Alberti S, Halfmann R, King O, Kapila A, Lindquist S. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell. 2009;137:146–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brown JCS, Lindquist S. A heritable switch in carbon source utilization driven by an unusual yeast prion. Genes Dev. 2009;23:2320–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Volkov KV, Aksenova AY, Soom MJ, Osipov KV, Svitin AV, Kurischko C, et al. Novel non-Mendelian determinant involved in the control of translation accuracy in Saccharomyces cerevisiae. Genetics. 2002;160:25–36.
CAS
PubMed
PubMed Central
Google Scholar
Wickner RB. [URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae. Science. 1994;264:566–9.
Article
CAS
PubMed
Google Scholar
Hou F, Sun L, Zheng H, Skaug B, Jiang Q-X, Chen ZJ. MAVS forms functional prion-like aggregates to activate and propagate antiviral innate immune response. Cell. 2011;146:448–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chakravarty AK, Jarosz DF. More than just a phase: prions at the crossroads of epigenetic inheritance and evolutionary change. J Mol Biol. 2018;430:4607–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hake LE, Richter JD. CPEB is a specificity factor that mediates cytoplasmic polyadenylation during Xenopus oocyte maturation. Cell. 1994;79:617–27.
Article
CAS
PubMed
Google Scholar
Si K, Choi Y-B, White-Grindley E, Majumdar A, Kandel ER. Aplysia CPEB can form prion-like multimers in sensory neurons that contribute to long-term facilitation. Cell. 2010;140:421–35.
Article
CAS
PubMed
Google Scholar
Fioriti L, Myers C, Huang Y-Y, Li X, Stephan JS, Trifilieff P, et al. The persistence of hippocampal-based memory requires protein synthesis mediated by the prion-like protein CPEB3. Neuron. 2015;86:1433–48.
Article
CAS
PubMed
Google Scholar
Majumdar A, Cesario WC, White-Grindley E, Jiang H, Ren F, Khan MR, et al. Critical role of amyloid-like oligomers of Drosophila Orb2 in the persistence of memory. Cell. 2012;148:515–29.
Article
CAS
PubMed
Google Scholar
Khan MR, Li L, Perez-Sanchez C, Saraf A, Florens L, Slaughter BD, et al. Amyloidogenic oligomerization transforms Drosophila Orb2 from a translation repressor to an activator. Cell. 2015;163:1468–83.
Article
CAS
PubMed
Google Scholar
Kruttner S, Stepien B, Noordermeer JN, Mommaas MA, Mechtler K, Dickson BJ, et al. Drosophila CPEB Orb2A mediates memory independent of Its RNA-binding domain. Neuron. 2012;76:383–95.
Article
PubMed
CAS
Google Scholar
Kruttner S, Traunmuller L, Dag U, Jandrasits K, Stepien B, Iyer N, et al. Synaptic Orb2A bridges memory acquisition and late memory consolidation in Drosophila. Cell Rep. 2015;11:1953–65.
Article
PubMed
PubMed Central
CAS
Google Scholar
Keleman K, Kruttner S, Alenius M, Dickson BJ. Function of the Drosophila CPEB protein Orb2 in long-term courtship memory. Nat Neurosci. 2007;10:1587–93.
Article
CAS
PubMed
Google Scholar
Li L, Sanchez CP, Slaughter BD, Zhao Y, Khan MR, Unruh JR, et al. A putative biochemical engram of long-term memory. Curr Biol. 2016;26:3143–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hervas R, Li L, Majumdar A, Fernandez-Ramirez MDC, Unruh JR, Slaughter BD, et al. Molecular basis of Orb2 amyloidogenesis and blockade of memory consolidation. PLoS Biol. 2016;14:e1002361.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hervas R, Rau MJ, Park Y, Zhang W, Murzin AG, Fitzpatrick JAJ, et al. Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in Drosophila. Science. 2020;367:1230–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hake LE, Mendez R, Richter JD. Specificity of RNA binding by CPEB: requirement for RNA recognition motifs and a novel zinc finger. Mol Cell Biol. 1998; 18:685–93.
