Protein aggregation: Mechanisms and functional consequences

Abeliovich, 2000, Mice lacking alpha-synuclein display functional deficits in the nigrostriatal dopamine system, Neuron, 25, 239, 10.1016/S0896-6273(00)80886-7 Aggeli, 2001, Hierarchical self-assembly of chiral rod-like molecules as a model for peptide beta-sheet tapes, ribbons, fibrils, and fibers, Proceedings of the National Academy of Sciences of the United States of America, 98, 11857, 10.1073/pnas.191250198 Aguzzi, 2008, Unraveling prion strains with cell biology and organic chemistry, Proceedings of the National Academy of Sciences of the United States of America, 105, 11, 10.1073/pnas.0710824105 Aguzzi, 2009, Prions: protein aggregation and infectious diseases, Physiological Reviews, 89, 1105, 10.1152/physrev.00006.2009 Almstedt, 2009, Amyloid fibrils of human prion protein are spun and woven from morphologically disordered aggregates, Prion, 3, 224, 10.4161/pri.3.4.10112 Alvarez-Martinez, 2011, Dynamics of polymerization shed light on the mechanisms that lead to multiple amyloid structures of the prion protein, Biochimica et Biophysica Acta, 1814, 1305, 10.1016/j.bbapap.2011.05.016 Andersen, 2009, Branching in amyloid fibril growth, Biophysical Journal, 96, 1529, 10.1016/j.bpj.2008.11.024 Atwood, 1998, Dramatic aggregation of Alzheimer abeta by Cu(II) is induced by conditions representing physiological acidosis, Journal of Biological Chemistry, 273, 12817, 10.1074/jbc.273.21.12817 Auer, 2008, Self-templated nucleation in peptide and protein aggregation, Physical Review Letters, 101, 10.1103/PhysRevLett.101.258101 Austin, 1998, Thin aggregative fimbriae enhance Salmonella enteritidis biofilm formation, FEMS Microbiology Letters, 162, 295, 10.1111/j.1574-6968.1998.tb13012.x Avila, 2011, Multiscale molecular dynamics of protein aggregation, Current Protein & Peptide Science, 12, 221, 10.2174/138920311795860205 Azevedo, 2011, Biochemistry, 50, 11070, 10.1021/bi201365r Balducci, 2010, Synthetic amyloid-beta oligomers impair long-term memory independently of cellular prion protein, Proceedings of the National Academy of Sciences of the United States of America, 107, 2295, 10.1073/pnas.0911829107 Ballard, 2011, Alzheimer's disease, Lancet, 377, 1019, 10.1016/S0140-6736(10)61349-9 Ballatore, 2007, Tau-mediated neurodegeneration in Alzheimer's disease and related disorders, Nature Reviews Neuroscience, 8, 663, 10.1038/nrn2194 Barducci, 2010, Linking well-tempered metadynamics simulations with experiments, Biophysical Journal, 98, L44, 10.1016/j.bpj.2010.01.033 Barducci, 2006, Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding, Journal of the American Chemical Society, 128, 2705, 10.1021/ja057076l Bartels, 2011, α-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation, Nature, 477, 107, 10.1038/nature10324 Bellesia, 2009, Diversity of kinetic pathways in amyloid fibril formation, Journal of Chemical Physics, 131, 111102, 10.1063/1.3216103 Bernstein, 2009, Amyloid-beta protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease, Nature Chemistry, 1, 326, 10.1038/nchem.247 Bero, 2011, Neuronal activity regulates the regional vulnerability to amyloid-beta deposition, Nature Neuroscience, 14, 750, 10.1038/nn.2801 Berryman, 2009, Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation, Biophysical Journal, 97, 1, 10.1016/j.bpj.2009.03.062 Berryman, 2011, Systematic examination of polymorphism in amyloid fibrils by molecular-dynamics simulation, Biophysical Journal, 100, 2234, 10.1016/j.bpj.2011.02.060 Berson, 2003, Proprotein convertase cleavage liberates a fibrillogenic fragment of a resident glycoprotein to initiate melanosome biogenesis, Journal of Cell Biology, 161, 521, 10.1083/jcb.200302072 Bhak, 2009, Mechanism of amyloidogenesis: nucleation-dependent fibrillation versus double-concerted fibrillation, BMB Reports, 42, 541, 10.5483/BMBRep.2009.42.9.541 Bonomi, 2009, Reconstructing the equilibrium boltzmann distribution from well-tempered metadynamics, Journal of Computational Chemistry, 30, 1615, 10.1002/jcc.21305 Bonomi, 2010, Enhanced sampling in the well-tempered ensemble, Physical Review Letters, 104, 10.1103/PhysRevLett.104.190601 Bremer, 2010, Axonal prion protein is required for peripheral myelin maintenance, Nature Neuroscience, 13, 310, 10.1038/nn.2483 Bucciantini, 2002, Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases, Nature, 416, 507, 10.1038/416507a Burré, 2010, Alpha-synuclein promotes SNARE-complex assembly in vivo and in vitro, Science, 329, 1663, 10.1126/science.1195227 Bush, 1994, Modulation of A beta adhesiveness and secretase site cleavage by zinc, Journal of Biological Chemistry, 269, 12152, 10.1016/S0021-9258(17)32694-7 