Proteomics applications in prion biology and structure

References

• Chesebro B. Introduction to the transmissible spongiform encephalopathies or prion diseases. Br Med Bull 2003;66:1-20
   PubMed Web of Science ®Google Scholar
• Caughey B, Baron GS, Chesebro B, Jeffrey M. Getting a grip on prions: oligomers, amyloids, and pathological membrane interactions. Annu Rev Biochem 2009;78:177-204
   PubMed Web of Science ®Google Scholar
• Zomosa-Signoret V, Arnaud JD, Fontes P, et al. Physiological role of the cellular prion protein. Vet Res 2008;39(4):9
   PubMedGoogle Scholar
• Didonna A. Prion protein and its role in signal transduction. Cell Mol Biol Lett 2013;18(2):209-30
   PubMedGoogle Scholar
• Caughey BW, Dong A, Bhat KS, et al. Secondary Structure-Analysis of the Scrapie-Associated Protein Prp 27-30 in Water by Infrared-Spectroscopy. Biochemistry 1991;30(31):7672-80
   PubMedGoogle Scholar
• Pan K-M, Baldwin M, Nguyen J, et al. Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion protein. Proc Natl Acad Sci USA 1993;90:10962-6
   PubMed Web of Science ®Google Scholar
• Groveman BR, Dolan MA, Taubner LM, et al. Parallel In-register Intermolecular beta-Sheet Architectures for Prion-seeded Prion Protein (PrP) Amyloids. J Biol Chem 2014;289(35):24129-42
   PubMed Web of Science ®Google Scholar
• Griffith JS. Self-replication and scrapie. Nature 1967;215:1043-4
   PubMed Web of Science ®Google Scholar
• Deleault NR, Harris BT, Rees JR, Supattapone S. Formation of native prions from minimal components in vitro. Proc Natl Acad Sci USA 2007;104:9741-6
   PubMed Web of Science ®Google Scholar
• Wang F, Wang X, Yuan CG, Ma J. Generating a prion with bacterially expressed recombinant prion protein. Science 2010;327(5969):1132-5
   PubMed Web of Science ®Google Scholar
• Raymond GJ, Race B, Hollister JR, et al. Isolation of novel synthetic prion strains by amplification in transgenic mice coexpressing wild-type and anchorless prion proteins. J Virol 2012;86(21):11763-78
   PubMedGoogle Scholar
• Prusiner SB. Novel proteinaceous infectious particles cause scrapie. Science 1982;216:136-44
   PubMed Web of Science ®Google Scholar
• Kimberlin RH, Walker CA. Evidence that the transmission of one source of scrapie agent to hamsters involves separation of agent strains from a mixture. J Gen Virol 1978;39:487-96
   PubMed Web of Science ®Google Scholar
• Moore RA, Taubner LM, Priola SA. Prion protein misfolding and disease. Curr Opin Struct Biol 2009;19(1):14-22
   PubMed Web of Science ®Google Scholar
• Silveira JR, Raymond GJ, Hughson AG, et al. The most infectious prion protein particles. Nature 2005;437(7056):257-61
   PubMed Web of Science ®Google Scholar
• Simoneau S, Rezaei H, Sales N, et al. In vitro and in vivo neurotoxicity of prion protein oligomers. PLoS Pathog 2007;3(8):e125
   PubMed Web of Science ®Google Scholar
• Sikorska B, Knight R, Ironside JW, Liberski PP. Creutzfeldt-Jakob disease. Adv Exp Med Biol 2012;724:76-90
   Google Scholar
• Head MW, Ironside JW. Review: Creutzfeldt-Jakob disease: prion protein type, disease phenotype and agent strain. Neuropathol Appl Neurobiol 2012;38(4):296-310
   PubMed Web of Science ®Google Scholar
• Liberski PP. Gerstmann- Sträussler-Scheinker disease. Adv Exp Med Biol 2012;724:128-37
   PubMed Web of Science ®Google Scholar
• Capellari S, Strammiello R, Saverioni D, et al. Genetic Creutzfeldt-Jakob disease and fatal familial insomnia: insights into phenotypic variability and disease pathogenesis. Acta Neuropathol 2011;121(1):21-37
   PubMed Web of Science ®Google Scholar
• Gambetti P, Kong Q, Zou W, et al. Sporadic and familial CJD: classification and characterisation. Br Med Bull 2003;66:213-39
   PubMed Web of Science ®Google Scholar
• Zigas V, Gajdusek DC. Kuru: clinical study of a new syndrome resembling paralysis agitans in natives of the Eastern Highlands of Australian New Guinea. Med J Aust 1957;2:745-54
   Google Scholar
• Liberski PP, Sikorska B, Brown P. Kuru: the first prion disease. Adv Exp Med Biol 2012;724:143-53
   PubMedGoogle Scholar
• Diack AB, Head MW, McCutcheon S, et al. Variant CJD: 18 years of research and surveillance. Prion 2014;8:3
   PubMedGoogle Scholar
• Ironside JW. Variant Creutzfeldt-Jakob disease. Haemophilia 2010;16(Suppl 5):175-80
   PubMedGoogle Scholar
• Appleby BS, Lu M, Bizzi A, et al. Iatrogenic Creutzfeldt-Jakob disease from commercial cadaveric human growth hormone. Emerg Infect Dis 2013;19(4):682-4
   PubMedGoogle Scholar