Stephan JS, Fioriti L, Lamba N, Colnaghi L, Karl K, Derkatch IL, et al. The CPEB3 protein is a functional prion that interacts with the actin cytoskeleton. Cell Rep. 2015;11:1772–85.
Article
CAS
PubMed
Google Scholar
Si K, Lindquist S. Kandel ER. A neuronal isoform of the aplysia CPEB has prion-like properties. Cell. 2003;115:879–91.
Article
CAS
PubMed
Google Scholar
Raveendra BL, Siemer AB, Puthanveettil SV, Hendrickson WA, Kandel ER, McDermott AE. Characterization of prion-like conformational changes of the neuronal isoform of Aplysia CPEB. Nat Struct Mol Biol. 2013;20:495–501.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fiumara F, Fioriti L, Kandel ER, Hendrickson WA. Essential role of coiled coils for aggregation and activity of Q/N-rich prions and PolyQ proteins. Cell. 2010;143:1121–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wickner RB, Edskes HK, Shewmaker F, Nakayashiki T. Prions of fungi: inherited structures and biological roles. Nat Rev Microbiol. 2007;5:611–8.
Lupas A, Van Dyke M, Stock J. Predicting coiled coils from protein sequences. Science. 1991;252:1162–4.
Article
CAS
PubMed
Google Scholar
McDonnell AV, Jiang T, Keating AE, Berger B. Paircoil2: improved prediction of coiled coils from sequence. Bioinformatics. 2006;22:356–8.
Article
CAS
PubMed
Google Scholar
Delorenzi M, Speed T. An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics. 2002;18:617–25.
Article
CAS
PubMed
Google Scholar
Gruber M, Söding J, Lupas AN. Comparative analysis of coiled-coil prediction methods. J Struct Biol. 2006;155:140–5.
Nagai Y, Inui T, Popiel HA, Fujikake N, Hasegawa K, Urade Y, et al. A toxic monomeric conformer of the polyglutamine protein. Nat Struct Mol Biol. 2007;14:332–40.
Article
CAS
PubMed
Google Scholar
Ramos-Martin F, Hervas R, Carrion-Vazquez M, Laurents DV. NMR spectroscopy reveals a preferred conformation with a defined hydrophobic cluster for polyglutamine binding peptide 1. Arch Biochem Biophys. 2014;558:104–10.
Article
CAS
PubMed
Google Scholar
Hervas R, Oroz J, Galera-Prat A, Goni O, Valbuena A, Vera AM, et al. Common features at the start of the neurodegeneration cascade. PLoS Biol. 2012;10:e1001335.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tomita K, Popiel HA, Nagai Y, Toda T, Yoshimitsu Y, Ohno H, et al. Structure-activity relationship study on polyglutamine binding peptide QBP1. Bioorg Med Chem. 2009;17:1259–63.
Article
CAS
PubMed
Google Scholar
Fernandez-Ramirez MDC, Hervas R, Galera-Prat A, Laurents DV, Carrion-Vazquez M. Efficient and simplified nanomechanical analysis of intrinsically disordered proteins. Nanoscale. 2018;10:16857–67.
Article
CAS
PubMed
Google Scholar
Fernández-Ramírez MDC, Hervás R, Menéndez M, Laurents D, Carrión-Vázquez M. Tau amyloidogenesis begins with a loss of its conformational polymorphism; 2020. bioRxiv doi: https://doi.org/10.1101/2020.06.18.158923.
Oroz J, Hervas R, Carrion-Vazquez M. Unequivocal single-molecule force spectroscopy of proteins by AFM using pFS vectors. Biophys J. 2012;102:682–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carrion-Vazquez M, Li H, Lu H, Marszalek PE, Oberhauser AF, Fernandez JM. The mechanical stability of ubiquitin is linkage dependent. Nat Struct Biol. 2003;10:738–43.
Article
CAS
PubMed
Google Scholar
Carrion-Vazquez M, Oberhauser AF, Fisher TE, Marszalek PE, Li H, Fernandez JM. Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering. Prog Biophys Mol Biol. 2000;74:63–91.
Article
CAS
PubMed
Google Scholar
Bustamante C, Chemla YR, Forde NR, Izhaky D. Mechanical processes in biochemistry. Annu Rev Biochem. 2004;73:705–48.