Butterfield, 2010, Amyloidogenic protein–membrane interactions: mechanistic insight from model systems, Angewandte Chemie: International Edition in English, 49, 5628, 10.1002/anie.200906670 Cabriolu, 2011, Amyloid fibrillation kinetics: insight from atomistic nucleation theory, Journal of Molecular Biology, 411, 275, 10.1016/j.jmb.2011.05.032 Calabrese, 2007, Formation of a stable oligomer of beta-2 microglobulin requires only transient encounter with Cu(II), Journal of Molecular Biology, 367, 1, 10.1016/j.jmb.2006.12.034 Calabrese, 2009, Metal binding sheds light on mechanisms of amyloid assembly, Prion, 3, 1, 10.4161/pri.3.1.8601 Camilloni, 2012, Energy landscape of the prion protein helix 1 probed by metadynamics and NMR, Biophysical Journal, 102, 158, 10.1016/j.bpj.2011.12.003 Carulla, 2005, Molecular recycling within amyloid fibrils, Nature, 436, 554, 10.1038/nature03986 Castillo, 2009, Amyloidogenic regions and interaction surfaces overlap in globular proteins related to conformational diseases, PLoS Computational Biology, 5, e1000476, 10.1371/journal.pcbi.1000476 Castro, 2011, Physical properties of polymorphic yeast prion amyloid fibers, Biophysical Journal, 101, 439, 10.1016/j.bpj.2011.06.016 Cavigiolio, 2010, Exchange of apolipoprotein A-I between lipid-associated and lipid-free states: a potential target for oxidative generation of dysfunctional high density lipoproteins, Journal of Biological Chemistry, 285, 18847, 10.1074/jbc.M109.098434 Chapman, 2002, Role of Escherichia coli curli operons in directing amyloid fiber formation, Science, 295, 851, 10.1126/science.1067484 Chauhan, 2008, Anti-amyloidogenic, anti-oxidant and anti-apoptotic role of gelsolin in Alzheimer's disease, Biogerontology, 9, 381, 10.1007/s10522-008-9169-z Cheon, 2010, Extending the PRIME model for protein aggregation to all 20 amino acids, Proteins: Structure Function and Bioinformatics, 78, 2950, 10.1002/prot.22817 Cheon, 2011, Spontaneous formation of twisted A beta(16–22) fibrils in large-scale molecular-dynamics simulations, Biophysical Journal, 101, 2493, 10.1016/j.bpj.2011.08.042 Chiti, 2006, Protein misfolding, functional amyloid, and human disease, Annual Review of Biochemistry, 75, 333, 10.1146/annurev.biochem.75.101304.123901 Chiti, 2009, Amyloid formation by globular proteins under native conditions, Nature Chemical Biology, 5, 15, 10.1038/nchembio.131 Claessen, 2003, A novel class of secreted hydrophobic proteins is involved in aerial hyphae formation in Streptomyces coelicolor by forming amyloid-like fibrils, Genes & Development, 17, 1714, 10.1101/gad.264303 Colby, 2011, Prions, Cold Spring Harbor Perspectives in Biology, 3, a006833, 10.1101/cshperspect.a006833 Conway, 2000, Acceleration of oligomerization, not fibrillization, is a shared property of both alpha-synuclein mutations linked to early-onset Parkinson's disease: implications for pathogenesis and therapy, Proceedings of the National Academy of Sciences of the United States of America, 97, 571, 10.1073/pnas.97.2.571 Dasari, 2011, Bacterial inclusion bodies of Alzheimer's disease beta-amyloid peptides can be employed to study native-like aggregation intermediate states, Chembiochem: A European Journal of Chemical Biology, 12, 407, 10.1002/cbic.201000602 de Jong, 2009, Attachment of Streptomyces coelicolor is mediated by amyloidal fimbriae that are anchored to the cell surface via cellulose, Molecular Microbiology, 73, 1128, 10.1111/j.1365-2958.2009.06838.x de Koning, 1993, Diabetes mellitus in Macaca mulatta monkeys is characterised by islet amyloidosis and reduction in beta-cell population, Diabetologia, 36, 378, 10.1007/BF00402271 De Simone, 2008, Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses, Biophysical Journal, 95, 1965, 10.1529/biophysj.108.129213 Dobson, 2003, Protein folding and misfolding, Nature, 426, 884, 10.1038/nature02261 Dodson, 2008, Molecular simulations of protein dynamics: new windows on mechanisms in biology, EMBO Reports, 9, 144, 10.1038/sj.embor.7401160 Duennwald, 2006, Flanking sequences profoundly alter polyglutamine toxicity in yeast, Proceedings of the National Academy of Sciences of the United States of America, 103, 11045, 10.1073/pnas.0604547103 Edgeworth, 2010, Spontaneous generation of mammalian prions, Proceedings of the National Academy of Sciences of the United States of America, 107, 14402, 10.1073/pnas.1004036107 Eichner, 2011, Conformational conversion during amyloid formation at atomic resolution, Molecular Cell, 41, 161, 10.1016/j.molcel.2010.11.028 Eichner, 2009, A generic mechanism of beta2-microglobulin amyloid assembly at neutral pH involving a specific proline switch, Journal of Molecular