• Thomas JG, Chenoweth CE, Sullivan SE. Iatrogenic Creutzfeldt-Jakob disease via surgical instruments. J Clin Neurosci 2013;20(9):1207-12
   PubMedGoogle Scholar
• Liberski PP, Ironside JW. An outline of the neuropathology of transmissible spongiform encephalopathies (prion diseases). Folia Neuropathol 2004;42(Suppl B):39-58
   PubMedGoogle Scholar
• Budka H, Aguzzi A, Brown P, et al. Neuropathological diagnostic criteria for Creutzfeldt-Jakob disease (CJD) and other human spongiform encephalopathies (prion diseases). Brain Pathol 1995;5(4):459-66
   PubMedGoogle Scholar
• Brown KL, Ritchie DL, McBride PA, Bruce ME. Detection of PrP in extraneural tissues. Microsc Res Tech 2000;50(1):40-5
   PubMedGoogle Scholar
• Lee J, Hyeon JW, Kim SY, et al. Review: laboratory diagnosis and surveillance of Creutzfeldt-Jakob disease. J Med Virol 2015;87(1):175-86
   PubMedGoogle Scholar
• Tribouillard-Tanvier D, Race B, Striebel JF, et al. Early cytokine elevation, PrPres deposition, and gliosis in mouse scrapie: no effect on disease by deletion of cytokine genes IL-12p40 and IL-12p35. J Virol 2012;86(19):10377-83
   PubMed Web of Science ®Google Scholar
• Jendroska K, Heinzel FP, Torchia M, et al. Proteinase-resistant prion protein accumulation in Syrian hamster brain correlates with regional pathology and scrapie infectivity. Neurology 1991;41(9):1482-90
   PubMed Web of Science ®Google Scholar
• Onisko BC, Silva CJ, Dynin I, et al. Sensitive, preclinical detection of prions in brain by nanospray liquid chromatography/tandem mass spectrometry. Rapid Commun Mass Spectrom 2007;21(24):4023-6
   PubMedGoogle Scholar
• Castilla J, Saa P, Hetz C, Soto C. In vitro generation of infectious scrapie prions. Cell 2005;121(2):195-206
   PubMed Web of Science ®Google Scholar
• Atarashi R, Moore RA, Sim VL, et al. Ultrasensitive detection of scrapie prion protein using seeded conversion of recombinant prion protein. Nat Methods 2007;4(8):645-50
   PubMed Web of Science ®Google Scholar
• Atarashi R, Wilham JM, Christensen L, et al. Simplified ultrasensitive prion detection by recombinant PrP conversion with shaking. Nat Methods 2008;5(3):211-12
   PubMed Web of Science ®Google Scholar
• Orru CD, Bongianni M, Tonoli G, et al. A test for Creutzfeldt-Jakob disease using nasal brushings. N Engl J Med 2014;371(6):519-29
   PubMed Web of Science ®Google Scholar
• Moda F, Gambetti P, Notari S, et al. Prions in the urine of patients with variant Creutzfeldt-Jakob disease. N Engl J Med 2014;371(6):530-9
   PubMed Web of Science ®Google Scholar
• Saa P, Castilla J, Soto C. Ultra-efficient replication of infectious prions by automated protein misfolding cyclic amplification. J Biol Chem 2006;281(46):35245-52
   PubMed Web of Science ®Google Scholar
• Peden AH, McGuire LI, Appleford NE, et al. Sensitive and specific detection of sporadic Creutzfeldt-Jakob disease brain prion protein using real-time quaking-induced conversion. J Gen Virol 2012;93(Pt 2):438-49
   PubMedGoogle Scholar
• Onisko B, Dynin I, Requena JR, et al. Mass spectrometric detection of attomole amounts of the prion protein by nanoLC/MS/MS. J Am Soc Mass Spectrom 2007;18(6):1070-9
   PubMedGoogle Scholar
• Silva CJ, Onisko BC, Dynin I, et al. Utility of mass spectrometry in the diagnosis of prion diseases. Anal Chem 2011;83(5):1609-15
   PubMedGoogle Scholar
• Sturm R, Sheynkman G, Booth C, et al. Absolute quantification of prion protein (90-231) using stable isotope-labeled chymotryptic peptide standards in a LC-MRM AQUA workflow. J Am Soc Mass Spectrom 2012;23(9):1522-33
   PubMedGoogle Scholar
• Diringer H, Beekes M, Ozel M, et al. Highly infectious purified preparations of disease-specific amyloid of transmissible spongiform encephalopathies are not devoid of nucleic acids of viral size. Intervirology 1997;40(4):238-46
   PubMedGoogle Scholar
• Van Dorsselaer A, Carapito C, Delalande F, et al. Detection of prion protein in urine-derived injectable fertility products by a targeted proteomic approach. PLoS One 2011;6(3):e17815
   PubMed Web of Science ®Google Scholar
• Gielbert A, Davis LA, Sayers AR, et al. High-resolution differentiation of transmissible spongiform encephalopathy strains by quantitative N-terminal amino acid profiling (N-TAAP) of PK-digested abnormal prion protein. J Mass Spectrom 2009;44(3):384-96
   PubMedGoogle Scholar
• Howells LC, Anderson S, Coldham NG, Sauer MJ. Transmissible spongiform encephalopathy strain-associated diversity of N-terminal proteinase K cleavage sites of PrP(Sc) from scrapie-infected and bovine spongiform encephalopathy-infected mice. Biomarkers 2008;13(4):393-412
