{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T01:27:52Z","timestamp":1792805272646,"version":"4.5.0"},"reference-count":494,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T00:00:00Z","timestamp":1728345600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Balvi Foundation","award":["18"],"award-info":[{"award-number":["18"]}]},{"name":"Balvi Foundation","award":["NNF20CC0035580"],"award-info":[{"award-number":["NNF20CC0035580"]}]},{"name":"Balvi Foundation","award":["142142"],"award-info":[{"award-number":["142142"]}]},{"name":"Novo Nordisk Foundation","award":["18"],"award-info":[{"award-number":["18"]}],"id":[{"id":"https:\/\/ror.org\/04txyc737","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Novo Nordisk Foundation","award":["NNF20CC0035580"],"award-info":[{"award-number":["NNF20CC0035580"]}],"id":[{"id":"https:\/\/ror.org\/04txyc737","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Novo Nordisk Foundation","award":["142142"],"award-info":[{"award-number":["142142"]}],"id":[{"id":"https:\/\/ror.org\/04txyc737","id-type":"ROR","asserted-by":"crossref"}]},{"name":"NRF of South Africa","award":["18"],"award-info":[{"award-number":["18"]}]},{"name":"NRF of South Africa","award":["NNF20CC0035580"],"award-info":[{"award-number":["NNF20CC0035580"]}]},{"name":"NRF of South Africa","award":["142142"],"award-info":[{"award-number":["142142"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>In classical amyloidoses, amyloid fibres form through the nucleation and accretion of protein monomers, with protofibrils and fibrils exhibiting a cross-\u03b2 motif of parallel or antiparallel \u03b2-sheets oriented perpendicular to the fibre direction. These protofibrils and fibrils can intertwine to form mature amyloid fibres. Similar phenomena can occur in blood from individuals with circulating inflammatory molecules (and also some originating from viruses and bacteria). Such pathological clotting can result in an anomalous amyloid form termed fibrinaloid microclots. Previous proteomic analyses of these microclots have shown the presence of non-fibrin(ogen) proteins, suggesting a more complex mechanism than simple entrapment. We thus provide evidence against such a simple entrapment model, noting that clot pores are too large and centrifugation would have removed weakly bound proteins. Instead, we explore whether co-aggregation into amyloid fibres may involve axial (multiple proteins within the same fibril), lateral (single-protein fibrils contributing to a fibre), or both types of integration. Our analysis of proteomic data from fibrinaloid microclots in different diseases shows no significant quantitative overlap with the normal plasma proteome and no correlation between plasma protein abundance and their presence in fibrinaloid microclots. Notably, abundant plasma proteins like \u03b1-2-macroglobulin, fibronectin, and transthyretin are absent from microclots, while less abundant proteins such as adiponectin, periostin, and von Willebrand factor are well represented. Using bioinformatic tools, including AmyloGram and AnuPP, we found that proteins entrapped in fibrinaloid microclots exhibit high amyloidogenic tendencies, suggesting their integration as cross-\u03b2 elements into amyloid structures. This integration likely contributes to the microclots\u2019 resistance to proteolysis. Our findings underscore the role of cross-seeding in fibrinaloid microclot formation and highlight the need for further investigation into their structural properties and implications in thrombotic and amyloid diseases. These insights provide a foundation for developing novel diagnostic and therapeutic strategies targeting amyloidogenic cross-seeding in blood clotting disorders.<\/jats:p>","DOI":"10.3390\/ijms251910809","type":"journal-article","created":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T12:01:54Z","timestamp":1728388914000},"page":"10809","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Proteomic Evidence for Amyloidogenic Cross-Seeding in Fibrinaloid Microclots"],"prefix":"10.3390","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5838-7963","authenticated-orcid":false,"given":"Douglas B.","family":"Kell","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK"},{"name":"The Novo Nordisk Foundation Centre for Biosustainability, Building 220, S\u00f8ltofts Plads 200, Technical University of Denmark, 2800 Kongens Lyngby, Denmark"},{"name":"Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9108-2384","authenticated-orcid":false,"given":"Etheresia","family":"Pretorius","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK"},{"name":"Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,10,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1136\/bmj.1.6157.153","article-title":"Characteristics affecting fibrinolytic activity and plasma fibrinogen concentrations","volume":"1","author":"Meade","year":"1979","journal-title":"Br. Med. J."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2300","DOI":"10.1161\/01.STR.0000141701.36371.d1","article-title":"Fibrinogen concentration and risk of ischemic stroke and acute coronary events in 5113 patients with transient ischemic attack and minor ischemic stroke","volume":"35","author":"Rothwell","year":"2004","journal-title":"Stroke"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e13","DOI":"10.1161\/ATVBAHA.117.308564","article-title":"Fibrinogen and Fibrin in Hemostasis and Thrombosis","volume":"37","author":"Kattula","year":"2017","journal-title":"Arterioscler. Thromb. Vasc. Biol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Fan, D.Y., Sun, H.L., Sun, P.Y., Jian, J.M., Li, W.W., Shen, Y.Y., Zeng, F., Wang, Y.J., and Bu, X.L. (2020). The Correlations between Plasma Fibrinogen with Amyloid-Beta and Tau Levels in Patients with Alzheimer\u2019s Disease. Front. Neurosci., 14.","DOI":"10.3389\/fnins.2020.625844"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/S0065-3233(05)70008-5","article-title":"Fibrinogen and fibrin","volume":"70","author":"Weisel","year":"2005","journal-title":"Adv. Protein Chem."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1007\/978-3-319-49674-0_13","article-title":"Fibrin Formation, Structure and Properties","volume":"82","author":"Weisel","year":"2017","journal-title":"Subcell. Biochem."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"G\u00f6bel, K., Eichler, S., Wiendl, H., Chavakis, T., Kleinschnitz, C., and Meuth, S.G. (2018). The Coagulation Factors Fibrinogen, Thrombin, and Factor XII in Inflammatory Disorders\u2014A Systematic Review. Front. Immunol., 9.","DOI":"10.3389\/fimmu.2018.01731"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1007\/978-3-030-58971-4_15","article-title":"Fibrinogen and Fibrin","volume":"96","author":"Litvinov","year":"2021","journal-title":"Subcell. Biochem."},{"key":"ref_9","first-page":"H1069","article-title":"Fibrin has larger pores when formed in the presence of erythrocytes","volume":"253","author":"Carr","year":"1987","journal-title":"Am. J. Physiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"21331","DOI":"10.1074\/jbc.M212734200","article-title":"Dynamic changes of fibrin architecture during fibrin formation and intrinsic fibrinolysis of fibrin-rich clots","volume":"278","author":"Collet","year":"2003","journal-title":"J. Biol. Chem."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1016\/j.bpj.2012.10.036","article-title":"Fibrin clot structure and mechanics associated with specific oxidation of methionine residues in fibrinogen","volume":"103","author":"Weigandt","year":"2012","journal-title":"Biophys. J."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1007\/s10856-024-06775-1","article-title":"Flow affects the structural and mechanical properties of the fibrin network in plasma clots","volume":"35","author":"Eyisoylu","year":"2024","journal-title":"J. Mater. Sci. Mater. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"eadh1265","DOI":"10.1126\/sciadv.adh1265","article-title":"Clots reveal anomalous elastic behavior of fiber networks","volume":"10","author":"Zakharov","year":"2024","journal-title":"Sci. Adv."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1016\/j.bpj.2013.02.055","article-title":"The hydraulic permeability of blood clots as a function of fibrin and platelet density","volume":"104","author":"Wufsus","year":"2013","journal-title":"Biophys. J."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"100081","DOI":"10.1016\/j.rpth.2023.100081","article-title":"Fibrinolysis: An illustrated review","volume":"7","author":"Risman","year":"2023","journal-title":"Res. Pract. Thromb. Haemost."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1073\/pnas.47.9.1309","article-title":"The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain","volume":"47","author":"Anfinsen","year":"1961","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.181.4096.223","article-title":"Principles that govern the folding of protein chains","volume":"181","author":"Anfinsen","year":"1973","journal-title":"Science"},{"key":"ref_18","unstructured":"Levinthal, C. (1969, January 17\u201318). How to Fold Graciously. Proceedings of the Mossbauer Spectroscopy in Biological Systems, Monticello, IL, USA."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1918","DOI":"10.1021\/ed300302h","article-title":"Introducing the Levinthal\u2019s Protein Folding Paradox and Its Solution","volume":"91","year":"2014","journal-title":"J. Chem. Educ."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.tcb.2015.08.007","article-title":"Cell Biology of Prions and Prionoids: A Status Report","volume":"26","author":"Aguzzi","year":"2016","journal-title":"Trends Cell Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.pbiomolbio.2016.08.006","article-title":"Proteins behaving badly. Substoichiometric molecular control and amplification of the initiation and nature of amyloid fibril formation: Lessons from and for blood clotting","volume":"123","author":"Kell","year":"2017","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1042\/BCJ20230241","article-title":"Are fibrinaloid microclots a cause of autoimmunity in Long Covid and other post-infection diseases?","volume":"480","author":"Kell","year":"2023","journal-title":"Biochem. J."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/s41576-018-0011-4","article-title":"Prions, prionoids and protein misfolding disorders","volume":"19","author":"Scheckel","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"5968","DOI":"10.1073\/pnas.1800168115","article-title":"Extant fold-switching proteins are widespread","volume":"115","author":"Porter","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"LiWang, A., Porter, L.L., and Wang, L.P. (2021). Fold-switching proteins. Biopolymers, 112.","DOI":"10.1002\/bip.23478"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Porter, L.L. (2023). Fluid protein fold space and its implications. Bioessays, 45.","DOI":"10.1002\/bies.202300057"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1016\/j.str.2020.10.006","article-title":"Functional and Regulatory Roles of Fold-Switching Proteins","volume":"29","author":"Kim","year":"2021","journal-title":"Structure"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1380","DOI":"10.1016\/j.bpj.2020.07.034","article-title":"Sequence-Based Prediction of Metamorphic Behavior in Proteins","volume":"119","author":"Chen","year":"2020","journal-title":"Biophys. J."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Das, M., Chen, N., LiWang, A., and Wang, L.P. (2021). Identification and characterization of metamorphic proteins: Current and future perspectives. Biopolymers, 112.","DOI":"10.1002\/bip.23473"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"5824","DOI":"10.1016\/j.csbj.2022.10.024","article-title":"Metamorphic proteins under a computational microscope: Lessons from a fold-switching RfaH protein","volume":"20","author":"Artsimovitch","year":"2022","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1007\/s12551-023-01087-0","article-title":"Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models","volume":"15","author":"Rivera","year":"2023","journal-title":"Biophys. Rev."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Porter, L.L., Artsimovitch, I., and Ramirez-Sarmiento, C.A. (2024). Metamorphic proteins and how to find them. Curr. Opin. Struct. Biol., 86.","DOI":"10.1016\/j.sbi.2024.102807"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Strodel, B. (2021). Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins. J. Mol. Biol., 433.","DOI":"10.1016\/j.jmb.2021.167182"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Schafer, J.W., Chakravarty, D., Chen, E.A., and Porter, L.L. (2024). Sequence clustering confounds AlphaFold2. bioRxiv.","DOI":"10.1101\/2024.01.05.574434"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e4426","DOI":"10.1002\/pro.4426","article-title":"Estimating conformational heterogeneity of tryptophan synthase with a template-based Alphafold2 approach","volume":"31","author":"Casadevall","year":"2022","journal-title":"Protein Sci."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Mishra, S., Looger, L.L., and Porter, L.L. (2021). A sequence-based method for predicting extant fold switchers that undergo alpha-helix <--> beta-strand transitions. Biopolymers, 112.","DOI":"10.1002\/bip.23471"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Porter, L.L., Chakravarty, D., Schafer, J.W., and Chen, E.A. (2023). ColabFold predicts alternative protein structures from single sequences, coevolution unnecessary for AF-cluster. bioRxiv.","DOI":"10.1101\/2023.11.21.567977"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1126\/science.1260031","article-title":"Circadian rhythms. A protein fold switch joins the circadian oscillator to clock output in cyanobacteria","volume":"349","author":"Chang","year":"2015","journal-title":"Science"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3177","DOI":"10.1038\/s41467-023-38519-0","article-title":"Identification of a covert evolutionary pathway between two protein folds","volume":"14","author":"Chakravarty","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"5478","DOI":"10.1038\/s41467-023-41237-2","article-title":"Evolutionary selection of proteins with two folds","volume":"14","author":"Schafer","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1080\/10409238.2022.2113030","article-title":"What makes functional amyloids work?","volume":"57","author":"Siemer","year":"2022","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.bpj.2014.10.073","article-title":"Subdomain interactions foster the design of two protein pairs with approximately 80% sequence identity but different folds","volume":"108","author":"Porter","year":"2015","journal-title":"Biophys. J."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1723","DOI":"10.1002\/pro.4097","article-title":"Predictable fold switching by the SARS-CoV-2 protein ORF9b","volume":"30","author":"Porter","year":"2021","journal-title":"Protein Sci."