Biology, 386, 1312, 10.1016/j.jmb.2009.01.013 Elliot, 2003, The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation in Streptomyces coelicolor, Genes & Development, 17, 1727, 10.1101/gad.264403 Ellisdon, 2006, The two-stage pathway of ataxin-3 fibrillogenesis involves a polyglutamine-independent step, Journal of Biological Chemistry, 281, 16888, 10.1074/jbc.M601470200 Eriksson, 2009, Hereditary apolipoprotein AI-associated amyloidosis in surgical pathology specimens: identification of three novel mutations in the APOA1 gene, Journal of Molecular Diagnostics, 11, 257, 10.2353/jmoldx.2009.080161 Esposito, 2000, Removal of the N-terminal hexapeptide from human beta2-microglobulin facilitates protein aggregation and fibril formation, Protein Science, 9, 831, 10.1110/ps.9.5.831 Fauvet, 2012, Alpha-synuclein in the central nervous system and from erythrocytes, mammalian cells and E. coli exists predominantly as a disordered monomer, Journal of Biological Chemistry, 287, 15345, 10.1074/jbc.M111.318949 Feng, 2008, Small-molecule aggregates inhibit amyloid polymerization, Nature Chemical Biology, 4, 197, 10.1038/nchembio.65 Ferrone, 1999, Analysis of protein aggregation kinetics, Methods in Enzymology, 309, 256, 10.1016/S0076-6879(99)09019-9 Floege, 1991, Clearance and synthesis rates of beta 2-microglobulin in patients undergoing hemodialysis and in normal subjects, Journal of Laboratory and Clinical Medicine, 118, 153 Fowler, 2006, Functional amyloid formation within mammalian tissue, PLoS Biology, 4, e6, 10.1371/journal.pbio.0040006 Friedman, 2011, Aggregation of amyloids in a cellular context: modelling and experiment, Biochemical Journal, 438, 415, 10.1042/BJ20110369 Gatchel, 2005, Diseases of unstable repeat expansion: mechanisms and common principles, Nature Reviews Genetics, 6, 743, 10.1038/nrg1691 Gilch, 2001, Intracellular re-routing of prion protein prevents propagation of PrP(Sc) and delays onset of prion disease, EMBO Journal, 20, 3957, 10.1093/emboj/20.15.3957 Giorgetti, 2005, Beta2-microglobulin isoforms display an heterogeneous affinity for type I collagen, Protein Science, 14, 696, 10.1110/ps.041194005 Giurleo, 2008, Beta-lactoglobulin assembles into amyloid through sequential aggregated intermediates, Journal of Molecular Biology, 381, 1332, 10.1016/j.jmb.2008.06.043 Glabe, 2006, Common mechanisms of amyloid oligomer pathogenesis in degenerative disease, Neurobiology of Aging, 27, 570, 10.1016/j.neurobiolaging.2005.04.017 Gomaraschi, 2011, Effect of the amyloidogenic L75P apolipoprotein A-I variant on HDL subpopulations, Clinica Chimica Acta, 412, 1262, 10.1016/j.cca.2011.03.027 Gorbenko, 2011, Protein aggregation in a membrane environment, Advances in Protein Chemistry and Structural Biology, 84, 113, 10.1016/B978-0-12-386483-3.00002-1 Gotz, 2001, Formation of neurofibrillary tangles in P301l tau transgenic mice induced by Abeta 42 fibrils, Science, 293, 1491, 10.1126/science.1062097 Guha, 2008, Correlation of structural stability with functional remodeling of high-density lipoproteins: the importance of being disordered, Biochemistry, 47, 11393, 10.1021/bi8014746 Gursky, 2012, The crystal structure of the C-terminal truncated apolipoprotein A-I sheds new light on amyloid formation by the N-terminal fragment, Biochemistry, 51, 10, 10.1021/bi2017014 Haigh, 2006, Prion protein reduces both oxidative and non-oxidative copper toxicity, Journal of Neurochemistry, 98, 677, 10.1111/j.1471-4159.2006.03906.x Harper, 1997, Models of amyloid seeding in Alzheimer's disease and scrapie: mechanistic truths and physiological consequences of the time-dependent solubility of amyloid proteins, Annual Review of Biochemistry, 66, 385, 10.1146/annurev.biochem.66.1.385 Harper, 1997, Atomic force microscopic imaging of seeded fibril formation and fibril branching by the Alzheimer's disease amyloid-beta protein, Chemistry and Biology, 4, 951, 10.1016/S1074-5521(97)90303-3 Hasegawa, 2008, Growth of beta(2)-microglobulin-related amyloid fibrils by non-esterified fatty acids at a neutral pH, Biochemical Journal, 416, 307, 10.1042/BJ20080543 Haspel, 2005, A comparative study of amyloid fibril formation by residues 15–19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core, Journal of Molecular Biology, 345, 1213, 10.1016/j.jmb.2004.11.002 Hills, 2010, Multiscale coarse-graining of the protein energy landscape, PLoS Computational Biology, 6, 10.1371/journal.pcbi.1000827 Hoashi, 2006, The repeat domain of the melanosomal matrix protein PMEL17/GP100 is required for the formation of organellar fibers, Journal of Biological Chemistry, 281, 21198, 10.1074/jbc.M601643200 Hou, 2007, Transthyretin and familial amyloidotic