   PubMed Web of Science ®Google Scholar
• Gielbert A, Davis LA, Sayers AR, et al. Quantitative profiling of PrP(Sc) peptides by high-performance liquid chromatography mass spectrometry to investigate the diversity of prions. Anal Biochem 2013;436(1):36-44
   PubMedGoogle Scholar
• Parchi P, Zou W, Wang W, et al. Genetic influence on the structural variations of the abnormal prion protein. Proc Natl Acad Sci USA 2000;97(18):10168-72
   PubMed Web of Science ®Google Scholar
• Chen SG, Zou W, Parchi P, Gambetti P. PrP(Sc) typing by N-terminal sequencing and mass spectrometry. Arch Virol 2000(16):209-16
   Google Scholar
• McGuire LI, Peden AH, Orru CD, et al. Real time quaking-induced conversion analysis of cerebrospinal fluid in sporadic Creutzfeldt-Jakob disease. Ann Neurol 2012;72(2):278-85
   PubMed Web of Science ®Google Scholar
• Qualtieri A, Urso E, Le Pera M, et al. Proteomic profiling of cerebrospinal fluid in Creutzfeldt-Jakob disease. Expert Rev Proteomics 2010;7(6):907-17
   PubMed Web of Science ®Google Scholar
• Cramm M, Schmitz M, Karch A, et al. Characteristic CSF prion seeding efficiency in humans with prion diseases. Mol Neurobiol 2015;51(1):396-405
   PubMed Web of Science ®Google Scholar
• Orru CD, Wilham JM, Raymond LD, et al. Prion disease blood test using immunoprecipitation and improved quaking-induced conversion. MBio 2011;2(3):e00078-11
   PubMed Web of Science ®Google Scholar
• Lamoureux L, Simon SL, Plews M, et al. Urine proteins identified by two-dimensional differential gel electrophoresis facilitate the differential diagnoses of scrapie. PLoS One 2013;8(5):e64044
   PubMed Web of Science ®Google Scholar
• Miele G, Seeger H, Marino D, et al. Urinary alpha1-antichymotrypsin: a biomarker of prion infection. PLoS One 2008;3(12):e3870
   Google Scholar
• Huzarewich RL, Siemens CG, Booth SA. Application of “omics” to prion biomarker discovery. J Biomed Biotechnol 2010;2010:613504
   PubMed Web of Science ®Google Scholar
• Ma D, Li L. Searching for reliable premortem protein biomarkers for prion diseases: progress and challenges to date. Expert Rev Proteomics 2012;9(3):267-80
   PubMed Web of Science ®Google Scholar
• Stoeck K, Sanchez-Juan P, Gawinecka J, et al. Cerebrospinal fluid biomarker supported diagnosis of Creutzfeldt-Jakob disease and rapid dementias: a longitudinal multicentre study over 10 years. Brain 2012;135(Pt 10):3051-61
   PubMed Web of Science ®Google Scholar
• Hsich G, Kenney K, Gibbs CJ, et al. The 14-3-3 brain protein in cerebrospinal fluid as a marker for transmissible spongiform encephalopathies. N Engl J Med 1996;335(13):924-30
   PubMed Web of Science ®Google Scholar
• Satoh K, Tobiume M, Matsui Y, et al. Establishment of a standard 14-3-3 protein assay of cerebrospinal fluid as a diagnostic tool for Creutzfeldt-Jakob disease. Lab Invest 2010;90(11):1637-44
   PubMedGoogle Scholar
• Zerr I, Pocchiari M, Collins S, et al. Analysis of EEG and CSF 14-3-3 proteins as aids to the diagnosis of Creutzfeldt-Jakob disease. Neurology 2000;55(6):811-15
   PubMed Web of Science ®Google Scholar
• Geschwind MD, Martindale J, Miller D, et al. Challenging the clinical utility of the 14-3-3 protein for the diagnosis of sporadic Creutzfeldt-Jakob disease. Arch Neurol 2003;60(6):813-16
   PubMedGoogle Scholar
• Hamlin C, Puoti G, Berri S, et al. A comparison of tau and 14-3-3 protein in the diagnosis of Creutzfeldt-Jakob disease. Neurology 2012;79(6):547-52
   PubMed Web of Science ®Google Scholar
• Gmitterova K, Heinemann U, Bodemer M, et al. 14-3-3 CSF levels in sporadic Creutzfeldt-Jakob disease differ across molecular subtypes. Neurobiol Aging 2009;30(11):1842-50
   PubMed Web of Science ®Google Scholar
• Bahl JM, Heegaard NH, Falkenhorst G, et al. The diagnostic efficiency of biomarkers in sporadic Creutzfeldt-Jakob disease compared to Alzheimer’s disease. Neurobiol Aging 2009;30(11):1834-41
   PubMed Web of Science ®Google Scholar
• Gawinecka J, Ciesielczyk B, Sanchez-Juan P, et al. Desmoplakin as a potential candidate for cerebrospinal fluid marker to rule out 14-3-3 false positive rates in sporadic Creutzfeldt-Jakob disease differential diagnosis. Neurodegener Dis 2012;9(3):139-44
   PubMedGoogle Scholar
• Satoh K, Shirabe S, Eguchi H, et al. 14-3-3 protein, total tau and phosphorylated tau in cerebrospinal fluid of patients with Creutzfeldt-Jakob disease and neurodegenerative disease in Japan. Cell Mol Neurobiol 2006;26(1):45-52