Article
CAS
PubMed
Google Scholar
Oberhauser AF, Carrion-Vazquez M. Mechanical biochemistry of proteins one molecule at a time. J Biol Chem. 2008;283:6617–21.
Article
CAS
PubMed
Google Scholar
Brown AEX, Litvinov RI, Discher DE, Weisel JW. Forced unfolding of coiled-coils in fibrinogen by single-molecule AFM. Biophysical Journal. 2007;92:L39-L41.
Goktas M, Luo C, Sullan RMA, Bergues-Pupo AE, Lipowsky R, Vila Verde A, et al. Molecular mechanics of coiled coils loaded in the shear geometry. Chemical Science. 2018;9:4610–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bornschlogl T, Rief M. Single-molecule dynamics of mechanical coiled-coil unzipping. Langmuir. 2008;24:1338–42.
Article
PubMed
CAS
Google Scholar
Schwaiger I, Sattler C, Hostetter DR, Rief M. The myosin coiled-coil is a truly elastic protein structure. Nat Mater. 2002;1:232–5.
Article
CAS
PubMed
Google Scholar
Oroz J, Félix SS, Cabrita EJ, Laurents DV. Structural transitions in Orb2 prion-like domain relevant for functional aggregation in memory consolidation; J Biol Chem. 2020;295:18122-33.
Lilliu E, Villeri V, Pelassa I, Cesano F, Scarano D, Fiumara F. Polyserine repeats promote coiled coil-mediated fibril formation and length-dependent protein aggregation. J Struct Biol. 2018;204:572–84.
Article
CAS
PubMed
Google Scholar
Lau SYM, Taneja AK, Hodges RS. Synthesis of a model protein of defined secondary and quaternary structure. J Biol Chem. 1984;259:13253-61.
Jeffrey YS, Hodges RS, Kay CM. Effect of chain length on the formation and stability of synthetic α-helical coiled coils. Biochemistry. 1994;33:15501-10.
Chen M, Zheng W, Wolynes PG. Energy landscapes of a mechanical prion and their implications for the molecular mechanism of long-term memory. Proc Natl Acad Sci U S A. 2016;113:5006–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kayed R, Head E, Thompson JL, McIntire TM, Milton SC, Cotman CW, et al. Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science. 2003;300:486–9.
Article
CAS
PubMed
Google Scholar
Kayed R, Head E, Sarsoza F, Saing T, Cotman CW, Necula M, et al. Fibril specific, conformation dependent antibodies recognize a generic epitope common to amyloid fibrils and fibrillar oligomers that is absent in prefibrillar oligomers. Mol Neurodegener. 2007;2:18.
Article
PubMed
PubMed Central
CAS
Google Scholar
Linke RP. Highly sensitive diagnosis of amyloid and various amyloid syndromes using Congo red fluorescence. Virchows Arch. 2000.
Şen S, Başdemir G. Diagnosis of renal amyloidosis using Congo red fluorescence. Pathol Int. 2003;53:534-8.
Krishnan R, Goodman JL, Mukhopadhyay S, Pacheco CD, Lemke EA, Deniz AA, et al. Conserved features of intermediates in amyloid assembly determine their benign or toxic states. Proc Natl Acad Sci U S A. 2012;109:11172–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sackett DL, Wolff J. Nile red as a polarity-sensitive fluorescent probe of hydrophobic protein surfaces. Anal Biochem. 1987;167:228–34.
Article
CAS
PubMed
Google Scholar
Campioni S, Mannini B, Zampagni M, Pensalfini A, Parrini C, Evangelisti E, et al. A causative link between the structure of aberrant protein oligomers and their toxicity. Nat Chem Biol. 2010;6:140–7.
Article
CAS
PubMed
Google Scholar
Chen SW, Drakulic S, Deas E, Ouberai M, Aprile FA, Arranz R, et al. Structural characterization of toxic oligomers that are kinetically trapped during alpha-synuclein fibril formation. Proc Natl Acad Sci U S A. 2015;112:E1994–2003.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu C, Zhao M, Jiang L, Cheng P-N, Park J, Sawaya MR, et al. Out-of-register beta-sheets suggest a pathway to toxic amyloid aggregates. Proc Natl Acad Sci U S A. 2012;109:20913–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mukhopadhyay S, Krishnan R, Lemke EA, Lindquist S, Deniz AA. A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. Proc Natl Acad Sci U S A. 2007;104:2649–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ferreon ACM, Moran CR, Gambin Y, Deniz AA. Single-molecule fluorescence studies of intrinsically disordered proteins. Methods Enzymol. 2010;472:179–204.