polyneuropathy. Recent progress in understanding the molecular mechanism of neurodegeneration, FEBS Journal, 274, 1637, 10.1111/j.1742-4658.2007.05712.x Hu, 2008, Soluble amyloid-beta peptides potently disrupt hippocampal synaptic plasticity in the absence of cerebrovascular dysfunction in vivo, Brain, 131, 2414, 10.1093/brain/awn174 Hubbell, 2000, Identifying conformational changes with site-directed spin labeling, Natural Structural Biology, 7, 735, 10.1038/78956 Hughes, 1997, Misfolded major histocompatibility complex class I heavy chains are translocated into the cytoplasm and degraded by the proteasome, Proceedings of the National Academy of Sciences of the United States of America, 94, 1896, 10.1073/pnas.94.5.1896 Hung, 2011, Inhibition of peptide aggregation by lipids: insights from coarse-grained molecular simulations, Journal of Molecular Graphics & Modelling, 29, 597, 10.1016/j.jmgm.2010.11.001 Iconomidou, 2006, Amyloid fibril formation propensity is inherent into the hexapeptide tandemly repeating sequence of the central domain of silkmoth chorion proteins of the A-family, Journal of Structural Biology, 156, 480, 10.1016/j.jsb.2006.08.011 Iconomidou, 2001, Amyloid-like fibrils from an 18-residue peptide analogue of a part of the central domain of the B-family of silkmoth chorion proteins, FEBS Letters, 499, 268, 10.1016/S0014-5793(01)02510-8 Iconomidou, 2011, The silkmoth eggshell as a natural amyloid shield for the safe development of insect oocyte and embryo: insights from studies of silkmoth chorion protein peptide-analogues of the B family, Biopolymers, 96, 723, 10.1002/bip.21606 Iconomidou, 2000, Amyloids protect the silkmoth oocyte and embryo, FEBS Letters, 479, 141, 10.1016/S0014-5793(00)01888-3 Ittner, 2011, Amyloid-beta and tau – a toxic pas de deux in Alzheimer's disease, Nature Reviews Neuroscience, 12, 65, 10.1038/nrn2967 Ittner, 2010, Dendritic function of tau mediates amyloid-beta toxicity in Alzheimer's disease mouse models, Cell, 142, 387, 10.1016/j.cell.2010.06.036 Jahn, 2008, Folding versus aggregation: polypeptide conformations on competing pathways, Archives of Biochemistry and Biophysics, 469, 100, 10.1016/j.abb.2007.05.015 Jarrett, 1993, Seeding one-dimensional crystallization of amyloid: a pathogenic mechanism in Alzheimer's disease and scrapie?, Cell, 73, 1055, 10.1016/0092-8674(93)90635-4 Jin, 2011, Soluble amyloid beta-protein dimers isolated from Alzheimer cortex directly induce Tau hyperphosphorylation and neuritic degeneration, Proceedings of the National Academy of Sciences of the United States of America, 108, 5819, 10.1073/pnas.1017033108 Kahle, 2008, alpha-Synucleinopathy models and human neuropathology: similarities and differences, Acta Neuropathologica, 115, 87, 10.1007/s00401-007-0302-x Karplus, 2005, Molecular dynamics and protein function, Proceedings of the National Academy of Sciences of the United States of America, 102, 6679, 10.1073/pnas.0408930102 Kashchiev, 2010, Nucleation of amyloid fibrils, Journal of Chemical Physics, 132, 10.1063/1.3447891 Kenney, 2002, Amyloidogenic nature of spider silk, European Journal of Biochemistry, 269, 4159, 10.1046/j.1432-1033.2002.03112.x Kodali, 2007, Polymorphism in the intermediates and products of amyloid assembly, Current Opinion in Structural Biology, 17, 48, 10.1016/j.sbi.2007.01.007 Kumar, 2011, Extracellular phosphorylation of the amyloid beta-peptide promotes formation of toxic aggregates during the pathogenesis of Alzheimer's disease, EMBO Journal, 30, 2255, 10.1038/emboj.2011.138 Kwan, 2006, Structural basis for rodlet assembly in fungal hydrophobins, Proceedings of the National Academy of Sciences of the United States of America, 103, 3621, 10.1073/pnas.0505704103 Laio, 2008, Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science, Reports on Progress in Physics, 71, 10.1088/0034-4885/71/12/126601 Larsen, 2006, Alpha-synuclein overexpression in PC12 and chromaffin cells impairs catecholamine release by interfering with a late step in exocytosis, Journal of Neuroscience, 26, 11915, 10.1523/JNEUROSCI.3821-06.2006 Laurén, 2009, Cellular prion protein mediates impairment of synaptic plasticity by amyloid-beta oligomers, Nature, 457, 1128, 10.1038/nature07761 Lee, 2009, Elongation dynamics of amyloid fibrils: a rugged energy landscape picture, Physical Review E, 80, 10.1103/PhysRevE.80.041906 Lee, 2011, Dopamine promotes formation and secretion of non-fibrillar alpha-synuclein oligomers, Experimental and Molecular Medicine, 43, 216, 10.3858/emm.2011.43.4.026 Lee, 2011, Protein aggregate spreading in neurodegenerative diseases: problems and perspectives, Neuroscience Research, 70, 339, 10.1016/j.neures.2011.05.008 