   PubMed Web of Science ®Google Scholar
• Skillback T, Rosen C, Asztely F, et al. Diagnostic performance of cerebrospinal fluid total tau and phosphorylated tau in Creutzfeldt-Jakob disease: results from the Swedish Mortality Registry. JAMA Neurol 2014;71(4):476-83
   PubMed Web of Science ®Google Scholar
• Jimi T, Wakayama Y, Shibuya S, et al. High levels of nervous system-specific proteins in cerebrospinal fluid in patients with early stage Creutzfeldt-Jakob disease. Clin Chim Acta 1992;211(1-2):37-46
   PubMedGoogle Scholar
• Baldeiras IE, Ribeiro MH, Pacheco P, et al. Diagnostic value of CSF protein profile in a Portuguese population of sCJD patients. J Neurol 2009;256(9):1540-50
   PubMed Web of Science ®Google Scholar
• Diringer H, Hilmert H, Simon D, et al. Towards purification of the scrapie agent. Eur J Biochem 1983;134:555-60
   PubMedGoogle Scholar
• Prusiner SB, Hadlow WJ, Garfin DE, et al. Partial purification and evidence for multiple molecular forms of the scrapie agent. Biochemistry 1978;17:4993-9
   PubMedGoogle Scholar
• Prusiner SB, Hadlow WJ, Eklund CM, et al. Sedimentation characteristics of the scrapie agent from murine spleen and brain. Biochemistry 1978;17:4987-92
   PubMed Web of Science ®Google Scholar
• Prusiner SB, Bolton DC, Groth DF, et al. Further purification and characterization of scrapie prions. Biochemistry 1982;21:6942-50
   PubMed Web of Science ®Google Scholar
• Hilmert H, Diringer H. A rapid and efficient method to enrich saf-protein from scrapie brains of hamsters. Biosci Rep 1984;4(2):165-70
   PubMedGoogle Scholar
• Raymond GJ, Chabry J. Purification of the pathological isoform of prion protein (PrPSc or PrPres) from transmissible spongiform encephalopathy-affected brain tissue. In: Lehmann S, Grassi J, Eds Techniques in Prion Research. Birkhauser Verlag; Basel: 2004. 16-26
   Google Scholar
• Gabizon R, McKinley MP, Groth D, Prusiner SB. Immuno-affinity purification and neutralization of scrapie prion infectivity. Proc Natl Acad Sci USA 1988;85:6617-21
   PubMed Web of Science ®Google Scholar
• Wadsworth JD, Joiner S, Hill AF, et al. Tissue distribution of protease resistant prion protein in variant Creutzfeldt-Jakob disease using a highly sensitive immunoblotting assay. Lancet 2001;358(9277):171-80
   PubMedGoogle Scholar
• Bolton DC, Bendheim PE, Marmostein AD, Potempska A. Isolation and structural studies of the intact scrapie agent protein. Arch Biochem Biophys 1987;258:579-90
   PubMed Web of Science ®Google Scholar
• Akowitz A, Sklaviadis T, Manuelidis EE, Manuelidis L. Nuclease-resistant polyadenylated RNAs of significant size are detected by PCR in highly purified Creutzfeldt-Jakob disease preparations. Microb Pathog 1990;9:33-45
   PubMedGoogle Scholar
• Stahl N, Borchelt DR, Hsiao K, Prusiner SB. Scrapie prion protein contains a phosphatidylinositol glycolipid. Cell 1987;51:229-40
   PubMed Web of Science ®Google Scholar
• Appel TR, Dumpitak C, Matthiesen U, Riesner D. Prion rods contain an inert polysaccharide scaffold. Biol Chem 1999;380(11):1295-306
   PubMedGoogle Scholar
• Wadsworth JD, Hill AF, Joiner S, et al. Strain-specific prion-protein conformation determined by metal ions. Nat Cell Biol 1999;1(1):55-9
   PubMedGoogle Scholar
• Johnson CJ, Gilbert PU, Abrecht M, et al. Low copper and high manganese levels in prion protein plaques. Viruses 2013;5(2):654-62
   PubMedGoogle Scholar
• Giorgi A, Di FL, Principe S, et al. Proteomic profiling of PrP27-30-enriched preparations extracted from the brain of hamsters with experimental scrapie. Proteomics 2009;9(15):3802-14
   PubMedGoogle Scholar
• Moore RA, Timmes A, Wilmarth PA, Priola SA. Comparative profiling of highly enriched 22L and Chandler mouse scrapie prion protein preparations. Proteomics 2010;10(15):2858-69
   PubMedGoogle Scholar
• Moore RA, Timmes AG, Wilmarth PA, et al. Identification and removal of proteins that co-purify with infectious prion protein improves the analysis of its secondary structure. Proteomics 2011;11(19):3853-65
   PubMedGoogle Scholar
• Graham JF, Kurian D, Agarwal S, et al. Na+/K+-ATPase is present in scrapie-associated fibrils, modulates PrP misfolding in vitro and links PrP function and dysfunction. PLoS One 2011;6(11):e26813
   Google Scholar
• Petrakis S, Malinowska A, Dadlez M, Sklaviadis T. Identification of proteins co-purifying with scrapie infectivity. J Proteomics 2009;72(4):690-4
   PubMedGoogle Scholar
