Peng, C., Trojanowski, J. Q. & Lee, V. M.-Y. Protein transmission in neurodegenerative illness. Nat. Rev. Neurol. 16, 199–212 (2020).
Wilson, D. M. et al. Hallmarks of neurodegenerative illnesses. Cell 186, 693–714 (2023).
Lövestam, S. et al. Meeting of recombinant tau into filaments equivalent to these of Alzheimer’s illness and persistent traumatic encephalopathy. Elife 11, e76494 (2022).
Arseni, D. et al. TDP-43 varieties amyloid filaments with a definite fold in sort A FTLD-TDP. Nature 620, 898–903 (2023).
Arseni, D. et al. Construction of pathological TDP-43 filaments from ALS with FTLD. Nature 601, 139–143 (2022).
Falcon, B. et al. Novel tau filament fold in persistent traumatic encephalopathy encloses hydrophobic molecules. Nature 568, 420–423 (2019).
Falcon, B. et al. Buildings of filaments from Choose’s illness reveal a novel tau protein fold. Nature 561, 137–140 (2018).
Fitzpatrick, A. W. P. et al. Cryo-EM constructions of tau filaments from Alzheimer’s illness. Nature 547, 185–190 (2017).
Schweighauser, M. et al. Buildings of α-synuclein filaments from a number of system atrophy. Nature 585, 464–469 (2020).
Shi, Y. et al. Construction-based classification of tauopathies. Nature 598, 359–363 (2021).
Yang, Y. et al. Buildings of α-synuclein filaments from human brains with Lewy pathology. Nature 610, 791–795 (2022).
Zhang, W. et al. Novel tau filament fold in corticobasal degeneration. Nature 580, 283–287 (2020).
Kayed, R. et al. Frequent construction of soluble amyloid oligomers implies widespread mechanism of pathogenesis. Science 300, 486–489 (2003).
van Dyck, C. H. et al. Lecanemab in early Alzheimer’s illness. N. Engl. J. Med. 388, 9–21 (2023).
Lannfelt, L. et al. Views on future Alzheimer therapies: amyloid-β protofibrils – a brand new goal for immunotherapy with BAN2401 in Alzheimer’s illness. Alzheimers Res. Ther. 6, 16 (2014).
Hartley, D. M. et al. Protofibrillar intermediates of amyloid β-protein induce acute electrophysiological modifications and progressive neurotoxicity in cortical neurons. J. Neurosci. 19, 8876–8884 (1999).
Lambert, M. P. et al. Diffusible, nonfibrillar ligands derived from Aβ1–42 are potent central nervous system neurotoxins. Proc. Natl Acad. Sci. USA 95, 6448–6453 (1998).
Maeda, S. et al. Granular tau oligomers as intermediates of tau filaments. Biochemistry 46, 3856–3861 (2007).
Conway, Ok. A., Harper, J. D. & Lansbury, P. T. Accelerated in vitro fibril formation by a mutant α-synuclein linked to early-onset Parkinson illness. Nat. Med. 4, 1318–1320 (1998).
Yang, Y. et al. Cryo-EM constructions of amyloid-β 42 filaments from human brains. Science 375, 167–172 (2022).
Wischik, C. M. et al. Isolation of a fraction of tau derived from the core of the paired helical filament of Alzheimer illness. Proc. Natl Acad. Sci. USA 85, 4506–4510 (1988).
Mukrasch, M. D. et al. Structural polymorphism of 441-residue Tau at single residue decision. PLoS Biol. 7, e1000034 (2009).
Daebel, V. et al. β-Sheet core of tau paired helical filaments revealed by solid-state NMR. J. Am. Chem. Soc. 134, 13982–13989 (2012).
Mukrasch, M. D. et al. Websites of tau essential for aggregation populate β-structure and bind to microtubules and polyanions. J. Biol. Chem. 280, 24978–24986 (2005).
Khan, S. N. et al. Distribution of pico- and nanosecond motions in disordered proteins from nuclear spin leisure. Biophys. J. 109, 988–999 (2015).
Jarrett, J. T. & Lansbury, P. T. Seeding ‘one-dimensional crystallization’ of amyloid: a pathogenic mechanism in Alzheimer’s illness and scrapie? Cell 73, 1055–1058 (1993).
Stern, A. M. et al. Ample Aβ fibrils in ultracentrifugal supernatants of aqueous extracts from Alzheimer’s illness brains. Neuron 111, 2012–2020 (2023).
Weismiller, H. A. et al. Structural dysfunction in four-repeat Tau fibrils reveals a brand new mechanism for boundaries to cross-seeding of Tau isoforms. J. Biol. Chem. 293, 17336–17348 (2018).