Legge, 2009, Effect of oxidation and mutation on the conformational dynamics and fibril assembly of amyloidogenic peptides derived from apolipoprotein C-II, Journal of Physical Chemistry B, 113, 14006, 10.1021/jp903842u Leone, 2010, Targeting biomolecular flexibility with metadynamics, Current Opinion in Structural Biology, 20, 148, 10.1016/j.sbi.2010.01.011 Li, 2011, Transthyretin and the brain re-visited: is neuronal synthesis of transthyretin protective in Alzheimer's disease?, Molecular Neurodegeneration, 6, 79, 10.1186/1750-1326-6-79 Li, 2006, Simulation of molecular crowding effects on an Alzheimer's beta-amyloid peptide, Cell Biochemistry and Biophysics, 46, 123, 10.1385/CBB:46:2:123 Linder, 2005, Hydrophobins: the protein-amphiphiles of filamentous fungi, FEMS Microbiology Reviews, 29, 877, 10.1016/j.femsre.2005.01.004 Lindorff-Larsen, 2011, How fast-folding proteins fold, Science (New York, NY), 334, 517, 10.1126/science.1208351 Liu, 2011, Iron promotes the toxicity of amyloid beta peptide by impeding its ordered aggregation, Journal of Biological Chemistry, 286, 4248, 10.1074/jbc.M110.158980 Liu, 2010, Mapping an aggregation nucleus one protein at a time, Journal of Physical Chemistry Letters, 1, 16, 10.1021/jz9000856 Liwo, 2008, Computational techniques for efficient conformational sampling of proteins, Current Opinion in Structural Biology, 18, 134, 10.1016/j.sbi.2007.12.001 Loferer, 1997, Availability of the fibre subunit CsgA and the nucleator protein CsgB during assembly of fibronectin-binding curli is limited by the intracellular concentration of the novel lipoprotein CsgG, Molecular Microbiology, 26, 11, 10.1046/j.1365-2958.1997.5231883.x Lugones, 1998, A hydrophobin (ABH3) specifically secreted by vegetatively growing hyphae of Agaricus bisporus (common white button mushroom), Microbiology, 144, 2345, 10.1099/00221287-144-8-2345 Luheshi, 2009, Bridging the gap: from protein misfolding to protein misfolding diseases, FEBS Letters, 583, 2581, 10.1016/j.febslet.2009.06.030 Ma, 2006, Simulations as analytical tools to understand protein aggregation and predict amyloid conformation, Current Opinion in Chemical Biology, 10, 445, 10.1016/j.cbpa.2006.08.018 Macindoe, 2012, Self-assembly of functional, amphipathic amyloid monolayers by the fungal hydrophobin EAS, Proceedings of the National Academy of Sciences of the United States of America, 104, 20908 Magno, 2010, Crowding effects on amyloid aggregation kinetics, Journal of Physical Chemistry Letters, 1, 3027, 10.1021/jz100967z Mahal, 2007, Prion strain discrimination in cell culture: the cell panel assay, Proceedings of the National Academy of Sciences of the United States of America, 104, 20908, 10.1073/pnas.0710054104 Maji, 2009, Functional amyloids as natural storage of peptide hormones in pituitary secretory granules, Science, 325, 328, 10.1126/science.1173155 Málaga-Trillo, 2009, Regulation of embryonic cell adhesion by the prion protein, PLoS Biology, 7, e55, 10.1371/journal.pbio.1000055 Marzban, 2006, Impaired NH2-terminal processing of human proislet amyloid polypeptide by the prohormone convertase PC2 leads to amyloid formation and cell death, Diabetes, 55, 2192, 10.2337/db05-1566 Maury, 1990, Finnish hereditary amyloidosis. Amino acid sequence homology between the amyloid fibril protein and human plasma gelsoline, FEBS Letters, 260, 85, 10.1016/0014-5793(90)80072-Q Maury, 2003, Fibrillogenesis in gelsolin-related familial amyloidosis, Amyloid, 10, 21, 10.1080/13506129.2003.12088564 McGlinchey, 2009, The repeat domain of the melanosome fibril protein Pmel17 forms the amyloid core promoting melanin synthesis, Proceedings of the National Academy of Sciences of the United States of America, 106, 13731, 10.1073/pnas.0906509106 McParland, 2000, Partially unfolded states of beta(2)-microglobulin and amyloid formation in vitro, Biochemistry, 39, 8735, 10.1021/bi000276j Miller, 2011, The unique Alzheimer's beta-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions, Journal of the American Chemical Society, 133, 2742, 10.1021/ja1100273 Monsellier, 2007, Prevention of amyloid-like aggregation as a driving force of protein evolution, EMBO Reports, 8, 737, 10.1038/sj.embor.7401034 Morell, 2008, Inclusion bodies: specificity in their aggregation process and amyloid-like structure, Biochimica et Biophysica Acta, 1783, 1815, 10.1016/j.bbamcr.2008.06.007 Moroni, 2009, Structure and sequence determinants of aggregation investigated with molecular dynamics, Frontiers in Bioscience, 14, 523, 10.2741/3260 Mousseau, 2008, Exploring energy landscapes of protein folding and aggregation, Frontiers in Bioscience, 13, 4495, 10.2741/3019 Myers, 2006, A systematic