• Hanson PI, Schulman H. Neuronal Ca2+/calmodulin-dependent protein kinases. Annu Rev Biochem 1992;61:559-601
   PubMed Web of Science ®Google Scholar
• Lee IS, Long JR, Prusiner SB, Safar JG. Selective precipitation of prions by polyoxometalate complexes. J Am Chem Soc 2005;127(40):13802-3
   PubMedGoogle Scholar
• Holtzman DM, Pitas RE, Kilbridge J, et al. Low density lipoprotein receptor-related protein mediates apolipoprotein E-dependent neurite outgrowth in a central nervous system-derived neuronal cell line. Proc Natl Acad Sci USA 1995;92(21):9480-4
   PubMed Web of Science ®Google Scholar
• Skinner PJ, Abbassi H, Chesebro B, et al. Gene expression alterations in brains of mice infected with three strains of scrapie. BMC Genomics 2006;7:114
   PubMed Web of Science ®Google Scholar
• Sorensen G, Medina S, Parchaliuk D, et al. Comprehensive transcriptional profiling of prion infection in mouse models reveals networks of responsive genes. BMC Genomics 2008;9:114
   PubMed Web of Science ®Google Scholar
• Lashley T, Holton JL, Verbeek MM, et al. Molecular chaperons, amyloid and preamyloid lesions in the BRI2 gene-related dementias: a morphological study. Neuropathol Appl Neurobiol 2006;32(5):492-504
   PubMedGoogle Scholar
• Yamaguchi H, Ishiguro K, Sugihara S, et al. Presence of apolipoprotein E on extracellular neurofibrillary tangles and on meningeal blood vessels precedes the Alzheimer beta-amyloid deposition. Acta Neuropathol 1994;88(5):413-19
   PubMedGoogle Scholar
• Rangon CM, Haik S, Faucheux BA, et al. Different chromogranin immunoreactivity between prion and a-beta amyloid plaque. Neuroreport 2003;14(5):755-8
   PubMedGoogle Scholar
• Choe LH, Green A, Knight RS, et al. Apolipoprotein E and other cerebrospinal fluid proteins differentiate ante mortem variant Creutzfeldt-Jakob disease from ante mortem sporadic Creutzfeldt-Jakob disease. Electrophoresis 2002;23(14):2242-6
   PubMedGoogle Scholar
• Wei X, Herbst A, Ma D, et al. A quantitative proteomic approach to prion disease biomarker research: delving into the glycoproteome. J Proteome Res 2011;10(6):2687-702
   PubMedGoogle Scholar
• Merz PA, Somerville RA, Wisniewski HM, Iqbal K. Abnormal fibrils from scrapie-infected brain. Acta Neuropathol 1981;54:63-74
   PubMed Web of Science ®Google Scholar
• Sarroukh R, Goormaghtigh E, Ruysschaert JM, Raussens V. ATR-FTIR: a “rejuvenated” tool to investigate amyloid proteins. Biochim Biophys Acta 2013;1828(10):2328-38
   PubMedGoogle Scholar
• Zandomeneghi G, Krebs MR, McCammon MG, Fandrich M. FTIR reveals structural differences between native beta-sheet proteins and amyloid fibrils. Protein Sci 2004;13(12):3314-21
   PubMed Web of Science ®Google Scholar
• Caughey B, Raymond GJ, Bessen RA. Strain-dependent differences in beta-sheet conformations of abnormal prion protein. J Biol Chem 1998;273(48):32230-5
   PubMed Web of Science ®Google Scholar
• Spassov S, Beekes M, Naumann D. Structural differences between TSEs strains investigated by FT-IR spectroscopy. Biochim Biophys Acta 2006;1760(7):1138-49
   PubMedGoogle Scholar
• Thomzig A, Spassov S, Friedrich M, et al. Discriminating scrapie and bovine spongiform encephalopathy isolates by infrared spectroscopy of pathological prion protein. J Biol Chem 2004;279(32):33847-54
   PubMedGoogle Scholar
• Baron GS, Hughson AG, Raymond GJ, et al. Effect of glycans and the glycophosphatidylinositol anchor on strain dependent conformations of scrapie prion protein: improved purifications and infrared spectra. Biochemistry 2011;50(21):4479-90
   PubMedGoogle Scholar
• Gasset M, Baldwin MA, Fletterick RJ, Prusiner SB. Perturbation of the secondary structure of the scrapie prion protein under conditions that alter infectivity. Proc Natl Acad Sci USA 1993;90:1-5
   PubMed Web of Science ®Google Scholar
• Safar J, Roller PP, Gajdusek DC, Gibbs CJJr. Conformational transitions, dissociation, and unfolding of scrapie amyloid (prion) protein. J Biol Chem 1993;268:20276-84
   PubMed Web of Science ®Google Scholar
• Smirnovas V, Baron GS, Offerdahl DK, et al. Structural organization of brain-derived mammalian prions examined by hydrogen-deuterium exchange. Nat Struct Mol Biol 2011;18(4):504-6
   PubMedGoogle Scholar
• Demarco ML, Daggett V. From conversion to aggregation: protofibril formation of the prion protein. Proc Natl Acad Sci USA 2004;101(8):2293-8
   PubMedGoogle Scholar
• Govaerts C, Wille H, Prusiner SB, Cohen FE. Evidence for assembly of prions with left-handed beta-helices into trimers. Proc Natl Acad Sci USA 2004;101(22):8342-7