He, S. & Scheres, S. H. W. Helical reconstruction in RELION. J. Struct. Biol. 198, 163–176 (2017).
Sawaya, M. R. et al. Atomic constructions of amyloid cross-beta spines reveal different steric zippers. Nature 447, 453–457 (2007).
Wiltzius, J. J. W. et al. Molecular mechanisms for protein-encoded inheritance. Nat. Struct. Mol. Biol. 16, 973–978 (2009).
Ostwald, W. Studien über die Bildung und Umwandlung fester Körper: 1. Abhandlung: Übersättigung und Überkaltung. Z. Phys. Chem. 22U, 289–330 (1897).
von Bergen, M. et al. Meeting of tau protein into Alzheimer paired helical filaments will depend on a neighborhood sequence motif ((306)VQIVYK(311)) forming beta construction. Proc. Natl Acad. Sci. USA 97, 5129–5134 (2000).
Macdonald, J. A. et al. Meeting of transgenic human P301S Tau is important for neurodegeneration in murine spinal twine. Acta Neuropathol. Commun. 7, 44 (2019).
Falcon, B. et al. Conformation determines the seeding potencies of native and recombinant Tau aggregates. J. Biol. Chem. 290, 1049–1065 (2015).
Xie, C. et al. Identification of key amino acids liable for the distinct aggregation properties of microtubule‐related protein 2 and tau. J. Neurochem. 135, 19–26 (2015).
Goldsbury, C., Kistler, J., Aebi, U., Arvinte, T. & Cooper, G. J. Watching amyloid fibrils develop by time-lapse atomic pressure microscopy. J. Mol. Biol. 285, 33–39 (1999).
Chiti, F. et al. Kinetic partitioning of protein folding and aggregation. Nat. Struct. Mol. Biol. 9, 137–143 (2002).
Fernandez-Escamilla, A.-M., Rousseau, F., Schymkowitz, J. & Serrano, L. Prediction of sequence-dependent and mutational results on the aggregation of peptides and proteins. Nat. Biotechnol. 22, 1302–1306 (2004).
Giasson, B. I., Murray, I. V., Trojanowski, J. Q. & Lee, V. M. A hydrophobic stretch of 12 amino acid residues in the midst of α-synuclein is important for filament meeting. J. Biol. Chem. 276, 2380–2386 (2001).
Jiang, L.-L. et al. Structural transformation of the amyloidogenic core area of TDP-43 protein initiates its aggregation and cytoplasmic inclusion. J. Biol. Chem. 288, 19614–19624 (2013).
Ferrone, F. A., Hofrichter, J., Sunshine, H. R. & Eaton, W. A. Kinetic research on photolysis-induced gelation of sickle cell hemoglobin counsel a brand new mechanism. Biophys. J. 32, 361–380 (1980).
Törnquist, M. et al. Secondary nucleation in amyloid formation. Chem. Commun. 54, 8667–8684 (2018).
Zhang, W. et al. Heparin-induced tau filaments are polymorphic and differ from these in Alzheimer’s and Choose’s illnesses. Elife 8, e43584 (2019).
Radamaker, L. et al. Cryo-EM reveals structural breaks in a patient-derived amyloid fibril from systemic AL amyloidosis. Nat. Commun. 12, 875 (2021).
Robinson, J. L. et al. TDP-43 skeins present properties of amyloid in a subset of ALS circumstances. Acta Neuropathol. 125, 121–131 (2013).
LeVine, H. Thioflavine T interplay with amyloid β-sheet constructions. Amyloid 2, 1–6 (1995).
Prusiner, S. B. Prions. Proc. Natl Acad. Sci. USA 95, 13363–13383 (1998).
Knowles, T. P. J. et al. An analytical resolution to the kinetics of breakable filament meeting. Science 326, 1533–1537 (2009).
Lövestam, S. et al. Seeded meeting in vitro doesn’t replicate the constructions of α-synuclein filaments from a number of system atrophy. FEBS Open Bio 11, 999–1013 (2021).
Tarutani, A. et al. Cryo-EM constructions of tau filaments from SH-SY5Y cells seeded with mind extracts from circumstances of Alzheimer’s illness and corticobasal degeneration. FEBS Open Bio 13, 1394–1404 (2023).
Mirbaha, H. et al. Inert and seed-competent tau monomers counsel structural origins of aggregation. eLife 7, e36584 (2018).
Sharma, A. M., Thomas, T. L., Woodard, D. R., Kashmer, O. M. & Diamond, M. I. Tau monomer encodes strains. eLife 7, e37813 (2018).
Studier, F. W. Protein manufacturing by auto-induction in excessive density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005).
Schuck, P. On the evaluation of protein self-association by sedimentation velocity analytical ultracentrifugation. Anal. Biochem. 320, 104–124 (2003).