study of the effect of physiological factors on beta2-microglobulin amyloid formation at neutral pH, Biochemistry, 45, 2311, 10.1021/bi052434i Nalls, 2011, Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies, Lancet, 377, 641, 10.1016/S0140-6736(10)62345-8 Nasica-Labouze, 2011, A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35, PLoS Computational Biology, 7, e1002051, 10.1371/journal.pcbi.1002051 Natalello, 2011, A major role for side-chain polyglutamine hydrogen bonding in irreversible ataxin-3 aggregation, PLoS One, 6, e18789, 10.1371/journal.pone.0018789 Nelson, 2005, Structure of the cross-beta spine of amyloid-like fibrils, Nature, 435, 773, 10.1038/nature03680 Nenninger, 2009, Localized and efficient curli nucleation requires the chaperone-like amyloid assembly protein CsgF, Proceedings of the National Academy of Sciences of the United States of America, 106, 900, 10.1073/pnas.0812143106 Nguyen, 2011, Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16–22) dimer and trimer, Physical Chemistry Chemical Physics, 13, 9778, 10.1039/c1cp20323a Nielsen, 2001, Effect of environmental factors on the kinetics of insulin fibril formation: elucidation of the molecular mechanism, Biochemistry, 40, 6036, 10.1021/bi002555c Nishi, 1989, Conservation of the sequence of islet amyloid polypeptide in five mammals is consistent with its putative role as an islet hormone, Proceedings of the National Academy of Sciences of the United States of America, 86, 5738, 10.1073/pnas.86.15.5738 Nozaki, 2001, Amino acid sequences flanking polyglutamine stretches influence their potential for aggregate formation, Neuroreport, 12, 3357, 10.1097/00001756-200110290-00042 Obici, 2006, Structure, function and amyloidogenic propensity of apolipoprotein A-I, Amyloid, 13, 191, 10.1080/13506120600960288 Ohhashi, 2010, Differences in prion strain conformations result from non-native interactions in a nucleus, Nature Chemical Biology, 6, 225, 10.1038/nchembio.306 Oosawa, 1975 Opazo, 2002, Metalloenzyme-like activity of Alzheimer's disease beta-amyloid. Cu-dependent catalytic conversion of dopamine, cholesterol, and biological reducing agents to neurotoxic H(2)O(2), Journal of Biological Chemistry, 277, 40302, 10.1074/jbc.M206428200 Otsubo, 2009, Characteristics of dialysis-related amyloidosis in patients on haemodialysis therapy for more than 30 years, Nephrology, Dialysis, Transplantation, 24, 1593, 10.1093/ndt/gfn706 Otzen, 2010, Functional amyloid: turning swords into plowshares, Prion, 4, 256, 10.4161/pri.4.4.13676 Page, 2009, Secretion of amyloidogenic gelsolin progressively compromises protein homeostasis leading to the intracellular aggregation of proteins, Proceedings of the National Academy of Sciences of the United States of America, 106, 11125, 10.1073/pnas.0811753106 Pál-Gábor, 2009, Mechanism of lysophosphatidic acid-induced amyloid fibril formation of beta(2)-microglobulin in vitro under physiological conditions, Biochemistry, 48, 5689, 10.1021/bi900356r Pastore, 2012, The two faces of Janus: functional interactions and protein aggregation, Current Opinion in Structural Biology, 22, 30, 10.1016/j.sbi.2011.11.007 Pechmann, 2009, Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins, Proceedings of the National Academy of Sciences of the United States of America, 106, 10159, 10.1073/pnas.0812414106 Pedersen, 2006, The changing face of glucagon fibrillation: structural polymorphism and conformational imprinting, Journal of Molecular Biology, 355, 501, 10.1016/j.jmb.2005.09.100 Pelczer, 1997, Data processing in multidimensional NMR, Methods in Molecular Biology, 60, 71 Pellarin, 2010, Amyloid fibril polymorphism is under kinetic control, Journal of the American Chemical Society, 132, 14960, 10.1021/ja106044u Penney, 1997, CAG repeat number governs the development rate of pathology in Huntington's disease, Annals of Neurology, 41, 689, 10.1002/ana.410410521 Pfefferkorn, 2010, Effects of pH on aggregation kinetics of the repeat domain of a functional amyloid, Pmel17, Proceedings of the National Academy of Sciences of the United States of America, 107, 21447, 10.1073/pnas.1006424107 Pittner, 1994, Molecular physiology of amylin, Journal of Cellular Biochemistry, 55, 19, 10.1002/jcb.240550004 Planté-Bordeneuve, 2011, Familial amyloid polyneuropathy, Lancet Neurology, 10, 1086, 10.1016/S1474-4422(11)70246-0 Podrabsky, 2001, Survival of water stress in annual fish embryos: dehydration avoidance and egg envelope amyloid fibers, American Journal of Physiology: Regulatory Integrative and Comparative Physiology, 280, R123 Ramella, 2011, Human apolipoprotein A-I-derived amyloid: its association with atherosclerosis, PLoS One, 6, e22532, 