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"8945","DOI":"10.1021\/jacs.2c03925","article-title":"Amyloidogenesis of SARS-CoV-2 Spike Protein","volume":"144","year":"2022","journal-title":"J. Am. Chem. Soc."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1038\/s41467-023-36234-4","article-title":"Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes","volume":"14","author":"Bhardwaj","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1080\/13506120701461111","article-title":"Structural analyses of fibrinogen amyloid fibrils","volume":"14","author":"Serpell","year":"2007","journal-title":"Amyloid"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1182\/blood-2016-03-705228","article-title":"Biochemical and structural analysis of the interaction between beta-amyloid and fibrinogen","volume":"128","author":"Zamolodchikov","year":"2016","journal-title":"Blood"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1097\/MOH.0000000000000368","article-title":"Interactions of beta-amyloid peptide with fibrinogen and coagulation factor XII may contribute to Alzheimer\u2019s disease","volume":"24","author":"Ahn","year":"2017","journal-title":"Curr. Opin. Hematol."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Singh, P.K., Berk-Rauch, H.E., Soplop, N., Uryu, K., Strickland, S., and Ahn, H.J. (2018). Analysis of beta-Amyloid-induced Abnormalities on Fibrin Clot Structure by Spectroscopy and Scanning Electron Microscopy. J. Vis. Exp., e58475.","DOI":"10.3791\/58475-v"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"14482","DOI":"10.1073\/pnas.1921327117","article-title":"Cerebral amyloid angiopathy-linked beta-amyloid mutations promote cerebral fibrin deposits via increased binding affinity for fibrinogen","volume":"117","author":"Cajamarca","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1146\/annurev.biochem.67.1.793","article-title":"Pathologic conformations of prion proteins","volume":"67","author":"Cohen","year":"1998","journal-title":"Annu. Rev. Biochem."},{"key":"ref_52","first-page":"450","article-title":"Structure and Polymorphism of Amyloid and Amyloid-Like Aggregates","volume":"87","author":"Matiiv","year":"2022","journal-title":"Biochemistry"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/nature03680","article-title":"Structure of the cross-beta spine of amyloid-like fibrils","volume":"435","author":"Nelson","year":"2005","journal-title":"Nature"},{"key":"ref_54","first-page":"237","article-title":"Cross-beta-sheet supersecondary structure in amyloid folds: Techniques for detection and characterization","volume":"932","author":"Ventura","year":"2013","journal-title":"Methods Mol. Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"3541","DOI":"10.1016\/j.febslet.2015.10.015","article-title":"Structural stability of amyloid fibrils depends on the existence of the peripheral sequence near the core cross-beta region","volume":"589","author":"Saiki","year":"2015","journal-title":"FEBS Lett."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.sbi.2019.09.001","article-title":"Amyloid structures: Much more than just a cross-beta fold","volume":"60","author":"Gallardo","year":"2020","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Gonay, V., Dunne, M.P., Caceres-Delpiano, J., and Kajava, A.V. (2024). Developing machine-learning-based amyloid predictors with Cross-Beta DB. bioRxiv.","DOI":"10.1101\/2024.02.12.579644"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1016\/j.jmb.2009.09.039","article-title":"The common architecture of cross-beta amyloid","volume":"395","author":"Jahn","year":"2010","journal-title":"J. Mol. Biol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1006\/jsbi.2000.4221","article-title":"Review: History of the amyloid fibril","volume":"130","author":"Sipe","year":"2000","journal-title":"J. Struct. Biol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1111\/brv.12399","article-title":"Amyloids of multiple species: Are they helpful in survival?","volume":"93","author":"Upadhyay","year":"2018","journal-title":"Biol. Rev. Camb. Philos. Soc."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"8285","DOI":"10.1021\/acs.chemrev.1c00196","article-title":"Amyloid-type Protein Aggregation and Prion-like Properties of Amyloids","volume":"121","author":"Willbold","year":"2021","journal-title":"Chem. Rev."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1080\/10409238.2021.1937926","article-title":"The amyloid proteome: A systematic review and proposal of a protein classification system","volume":"56","author":"Gottwald","year":"2021","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1038\/s41580-023-00647-2","article-title":"Mechanisms and pathology of protein misfolding and aggregation","volume":"24","author":"Louros","year":"2023","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_64","first-page":"379","article-title":"Amyloid formation as a protein phase transition","volume":"5","author":"Michaels","year":"2023","journal-title":"Nat. Phys."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"4661","DOI":"10.1039\/C6CS00542J","article-title":"Self-assembling peptide and protein amyloids: From structure to tailored function in nanotechnology","volume":"46","author":"Wei","year":"2017","journal-title":"Chem. Soc. Rev."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"43","DOI":"10.3233\/JAD-220720","article-title":"Alzheimer-type dementia: A systems view provides a unifying explanation of its development","volume":"91","author":"Grobler","year":"2023","journal-title":"J. Alzheimer\u2019s Dis."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1146\/annurev-biochem-072611-130030","article-title":"Systemic amyloidoses","volume":"82","year":"2013","journal-title":"Annu. Rev. Biochem."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.jmb.2012.01.024","article-title":"A molecular history of the amyloidoses","volume":"421","author":"Buxbaum","year":"2012","journal-title":"J. Mol. Biol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.euprot.2016.02.003","article-title":"Systemic amyloidoses and proteomics: The state of the art","volume":"11","author":"Lavatelli","year":"2016","journal-title":"EuPA Open Proteom."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/j.ejim.2013.10.007","article-title":"Systemic amyloidoses: What an internist should know","volume":"24","author":"Palladini","year":"2013","journal-title":"Eur. J. Intern. Med."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Nevone, A., Merlini, G., and Nuvolone, M. (2020). Treating Protein Misfolding Diseases: Therapeutic Successes Against Systemic Amyloidoses. Front. Pharmacol., 11.","DOI":"10.3389\/fphar.2020.01024"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1007\/s00441-022-03609-w","article-title":"Yeast red pigment, protein aggregates, and amyloidoses: A review","volume":"388","author":"Nevzglyadova","year":"2022","journal-title":"Cell Tissue Res."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"12132","DOI":"10.1021\/acs.chemrev.1c00941","article-title":"Second Sphere Interactions in Amyloidogenic Diseases","volume":"122","author":"Roy","year":"2022","journal-title":"Chem. Rev."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Burdukiewicz, M., Sobczyk, P., R\u00f6diger, S., Duda-Madej, A., Mackiewicz, P., and Kotulska, M. (2017). Amyloidogenic motifs revealed by n-gram analysis. Sci. Rep., 7.","DOI":"10.1038\/s41598-017-13210-9"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"40235","DOI":"10.1074\/jbc.M506372200","article-title":"Direct observation of protein folding, aggregation, and a prion-like conformational conversion","volume":"280","author":"Ding","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Sulatskaya, A.I., Kosolapova, A.O., Bobylev, A.G., Belousov, M.V., Antonets, K.S., Sulatsky, M.I., Kuznetsova, I.M., Turoverov, K.K., Stepanenko, O.V., and Nizhnikov, A.A. (2021). beta-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222111316"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1038\/nchembio.131","article-title":"Amyloid formation by globular proteins under native conditions","volume":"5","author":"Chiti","year":"2009","journal-title":"Nat. Chem. Biol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1687","DOI":"10.1016\/j.bbamem.2018.03.011","article-title":"Structures and dynamics of beta-barrel oligomer intermediates of amyloid-beta16-22 aggregation","volume":"1860","author":"Ge","year":"2018","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1021\/acschemneuro.7b00396","article-title":"Islet Amyloid Polypeptide Promotes Amyloid-Beta Aggregation by Binding-Induced Helix-Unfolding of the Amyloidogenic Core","volume":"9","author":"Ge","year":"2018","journal-title":"ACS Chem. Neurosci."},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Sun, Y., Ge, X., Xing, Y., Wang, B., and Ding, F. (2018). beta-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-beta Aggregates. Sci. Rep., 8.","DOI":"10.1038\/s41598-018-28649-7"},{"key":"ref_81","first-page":"155","article-title":"Protein design by binary patterning of polar and nonpolar amino acids","volume":"352","author":"Bradley","year":"2007","journal-title":"Methods Mol. Biol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"2066","DOI":"10.1007\/s00018-007-7110-2","article-title":"On the structural definition of amyloid fibrils and other polypeptide aggregates","volume":"64","year":"2007","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"35532","DOI":"10.1021\/acsomega.2c02513","article-title":"Succinct Amyloid and Nonamyloid Patterns in Hexapeptides","volume":"7","author":"Keresztes","year":"2022","journal-title":"ACS Omega"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-0716-1546-1_1","article-title":"Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins","volume":"2340","author":"Kotulska","year":"2022","journal-title":"Methods Mol. Biol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"e1703","DOI":"10.1002\/wcms.1703","article-title":"A brief history of amyloid aggregation simulations","volume":"14","author":"Fatafta","year":"2024","journal-title":"Wires Comput. Mol. Sci."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"1698","DOI":"10.1093\/bioinformatics\/btv027","article-title":"WALTZ-DB: A benchmark database of amyloidogenic hexapeptides","volume":"31","author":"Beerten","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"D352","DOI":"10.1093\/nar\/gkac882","article-title":"AmyloGraph: A comprehensive database of amyloid-amyloid interactions","volume":"51","author":"Burdukiewicz","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1111\/j.1432-1033.1982.tb07002.x","article-title":"Structural prediction of membrane-bound proteins","volume":"128","author":"Argos","year":"1982","journal-title":"Eur. J. Biochem."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1111\/j.1399-3011.1988.tb01258.x","article-title":"Positional flexibilities of amino acid residues in globular proteins","volume":"32","author":"Bhaskaran","year":"1988","journal-title":"Int. J. Pept. Protein Res."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/0022-5193(82)90191-6","article-title":"The structural dependence of amino acid hydrophobicity parameters","volume":"99","author":"Charton","year":"1982","journal-title":"J. Theor. Biol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/362267a0","article-title":"Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide","volume":"362","author":"Kim","year":"1993","journal-title":"Nature"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"W159","DOI":"10.1093\/nar\/gkae420","article-title":"AggreProt: A web server for predicting and engineering aggregation prone regions in proteins","volume":"52","author":"Borko","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Conchillo-Sol\u00e9, O., de Groot, N.S., Avil\u00e9s, F.X., Vendrell, J., Daura, X., and Ventura, S. (2007). AGGRESCAN: A server for the prediction and evaluation of \u201chot spots\u201d of aggregation in polypeptides. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-65"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"W306","DOI":"10.1093\/nar\/gkv359","article-title":"AGGRESCAN3D (A3D): Server for prediction of aggregation properties of protein structures","volume":"43","author":"Zambrano","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"W170","DOI":"10.1093\/nar\/gkae382","article-title":"Aggrescan4D: Structure-informed analysis of pH-dependent protein aggregation","volume":"52","author":"Kuriata","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1021\/acs.jcim.3c02035","article-title":"AMYGNN: A Graph Convolutional Neural Network-Based Approach for Predicting Amyloid Formation from Polypeptides","volume":"64","author":"Yang","year":"2024","journal-title":"J. Chem. Inf. Model."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"3395","DOI":"10.1093\/bioinformatics\/btv375","article-title":"AmyLoad: Website dedicated to amyloidogenic protein fragments","volume":"31","author":"Wozniak","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Bondarev, S.A., Uspenskaya, M.V., Leclercq, J., Falgarone, T., Zhouravleva, G.A., and Kajava, A.V. (2024). AmyloComp: A Bioinformatic Tool for Prediction of Amyloid Co-aggregation. J. Mol. Biol., 436.","DOI":"10.1016\/j.jmb.2024.168437"},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Szulc, N., Burdukiewicz, M., G\u0105sior-G\u0142ogowska, M., Wojciechowski, J.W., Chilimoniuk, J., Mackiewicz, P., \u0160neideris, T., Smirnovas, V., and Kotulska, M. (2021). Bioinformatics methods for identification of amyloidogenic peptides show robustness to misannotated training data. Sci. Rep., 11.","DOI":"10.1038\/s41598-021-86530-6"},{"key":"ref_100","doi-asserted-by":"crossref","unstructured":"Charoenkwan, P., Ahmed, S., Nantasenamat, C., Quinn, J.M.W., Moni, M.A., Lio, P., and Shoombuatong, W. (2022). AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning. Sci. Rep., 12.","DOI":"10.1038\/s41598-022-11897-z"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gkx950","article-title":"AmyPro: A database of proteins with validated amyloidogenic regions","volume":"46","author":"Varadi","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1016\/j.jalz.2014.06.007","article-title":"A structure-based approach to predict predisposition to amyloidosis","volume":"11","author":"Ahmed","year":"2015","journal-title":"Alzheimer\u2019s Dement."},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Falgarone, T., Villain, E., Guettaf, A., Leclercq, J., and Kajava, A.V. (2022). TAPASS: Tool for annotation of protein amyloidogenicity in the context of other structural states. J. Struct. Biol., 214.","DOI":"10.1016\/j.jsb.2022.107840"},{"key":"ref_104","doi-asserted-by":"crossref","unstructured":"Prabakaran, R., Rawat, P., Kumar, S., and Michael Gromiha, M. (2021). ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins. J. Mol. Biol., 433.","DOI":"10.1016\/j.jmb.2020.11.006"},{"key":"ref_105","doi-asserted-by":"crossref","unstructured":"Bryan, A.W., Menke, M., Cowen, L.J., Lindquist, S.L., and Berger, B. (2009). BETASCAN: Probable beta-amyloids identified by pairwise probabilistic analysis. PLoS Comput. Biol., 5.","DOI":"10.1371\/journal.pcbi.1000333"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1093\/bioinformatics\/btx629","article-title":"BetaSerpentine: A bioinformatics tool for reconstruction of amyloid structures","volume":"34","author":"Bondarev","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_107","doi-asserted-by":"crossref","unstructured":"Keresztes, L., Szogi, E., Varga, B., Farkas, V., Perczel, A., and Grolmusz, V. (2021). The Budapest Amyloid Predictor and Its Applications. Biomolecules, 11.","DOI":"10.3390\/biom11040500"},{"key":"ref_108","doi-asserted-by":"crossref","unstructured":"Louros, N., Rousseau, F., and Schymkowitz, J. (2024). CORDAX web server: An online platform for the prediction and 3D visualization of aggregation motifs in protein sequences. Bioinformatics, 40.","DOI":"10.1093\/bioinformatics\/btae279"},{"key":"ref_109","doi-asserted-by":"crossref","unstructured":"Thangakani, A.M., Nagarajan, R., Kumar, S., Sakthivel, R., Velmurugan, D., and Gromiha, M.M. (2016). CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0152949"},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Citarella, A.A., Di Biasi, L., De Marco, F., and Tortora, G. (2022). ENTAIL: yEt aNoTher amyloid fIbrils cLassifier. BMC Bioinform., 23.","DOI":"10.21203\/rs.3.rs-2041454\/v1"},{"key":"ref_111","doi-asserted-by":"crossref","unstructured":"Gasior, P., and Kotulska, M. (2014). FISH Amyloid\u2014A new method for finding amyloidogenic segments in proteins based on site specific co-occurrence of aminoacids. BMC Bioinform., 15.","DOI":"10.1186\/1471-2105-15-54"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1093\/bioinformatics\/btp691","article-title":"FoldAmyloid: A method of prediction of amyloidogenic regions from protein sequence","volume":"26","author":"Garbuzynskiy","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1093\/bioinformatics\/btu167","article-title":"GAP: Towards almost 100 percent prediction for beta-strand-mediated aggregating peptides with distinct morphologies","volume":"30","author":"Thangakani","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.1109\/TCBB.2019.2936846","article-title":"MILAMP: Multiple Instance Prediction of Amyloid Proteins","volume":"18","author":"Munir","year":"2021","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"ref_115","doi-asserted-by":"crossref","unstructured":"Wojciechowski, J.W., Szczurek, W., Szulc, N., Szefczyk, M., and Kotulska, M. (2023). PACT\u2014Prediction of amyloid cross-interaction by threading. Sci. Rep., 13.","DOI":"10.1038\/s41598-023-48886-9"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1038\/nbt1012","article-title":"Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins","volume":"22","author":"Rousseau","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"W301","DOI":"10.1093\/nar\/gku399","article-title":"PASTA 2.0: An improved server for protein aggregation prediction","volume":"42","author":"Walsh","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_118","doi-asserted-by":"crossref","unstructured":"Teng, Z., Zhang, Z., Tian, Z., Li, Y., and Wang, G. (2021). ReRF-Pred: Predicting amyloidogenic regions of proteins based on their pseudo amino acid composition and tripeptide composition. BMC Bioinform., 22.","DOI":"10.1186\/s12859-021-04446-4"},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"Niu, M., Li, Y., Wang, C., and Han, K. (2018). RFAmyloid: A Web Server for Predicting Amyloid Proteins. Int. J. Mol. Sci., 19.","DOI":"10.3390\/ijms19072071"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1038\/nmeth.1432","article-title":"Exploring the sequence determinants of amyloid structure using position-specific scoring matrices","volume":"7","author":"Debulpaep","year":"2010","journal-title":"Nat. Methods"},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"D389","DOI":"10.1093\/nar\/gkz758","article-title":"WALTZ-DB 2.0: An updated database containing structural information of experimentally determined amyloid-forming peptides","volume":"48","author":"Louros","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"3487","DOI":"10.1073\/pnas.0915166107","article-title":"Identifying the amylome, proteins capable of forming amyloid-like fibrils","volume":"107","author":"Goldschmidt","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1002\/prot.25276","article-title":"Aggregation prone regions in human proteome: Insights from large-scale data analyses","volume":"85","author":"Prabakaran","year":"2017","journal-title":"Proteins"},{"key":"ref_124","doi-asserted-by":"crossref","unstructured":"Danilov, L.G., Sukhanova, X.V., Rogoza, T.M., Antonova, E.Y., Trubitsina, N.P., Zhouravleva, G.A., and Bondarev, S.A. (2023). Identification of New FG-Repeat Nucleoporins with Amyloid Properties. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24108571"},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Falgarone, T., Villain, E., Richard, F., Osmanli, Z., and Kajava, A.V. (2023). Census of exposed aggregation-prone regions in proteomes. Brief. Bioinform., 24.","DOI":"10.1093\/bib\/bbad183"},{"key":"ref_126","first-page":"1127","article-title":"Amyloids: From Pathogenesis to Function","volume":"80","author":"Nizhnikov","year":"2015","journal-title":"Biochemistry"},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1016\/j.jmb.2005.02.030","article-title":"Amyloid-like properties of bacterial inclusion bodies","volume":"347","author":"Vera","year":"2005","journal-title":"J. Mol. Biol."},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1021\/acsptsci.2c00174","article-title":"Amyloid Fibrillation of Insulin: Amelioration Strategies and Implications for Translation","volume":"5","author":"Fagihi","year":"2022","journal-title":"ACS Pharmacol. Transl. Sci."},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Miller, Y. (2022). Advancements and future directions in research of the roles of insulin in amyloid diseases. Biophys. Chem., 281.","DOI":"10.1016\/j.bpc.2021.106720"},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"21449","DOI":"10.1074\/jbc.M314141200","article-title":"Mechanism of insulin fibrillation: The structure of insulin under amyloidogenic conditions resembles a protein-folding intermediate","volume":"279","author":"Hua","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.ijbiomac.2017.01.110","article-title":"Investigating the effects of erythrosine B on amyloid fibril formation derived from lysozyme","volume":"98","author":"Kuo","year":"2017","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.ijbiomac.2019.07.055","article-title":"Exploring the influence of brilliant blue G on amyloid fibril formation of lysozyme","volume":"38","author":"How","year":"2019","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"5678","DOI":"10.1021\/acs.jpcb.9b02338","article-title":"Mechanism of Fibril and Soluble Oligomer Formation in Amyloid Beta and Hen Egg White Lysozyme Proteins","volume":"123","author":"Perez","year":"2019","journal-title":"J. Phys. Chem. B"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"16439","DOI":"10.1021\/acsomega.3c01531","article-title":"Manganese Ion-Induced Amyloid Fibrillation Kinetics of Hen Egg White-Lysozyme in Thermal and Acidic Conditions","volume":"8","author":"Chen","year":"2023","journal-title":"ACS Omega"},{"key":"ref_135","doi-asserted-by":"crossref","unstructured":"Gancar, M., Kurin, E., Bednarikova, Z., Marek, J., Mucaji, P., Nagy, M., and Gazova, Z. (2023). Green tea leaf constituents inhibit the formation of lysozyme amyloid aggregates: An effect of mutual interactions. Int. J. Biol. Macromol., 242.","DOI":"10.1016\/j.ijbiomac.2023.124856"},{"key":"ref_136","doi-asserted-by":"crossref","unstructured":"Khan, A.N., Nabi, F., and Khan, R.H. (2023). Mechanistic and biophysical insight into the inhibitory and disaggregase role of antibiotic moxifloxacin on human lysozyme amyloid formation. Biophys. Chem., 298.","DOI":"10.1016\/j.bpc.2023.107029"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/B978-0-12-386483-3.00003-3","article-title":"Lysozyme: A model protein for amyloid research","volume":"84","author":"Swaminathan","year":"2011","journal-title":"Adv. Protein Chem. Struct. Biol."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"103205","DOI":"10.1016\/j.cis.2024.103205","article-title":"Molecular insights into the phase transition of lysozyme into amyloid nanostructures: Implications of therapeutic strategies in diverse pathological conditions","volume":"331","author":"Roy","year":"2024","journal-title":"Adv. Colloid. Interface Sci."},{"key":"ref_139","doi-asserted-by":"crossref","unstructured":"Muthu, S.A., Qureshi, A., Sharma, R., Bisaria, I., Parvez, S., Grover, S., and Ahmad, B. (2024). Redesigning the kinetics of lysozyme amyloid aggregation by cephalosporin molecules. J. Biomol. Struct. Dyn., 1\u201316.","DOI":"10.1080\/07391102.2024.2335304"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"2502","DOI":"10.1039\/D1NR05571B","article-title":"Hierarchical propagation of structural features in protein nanomaterials","volume":"14","author":"Kamada","year":"2022","journal-title":"Nanoscale"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1038\/s43016-019-0009-x","article-title":"Design principles of food gels","volume":"1","author":"Cao","year":"2020","journal-title":"Nat. Food"},{"key":"ref_142","doi-asserted-by":"crossref","unstructured":"Rahman, M.M., Pires, R.S., Herneke, A., Gowda, V., Langton, M., Biverstal, H., and Lendel, C. (2023). Food protein-derived amyloids do not accelerate amyloid beta aggregation. Sci. Rep., 13.","DOI":"10.1038\/s41598-023-28147-5"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1042\/bse0560193","article-title":"Amyloid diseases of yeast: Prions are proteins acting as genes","volume":"56","author":"Wickner","year":"2014","journal-title":"Essays Biochem."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/bs.adgen.2015.12.003","article-title":"Yeast and Fungal Prions: Amyloid-Handling Systems, Amyloid Structure, and Prion Biology","volume":"93","author":"Wickner","year":"2016","journal-title":"Adv. Genet."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/s41589-021-00951-y","article-title":"Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system","volume":"18","author":"Nakagawa","year":"2022","journal-title":"Nat. Chem. Biol."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"3685","DOI":"10.1016\/j.jmb.2018.05.004","article-title":"Ecology and Biogenesis of Functional Amyloids in Pseudomonas","volume":"430","author":"Rouse","year":"2018","journal-title":"J. Mol. Biol."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"2461","DOI":"10.1002\/cphc.201600246","article-title":"Binding Modes of Thioflavin T on the Surface of Amyloid Fibrils by NMR","volume":"17","author":"Ivancic","year":"2016","journal-title":"ChemPhysChem"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1146\/annurev-physchem-032210-103539","article-title":"Solid-state NMR studies of amyloid fibril structure","volume":"62","author":"Tycko","year":"2011","journal-title":"Annu. Rev. Phys. Chem."},{"key":"ref_149","doi-asserted-by":"crossref","unstructured":"Artikis, E., Kraus, A., and Caughey, B. (2022). Structural biology of ex vivo mammalian prions. J. Biol. Chem., 298.","DOI":"10.1016\/j.jbc.2022.102181"},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1007\/s12551-018-0427-2","article-title":"Understanding amyloid fibril formation using protein fragments: Structural investigations via vibrational spectroscopy and solid-state NMR","volume":"10","author":"Martial","year":"2018","journal-title":"Biophys. Rev."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1016\/bs.mie.2024.01.025","article-title":"Solid-state NMR spectroscopic analysis for structure determination of a zinc-bound catalytic amyloid fibril","volume":"697","author":"Baek","year":"2024","journal-title":"Methods Enzymol."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1039\/D2FD00034B","article-title":"High-throughput cryo-EM structure determination of amyloids","volume":"240","author":"Scheres","year":"2022","journal-title":"Faraday Discuss."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1126\/science.abm7285","article-title":"Cryo-EM structures of amyloid-beta 42 filaments from human brains","volume":"375","author":"Yang","year":"2022","journal-title":"Science"},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"4356","DOI":"10.1038\/s41467-022-32039-z","article-title":"The Cryo-EM structures of two amphibian antimicrobial cross-beta amyloid fibrils","volume":"13","author":"Seuring","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_155","doi-asserted-by":"crossref","unstructured":"Heerde, T., Bansal, A., Schmidt, M., and F\u00e4ndrich, M. (2023). Cryo-EM structure of a catalytic amyloid fibril. Sci. Rep., 13.","DOI":"10.1038\/s41598-023-30711-y"},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1038\/s41594-024-01252-3","article-title":"Cryo-EM structures of amyloid-beta and tau filaments in Down syndrome","volume":"31","author":"Fernandez","year":"2024","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/s41467-023-44489-0","article-title":"Cryo-EM observation of the amyloid key structure of polymorphic TDP-43 amyloid fibrils","volume":"15","author":"Sharma","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1002\/pro.5560020312","article-title":"Thioflavine T interaction with synthetic Alzheimer\u2019s disease beta-amyloid peptides: Detection of amyloid aggregation in solution","volume":"2","author":"LeVine","year":"1993","journal-title":"Protein Sci."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.jsb.2005.06.006","article-title":"Mechanism of thioflavin T binding to amyloid fibrils","volume":"151","author":"Khurana","year":"2005","journal-title":"J. Struct. Biol."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1007\/s11095-007-9516-9","article-title":"Extrinsic fluorescent dyes as tools for protein characterization","volume":"25","author":"Hawe","year":"2008","journal-title":"Pharm. Res."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1016\/j.bbapap.2010.04.001","article-title":"Molecular mechanism of Thioflavin-T binding to amyloid fibrils","volume":"1804","author":"Biancalana","year":"2010","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.1021\/ar300053p","article-title":"Molecular rotors: What lies behind the high sensitivity of the thioflavin-T fluorescent marker","volume":"45","author":"Amdursky","year":"2012","journal-title":"Acc. Chem. Res."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1021\/acs.analchem.5b02747","article-title":"High Fluorescence Anisotropy of Thioflavin T in Aqueous Solution Resulting from Its Molecular Rotor Nature","volume":"88","author":"Kuznetsova","year":"2016","journal-title":"Anal. Chem."