   PubMed Web of Science ®Google Scholar
• Cobb NJ, Sonnichsen FD, McHaourab H, Surewicz WK. Molecular architecture of human prion protein amyloid: a parallel, in-register beta-structure. Proc Natl Acad Sci USA 2007;104(48):18946-51
   PubMedGoogle Scholar
• Smirnovas V, Kim JI, Lu X, et al. Distinct structures of scrapie prion protein (PrPSc)-seeded versus spontaneous recombinant prion protein fibrils revealed by hydrogen/deuterium exchange. J Biol Chem 2009;284(36):24233-41
   PubMedGoogle Scholar
• Serpa JJ, Patterson AP, Pan J, et al. Using multiple structural proteomics approaches for the characterization of prion proteins. J Proteomics 2013;81:31-42
   PubMedGoogle Scholar
• Tycko R, Savtchenko R, Ostapchenko VG, et al. The alpha-helical C-terminal domain of full-length recombinant PrP converts to an in-register parallel beta-sheet structure in PrP fibrils: evidence from solid state nuclear magnetic resonance. Biochemistry 2010;49(44):9488-97
   PubMedGoogle Scholar
• 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(7):e71081
   Google Scholar
• Kim JI, Cali I, Surewicz K, et al. Mammalian prions generated from bacterially expressed prion protein in the absence of any mammalian cofactors. J Biol Chem 2010;285(19):14083-7
   PubMedGoogle Scholar
• Makarava N, Kovacs GG, Bocharova O, et al. Recombinant prion protein induces a new transmissible prion disease in wild-type animals. Acta Neuropathol 2010;119(2):177-87
   PubMedGoogle Scholar
• Legname G, Baskakov IV, Nguyen HO, et al. Synthetic mammalian prions. Science 2004;305(5684):673-6
   PubMed Web of Science ®Google Scholar
• Onisko B, Fernandez EG, Freire ML, et al. Probing PrPSc structure using chemical cross-linking and mass spectrometry: evidence of the proximity of Gly90 amino termini in the PrP 27-30 aggregate. Biochemistry 2005;44(30):10100-9
   PubMedGoogle Scholar
• Kocisko DA, Lansbury PTJr, Caughey B. Partial unfolding and refolding of scrapie-associated prion protein: evidence for a critical 16-kDa C-terminal domain. Biochemistry 1996;35:13434-42
   PubMed Web of Science ®Google Scholar
• Lawson VA, Priola SA, Meade-White K, et al. Flexible N-terminal region of prion protein influences conformation of protease-resistant prion protein isoforms associated with cross-species scrapie infection in vivo and in vitro. J Biol Chem 2004;279(14):13689-95
   PubMedGoogle Scholar
• Sajnani G, Pastrana MA, Dynin I, et al. Scrapie prion protein structural constraints obtained by limited proteolysis and mass spectrometry. J Mol Biol 2008;382(1):88-98
   PubMedGoogle Scholar
• Vazquez-Fernandez E, Alonso J, Pastrana MA, et al. Structural organization of mammalian prions as probed by limited proteolysis. PLoS One 2012;7(11):e50111
   PubMedGoogle Scholar
• Prusiner SB, Groth DF, Bolton DC, et al. Purification and structural studies of a major scrapie prion protein. Cell 1984;38:127-34
   PubMedGoogle Scholar
• Bessen RA, Marsh RF. Identification of two biologically distinct strains of transmissible mink encephalopathy in hamsters. J Gen Virol 1992;73:329-34
   PubMed Web of Science ®Google Scholar
• Bessen RA, Marsh RF. Distinct PrP properties suggest the molecular basis of strain variation in transmissible mink encephalopathy. J Virol 1994;68:7859-68
   PubMed Web of Science ®Google Scholar
• Stahl N, Baldwin MA, Prusiner SB. Electrospray mass spectrometry of the glycosylinositol phospholipid of the scrapie prion protein. Cell Biol Int Rep 1991;15(9):853-62
   PubMedGoogle Scholar
• Bolton DC, Meyer RK, Prusiner SB. Scrapie PrP 27-30 is a sialoglycoprotein. J Virol 1985;53:596-606
   PubMed Web of Science ®Google Scholar
• Stimson E, Hope J, Chong A, Burlingame AL. Site-specific characterization of the N-linked glycans of murine prion protein by high-performance liquid chromatography/electrospray mass spectrometry and exoglycosidase digestions. Biochemistry 1999;38(15):4885-95
   PubMedGoogle Scholar
• Turk E, Teplow DB, Hood LE, Prusiner SB. Purification and properties of the cellular and scrapie hamster prion proteins. Eur J Biochem 1988;176:21-30
   PubMedGoogle Scholar
• Stahl N, Baldwin MA, Teplow DB, et al. Structural studies of the scrapie prion protein using mass spectrometry and amino acid sequencing. Biochemistry 1993;32:1991-2002
   PubMed Web of Science ®Google Scholar
• Hope J, Morton LJD, Farquhar CF, et al. The major polypeptide of scrapie-associated fibrils (SAF) has the same size, charge distribution and N-terminal protein sequence as predicted for the normal brain protein (PrP). EMBO J 1986;5:2591-7