Article
CAS
PubMed
Google Scholar
Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem. 2006;75:333–66.
Article
CAS
PubMed
Google Scholar
Si K. Prions: what are they good for? Ann Rev Cell Dev Biol. 2015;31:149–69.
Article
CAS
Google Scholar
Ramírez de Mingo D, López-García P, Hervás R, Laurents DV, Carrión-Vázquez M. Molecular determinants of liquid demixing and amyloidogenesis in human CPEB3; 2020. bioRxiv doi: https://doi.org/10.1101/2020.06.02.129783.
Ramírez de Mingo D, Pantoja-Uceda D, Hervás R, Vázquez MC, Laurents D. Preferred conformations in the intrinsically disordered region of human CPEB3 explain its role in memory consolidation; 2020. bioRxiv doi:https://doi.org/10.1101/2020.05.12.091587.
Drisaldi B, Colnaghi L, Fioriti L, Rao N, Myers C, Snyder AM, et al. SUMOylation is an inhibitory constraint that regulates the prion-like aggregation and activity of CPEB3. Cell Rep. 2015;11:1694–702.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fiumara F, Rajasethupathy P, Antonov I, Kosmidis S, Sossin WS, Kandel ER. MicroRNA-22 gates long-term heterosynaptic plasticity in Aplysia through presynaptic regulation of CPEB and downstream targets. Cell Rep. 2015;11:1866–75.
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44:D279–85.
Article
CAS
PubMed
Google Scholar
Mitchell A, Chang H-Y, Daugherty L, Fraser M, Hunter S, Lopez R, et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 2015;43(Database issue):D213–21.
Article
PubMed
Google Scholar
Goldschmidt L, Teng PK, Riek R, Eisenberg D. Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proc Natl Acad Sci U S A. 2010;107:3487–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta. 2010;1804:996–1010.
Article
CAS
PubMed
PubMed Central
Google Scholar
Piotto M, Saudek V, Sklenar V. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J Biomol NMR. 1992;2:661–5.
Article
CAS
PubMed
Google Scholar
Improta S, Politou AS, Pastore A. Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity. Structure. 1996;4:323–37.
Article
CAS
PubMed
Google Scholar
Bohm G, Muhr R, Jaenicke R. Quantitative analysis of protein far UV circular dichroism spectra by neural networks. Protein Eng. 1992;5:191–5.
Article
CAS
PubMed
Google Scholar
Wurth C, Guimard NK, Hecht MH. Mutations that reduce aggregation of the Alzheimer’s Abeta42 peptide: an unbiased search for the sequence determinants of Abeta amyloidogenesis. J Mol Biol. 2002;319:1279–90.
Article
CAS
PubMed
Google Scholar
Valbuena A, Oroz J, Hervas R, Vera AM, Rodriguez D, Menendez M, et al. On the remarkable mechanostability of scaffoldins and the mechanical clamp motif. Proc Natl Acad Sci U S A. 2009;106:13791–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Florin EL, Rief M, Lehmann H, Ludwig M, Dornmair C, Moy VT, et al. Sensing specific molecular interactions with the atomic force microscope. Biosens Bioelectron. 1995;10:895–901.
Article
CAS
Google Scholar
Carrión-Vázquez M, Oberhauser A, Diez H, Hervás R, Oroz J, Fernández J, et al. Protein nanomechanics - as studied by AFM single-molecule force spectroscopy. In: Advanced Techniques in Biophysics; 2007. p. 163–245.
Google Scholar
Ainavarapu SRK, Brujic J, Huang HH, Wiita AP, Lu H, Li L, et al. Contour length and refolding rate of a small protein controlled by engineered disulfide bonds. Biophys J. 2007;92:225–33.
Article
CAS
PubMed
Google Scholar