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/13506129.2017.1304905","article-title":"ThT 101: A primer on the use of thioflavin T to investigate amyloid formation","volume":"24","author":"Weber","year":"2017","journal-title":"Amyloid"},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"160696","DOI":"10.1098\/rsos.160696","article-title":"Thioflavin T as an amyloid dye: Fibril quantification, optimal concentration and effect on aggregation","volume":"4","author":"Xue","year":"2017","journal-title":"R. Soc. Open Sci."},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"11819","DOI":"10.1021\/acs.chemrev.9b00404","article-title":"Interrogating Amyloid Aggregates using Fluorescent Probes","volume":"119","author":"Aliyan","year":"2019","journal-title":"Chem. Rev."},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"1156","DOI":"10.1039\/b912396b","article-title":"Crystal structure of thioflavin-T and its binding to amyloid fibrils: Insights at the molecular level","volume":"46","author":"Rimola","year":"2010","journal-title":"Chem. Commun."},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"6674","DOI":"10.1021\/jp402807g","article-title":"Insights on the binding of Thioflavin derivative markers to amyloid-like fibril models from quantum chemical calculations","volume":"117","author":"Rimola","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"11560","DOI":"10.1021\/acs.jpcb.5b05964","article-title":"Investigation of the Binding Profiles of AZD2184 and Thioflavin T with Amyloid-beta(1-42) Fibril by Molecular Docking and Molecular Dynamics Methods","volume":"119","author":"Kuang","year":"2015","journal-title":"J. Phys. Chem. B"},{"key":"ref_170","doi-asserted-by":"crossref","unstructured":"Shaban, H.A., Valades-Cruz, C.A., Savatier, J., and Brasselet, S. (2017). Polarized super-resolution structural imaging inside amyloid fibrils using Thioflavine T. Sci. Rep., 7.","DOI":"10.1038\/s41598-017-12864-9"},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"7589","DOI":"10.1039\/D0CC01161D","article-title":"Binding modes of thioflavin T and Congo red to the fibril structure of amyloid-beta(1-42)","volume":"56","author":"Frieg","year":"2020","journal-title":"Chem. Commun."},{"key":"ref_172","doi-asserted-by":"crossref","unstructured":"Sulatskaya, A.I., Rychkov, G.N., Sulatsky, M.I., Mikhailova, E.V., Melnikova, N.M., Andozhskaya, V.S., Kuznetsova, I.M., and Turoverov, K.K. (2022). New Evidence on a Distinction between A beta 40 and A beta 42 Amyloids: Thioflavin T Binding Modes, Clustering Tendency, Degradation Resistance, and Cross-Seeding. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23105513"},{"key":"ref_173","doi-asserted-by":"crossref","unstructured":"Sulatskaya, A.I., Kuznetsova, I.M., Belousov, M.V., Bondarev, S.A., Zhouravleva, G.A., and Turoverov, K.K. (2016). Stoichiometry and Affinity of Thioflavin T Binding to Sup35p Amyloid Fibrils. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0156314"},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"1354","DOI":"10.1039\/D3CS00518F","article-title":"A closer look at amyloid ligands, and what they tell us about protein aggregates","volume":"53","author":"Chisholm","year":"2024","journal-title":"Chem. Soc. Rev."},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"7856","DOI":"10.1021\/ja7109822","article-title":"Crystal structure of thioflavin T bound to the peripheral site of Torpedo californica acetylcholinesterase reveals how thioflavin T acts as a sensitive fluorescent reporter of ligand binding to the acylation site","volume":"130","author":"Harel","year":"2008","journal-title":"J. Am. Chem. Soc."},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"5960","DOI":"10.1111\/j.1742-4658.2009.07307.x","article-title":"The thioflavin T fluorescence assay for amyloid fibril detection can be biased by the presence of exogenous compounds","volume":"276","author":"Hudson","year":"2009","journal-title":"FEBS J."},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/j.bbrc.2015.01.132","article-title":"Steady-state and time-resolved Thioflavin-T fluorescence can report on morphological differences in amyloid fibrils formed by Abeta(1-40) and Abeta(1-42)","volume":"458","author":"Lindberg","year":"2015","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1021\/cb700116u","article-title":"Imaging distinct conformational states of amyloid-beta fibrils in Alzheimer\u2019s disease using novel luminescent probes","volume":"2","author":"Nilsson","year":"2007","journal-title":"ACS Chem. Biol."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"563","DOI":"10.2353\/ajpath.2010.080797","article-title":"Structural typing of systemic amyloidoses by luminescent-conjugated polymer spectroscopy","volume":"176","author":"Nilsson","year":"2010","journal-title":"Am. J. Pathol."},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"1860","DOI":"10.1021\/bc700180g","article-title":"Studies of luminescent conjugated polythiophene derivatives: Enhanced spectral discrimination of protein conformational states","volume":"18","author":"Herland","year":"2007","journal-title":"Bioconjug. Chem."},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"8356","DOI":"10.1039\/c1ob05637a","article-title":"Synthesis of a library of oligothiophenes and their utilization as fluorescent ligands for spectral assignment of protein aggregates","volume":"9","author":"Klingstedt","year":"2011","journal-title":"Org. Biomol. Chem."},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"10179","DOI":"10.1002\/chem.201301463","article-title":"The structural basis for optimal performance of oligothiophene-based fluorescent amyloid ligands: Conformational flexibility is essential for spectral assignment of a diversity of protein aggregates","volume":"19","author":"Klingstedt","year":"2013","journal-title":"Chemistry"},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"12537","DOI":"10.1002\/chem.201402890","article-title":"Pentameric thiophene-based ligands that spectrally discriminate amyloid-beta and tau aggregates display distinct solvatochromism and viscosity-induced spectral shifts","volume":"20","author":"Simon","year":"2014","journal-title":"Chemistry"},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"5452","DOI":"10.1002\/anie.200500845","article-title":"In vivo optical Imaging of amyloid aggregates in brain: Design of fluorescent markers","volume":"44","author":"Nesterov","year":"2005","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.cplett.2015.05.010","article-title":"Torsion-dependent fluorescence switching of amyloid-binding dye NIAD-4","volume":"633","author":"Bae","year":"2015","journal-title":"Chem. Phys. Lett."},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1039\/C1MB05370A","article-title":"Specific in situ discrimination of amyloid fibrils versus alpha-helical fibres by the fluorophore NIAD-4","volume":"8","author":"Brandenburg","year":"2012","journal-title":"Mol. Biosyst."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"1807","DOI":"10.1039\/C4CS00337C","article-title":"Imaging of beta-amyloid plaques by near infrared fluorescent tracers: A new frontier for chemical neuroscience","volume":"44","author":"Staderini","year":"2015","journal-title":"Chem. Soc. Rev."},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1002\/ijch.201600114","article-title":"Fluorescent Markers for Amyloid-beta Detection: Computational Insights","volume":"57","author":"Peccati","year":"2017","journal-title":"Isr. J. Chem."},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"15849","DOI":"10.1039\/C7CP02268A","article-title":"The influence of hydrogen bonds on NIAD-4 for use in the optical imaging of amyloid fibrils","volume":"19","author":"Li","year":"2017","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"2736","DOI":"10.2174\/0929867325666180214110024","article-title":"Fluorescent Imaging of Amyloid-beta Deposits in Brain: An Overview of Probe Development and a Highlight of the Applications for In Vivo Imaging","volume":"25","author":"Fu","year":"2018","journal-title":"Curr. Med. Chem."},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"111982","DOI":"10.1016\/j.ejmech.2019.111982","article-title":"Biological applications of near infrared fluorescence dye probes in monitoring Alzheimer\u2019s disease","volume":"187","author":"Gyasi","year":"2020","journal-title":"Eur. J. Med. Chem."},{"key":"ref_192","doi-asserted-by":"crossref","first-page":"1986","DOI":"10.1039\/C9TB00161A","article-title":"Versatile fluorescent probes for near-infrared imaging of amyloid-beta species in Alzheimer\u2019s disease mouse model","volume":"7","author":"Peng","year":"2022","journal-title":"J. Mater. Chem. B"},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/j.ccr.2018.11.003","article-title":"Brain imaging with near-infrared fluorophores","volume":"380","author":"Wang","year":"2019","journal-title":"Coord. Chem. Rev."},{"key":"ref_194","doi-asserted-by":"crossref","first-page":"20160539","DOI":"10.1098\/rsif.2016.0539","article-title":"Acute induction of anomalous and amyloidogenic blood clotting by molecular amplification of highly substoichiometric levels of bacterial lipopolysaccharide","volume":"123","author":"Pretorius","year":"2016","journal-title":"J. R. Soc. Interface"},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"20170941","DOI":"10.1098\/rsif.2017.0941","article-title":"Both lipopolysaccharide and lipoteichoic acids potently induce anomalous fibrin amyloid formation: Assessment with novel Amytracker\u2122 stains","volume":"15","author":"Pretorius","year":"2018","journal-title":"J. R. Soc. Interface"},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1186\/s12933-017-0624-5","article-title":"Substantial fibrin amyloidogenesis in type 2 diabetes assessed using amyloid-selective fluorescent stains","volume":"16","author":"Pretorius","year":"2017","journal-title":"Cardiovasc. Diabetol."},{"key":"ref_197","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1186\/s12933-020-01165-7","article-title":"Prevalence of readily detected amyloid blood clots in \u2018unclotted\u2019 Type 2 Diabetes Mellitus and COVID-19 plasma: A preliminary report","volume":"19","author":"Pretorius","year":"2020","journal-title":"Cardiovasc. Diabetol."},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1042\/BCJ20220016","article-title":"A central role for amyloid fibrin microclots in long COVID\/PASC: Origins and therapeutic implications","volume":"479","author":"Kell","year":"2022","journal-title":"Biochem. J."},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1186\/s12933-022-01579-5","article-title":"Prevalence of symptoms, comorbidities, fibrin amyloid microclots and platelet pathology in individuals with Long COVID\/ Post-Acute Sequelae of COVID-19 (PASC)","volume":"21","author":"Pretorius","year":"2022","journal-title":"Cardiovasc. Diabetol."},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.tem.2023.03.002","article-title":"Long COVID: Pathophysiological factors and abnormal coagulation","volume":"34","author":"Turner","year":"2023","journal-title":"Trends Endocrinol. Metab."},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"e19605","DOI":"10.1016\/j.heliyon.2023.e19605","article-title":"Accelerating discovery: A novel flow cytometric method for detecting fibrin(ogen) amyloid microclots using long COVID as a model","volume":"9","author":"Turner","year":"2023","journal-title":"Heliyon"},{"key":"ref_202","doi-asserted-by":"crossref","unstructured":"Kell, D.B., Khan, M.A., Kane, B., Lip, G.Y.H., and Pretorius, E. (2024). Possible role of fibrinaloid microclots in Postural Orthostatic Tachycardia Syndrome (POTS): Focus on Long COVID. J. Pers. Med., 14.","DOI":"10.3390\/jpm14020170"},{"key":"ref_203","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1055\/s-0043-1774796","article-title":"A Perspective on How Fibrinaloid Microclots and Platelet Pathology May be Applied in Clinical Investigations","volume":"50","author":"Pretorius","year":"2024","journal-title":"Semin. Thromb. Hemost."},{"key":"ref_204","doi-asserted-by":"crossref","unstructured":"Dalton, C.F., de Oliveira, M.I.R., Stafford, P., Peake, N., Kane, B., Higham, A., Singh, D., Jackson, N., Davies, H., and Price, D. (2024). Increased fibrinaloid microclot counts in platelet-poor plasma are associated with Long COVID. medRxiv.","DOI":"10.1101\/2024.04.04.24305318"},{"key":"ref_205","doi-asserted-by":"crossref","first-page":"2499","DOI":"10.1182\/bloodadvances.2023012473","article-title":"Amyloid-fibrinogen aggregates (\u201cmicroclots\u201d) predict risks of Disseminated Intravascular Coagulation and mortality","volume":"8","author":"Schofield","year":"2024","journal-title":"Blood Adv."},{"key":"ref_206","doi-asserted-by":"crossref","first-page":"3967","DOI":"10.1021\/bi900015n","article-title":"Alpha(E)C, the C-terminal extension of fibrinogen, has chaperone-like activity","volume":"48","author":"Tang","year":"2009","journal-title":"Biochemistry"},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1016\/j.bbrc.2008.11.112","article-title":"Fibrinogen has chaperone-like activity","volume":"378","author":"Tang","year":"2009","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_208","doi-asserted-by":"crossref","unstructured":"Yamamoto, N., and Chatani, E. (2022). Multistep growth of amyloid intermediates and its inhibition toward exploring therapeutic way: A case study using insulin B chain and fibrinogen. Biophys. Physicobiol., 19.","DOI":"10.2142\/biophysico.bppb-v19.0017"},{"key":"ref_209","doi-asserted-by":"crossref","first-page":"4313","DOI":"10.1182\/blood-2010-01-261750","article-title":"Hereditary fibrinogen A alpha-chain amyloidosis: Clinical phenotype and role of liver transplantation","volume":"115","author":"Gillmore","year":"2010","journal-title":"Blood"},{"key":"ref_210","doi-asserted-by":"crossref","first-page":"2998","DOI":"10.1182\/blood-2009-06-223792","article-title":"Hereditary fibrinogen A alpha-chain amyloidosis: Phenotypic characterization of a systemic disease and the role of liver transplantation","volume":"115","author":"Stangou","year":"2010","journal-title":"Blood"},{"key":"ref_211","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1080\/14789450.2019.1659137","article-title":"Fibrinogen alpha amyloidosis: Insights from proteomics","volume":"16","author":"Chapman","year":"2019","journal-title":"Expert. Rev. Proteom."},{"key":"ref_212","doi-asserted-by":"crossref","first-page":"6025","DOI":"10.1021\/ja800834y","article-title":"EP-2104R: A fibrin-specific gadolinium-Based MRI contrast agent for detection of thrombus","volume":"130","author":"Koerner","year":"2008","journal-title":"J. Am. Chem. Soc."