   PubMed Web of Science ®Google Scholar
• Gill AC, Ritchie MA, Hunt LG, et al. Post-translational hydroxylation at the N-terminus of the prion protein reveals presence of PPII structure in vivo. EMBO J 2000;19(20):5324-31
   PubMedGoogle Scholar
• Arsenault PR, Heaton-Johnson KJ, Li LS, et al. Identification of prolyl hydroxylation modifications in mammalian cell proteins. Proteomics 2014. [Epub ahead of print]
   Google Scholar
• Squier TC. Oxidative stress and protein aggregation during biological aging. Exp Gerontol 2001;36(9):1539-50
   PubMed Web of Science ®Google Scholar
• Li S, Nguyen TH, Schoneich C, Borchardt RT. Aggregation and precipitation of human relaxin induced by metal-catalyzed oxidation. Biochemistry 1995;34(17):5762-72
   PubMedGoogle Scholar
• Feng B, Wang Z, Liu T, et al. Methionine oxidation accelerates the aggregation and enhances the neurotoxicity of the D178N variant of the human prion protein. Biochim Biophys Acta 2014;1842(12 Pt A):2345-56
   PubMedGoogle Scholar
• Requena JR, Dimitrova MN, Legname G, et al. Oxidation of methionine residues in the prion protein by hydrogen peroxide. Arch Biochem Biophys 2004;432(2):188-95
   PubMedGoogle Scholar
• Canello T, Engelstein R, Moshel O, et al. Methionine sulfoxides on PrPSc: a prion-specific covalent signature. Biochemistry 2008;47(34):8866-73
   PubMed Web of Science ®Google Scholar
• Colombo G, Meli M, Morra G, et al. Methionine sulfoxides on prion protein Helix-3 switch on the alpha-fold destabilization required for conversion. PLoS One 2009;4(1):e4296
   Google Scholar
• Canello T, Frid K, Gabizon R, et al. Oxidation of Helix-3 methionines precedes the formation of PK resistant PrP. PLoS Pathog 2010;6(7):e1000977
   PubMed Web of Science ®Google Scholar
• Silva CJ, Onisko BC, Dynin I, et al. Assessing the role of oxidized methionine at position 213 in the formation of prions in hamsters. Biochemistry 2010;49(9):1854-61
   PubMed Web of Science ®Google Scholar
• Chen M, Cook KD. Oxidation artifacts in the electrospray mass spectrometry of Abeta Peptide. Anal Chem 2007;79(5):2031-6
   PubMed Web of Science ®Google Scholar
• Cohen SL. Ozone in ambient air as a source of adventitious oxidation. A mass spectrometric study. Anal Chem 2006;78(13):4352-62
   PubMedGoogle Scholar
• Crecelius AC, Helmstetter D, Strangmann J, et al. The brain proteome profile is highly conserved between Prnp-/- and Prnp+/+ mice. Neuroreport 2008;19(10):1027-31
   PubMedGoogle Scholar
• Schmitz M, Greis C, Ottis P, et al. Loss of prion protein leads to age-dependent behavioral abnormalities and changes in cytoskeletal protein expression. Mol Neurobiol 2014;50(3):923-36
   PubMed Web of Science ®Google Scholar
• Zafar S, von Ahsen N, Oellerich M, et al. Proteomics approach to identify the interacting partners of cellular prion protein and characterization of Rab7a interaction in neuronal cells. J Proteome Res 2011;10(7):3123-35
   PubMedGoogle Scholar
• Zafar S, Asif AR, Ramljak S, et al. Anchorless 23-230 PrPC interactomics for elucidation of PrPC protective role. Mol Neurobiol 2014;49(3):1385-99
   PubMedGoogle Scholar
• Weiss E, Ramljak S, Asif AR, et al. Cellular prion protein overexpression disturbs cellular homeostasis in SH-SY5Y neuroblastoma cells but does not alter p53 expression: a proteomic study. Neurosci 2010;169(4):1640-50
   Google Scholar
• Reutelingsperger CP, van Heerde WL. Annexin V. The regulator of phosphatidylserine-catalyzed inflammation and coagulation during apoptosis. Cell Mol Life Sci 1997;53(6):527-32
   PubMed Web of Science ®Google Scholar
• Giese A, Kretzschmar HA. Prion-induced neuronal damage – the mechanisms of neuronal destruction in the subacute spongiform encephalopathies. Curr Top Microbiol Immunol 2001;253:203-17
   PubMed Web of Science ®Google Scholar
• Eikelenboom P, Bate C, van Gool WA, et al. Neuroinflammation in Alzheimer’s disease and prion disease. Glia 2002;40(2):232-9
   PubMed Web of Science ®Google Scholar
• Llorens F, Lopez-Gonzalez I, Thune K, et al. Subtype and regional-specific neuroinflammation in sporadic Creutzfeldt-Jakob disease. Front Aging Neurosci 2014;6:198
   PubMed Web of Science ®Google Scholar
• Riemer C, Gultner S, Heise I, et al. Neuroinflammation in prion diseases: concepts and targets for therapeutic intervention. CNS Neurol Disord Drug Targets 2009;8(5):329-41
   PubMedGoogle Scholar