Laue, T. M., Shah, B. D., Ridgeway, T. M. & Pelletier, S. L. Pc-aided interpretation of sedimentation information for proteins. In Analytical Ultracentrifugation in Biochemistry and Polymer Science (eds Harding, S. E., Horton, J. C. & Rowe, A. J.) 90–125 (Royal Society of Chemistry, 1992).
Brautigam, C. A. Calculations and publication-quality illustrations for analytical ultracentrifugation information. Strategies Enzymol. 562, 109–133 (2015).
Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system primarily based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).
Kazimierczuk, Ok. & Orekhov, V. Y. Accelerated NMR spectroscopy by utilizing compressed sensing. Angew. Chem. Int. Ed. Engl. 50, 5556–5559 (2011).
Jung, Y.-S. & Zweckstetter, M. Mars – sturdy computerized spine project of proteins. J. Biomol. NMR 30, 11–23 (2004).
Kjaergaard, M., Brander, S. & Poulsen, F. M. Random coil chemical shift for intrinsically disordered proteins: results of temperature and pH. J. Biomol. NMR 49, 139–149 (2011).
Kjaergaard, M. & Poulsen, F. M. Sequence correction of random coil chemical shifts: correlation between neighbor correction components and modifications within the Ramachandran distribution. J. Biomol. NMR 50, 157–165 (2011).
Schwarzinger, S. et al. Sequence-dependent correction of random coil NMR chemical shifts. J. Am. Chem. Soc. 123, 2970–2978 (2001).
Pelupessy, P., Ferrage, F. & Bodenhausen, G. Correct measurement of longitudinal cross-relaxation charges in nuclear magnetic resonance. J. Chem. Phys. 126, 134508 (2007).
Rezaei-Ghaleh, N., Giller, Ok., Becker, S. & Zweckstetter, M. Impact of zinc binding on β-amyloid construction and dynamics: implications for Aβ aggregation. Biophys. J. 101, 1202–1211 (2011).
Zivanov, J. et al. New instruments for automated high-resolution cryo-EM construction willpower in RELION-3. Elife 7, e42166 (2018).
Zivanov, J., Nakane, T. & Scheres, S. H. W. A Bayesian strategy to beam-induced movement correction in cryo-EM single-particle evaluation. IUCrJ 6, 5–17 (2019).
Rohou, A. & Grigorieff, N. CTFFIND4: quick and correct defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
Kimanius, D., Dong, L., Sharov, G., Nakane, T. & Scheres, S. H. W. New instruments for automated cryo-EM single-particle evaluation in RELION-4.0. Biochem. J. 478, 4169–4185 (2021).
Bepler, T. et al. Constructive-unlabeled convolutional neural networks for particle selecting in cryo-electron micrographs. Nat. Strategies 16, 1153–1160 (2019).
Lövestam, S. & Scheres, S. H. W. Excessive-throughput cryo-EM construction willpower of amyloids. Faraday Talk about. 240, 243–260 (2022).
Pothula, Ok. R., Geraets, J. A., Ferber, I. I. & Schröder, G. F. Clustering polymorphs of tau and IAPP fibrils with the CHEP algorithm. Prog. Biophys. Mol. Biol. 160, 16–25 (2021).
Scheres, S. H. W. Amyloid construction willpower in RELION-3.1. Acta Crystallogr. D 76, 94–101 (2020).
Kimanius, D. et al. Information-driven regularisation lowers the scale barrier of cryo-EM construction willpower. Preprint at bioRxiv https://doi.org/10.1101/2023.10.23.563586 (2023).
Zivanov, J., Nakane, T. & Scheres, S. H. W. Estimation of high-order aberrations and anisotropic magnification from cryo-EM information units in RELION-3.1. IUCrJ 7, 253–267 (2020).
Casañal, A., Lohkamp, B. & Emsley, P. Present developments in Coot for macromolecular mannequin constructing of electron cryo-microscopy and crystallographic information. Protein Sci. 29, 1069–1078 (2020).
Jamali, Ok. et al. Automated mannequin constructing and protein identification in cryo-EM maps. Preprint at bioRxiv https://doi.org/10.1101/2023.05.16.541002 (2023).
Croll, T. I. ISOLDE: a bodily life like setting for mannequin constructing into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018).
Pettersen, E. F. et al. UCSF ChimeraX: construction visualization for researchers, educators, and builders. Protein Sci. 30, 70–82 (2021).
Sawaya, M. R., Hughes, M. P., Rodriguez, J. A., Riek, R. & Eisenberg, D. S. The increasing amyloid household: construction, stability, perform, and pathogenesis. Cell 184, 4857–4873 (2021).