},{"key":"ref_213","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.jcmg.2012.01.017","article-title":"Molecular imaging of fibrin deposition in deep vein thrombosis using fibrin-targeted near-infrared fluorescence","volume":"5","author":"Hara","year":"2012","journal-title":"JACC Cardiovasc. Imaging"},{"key":"ref_214","first-page":"276","article-title":"FITC-linked Fibrin-Binding Peptide and real-time live confocal microscopy as a novel tool to visualize fibrin(ogen) in coagulation","volume":"3","author":"Weiss","year":"2017","journal-title":"J. Clin. Transl. Res."},{"key":"ref_215","doi-asserted-by":"crossref","first-page":"112","DOI":"10.4161\/pri.2.3.7488","article-title":"Amyloid fibrils: Abnormal protein assembly","volume":"2","author":"Rambaran","year":"2008","journal-title":"Prion"},{"key":"ref_216","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.jalz.2009.06.002","article-title":"Characterization of tau fibrillization in vitro","volume":"6","author":"Xu","year":"2010","journal-title":"Alzheimer\u2019s Dement."},{"key":"ref_217","doi-asserted-by":"crossref","first-page":"496","DOI":"10.4161\/pri.27190","article-title":"SAXS structural study of PrP(Sc) reveals ~11 nm diameter of basic double intertwined fibers","volume":"7","author":"Amenitsch","year":"2013","journal-title":"Prion"},{"key":"ref_218","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1038\/s41586-022-05319-3","article-title":"Structures of alpha-synuclein filaments from human brains with Lewy pathology","volume":"610","author":"Yang","year":"2022","journal-title":"Nature"},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"2750","DOI":"10.1038\/s41467-024-46832-5","article-title":"Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue","volume":"15","author":"Dhavale","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_220","doi-asserted-by":"crossref","unstructured":"He, S., He, X., Liu, L., Zhang, W., Yu, L., Deng, Z., Feiyi, Z., Mo, S., Fan, Y., and Zhao, X. (2021). The Structural Understanding of Transthyretin Misfolding and the Inspired Drug Approaches for the Treatment of Heart Failure Associated with Transthyretin Amyloidosis. Front. Pharmacol., 12.","DOI":"10.3389\/fphar.2021.628184"},{"key":"ref_221","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1021\/bm101122g","article-title":"High-resolution visualization of fibrinogen molecules and fibrin fibers with atomic force microscopy","volume":"12","author":"Yermolenko","year":"2011","journal-title":"Biomacromolecules"},{"key":"ref_222","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1054\/fipr.2000.0085","article-title":"Atomic force microscopy of fibrin networks and plasma clots during fibrinolysis","volume":"14","author":"Blinc","year":"2000","journal-title":"Fibrinolysis Proteolysis"},{"key":"ref_223","doi-asserted-by":"crossref","first-page":"1354","DOI":"10.1161\/01.ATV.20.5.1354","article-title":"Influence of fibrin network conformation and fibrin fiber diameter on fibrinolysis speed: Dynamic and structural approaches by confocal microscopy","volume":"20","author":"Collet","year":"2000","journal-title":"Arterioscler. Thromb. Vasc. Biol."},{"key":"ref_224","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1016\/j.bpj.2016.02.021","article-title":"Fibrin Fiber Stiffness Is Strongly Affected by Fiber Diameter, but Not by Fibrinogen Glycation","volume":"110","author":"Li","year":"2016","journal-title":"Biophys. J."},{"key":"ref_225","doi-asserted-by":"crossref","unstructured":"Li, W., Sigley, J., Baker, S.R., Helms, C.C., Kinney, M.T., Pieters, M., Brubaker, P.H., Cubcciotti, R., and Guthold, M. (2017). Nonuniform Internal Structure of Fibrin Fibers: Protein Density and Bond Density Strongly Decrease with Increasing Diameter. Biomed. Res. Int., 2017.","DOI":"10.1155\/2017\/6385628"},{"key":"ref_226","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1016\/j.str.2018.04.005","article-title":"Atomic Structural Models of Fibrin Oligomers","volume":"26","author":"Zhmurov","year":"2018","journal-title":"Structure"},{"key":"ref_227","doi-asserted-by":"crossref","first-page":"20396","DOI":"10.1021\/ja3076428","article-title":"Mechanical transition from alpha-helical coiled coils to beta-sheets in fibrin(ogen)","volume":"134","author":"Zhmurov","year":"2012","journal-title":"J. Am. Chem. Soc."},{"key":"ref_228","doi-asserted-by":"crossref","first-page":"16168","DOI":"10.1021\/jacs.7b06883","article-title":"Dynamic Transition from alpha-Helices to beta-Sheets in Polypeptide Coiled-Coil Motifs","volume":"139","author":"Minin","year":"2017","journal-title":"J. Am. Chem. Soc."},{"key":"ref_229","doi-asserted-by":"crossref","unstructured":"Risman, R.A., Belcher, H.A., Ramanujam, R.K., Weisel, J.W., Hudson, N.E., and Tutwiler, V. (2024). Comprehensive Analysis of the Role of Fibrinogen and Thrombin in Clot Formation and Structure for Plasma and Purified Fibrinogen. Biomolecules, 14.","DOI":"10.3390\/biom14020230"},{"key":"ref_230","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.blre.2006.11.001","article-title":"Thrombin generation and fibrin clot structure","volume":"21","author":"Wolberg","year":"2007","journal-title":"Blood Rev."},{"key":"ref_231","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1002\/jemt.22378","article-title":"Estrogen causes ultrastructural changes of fibrin networks during the menstrual cycle: A qualitative investigation","volume":"77","author":"Swanepoel","year":"2014","journal-title":"Microsc. Res. Tech."},{"key":"ref_232","doi-asserted-by":"crossref","first-page":"16968","DOI":"10.1021\/acsnano.3c04164","article-title":"Amyloid Fibrils Formed by Short Prion-Inspired Peptides Are Metalloenzymes","volume":"17","author":"Navarro","year":"2023","journal-title":"ACS Nano"},{"key":"ref_233","doi-asserted-by":"crossref","first-page":"5632","DOI":"10.1039\/D1SM01578H","article-title":"Unraveling gelation kinetics, arrested dynamics and relaxation phenomena in filamentous colloids by photon correlation imaging","volume":"18","author":"Usuelli","year":"2022","journal-title":"Soft Matter"},{"key":"ref_234","doi-asserted-by":"crossref","first-page":"6342","DOI":"10.1021\/acs.langmuir.7b00527","article-title":"Buffers Strongly Modulate Fibrin Self-Assembly into Fibrous Networks","volume":"33","author":"Kurniawan","year":"2017","journal-title":"Langmuir"},{"key":"ref_235","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/S0161-813X(02)00067-0","article-title":"Synergistic effects of pesticides and metals on the fibrillation of alpha-synuclein: Implications for Parkinson\u2019s disease","volume":"23","author":"Uversky","year":"2002","journal-title":"Neurotoxicology"},{"key":"ref_236","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1023\/A:1025024104862","article-title":"Protein aggregation in recombinant bacteria: Biological role of inclusion bodies","volume":"25","author":"Villaverde","year":"2003","journal-title":"Biotechnol. Lett."},{"key":"ref_237","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.tibtech.2006.02.007","article-title":"Protein quality in bacterial inclusion bodies","volume":"24","author":"Ventura","year":"2006","journal-title":"Trends Biotechnol."},{"key":"ref_238","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1016\/0167-7799(94)90021-3","article-title":"Recent developments in heterologous protein production in Escherichia coli","volume":"12","author":"Hockney","year":"1994","journal-title":"Trends Biotechnol."},{"key":"ref_239","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1007\/s10529-005-7184-6","article-title":"Monitoring and quantification of inclusion body formation in Escherichia coli by multi-parameter flow cytometry","volume":"27","author":"Ledung","year":"2005","journal-title":"Biotechnol. Lett."},{"key":"ref_240","first-page":"1898","article-title":"Modulation of the tendency towards inclusion body formation of recombinant protein by the addition of glucose in the araBAD promoter system of Escherichia coli","volume":"17","author":"Lee","year":"2007","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref_241","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-0716-2930-7_1","article-title":"Inclusion Bodies: Status Quo and Perspectives","volume":"2617","author":"Kopp","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_242","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1080\/10826068.2022.2155835","article-title":"Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: Insights from structure-function relationship for novel applications","volume":"53","author":"Kachhawaha","year":"2023","journal-title":"Prep. Biochem. Biotechnol."},{"key":"ref_243","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1111\/febs.16312","article-title":"A guide to studying protein aggregation","volume":"290","author":"Housmans","year":"2023","journal-title":"FEBS J."},{"key":"ref_244","doi-asserted-by":"crossref","unstructured":"Wang, L., Maji, S.K., Sawaya, M.R., Eisenberg, D., and Riek, R. (2008). Bacterial inclusion bodies contain amyloid-like structure. PLoS Biol., 6.","DOI":"10.4016\/7266.01"},{"key":"ref_245","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1016\/j.tibs.2009.03.009","article-title":"Amyloids in bacterial inclusion bodies","volume":"34","author":"Sabate","year":"2009","journal-title":"Trends Biochem. Sci."},{"key":"ref_246","doi-asserted-by":"crossref","first-page":"2419","DOI":"10.1111\/j.1742-4658.2011.08165.x","article-title":"Biological role of bacterial inclusion bodies: A model for amyloid aggregation","volume":"278","author":"Sabate","year":"2011","journal-title":"FEBS J."},{"key":"ref_247","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1093\/femsre\/fuy038","article-title":"Bacterial inclusion bodies are industrially exploitable amyloids","volume":"43","author":"Mitraki","year":"2019","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_248","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s12934-021-01524-3","article-title":"Insoluble proteins catch heterologous soluble proteins into inclusion bodies by intermolecular interaction of aggregating peptides","volume":"20","author":"Cisneros","year":"2021","journal-title":"Microb. Cell Fact."},{"key":"ref_249","doi-asserted-by":"crossref","first-page":"6134","DOI":"10.1016\/j.actbio.2012.11.033","article-title":"Supramolecular organization of protein-releasing functional amyloids solved in bacterial inclusion bodies","volume":"9","author":"Elizondo","year":"2013","journal-title":"Acta Biomater."},{"key":"ref_250","doi-asserted-by":"crossref","first-page":"2881","DOI":"10.2217\/nnm.15.125","article-title":"Functional protein aggregates: Just the tip of the iceberg","volume":"10","author":"Villaverde","year":"2015","journal-title":"Nanomedicine"},{"key":"ref_251","doi-asserted-by":"crossref","unstructured":"Hrabarova, E., Belkova, M., Koszagova, R., and Nahalka, J. (2022). Pull-Down Into Active Inclusion Bodies and Their Application in the Detection of (Poly)-Phosphates and Metal-Ions. Front. Bioeng. Biotechnol., 10.","DOI":"10.3389\/fbioe.2022.833192"},{"key":"ref_252","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1146\/annurev.biochem.75.101304.123901","article-title":"Protein misfolding, functional amyloid, and human disease","volume":"75","author":"Chiti","year":"2006","journal-title":"Annu. Rev. Biochem."},{"key":"ref_253","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1038\/nature02261","article-title":"Protein folding and misfolding","volume":"426","author":"Dobson","year":"2003","journal-title":"Nature"},{"key":"ref_254","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/nrm3810","article-title":"The amyloid state and its association with protein misfolding diseases","volume":"15","author":"Knowles","year":"2014","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_255","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1038\/s41580-018-0060-8","article-title":"A new era for understanding amyloid structures and disease","volume":"19","author":"Iadanza","year":"2018","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_256","doi-asserted-by":"crossref","unstructured":"Ghosh, D., Biswas, A., and Radhakrishna, M. (2024). Advanced computational approaches to understand protein aggregation. Biophys. Rev., 5.","DOI":"10.1063\/5.0180691"},{"key":"ref_257","doi-asserted-by":"crossref","first-page":"5326","DOI":"10.1039\/C4CS00082J","article-title":"Amyloid-based nanosensors and nanodevices","volume":"43","author":"Hauser","year":"2014","journal-title":"Chem. Soc. Rev."},{"key":"ref_258","doi-asserted-by":"crossref","first-page":"5473","DOI":"10.1039\/C9CS00199A","article-title":"Half a century of amyloids: Past, present and future","volume":"49","author":"Ke","year":"2020","journal-title":"Chem. Soc. Rev."},{"key":"ref_259","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/978-1-61779-551-0_9","article-title":"X-ray fibre diffraction studies of amyloid fibrils","volume":"849","author":"Morris","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"ref_260","doi-asserted-by":"crossref","first-page":"20170027","DOI":"10.1098\/rsfs.2017.0027","article-title":"The diversity and utility of amyloid fibrils formed by short amyloidogenic peptides","volume":"7","author":"Morris","year":"2017","journal-title":"Interface Focus."},{"key":"ref_261","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1006\/jmbi.2000.3908","article-title":"The protofilament substructure of amyloid fibrils","volume":"300","author":"Serpell","year":"2000","journal-title":"J. Mol. Biol."},{"key":"ref_262","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1073\/pnas.0406847102","article-title":"Molecular basis for amyloid fibril formation and stability","volume":"102","author":"Makin","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_263","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.nbd.2017.07.009","article-title":"The contribution of biophysical and structural studies of protein self-assembly to the design of therapeutic strategies for amyloid diseases","volume":"109","author":"Cremades","year":"2018","journal-title":"Neurobiol. Dis."},{"key":"ref_264","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1017\/S0033583598003400","article-title":"From the globular to the fibrous state: Protein structure and structural conversion in amyloid formation","volume":"31","author":"Sunde","year":"1998","journal-title":"Q. Rev. Biophys."},{"key":"ref_265","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1126\/science.1105850","article-title":"Self-propagating, molecular-level polymorphism in Alzheimer\u2019s beta-amyloid fibrils","volume":"307","author":"Petkova","year":"2005","journal-title":"Science"},{"key":"ref_266","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.sbi.2014.12.001","article-title":"The structure of fibrils from \u2018misfolded\u2019 proteins","volume":"30","author":"Meier","year":"2015","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_267","doi-asserted-by":"crossref","unstructured":"Lutter, L., Serpell, C.J., Tuite, M.F., and Xue, W.F. (2019). The molecular lifecycle of amyloid\u2014Mechanism of assembly, mesoscopic organisation, polymorphism, suprastructures, and biological consequences. Biochim. Biophys. Acta Proteins Proteom., 1867.","DOI":"10.1016\/j.bbapap.2019.07.010"},{"key":"ref_268","doi-asserted-by":"crossref","first-page":"343","DOI":"10.2174\/138920310791330631","article-title":"Structural polymorphism of amyloid oligomers and fibrils underlies different fibrillization pathways: Immunogenicity and cytotoxicity","volume":"11","author":"Stefani","year":"2010","journal-title":"Curr. Protein Pept. Sci."