10.1371/journal.pone.0022532 Relini, 2006, Collagen plays an active role in the aggregation of beta2-microglobulin under physiopathological conditions of dialysis-related amyloidosis, Journal of Biological Chemistry, 281, 16521, 10.1074/jbc.M513827200 Reynolds, 2011, Mechanism of membrane interaction and disruption by α-synuclein, Journal of the American Chemical Society, 133, 19366, 10.1021/ja2029848 Rivera, 2009, Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide, Biophysical Journal, 96, 4552, 10.1016/j.bpj.2009.03.039 Roberson, 2007, Reducing endogenous tau ameliorates amyloid beta-induced deficits in an Alzheimer's disease mouse model, Science, 316, 750, 10.1126/science.1141736 Roberts, 2012, The role of metallobiology and amyloid-beta peptides in Alzheimer's disease, Journal of Neurochemistry, 120, 149, 10.1111/j.1471-4159.2011.07500.x Rodrigues, 2010, Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: insights from molecular dynamics simulations, Protein Science, 19, 202, 10.1002/pro.289 Rojas, 2010, Mechanism of fiber assembly: treatment of a beta peptide aggregation with a coarse-grained united-residue force field, Journal of Molecular Biology, 404, 537, 10.1016/j.jmb.2010.09.057 Rossetti, 2011, Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations, FEBS Letters, 585, 3086, 10.1016/j.febslet.2011.08.036 Rowczenio, 2011, Amyloidogenicity and clinical phenotype associated with five novel mutations in apolipoprotein A-I, American Journal of Pathology, 179, 1978, 10.1016/j.ajpath.2011.06.024 Rueda, 2007, A consensus view of protein dynamics, Proceedings of the National Academy of Sciences of the United States of America, 104, 796, 10.1073/pnas.0605534104 Sabate, 2007, Prion and non-prion amyloids of the HET-s prion forming domain, Journal of Molecular Biology, 370, 768, 10.1016/j.jmb.2007.05.014 Sabate, 2005, Evidence of the existence of micelles in the fibrillogenesis of beta-amyloid peptide, Journal of Physical Chemistry B, 109, 11027, 10.1021/jp050716m Sabate, 2003, An autocatalytic reaction as a model for the kinetics of the aggregation of beta-amyloid, Biopolymers, 71, 190, 10.1002/bip.10441 Saraiva, 2001, Transthyretin mutations in hyperthyroxinemia and amyloid diseases, Human Mutation, 17, 493, 10.1002/humu.1132 Sasahara, 2008, Amyloid nucleation triggered by agitation of beta2-microglobulin under acidic and neutral pH conditions, Biochemistry, 47, 2650, 10.1021/bi701968g Saunders, 2009, Multi-domain misfolding: understanding the aggregation pathway of polyglutamine proteins, Protein Engineering, Design & Selection, 22, 447, 10.1093/protein/gzp033 Sawaya, 2007, Atomic structures of amyloid cross-beta spines reveal varied steric zippers, Nature, 447, 453, 10.1038/nature05695 Selkoe, 2003, Folding proteins in fatal ways, Nature, 426, 900, 10.1038/nature02264 Srikanth, 2009, Copper binding to beta-2-microglobulin and its pre-amyloid oligomers, Biochemistry, 48, 9871, 10.1021/bi901172y Stefani, 2010, Protein aggregation diseases: toxicity of soluble prefibrillar aggregates and their clinical significance, Methods in Molecular Biology, 648, 25, 10.1007/978-1-60761-756-3_2 Steward, 2008, Different disease-causing mutations in transthyretin trigger the same conformational conversion, Protein Engineering, Design & Selection, 21, 187, 10.1093/protein/gzm086 Stoppini, 2005, Proteomics of beta2-microglobulin amyloid fibrils, Biochimica et Biophysica Acta, 1753, 23, 10.1016/j.bbapap.2005.07.019 Straub, 2011, Toward a molecular theory of early and late events in monomer to amyloid fibril formation, Annual Review of Physical Chemistry, 62, 437, 10.1146/annurev-physchem-032210-103526 Tabner, 2002, Formation of hydrogen peroxide and hydroxyl radicals from A(beta) and alpha-synuclein as a possible mechanism of cell death in Alzheimer's disease and Parkinson's disease, Free Radical Biology and Medicine, 32, 1076, 10.1016/S0891-5849(02)00801-8 Tanaka, 2004, Conformational variations in an infectious protein determine prion strain differences, Nature, 428, 323, 10.1038/nature02392 Tanaka, 2005, Mechanism of cross-species prion transmission: an infectious conformation compatible with two highly divergent yeast prion proteins, Cell, 121, 49, 10.1016/j.cell.2005.03.008 Tanaka, 2006, The physical basis of how prion conformations determine strain phenotypes, Nature, 442, 585, 10.1038/nature04922 Tanskanen, 2008, Senile systemic amyloidosis affects 25% of the very aged and associates with genetic variation in alpha2-macroglobulin and tau: a population-based autopsy study, Annals of Medicine, 40, 232, 10.1080/07853890701842988 Tanzi, 2005, Twenty years of the Alzheimer's disease amyloid hypothesis: a genetic