oxidation may be used as an oxi-genetics tool to dissect specific protein function in situ.
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Affiliation(s)
- Zong Jie Cui
- Institute of Cell Biology, Beijing Normal University, Beijing 100875, China.
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21
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Silva CJ, Onisko BC, Dynin I, Erickson ML, Requena JR, Carter JM. Utility of mass spectrometry in the diagnosis of prion diseases. Anal Chem 2011; 83:1609-15. [PMID: 21288014 DOI: 10.1021/ac102527w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed a sensitive mass spectrometry-based method of quantitating the prions present in a variety of mammalian species. Calibration curves relating the area ratios of the integrated MRM signals from selected analyte peptides and their oxidized analogues to their homologous stable isotope labeled internal standards were prepared. The limit of detection (LOD) and limit of quantitation (LOQ) for the synthetic peptides from human, sheep, deer, cow, and mouse PrP were determined to be below 100 amol. Nonanalyte peptides that were characteristic of prions were included in the multiple reaction monitoring method, thereby allowing for both the quantitation and confirmation of the presence of prions in the attomole range. This method was used to quantitate the prions present in brains of hamsters or mice 5 weeks after inoculation (ic) with either four hamster-adapted prion strains (139H, drowsy, 22AH, and 22CH) or four mouse-adapted prion strains (Me7, Me7-298, RML, and 79A). The prions from different brain regions of a sheep naturally infected with scrapie were quantitated. All of the rodent-adapted prion strains were detectable in the asymptomatic animals. In sheep, prions were detectable in the obex, anterior portion of the cerebrum, and the nonobex/nonanterior portion of the cerebrum. This mass spectrometry-based approach can be used to quantitate and confirm the presence of prions before detectable pathology.
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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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van der Kamp MW, Daggett V. Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations. Top Curr Chem (Cham) 2011; 305:169-97. [PMID: 21526434 DOI: 10.1007/128_2011_158] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Computer simulation of protein dynamics offers unique high-resolution information that complements experiment. Using experimentally derived structures of the natively folded prion protein (PrP), physically realistic dynamics and conformational changes can be simulated, including the initial steps of misfolding. By introducing mutations in silico, the effect of pathogenic mutations on PrP conformation and dynamics can be assessed. Here, we briefly introduce molecular dynamics methods and review the application of molecular dynamics simulations to obtain insight into various aspects of the PrP, including the mechanism of misfolding, the response to changes in the environment, and the influence of disease-related mutations.
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Affiliation(s)
- Marc W van der Kamp
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
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23
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Canello T, Frid K, Gabizon R, Lisa S, Friedler A, Moskovitz J, Gasset M, Gabizon R. Oxidation of Helix-3 methionines precedes the formation of PK resistant PrP. PLoS Pathog 2010; 6:e1000977. [PMID: 20625387 PMCID: PMC2895666 DOI: 10.1371/journal.ppat.1000977] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 05/28/2010] [Indexed: 12/19/2022] Open
Abstract
While elucidating the peculiar epitope of the alpha-PrP mAb IPC2, we found that PrPSc exhibits the sulfoxidation of residue M213 as a covalent signature. Subsequent computational analysis predicted that the presence of sulfoxide groups at both Met residues 206 and 213 destabilize the alpha-fold, suggesting oxidation may facilitate the conversion of PrPC into PrPSc. To further study the effect of oxidation on prion formation, we generated pAbs to linear PrP peptides encompassing the Helix-3 region, as opposed to the non-linear complexed epitope of IPC2. We now show that pAbs, whose epitopes comprise Met residues, readily detected PrPC, but could not recognize most PrPSc bands unless they were vigorously reduced. Next, we showed that the alpha-Met pAbs did not recognize newly formed PrPSc, as is the case for the PK resistant PrP present in lines of prion infected cells. In addition, these reagents did not detect intermediate forms such as PK sensitive and partially aggregated PrPs present in infected brains. Finally, we show that PrP molecules harboring the pathogenic mutation E200K, which is linked to the most common form of familial CJD, may be spontaneously oxidized. We conclude that the oxidation of methionine residues in Helix-3 represents an early and important event in the conversion of PrPC to PrPSc. We believe that further investigation into the mechanism and role of PrP oxidation will be central in finally elucidating the mechanism by which a normal cell protein converts into a pathogenic entity that causes fatal brain degeneration.
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Affiliation(s)
- Tamar Canello
- Department of Neurology, The Agnes Ginges Center for Human Neurogenetics, Hadassah University Hospital, Jerusalem, Israel
| | - Kati Frid
- Department of Neurology, The Agnes Ginges Center for Human Neurogenetics, Hadassah University Hospital, Jerusalem, Israel
| | - Ronen Gabizon
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Jerusalem, Israel
| | - Silvia Lisa
- Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Jerusalem, Israel
| | - Jackob Moskovitz
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, United States of America
| | - María Gasset
- Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ruth Gabizon
- Department of Neurology, The Agnes Ginges Center for Human Neurogenetics, Hadassah University Hospital, Jerusalem, Israel
- * E-mail:
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