},{"key":"ref_269","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1002\/pro.2544","article-title":"Physical and structural basis for polymorphism in amyloid fibrils","volume":"23","author":"Tycko","year":"2014","journal-title":"Protein Sci."},{"key":"ref_270","doi-asserted-by":"crossref","unstructured":"Riek, R. (2017). The Three-Dimensional Structures of Amyloids. Cold Spring Harb. Perspect. Biol., 9.","DOI":"10.1101\/cshperspect.a023572"},{"key":"ref_271","doi-asserted-by":"crossref","first-page":"5798","DOI":"10.1016\/j.cell.2023.11.025","article-title":"Structural evolution of fibril polymorphs during amyloid assembly","volume":"186","author":"Wilkinson","year":"2023","journal-title":"Cell"},{"key":"ref_272","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/s41594-018-0045-5","article-title":"Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2","volume":"25","author":"Guenther","year":"2018","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_273","doi-asserted-by":"crossref","unstructured":"Ostermeier, L., de Oliveira, G.A.P., Dzwolak, W., Silva, J.L., and Winter, R. (2021). Exploring the polymorphism, conformational dynamics and function of amyloidogenic peptides and proteins by temperature and pressure modulation. Biophys. Chem., 268.","DOI":"10.1016\/j.bpc.2020.106506"},{"key":"ref_274","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/s41583-022-00603-7","article-title":"Conformational strains of pathogenic amyloid proteins in neurodegenerative diseases","volume":"23","author":"Li","year":"2022","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_275","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1016\/j.str.2023.08.006","article-title":"Molecular rules governing the structural polymorphism of amyloid fibrils in neurodegenerative diseases","volume":"31","author":"Li","year":"2023","journal-title":"Structure"},{"key":"ref_276","doi-asserted-by":"crossref","unstructured":"Taylor, A.I.P., and Staniforth, R.A. (2022). General Principles Underpinning Amyloid Structure. Front. Neurosci., 16.","DOI":"10.3389\/fnins.2022.878869"},{"key":"ref_277","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/s41586-023-06788-w","article-title":"Disease-specific tau filaments assemble via polymorphic intermediates","volume":"625","author":"Li","year":"2024","journal-title":"Nature"},{"key":"ref_278","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1016\/j.neuron.2015.03.017","article-title":"Amyloid polymorphism: Structural basis and neurobiological relevance","volume":"86","author":"Tycko","year":"2015","journal-title":"Neuron"},{"key":"ref_279","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1152\/physrev.00006.2009","article-title":"Prions: Protein aggregation and infectious diseases","volume":"89","author":"Aguzzi","year":"2009","journal-title":"Physiol. Rev."},{"key":"ref_280","doi-asserted-by":"crossref","unstructured":"Igel-Egalon, A., B\u00e9ringue, V., Rezaei, H., and Sibille, P. (2018). Prion Strains and Transmission Barrier Phenomena. Pathogens, 7.","DOI":"10.3390\/pathogens7010005"},{"key":"ref_281","doi-asserted-by":"crossref","unstructured":"Arifin, M.I., Hannaoui, S., Chang, S.C., Thapa, S., Schatzl, H.M., and Gilch, S. (2021). Cervid Prion Protein Polymorphisms: Role in Chronic Wasting Disease Pathogenesis. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22052271"},{"key":"ref_282","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1007\/s00441-022-03700-2","article-title":"Prion assemblies: Structural heterogeneity, mechanisms of formation, and role in species barrier","volume":"392","author":"Igel","year":"2023","journal-title":"Cell Tissue Res."},{"key":"ref_283","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/s00441-021-03572-y","article-title":"Cell biology of prion strains in vivo and in vitro","volume":"392","author":"Shoup","year":"2022","journal-title":"Cell Tissue Res."},{"key":"ref_284","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.neuron.2009.12.016","article-title":"The transcellular spread of cytosolic amyloids, prions, and prionoids","volume":"64","author":"Aguzzi","year":"2009","journal-title":"Neuron"},{"key":"ref_285","doi-asserted-by":"crossref","first-page":"55","DOI":"10.4161\/pri.23061","article-title":"Prions, prionoids and pathogenic proteins in Alzheimer disease","volume":"7","author":"Ashe","year":"2013","journal-title":"Prion"},{"key":"ref_286","doi-asserted-by":"crossref","first-page":"fcac145","DOI":"10.1093\/braincomms\/fcac145","article-title":"Prionoids in amyotrophic lateral sclerosis","volume":"4","author":"Gosset","year":"2022","journal-title":"Brain Commun."},{"key":"ref_287","first-page":"w14424","article-title":"Prions, prionoid complexes and amyloids: The bad, the good and something in between","volume":"147","year":"2017","journal-title":"Swiss Med. Wkly."},{"key":"ref_288","doi-asserted-by":"crossref","unstructured":"Wells, C., Brennan, S.E., Keon, M., and Saksena, N.K. (2019). Prionoid Proteins in the Pathogenesis of Neurodegenerative Diseases. Front. Mol. Neurosci., 12.","DOI":"10.3389\/fnmol.2019.00271"},{"key":"ref_289","doi-asserted-by":"crossref","first-page":"1070","DOI":"10.1111\/mmi.12518","article-title":"Direct assessment in bacteria of prionoid propagation and phenotype selection by Hsp70 chaperone","volume":"91","author":"Coquel","year":"2014","journal-title":"Mol. Microbiol."},{"key":"ref_290","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1038\/nature23002","article-title":"Cryo-EM structures of tau filaments from Alzheimer\u2019s disease","volume":"547","author":"Fitzpatrick","year":"2017","journal-title":"Nature"},{"key":"ref_291","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1021\/acs.biochem.9b01069","article-title":"Structural Diversity of Amyloid Fibrils and Advances in Their Structure Determination","volume":"59","author":"Li","year":"2020","journal-title":"Biochemistry"},{"key":"ref_292","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.sbi.2019.05.003","article-title":"Cryo-EM of amyloid fibrils and cellular aggregates","volume":"58","author":"Fitzpatrick","year":"2019","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_293","doi-asserted-by":"crossref","first-page":"1900","DOI":"10.1126\/science.1150057","article-title":"Role of intermolecular forces in defining material properties of protein nanofibrils","volume":"318","author":"Knowles","year":"2007","journal-title":"Science"},{"key":"ref_294","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1007\/s00249-022-01600-5","article-title":"Amyloid fibril length distribution from dynamic light scattering data","volume":"51","author":"Sokolov","year":"2022","journal-title":"Eur. Biophys. J."},{"key":"ref_295","doi-asserted-by":"crossref","unstructured":"Sharma, S., Modi, P., Sharma, G., and Deep, S. (2021). Kinetics theories to understand the mechanism of aggregation of a protein and to design strategies for its inhibition. Biophys. Chem., 278.","DOI":"10.1016\/j.bpc.2021.106665"},{"key":"ref_296","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.ijbiomac.2016.06.052","article-title":"Kinetics of protein fibril formation: Methods and mechanisms","volume":"100","author":"Kumar","year":"2017","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_297","doi-asserted-by":"crossref","first-page":"2556","DOI":"10.1016\/j.bpj.2023.05.009","article-title":"Distinct growth regimes of alpha-synuclein amyloid elongation","volume":"122","author":"Horvath","year":"2023","journal-title":"Biophys. J."},{"key":"ref_298","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1126\/science.1178250","article-title":"An analytical solution to the kinetics of breakable filament assembly","volume":"326","author":"Knowles","year":"2009","journal-title":"Science"},{"key":"ref_299","doi-asserted-by":"crossref","first-page":"1205","DOI":"10.1038\/aps.2017.28","article-title":"Amyloid beta: Structure, biology and structure-based therapeutic development","volume":"38","author":"Chen","year":"2017","journal-title":"Acta Pharmacol. Sin."},{"key":"ref_300","doi-asserted-by":"crossref","unstructured":"Wu, J., Cao, C., Loch, R.A., Tiiman, A., and Luo, J. (2020). Single-molecule studies of amyloid proteins: From biophysical properties to diagnostic perspectives. Q. Rev. Biophys., 53.","DOI":"10.1017\/S0033583520000086"},{"key":"ref_301","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1146\/annurev-physchem-050317-021322","article-title":"Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation","volume":"69","author":"Michaels","year":"2018","journal-title":"Annu. Rev. Phys. Chem."},{"key":"ref_302","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/978-1-4939-7816-8_12","article-title":"Kinetic Analysis of Amyloid Formation","volume":"1779","author":"Meisl","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"ref_303","doi-asserted-by":"crossref","first-page":"12087","DOI":"10.1073\/pnas.1922267117","article-title":"Kinetic diversity of amyloid oligomers","volume":"117","author":"Dear","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_304","doi-asserted-by":"crossref","first-page":"7606","DOI":"10.1039\/C4CP05563B","article-title":"On the lag phase in amyloid fibril formation","volume":"17","author":"Arosio","year":"2015","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_305","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/416507a","article-title":"Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases","volume":"416","author":"Bucciantini","year":"2002","journal-title":"Nature"},{"key":"ref_306","doi-asserted-by":"crossref","first-page":"31374","DOI":"10.1074\/jbc.M400348200","article-title":"Prefibrillar amyloid protein aggregates share common features of cytotoxicity","volume":"279","author":"Bucciantini","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_307","doi-asserted-by":"crossref","first-page":"24251","DOI":"10.1073\/pnas.2006684117","article-title":"Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors","volume":"117","author":"Michaels","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_308","doi-asserted-by":"crossref","unstructured":"Sulatskaya, A.I., Rodina, N.P., Sulatsky, M.I., Povarova, O.I., Antifeeva, I.A., Kuznetsova, I.M., and Turoverov, K.K. (2018). Investigation of alpha-Synuclein Amyloid Fibrils Using the Fluorescent Probe Thioflavin T. Int. J. Mol. Sci., 19.","DOI":"10.20944\/preprints201806.0463.v1"},{"key":"ref_309","unstructured":"Pirt, S.J. (1975). Principles of microbe and cell cultivation, Wiley."},{"key":"ref_310","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/s12933-021-01359-7","article-title":"Persistent clotting protein pathology in Long COVID\/ Post-Acute Sequelae of COVID-19 (PASC) is accompanied by increased levels of antiplasmin","volume":"20","author":"Pretorius","year":"2021","journal-title":"Cardiovasc. Diabetol."},{"key":"ref_311","doi-asserted-by":"crossref","first-page":"3850","DOI":"10.2741\/2973","article-title":"Proteomic identification of novel proteins associated with Lewy bodies","volume":"13","author":"Xia","year":"2008","journal-title":"Front. Biosci."},{"key":"ref_312","doi-asserted-by":"crossref","first-page":"101771","DOI":"10.1016\/j.arr.2022.101771","article-title":"From protein biomarkers to proteomics in dementia with Lewy Bodies","volume":"83","author":"Tsamourgelis","year":"2023","journal-title":"Ageing Res. Rev."},{"key":"ref_313","doi-asserted-by":"crossref","first-page":"12473","DOI":"10.1073\/pnas.1610371113","article-title":"Cross-talk between amyloidogenic proteins in type-2 diabetes and Parkinson\u2019s disease","volume":"113","author":"Horvath","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_314","first-page":"819","article-title":"Crosstalk between Alpha-Synuclein and Other Human and Non-Human Amyloidogenic Proteins: Consequences for Amyloid Formation in Parkinson\u2019s Disease","volume":"10","author":"Werner","year":"2020","journal-title":"J. Park. Dis."},{"key":"ref_315","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.sbi.2021.07.009","article-title":"Gut power: Modulation of human amyloid formation by amyloidogenic proteins in the gastrointestinal tract","volume":"72","year":"2022","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_316","doi-asserted-by":"crossref","first-page":"7112","DOI":"10.1038\/s41467-021-27416-z","article-title":"Plasmin activity promotes amyloid deposition in a transgenic model of human transthyretin amyloidosis","volume":"12","author":"Slamova","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_317","doi-asserted-by":"crossref","first-page":"e1800059","DOI":"10.1002\/pmic.201800059","article-title":"Formation of Heterotypic Amyloids: Alpha-Synuclein in Co-Aggregation","volume":"18","author":"Bhasne","year":"2018","journal-title":"Proteomics"},{"key":"ref_318","doi-asserted-by":"crossref","first-page":"2508","DOI":"10.1016\/j.jmb.2018.04.020","article-title":"Synergistic Amyloid Switch Triggered by Early Heterotypic Oligomerization of Intrinsically Disordered alpha-Synuclein and Tau","volume":"430","author":"Bhasne","year":"2018","journal-title":"J. Mol. Biol."},{"key":"ref_319","doi-asserted-by":"crossref","first-page":"1759","DOI":"10.1021\/acschemneuro.5b00192","article-title":"Cross-Seeding Interaction between beta-Amyloid and Human Islet Amyloid Polypeptide","volume":"6","author":"Hu","year":"2015","journal-title":"ACS Chem. Neurosci."},{"key":"ref_320","doi-asserted-by":"crossref","unstructured":"Ivanova, M.I., Lin, Y., Lee, Y.H., Zheng, J., and Ramamoorthy, A. (2021). Biophysical processes underlying cross-seeding in amyloid aggregation and implications in amyloid pathology. Biophys. Chem., 269.","DOI":"10.1016\/j.bpc.2020.106507"},{"key":"ref_321","doi-asserted-by":"crossref","first-page":"6098","DOI":"10.1073\/pnas.0501814102","article-title":"Protein fibrils in nature can enhance amyloid protein A amyloidosis in mice: Cross-seeding as a disease mechanism","volume":"102","author":"Lundmark","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_322","doi-asserted-by":"crossref","unstructured":"Morales, R., Moreno-Gonzalez, I., and Soto, C. (2013). Cross-Seeding of Misfolded Proteins: Implications for Etiology and Pathogenesis of Protein Misfolding Diseases. PLoS Pathog., 9.","DOI":"10.1371\/journal.ppat.1003537"},{"key":"ref_323","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1111\/j.1471-4159.2012.07847.x","article-title":"Cross-seeding effects of amyloid beta-protein and alpha-synuclein","volume":"122","author":"Ono","year":"2012","journal-title":"J. Neurochem."