perspective, Cell, 120, 545, 10.1016/j.cell.2005.02.008 Thakur, 2009, Polyglutamine disruption of the huntingtin exon 1 N terminus triggers a complex aggregation mechanism, Nature Structural & Molecular Biology, 16, 380, 10.1038/nsmb.1570 Tsigelny, 2012, Role of α-synuclein penetration into the membrane in the mechanisms of oligomer pore formation, FEBS Journal, 279, 1000, 10.1111/j.1742-4658.2012.08489.x Tycko, 2006, Molecular structure of amyloid fibrils: insights from solid-state NMR, Quarterly Reviews of Biophysics, 39, 1, 10.1017/S0033583506004173 Tycko, 2011, Solid-state NMR studies of amyloid fibril structure, Annual Review of Physical Chemistry, 62, 279, 10.1146/annurev-physchem-032210-103539 Ullman, 2011, Explaining the structural plasticity of α-synuclein, Journal of the American Chemical Society, 133, 19536, 10.1021/ja208657z Uversky, 2010, Mysterious oligomerization of the amyloidogenic proteins, FEBS Journal, 277, 2940, 10.1111/j.1742-4658.2010.07721.x van der Kamp, 2009, The consequences of pathogenic mutations to the human prion protein, Protein Engineering, Design & Selection, 22, 461, 10.1093/protein/gzp039 van der Vaart, 2006, Simulation of conformational transitions, Theoretical Chemistry Accounts, 116, 183, 10.1007/s00214-005-0004-1 van Rooijen, 2009, Lipid bilayer disruption by oligomeric alpha-synuclein depends on bilayer charge and accessibility of the hydrophobic core, Biochimica et Biophysica Acta, 1788, 1271, 10.1016/j.bbamem.2009.03.010 van Rooijen, 2010, Membrane permeabilization by oligomeric alpha-synuclein: in search of the mechanism, PLoS One, 5, e14292, 10.1371/journal.pone.0014292 Velayudhan, 2012, Plasma transthyretin as a candidate marker for Alzheimer's disease, Journal of Alzheimer's Disease, 28, 369, 10.3233/JAD-2011-110611 Wang, 2011, Molecular determinants and thermodynamics of the amyloid precursor protein transmembrane domain implicated in Alzheimer's disease, Journal of Molecular Biology, 408, 879, 10.1016/j.jmb.2011.03.028 Wang, 2008, Bacterial inclusion bodies contain amyloid-like structure, PLoS Biology, 6, e195, 10.1371/journal.pbio.0060195 Wasmer, 2008, Amyloid fibrils of the HET-s(218–289) prion form a beta solenoid with a triangular hydrophobic core, Science, 319, 1523, 10.1126/science.1151839 Wei, 2007, Computational simulations of the early steps of protein aggregation, Prion, 1, 3, 10.4161/pri.1.1.3969 Wei, 2010, Structural diversity of dimers of the Alzheimer amyloid-beta(25–35) peptide and polymorphism of the resulting fibrils, Physical Chemistry Chemical Physics, 12, 3622, 10.1039/c000755m Westermark, 2011, Islet amyloid polypeptide, islet amyloid, and diabetes mellitus, Physiological Reviews, 91, 795, 10.1152/physrev.00042.2009 Winner, 2011, In vivo demonstration that alpha-synuclein oligomers are toxic, Proceedings of the National Academy of Sciences of the United States of America, 108, 4194, 10.1073/pnas.1100976108 Wolfe, 2011, Amyloid in neurodegenerative diseases: friend or foe?, Seminars in Cell & Developmental Biology, 22, 476, 10.1016/j.semcdb.2011.03.011 Wosten, 1999, Structural proteins involved in emergence of microbial aerial hyphae, Fungal Genetics and Biology, 27, 153, 10.1006/fgbi.1999.1130 Wu, 2011, Coarse-grained models for protein aggregation, Current Opinion in Structural Biology, 21, 209, 10.1016/j.sbi.2011.02.002 Xu, 2011, Intrinsic determinants of A beta(12–24) pH-dependent self-assembly revealed by combined computational and experimental studies, PLoS One, 6, 10.1371/journal.pone.0024329 Xue, 2009, Fibril fragmentation enhances amyloid cytotoxicity, Journal of Biological Chemistry, 284, 34272, 10.1074/jbc.M109.049809 Xue, 2010, Fibril fragmentation in amyloid assembly and cytotoxicity: when size matters, Prion, 4, 20, 10.4161/pri.4.1.11378 Yong, 2002, Structure determination of micelle-like intermediates in amyloid beta-protein fibril assembly by using small angle neutron scattering, Proceedings of the National Academy of Sciences of the United States of America, 99, 150, 10.1073/pnas.012584899 You, 2012, Aβ neurotoxicity depends on interactions between copper ions, prion protein, and N-methyl-d-aspartate receptors, Proceedings of the National Academy of Sciences of the United States of America, 109, 1737, 10.1073/pnas.1110789109 Zhao, 2011, Amyloid beta peptides aggregation in a mixed membrane bilayer: a molecular dynamics study, Journal of Physical Chemistry B, 115, 12247, 10.1021/jp2065985 Zhu, 2002, Surface-catalyzed amyloid fibril formation, Journal of Biological Chemistry, 277, 50914, 10.1074/jbc.M207225200 Zijlstra, 1990, Beta 2-microglobulin deficient mice lack CD4-8+ cytolytic T cells, Nature, 344, 742, 10.1038/344742a0