• Levin EC, Acharya NK, Sedeyn JC, et al. Neuronal expression of vimentin in the Alzheimer’s disease brain may be part of a generalized dendritic damage-response mechanism. Brain Res 2009;1298:194-207
   PubMedGoogle Scholar
• Nezu T, Hosomi N, Aoki S, et al. Alpha2-macroglobulin as a promising biomarker for cerebral small vessel disease in acute ischemic stroke patients. J Neurol 2013;260(10):2642-9
   PubMedGoogle Scholar
• Wang H, Sama AE. Anti-inflammatory role of fetuin-A in injury and infection. Curr Mol Med 2012;12(5):625-33
   PubMed Web of Science ®Google Scholar
• Asuni AA, Gray B, Bailey J, et al. Analysis of the hippocampal proteome in me7 prion disease reveals a predominant astrocytic signature and highlights the brain-restricted production of clusterin in chronic neurodegeneration. J Biol Chem 2014;289(7):4532-45
   PubMedGoogle Scholar
• Piubelli C, Fiorini M, Zanusso G, et al. Searching for markers of Creutzfeldt-Jakob disease in cerebrospinal fluid by two-dimensional mapping. Proteomics 2006;6(Suppl 1):S256-61
   Google Scholar
• Lv Y, Chen C, Zhang BY, et al. Remarkable activation of the complement system and aberrant neuronal localization of the membrane attack complex in the brain tissues of scrapie-infected rodents. Mol Neurobiol 2014. [Epub ahead of print]
   Google Scholar
• Veerhuis R. Histological and direct evidence for the role of complement in the neuroinflammation of AD. Curr Alzheimer Res 2011;8(1):34-58
   PubMedGoogle Scholar
• Moore RA, Sturdevant DE, Chesebro B, Priola SA. Proteomics analysis of amyloid and nonamyloid prion disease phenotypes reveals both common and divergent mechanisms of neuropathogenesis. J Proteome Res 2014;13(11):4620-34
   PubMedGoogle Scholar
• Chesebro B, Race B, Meade-White K, et al. Fatal transmissible amyloid encephalopathy: a new type of prion disease associated with lack of prion protein membrane anchoring. PLoS Pathog 2010;6(3):e1000800
   PubMed Web of Science ®Google Scholar
• Klingeborn M, Race B, Meade-White KD, et al. Crucial role for prion protein membrane anchoring in the neuroinvasion and neural spread of prion infection. J Virol 2011;85(4):1484-94
   PubMed Web of Science ®Google Scholar
• Gawinecka J, Cardone F, Asif AR, et al. Sporadic Creutzfeldt-Jakob disease subtype-specific alterations of the brain proteome: impact on Rab3a recycling. Proteomics 2012;12(23-24):3610-20
   PubMedGoogle Scholar
• Norberg E, Orrenius S, Zhivotovsky B. Mitochondrial regulation of cell death: processing of apoptosis-inducing factor (AIF). Biochem Biophys Res Commun 2010;396(1):95-100
   PubMed Web of Science ®Google Scholar
• Choi SI, Ju WK, Choi EK, et al. Mitochondrial dysfunction induced by oxidative stress in the brains of hamsters infected with the 263 K scrapie agent. Acta Neuropathol 1998;96(3):279-86
   PubMed Web of Science ®Google Scholar
• Siskova Z, Mahad DJ, Pudney C, et al. Morphological and functional abnormalities in mitochondria associated with synaptic degeneration in prion disease. Am J Pathol 2010;177(3):1411-21
   PubMedGoogle Scholar
• Gawinecka J, Dieks J, Asif AR, et al. Codon 129 polymorphism specific cerebrospinal fluid proteome pattern in sporadic Creutzfeldt-Jakob disease and the implication of glycolytic enzymes in prion-induced pathology. J Proteome Res 2010;9(11):5646-57
   PubMedGoogle Scholar
• Gawinecka J, Nowak M, Carimalo J, et al. Subtype-specific synaptic proteome alterations in sporadic Creutzfeldt-Jakob disease. J Alzheimers Dis 2013;37(1):51-61
   PubMedGoogle Scholar
• Xiang W, Windl O, Westner IM, et al. Cerebral gene expression profiles in sporadic Creutzfeldt-Jakob disease. Ann Neurol 2005;58(2):242-57
   PubMed Web of Science ®Google Scholar
• Brinkmalm A, Brinkmalm G, Honer WG, et al. Targeting synaptic pathology with a novel affinity mass spectrometry approach. Mol Cell Proteomics 2014;13(10):2584-92
   PubMed Web of Science ®Google Scholar
• Provansal M, Roche S, Pastore M, et al. Proteomic consequences of expression and pathological conversion of the prion protein in inducible neuroblastoma N2a cells. Prion 2010;4(4):292-301
   PubMed Web of Science ®Google Scholar
• Aebersold R, Burlingame AL, Bradshaw RA. Western blots versus selected reaction monitoring assays: time to turn the tables? Mol Cell Proteomics 2013;12(9):2381-2
   PubMed Web of Science ®Google Scholar
• Lausted C, Lee I, Zhou Y, et al. Systems approach to neurodegenerative disease biomarker discovery. Annu Rev Pharmacol Toxicol 2014;54:457-81
   PubMedGoogle Scholar