},{"key":"ref_324","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1016\/j.ajpath.2014.11.016","article-title":"In vivo seeding and cross-seeding of localized amyloidosis: A molecular link between type 2 diabetes and Alzheimer disease","volume":"185","author":"Oskarsson","year":"2015","journal-title":"Am. J. Pathol."},{"key":"ref_325","doi-asserted-by":"crossref","unstructured":"Subedi, S., Sasidharan, S., Nag, N., Saudagar, P., and Tripathi, T. (2022). Amyloid Cross-Seeding: Mechanism, Implication, and Inhibition. Molecules, 27.","DOI":"10.3390\/molecules27061776"},{"key":"ref_326","doi-asserted-by":"crossref","first-page":"23245","DOI":"10.1039\/C5CP03329B","article-title":"Polymorphic cross-seeding amyloid assemblies of amyloid-beta and human islet amyloid polypeptide","volume":"17","author":"Zhang","year":"2015","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_327","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1021\/acs.biomac.2c01233","article-title":"Amyloid Protein Cross-Seeding Provides a New Perspective on Multiple Diseases In Vivo","volume":"24","author":"Ge","year":"2023","journal-title":"Biomacromolecules"},{"key":"ref_328","doi-asserted-by":"crossref","first-page":"3300","DOI":"10.1039\/D0TB02958K","article-title":"Dual amyloid cross-seeding reveals steric zipper-facilitated fibrillization and pathological links between protein misfolding diseases","volume":"9","author":"Zhang","year":"2021","journal-title":"J. Mater. Chem. B"},{"key":"ref_329","doi-asserted-by":"crossref","first-page":"7267","DOI":"10.1039\/C9TB01871A","article-title":"Fundamentals of cross-seeding of amyloid proteins: An introduction","volume":"7","author":"Ren","year":"2019","journal-title":"J. Mater. Chem. B"},{"key":"ref_330","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1007\/978-1-4939-7811-3_27","article-title":"Experimental and Computational Protocols for Studies of Cross-Seeding Amyloid Assemblies","volume":"1777","author":"Ren","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"ref_331","doi-asserted-by":"crossref","first-page":"736","DOI":"10.3724\/abbs.2023081","article-title":"Coaggregation of polyglutamine (polyQ) proteins is mediated by polyQ-tract interactions and impairs cellular proteostasis","volume":"55","author":"Hong","year":"2023","journal-title":"Acta Biochim. Biophys. Sin."},{"key":"ref_332","doi-asserted-by":"crossref","first-page":"100937","DOI":"10.1016\/j.arr.2019.100937","article-title":"Amyloid cross-seeding raises new dimensions to understanding of amyloidogenesis mechanism","volume":"56","author":"Chaudhuri","year":"2019","journal-title":"Ageing Res. Rev."},{"key":"ref_333","doi-asserted-by":"crossref","first-page":"e22493","DOI":"10.1096\/fj.202200235R","article-title":"Interactions of amyloid coaggregates with biomolecules and its relevance to neurodegeneration","volume":"36","author":"Murakami","year":"2022","journal-title":"FASEB J."},{"key":"ref_334","doi-asserted-by":"crossref","first-page":"a024323","DOI":"10.1101\/cshperspect.a024323","article-title":"Noncerebral Amyloidoses: Aspects on Seeding, Cross-Seeding, and Transmission","volume":"8","author":"Westermark","year":"2018","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_335","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1111\/j.1471-4159.2005.03444.x","article-title":"Cross-seeding of wild-type and hereditary variant-type amyloid beta-proteins in the presence of gangliosides","volume":"95","author":"Yamamoto","year":"2005","journal-title":"J. Neurochem."},{"key":"ref_336","doi-asserted-by":"crossref","first-page":"1801","DOI":"10.1110\/ps.062116206","article-title":"Mutagenic exploration of the cross-seeding and fibrillation propensity of Alzheimer\u2019s beta-amyloid peptide variants","volume":"15","author":"Peim","year":"2006","journal-title":"Protein Sci."},{"key":"ref_337","doi-asserted-by":"crossref","first-page":"229","DOI":"10.3109\/13506129.2011.630761","article-title":"Signs of cross-seeding: Aortic medin amyloid as a trigger for protein AA deposition","volume":"18","author":"Larsson","year":"2011","journal-title":"Amyloid"},{"key":"ref_338","doi-asserted-by":"crossref","first-page":"35092","DOI":"10.1074\/jbc.M112.383737","article-title":"Promiscuous cross-seeding between bacterial amyloids promotes interspecies biofilms","volume":"287","author":"Zhou","year":"2012","journal-title":"J. Biol. Chem."},{"key":"ref_339","doi-asserted-by":"crossref","first-page":"e5","DOI":"10.7717\/peerj.5","article-title":"Bacterial curli protein promotes the conversion of PAP248-286 into the amyloid SEVI: Cross-seeding of dissimilar amyloid sequences","volume":"1","author":"Hartman","year":"2013","journal-title":"PeerJ"},{"key":"ref_340","doi-asserted-by":"crossref","first-page":"7026","DOI":"10.1021\/jp5022246","article-title":"Structural and energetic insight into the cross-seeding amyloid assemblies of human IAPP and rat IAPP","volume":"118","author":"Zhang","year":"2014","journal-title":"J. Phys. Chem. B"},{"key":"ref_341","doi-asserted-by":"crossref","first-page":"1628","DOI":"10.1021\/acs.jcim.5b00166","article-title":"Polymorphic Associations and Structures of the Cross-Seeding of Abeta1-42 and hIAPP1-37 Polypeptides","volume":"55","author":"Zhang","year":"2015","journal-title":"J. Chem. Inf. Model."},{"key":"ref_342","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1080\/19336896.2016.1176659","article-title":"Wild type huntingtin toxicity in yeast: Implications for the role of amyloid cross-seeding in polyQ diseases","volume":"10","author":"Alexandrov","year":"2016","journal-title":"Prion"},{"key":"ref_343","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1021\/acsomega.6b00559","article-title":"Seed-Induced Heterogeneous Cross-Seeding Self-Assembly of Human and Rat Islet Polypeptides","volume":"2","author":"Hu","year":"2017","journal-title":"ACS Omega"},{"key":"ref_344","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1021\/acschemneuro.6b00247","article-title":"Molecular Understanding of Abeta-hIAPP Cross-Seeding Assemblies on Lipid Membranes","volume":"8","author":"Zhang","year":"2017","journal-title":"ACS Chem. Neurosci."},{"key":"ref_345","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.bbrc.2018.04.198","article-title":"Abeta(1-40) mediated aggregation of proteins and metabolites unveils the relevance of amyloid cross-seeding in amyloidogenesis","volume":"501","author":"Anand","year":"2018","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_346","first-page":"793","article-title":"Possible Role of Amyloid Cross-Seeding in Evolvability and Neurodegenerative Disease","volume":"9","author":"Hashimoto","year":"2019","journal-title":"J. Park. Dis."},{"key":"ref_347","doi-asserted-by":"crossref","unstructured":"Bardin, T., Daskalov, A., Barrouilhet, S., Granger-Farbos, A., Salin, B., Blancard, C., Kauffmann, B., Saupe, S.J., and Coustou, V. (2021). Partial Prion Cross-Seeding between Fungal and Mammalian Amyloid Signaling Motifs. mBio, 12.","DOI":"10.1128\/mBio.02782-20"},{"key":"ref_348","doi-asserted-by":"crossref","first-page":"e2014085118","DOI":"10.1073\/pnas.2014085118","article-title":"Structural and molecular basis of cross-seeding barriers in amyloids","volume":"118","author":"Daskalov","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_349","doi-asserted-by":"crossref","first-page":"e2104148118","DOI":"10.1073\/pnas.2104148118","article-title":"Amyloid particles facilitate surface-catalyzed cross-seeding by acting as promiscuous nanoparticles","volume":"118","author":"Aubrey","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_350","doi-asserted-by":"crossref","unstructured":"Nirwal, S., Bharathi, V., and Patel, B.K. (2021). Amyloid-like aggregation of bovine serum albumin at physiological temperature induced by cross-seeding effect of HEWL amyloid aggregates. Biophys. Chem., 278.","DOI":"10.1016\/j.bpc.2021.106678"},{"key":"ref_351","doi-asserted-by":"crossref","unstructured":"Vaneyck, J., Segers-Nolten, I., Broersen, K., and Claessens, M.M.A.E. (2021). Cross-seeding of alpha-synuclein aggregation by amyloid fibrils of food proteins. J. Biol. Chem., 296.","DOI":"10.1016\/j.jbc.2021.100358"},{"key":"ref_352","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1016\/j.bpj.2020.12.005","article-title":"Multistep Changes in Amyloid Structure Induced by Cross-Seeding on a Rugged Energy Landscape","volume":"120","author":"Yuzu","year":"2021","journal-title":"Biophys. J."},{"key":"ref_353","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1002\/pro.4247","article-title":"A new strategy to reconcile amyloid cross-seeding and amyloid prevention in a binary system of alpha-synuclein fragmental peptide and hIAPP","volume":"31","author":"Tang","year":"2022","journal-title":"Protein Sci."},{"key":"ref_354","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1021\/acschemneuro.2c00712","article-title":"Atrial Natriuretic Peptide Associated with Cardiovascular Diseases Inhibits Amyloid-beta Aggregation via Cross-Seeding","volume":"14","author":"Tang","year":"2023","journal-title":"ACS Chem. Neurosci."},{"key":"ref_355","doi-asserted-by":"crossref","first-page":"3143","DOI":"10.1021\/acschemneuro.3c00293","article-title":"Repurposing Antimicrobial Protegrin-1 as a Dual-Function Amyloid Inhibitor via Cross-seeding","volume":"14","author":"Tang","year":"2023","journal-title":"ACS Chem. Neurosci."},{"key":"ref_356","doi-asserted-by":"crossref","first-page":"5303","DOI":"10.1021\/acs.jcim.4c00859","article-title":"Computational Investigation of Coaggregation and Cross-Seeding between Abeta and hIAPP Underpinning the Cross-Talk in Alzheimer\u2019s Disease and Type 2 Diabetes","volume":"64","author":"Fan","year":"2024","journal-title":"J. Chem. Inf. Model."},{"key":"ref_357","doi-asserted-by":"crossref","unstructured":"Wang, Y., Bergstrom, J., Ingelsson, M., and Westermark, G.T. (2023). Studies on alpha-synuclein and islet amyloid polypeptide interaction. Front. Mol. Biosci., 10.","DOI":"10.3389\/fmolb.2023.1080112"},{"key":"ref_358","doi-asserted-by":"crossref","unstructured":"Wang, Y., and Westermark, G.T. (2021). The Amyloid Forming Peptides Islet Amyloid Polypeptide and Amyloid beta Interact at the Molecular Level. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222011153"},{"key":"ref_359","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1006\/jmbi.2001.4850","article-title":"Polyglutamine aggregation behavior in vitro supports a recruitment mechanism of cytotoxicity","volume":"311","author":"Chen","year":"2001","journal-title":"J. Mol. Biol."},{"key":"ref_360","doi-asserted-by":"crossref","first-page":"7391","DOI":"10.1021\/bi011772q","article-title":"Amyloid-like features of polyglutamine aggregates and their assembly kinetics","volume":"41","author":"Chen","year":"2002","journal-title":"Biochemistry"},{"key":"ref_361","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.jmb.2011.06.045","article-title":"Structural characterization of polyglutamine fibrils by solid-state NMR spectroscopy","volume":"412","author":"Schneider","year":"2011","journal-title":"J. Mol. Biol."},{"key":"ref_362","doi-asserted-by":"crossref","first-page":"3012","DOI":"10.1021\/acs.jpcb.5b11380","article-title":"Polyglutamine Fibrils: New Insights into Antiparallel beta-Sheet Conformational Preference and Side Chain Structure","volume":"120","author":"Punihaole","year":"2016","journal-title":"J. Phys. Chem. B"},{"key":"ref_363","doi-asserted-by":"crossref","first-page":"2134","DOI":"10.1016\/j.bpj.2014.03.047","article-title":"Conformational switching in PolyGln amyloid fibrils resulting from a single amino acid insertion","volume":"106","author":"Huang","year":"2014","journal-title":"Biophys. J."},{"key":"ref_364","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1007\/s00204-010-0577-x","article-title":"Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson\u2019s, Huntington\u2019s, Alzheimer\u2019s, prions, bactericides, chemical toxicology and others as examples","volume":"577","author":"Kell","year":"2010","journal-title":"Arch. Toxicol."},{"key":"ref_365","doi-asserted-by":"crossref","unstructured":"Bondarev, S.A., Antonets, K.S., Kajava, A.V., Nizhnikov, A.A., and Zhouravleva, G.A. (2018). Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification. Int. J. Mol. Sci., 19.","DOI":"10.3390\/ijms19082292"},{"key":"ref_366","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1096\/fj.09-145979","article-title":"Beta arcades: Recurring motifs in naturally occurring and disease-related amyloid fibrils","volume":"24","author":"Kajava","year":"2010","journal-title":"FASEB J."},{"key":"ref_367","doi-asserted-by":"crossref","first-page":"12741","DOI":"10.1002\/anie.201304699","article-title":"The conformation of the prion domain of Sup35p in isolation and in the full-length protein","volume":"52","author":"Luckgei","year":"2013","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_368","doi-asserted-by":"crossref","first-page":"17342","DOI":"10.1073\/pnas.0506723102","article-title":"3D structure of Alzheimer\u2019s amyloid-beta(1-42) fibrils","volume":"102","author":"Ritter","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_369","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.1042\/BST20120160","article-title":"Evolutionary selection for protein aggregation","volume":"40","author":"Torrent","year":"2012","journal-title":"Biochem. Soc. Trans."},{"key":"ref_370","doi-asserted-by":"crossref","unstructured":"Weirich, F., Gremer, L., Mirecka, E.A., Schiefer, S., Hoyer, W., and Heise, H. (2016). Structural Characterization of Fibrils from Recombinant Human Islet Amyloid Polypeptide by Solid-State NMR: The Central FGAILS Segment Is Part of the beta-Sheet Core. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0161243"},{"key":"ref_371","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.cell.2012.06.019","article-title":"The RIP1\/RIP3 necrosome forms a functional amyloid signaling complex required for programmed necrosis","volume":"150","author":"Li","year":"2012","journal-title":"Cell"},{"key":"ref_372","doi-asserted-by":"crossref","unstructured":"Kajava, A.V., Klopffleisch, K., Chen, S., and Hofmann, K. (2014). Evolutionary link between metazoan RHIM motif and prion-forming domain of fungal heterokaryon incompatibility factor HET-s\/HET-s. Sci. Rep., 4.","DOI":"10.1038\/srep07436"},{"key":"ref_373","doi-asserted-by":"crossref","unstructured":"Azizyan, R.A., Wang, W., Anikeenko, A., Radkova, Z., Bakulina, A., Garro, A., Charlier, L., Dumas, C., Ventura, S., and Kajava, A.V. (2020). Amyloidogenicity as a driving force for the formation of functional oligomers. J. Struct. Biol., 212.","DOI":"10.1016\/j.jsb.2020.107604"},{"key":"ref_374","doi-asserted-by":"crossref","first-page":"21812","DOI":"10.1073\/pnas.1010373107","article-title":"Alzheimer\u2019s disease peptide beta-amyloid interacts with fibrinogen and induces its oligomerization","volume":"107","author":"Ahn","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_375","doi-asserted-by":"crossref","unstructured":"Biza, K.V., Nastou, K.C., Tsiolaki, P.L., Mastrokalou, C.V., Hamodrakas, S.J., and Iconomidou, V.A. (2017). The amyloid interactome: Exploring protein aggregation. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0173163"},{"key":"ref_376","doi-asserted-by":"crossref","unstructured":"Kell, D.B., and Pretorius, E. (2024). Proteomic evidence for amyloidogenic cross-seeding in fibrinaloid microclots. bioRxiv.","DOI":"10.1101\/2024.07.16.603837"},{"key":"ref_377","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1186\/s12933-022-01623-4","article-title":"Proteomics of fibrin amyloid microclots in Long COVID\/ Post-Acute Sequelae of COVID-19 (PASC) shows many entrapped pro-inflammatory molecules that may also contribute to a failed fibrinolytic system","volume":"21","author":"Kruger","year":"2022","journal-title":"Cardiovasc. Diabetol."},{"key":"ref_378","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1373\/clinchem.2008.108175","article-title":"High-abundance polypeptides of the human plasma proteome comprising the top 4 logs of polypeptide abundance","volume":"54","author":"Hortin","year":"2008","journal-title":"Clin. Chem."},{"key":"ref_379","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1074\/mcp.R200007-MCP200","article-title":"The human plasma proteome: History, character, and diagnostic prospects","volume":"1","author":"Anderson","year":"2002","journal-title":"Mol. Cell. Proteom."},{"key":"ref_380","doi-asserted-by":"crossref","unstructured":"Khan, S.A., Joyce, J., and Tsuda, T. (2012). Quantification of active and total transforming growth factor-beta levels in serum and solid organ tissues by bioassay. BMC Res. Notes, 5.","DOI":"10.1186\/1756-0500-5-636"},{"key":"ref_381","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s11033-011-0746-x","article-title":"Periostin gene polymorphisms, protein levels and risk of incident coronary artery disease","volume":"39","author":"Wang","year":"2012","journal-title":"Mol. Biol. Rep."},{"key":"ref_382","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/0009-8981(83)90187-0","article-title":"Immunoradiometric assay for human complement component C9 utilising monoclonal antibodies","volume":"134","author":"Morgan","year":"1983","journal-title":"Clin. Chim. Acta"},{"key":"ref_383","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0022-1759(85)90161-9","article-title":"Measurement of C9 concentrations using an immunochemiluminometric assay","volume":"80","author":"Weeks","year":"1985","journal-title":"J. Immunol. Methods"},{"key":"ref_384","doi-asserted-by":"crossref","first-page":"46","DOI":"10.3390\/biom2010046","article-title":"Factor H: A complement regulator in health and disease, and a mediator of cellular interactions","volume":"2","author":"Kopp","year":"2012","journal-title":"Biomolecules"},{"key":"ref_385","unstructured":"Feingold, K.R., Anawalt, B., Blackman, M.R., Boyce, A., Chrousos, G., Corpas, E., de Herder, W.W., Dhatariya, K., Dungan, K., and Hofland, J. (2000). Thyroid Hormone Serum Transport Proteins. Endotext, MDText.com, Inc."},{"key":"ref_386","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.1172\/JCI105889","article-title":"Retinol-binding protein: The transport protein for vitamin A in human plasma","volume":"47","author":"Kanai","year":"1968","journal-title":"J. Clin. Investig."},{"key":"ref_387","doi-asserted-by":"crossref","unstructured":"Li, L., Zhang, L., Tian, Y., Zhang, T., Duan, G., Liu, Y., Yin, Y., Hua, D., Qi, X., and Mao, Y. (2019). Serum Chemokine CXCL7 as a Diagnostic Biomarker for Colorectal Cancer. Front. Oncol., 9.","DOI":"10.3389\/fonc.2019.00921"},{"key":"ref_388","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1055\/s-0040-1710013","article-title":"Role of Factor XIa and Plasma Kallikrein in Arterial and Venous Thrombosis","volume":"120","author":"Visser","year":"2020","journal-title":"Thromb. Haemost."},{"key":"ref_389","doi-asserted-by":"crossref","first-page":"e000026","DOI":"10.1136\/lupus-2014-000026","article-title":"Plasma levels of galectin-3-binding protein reflect type I interferon activity and are increased in patients with systemic lupus erythematosus","volume":"1","author":"Nielsen","year":"2014","journal-title":"Lupus Sci. Med."},{"key":"ref_390","doi-asserted-by":"crossref","first-page":"3515","DOI":"10.2147\/DDDT.S218428","article-title":"Thrombospondin-1 Serum Levels In Hypertensive Patients with Endothelial Dysfunction after One Year Of Treatment with Perindopril","volume":"13","author":"Buda","year":"2019","journal-title":"Drug Des. Dev. Ther."},{"key":"ref_391","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.1021\/acs.jproteome.4c00064","article-title":"Longitudinal Fluctuations in Protein Concentrations and Higher-Order Structures in the Plasma Proteome of Kidney Failure Patients Subjected to a Kidney Transplant","volume":"23","author":"Lukassen","year":"2024","journal-title":"J. Proteome Res."},{"key":"ref_392","doi-asserted-by":"crossref","unstructured":"Park, J.C., Han, S.H., Lee, H., Jeong, H., Byun, M.S., Bae, J., Kim, H., Lee, D.Y., Yi, D., and Shin, S.A. (2019). Prognostic plasma protein panel for Abeta deposition in the brain in Alzheimer\u2019s disease. Prog. Neurobiol., 183.","DOI":"10.1016\/j.pneurobio.2019.101690"},{"key":"ref_393","doi-asserted-by":"crossref","first-page":"3214","DOI":"10.1016\/j.neurobiolaging.2015.09.005","article-title":"Thrombospondin-1 prevents amyloid beta-mediated synaptic pathology in Alzheimer\u2019s disease","volume":"36","author":"Son","year":"2015","journal-title":"Neurobiol. Aging"},{"key":"ref_394","doi-asserted-by":"crossref","first-page":"207","DOI":"10.3109\/03602532.2014.882354","article-title":"Atomic force microscopy to study molecular mechanisms of amyloid fibril formation and toxicity in Alzheimer\u2019s disease","volume":"46","author":"Drolle","year":"2014","journal-title":"Drug Metab. Rev."},{"key":"ref_395","doi-asserted-by":"crossref","first-page":"3789","DOI":"10.1021\/acs.nanolett.1c00058","article-title":"Nanoaggregates Derived from Amyloid-beta and Alpha-synuclein Characterized by Sequential Quadruple Force Mapping","volume":"21","author":"Shin","year":"2021","journal-title":"Nano Lett."},{"key":"ref_396","doi-asserted-by":"crossref","first-page":"18276","DOI":"10.1021\/jacs.3c03212","article-title":"alpha-Synuclein Aggregation Is Triggered by Oligomeric Amyloid-beta 42 via Heterogeneous Primary Nucleation","volume":"145","author":"Vadukul","year":"2023","journal-title":"J. Am. Chem. Soc."},{"key":"ref_397","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/S1474-4422(05)70284-2","article-title":"Risk of dementia in diabetes mellitus: A systematic review","volume":"5","author":"Biessels","year":"2006","journal-title":"Lancet Neurol."},{"key":"ref_398","doi-asserted-by":"crossref","first-page":"6270","DOI":"10.1021\/acs.biochem.8b00841","article-title":"Human Fibrinogen Inhibits Amyloid Assembly of Biofilm-Forming CsgA","volume":"57","author":"Swasthi","year":"2018","journal-title":"Biochemistry"},{"key":"ref_399","doi-asserted-by":"crossref","first-page":"21960","DOI":"10.1021\/acsomega.1c02333","article-title":"Human Fibrinogen Inhibits Amyloid Assembly of Most Phenol-Soluble Modulins from Staphylococcus aureus","volume":"6","author":"Najarzadeh","year":"2021","journal-title":"ACS Omega"},{"key":"ref_400","doi-asserted-by":"crossref","first-page":"112217","DOI":"10.1016\/j.yexcr.2020.112217","article-title":"SERPINA1 modulates expression of amyloidogenic transthyretin","volume":"395","author":"Niemietz","year":"2020","journal-title":"Exp. Cell Res."},{"key":"ref_401","doi-asserted-by":"crossref","unstructured":"Bezerra, F., Niemietz, C., Schmidt, H.H.J., Zibert, A., Guo, S., Monia, B.P., Goncalves, P., Saraiva, M.J., and Almeida, M.R. (2021). In Vitro and In Vivo Effects of SerpinA1 on the Modulation of Transthyretin Proteolysis. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22179488"},{"key":"ref_402","doi-asserted-by":"crossref","first-page":"jcs.219824","DOI":"10.1242\/jcs.219824","article-title":"Hepatocyte-like cells reveal novel role of SERPINA1 in transthyretin amyloidosis","volume":"131","author":"Niemietz","year":"2018","journal-title":"J. Cell Sci."},{"key":"ref_403","doi-asserted-by":"crossref","unstructured":"Berndsen, Z.T., and Cassidy, C.K. (2024). The Structure of ApoB100 from Human Low-density Lipoprotein. bioRxiv.","DOI":"10.1101\/2024.02.28.582555"},{"key":"ref_404","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/0304-3940(92)90531-B","article-title":"Apolipoprotein B immunoreactivity in senile plaque and vascular amyloids and neurofibrillary tangles in the brains of patients with Alzheimer\u2019s disease","volume":"134","author":"Namba","year":"1992","journal-title":"Neurosci. Lett."},{"key":"ref_405","doi-asserted-by":"crossref","unstructured":"Grobler, C., Maphumulo, S.C., Grobbelaar, L.M., Bredenkamp`, J., Laubscher, J., Lourens, P.J., Steenkamp, J., Kell, D.B., and Pretorius, E. (2020). COVID-19: The Rollercoaster of Fibrin(ogen), D-dimer, von Willebrand Factor, P-selectin and Their Interactions with Endothelial Cells, Platelets and Erythrocytes. Int. J. Mol. Sci., 21.","DOI":"10.20944\/preprints202007.0142.v1"},{"key":"ref_406","first-page":"904","article-title":"Serum Adiponectin and In Vivo Brain Amyloid Deposition in Cognitively Normal Older Adults: A Cohort Study","volume":"14","author":"Kim","year":"2023","journal-title":"Aging Dis."},{"key":"ref_407","doi-asserted-by":"crossref","unstructured":"Chan, K.H., Lam, K.S., Cheng, O.Y., Kwan, J.S., Ho, P.W., Cheng, K.K., Chung, S.K., Ho, J.W., Guo, V.Y., and Xu, A. (2012). Adiponectin is protective against oxidative stress induced cytotoxicity in amyloid-beta neurotoxicity. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0052354"},{"key":"ref_408","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/s41420-017-0023-4","article-title":"Thrombospondin-1 protects against Abeta-induced mitochondrial fragmentation and dysfunction in hippocampal cells","volume":"4","author":"Kang","year":"2018","journal-title":"Cell Death Discov."},{"key":"ref_409","doi-asserted-by":"crossref","unstructured":"Kim, D.H., Lim, H., Lee, D., Choi, S.J., Oh, W., Yang, Y.S., Oh, J.S., Hwang, H.H., and Jeon, H.B. (2018). Thrombospondin-1 secreted by human umbilical cord blood-derived mesenchymal stem cells rescues neurons from synaptic dysfunction in Alzheimer\u2019s disease model. Sci. Rep., 8.","DOI":"10.1038\/s41598-017-18542-0"},{"key":"ref_410","doi-asserted-by":"crossref","unstructured":"Singh, S., Saleem, S., and Reed, G.L. (2020). Alpha2-Antiplasmin: The Devil You Don\u2019t Know in Cerebrovascular and Cardiovascular Disease. Front. Cardiovasc. Med., 7.","DOI":"10.3389\/fcvm.2020.608899"},{"key":"ref_411","doi-asserted-by":"crossref","first-page":"8951","DOI":"10.1021\/bi00449a001","article-title":"Implications of the three-dimensional structure of alpha 1-antitrypsin for structure and function of serpins","volume":"28","author":"Huber","year":"1989","journal-title":"Biochemistry"},{"key":"ref_412","doi-asserted-by":"crossref","first-page":"4751","DOI":"10.1021\/cr010170+","article-title":"Serpin structure, mechanism, and function","volume":"102","author":"Gettins","year":"2002","journal-title":"Chem. Rev."},{"key":"ref_413","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1111\/j.1538-7836.2011.04360.x","article-title":"Serpin structure, function and dysfunction","volume":"9","author":"Huntington","year":"2011","journal-title":"J. Thromb. Haemost."},{"key":"ref_414","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1111\/joim.12239","article-title":"Role of alpha-1 antitrypsin in human health and disease","volume":"276","author":"Blanco","year":"2014","journal-title":"J. Intern. Med."},{"key":"ref_415","doi-asserted-by":"crossref","first-page":"15674","DOI":"10.1074\/jbc.M116.727826","article-title":"Molecular Mechanism of Z alpha1-Antitrypsin Deficiency","volume":"291","author":"Huang","year":"2016","journal-title":"J. Biol. Chem."},{"key":"ref_416","doi-asserted-by":"crossref","first-page":"9264","DOI":"10.1074\/jbc.M311731200","article-title":"alpha1-Proteinase inhibitor forms initial non-covalent and final covalent complexes with elastase analogously to other serpin-proteinase pairs, suggesting a common mechanism of inhibition","volume":"279","author":"Gettins","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_417","doi-asserted-by":"crossref","first-page":"288","DOI":"10.2741\/1528","article-title":"A protein family under \u2018stress\u2019\u2014Serpin stability, folding and misfolding","volume":"10","author":"Devlin","year":"2005","journal-title":"Front. Biosci."},{"key":"ref_418","doi-asserted-by":"crossref","first-page":"12425","DOI":"10.1074\/jbc.M111.315465","article-title":"How the serpin alpha1-proteinase inhibitor folds","volume":"287","author":"Dolmer","year":"2012","journal-title":"J. Biol. Chem."},{"key":"ref_419","first-page":"253","article-title":"Analysis of the expression of the Serpina1 gene in SARS-CoV-2 infection: Study of a new biomarker","volume":"224","year":"2024","journal-title":"Rev. Cl\u00ednica Espa\u00f1ola"},{"key":"ref_420","doi-asserted-by":"crossref","first-page":"245ra292","DOI":"10.1126\/scitranslmed.3008808","article-title":"Protein misfolding, congophilia, oligomerization, and defective amyloid processing in preeclampsia","volume":"6","author":"Buhimschi","year":"2014","journal-title":"Sci. Transl. Med."},{"key":"ref_421","doi-asserted-by":"crossref","first-page":"2990","DOI":"10.1039\/C6CP07145G","article-title":"Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: Consideration as a possible model","volume":"19","author":"Kouza","year":"2017","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_422","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.resinv.2014.12.003","article-title":"Serum level of periostin can predict long-term outcome of idiopathic pulmonary fibrosis","volume":"53","author":"Tajiri","year":"2015","journal-title":"Respir. Investig."},{"key":"ref_423","doi-asserted-by":"crossref","first-page":"2116","DOI":"10.1111\/all.13814","article-title":"Periostin: An emerging biomarker for allergic diseases","volume":"74","author":"Izuhara","year":"2019","journal-title":"Allergy"},{"key":"ref_424","doi-asserted-by":"crossref","unstructured":"Yoshihara, T., Morimoto, T., Hirata, H., Murayama, M., Nonaka, T., Tsukamoto, M., Toda, Y., Kobayashi, T., Izuhara, K., and Mawatari, M. (2023). Mechanisms of tissue degeneration mediated by periostin in spinal degenerative diseases and their implications for pathology and diagnosis: A review. Front. Med., 10.","DOI":"10.3389\/fmed.2023.1276900"},{"key":"ref_425","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1067\/mob.2002.118157","article-title":"Novel chemiluminescence assay for serum periostin levels in women with preeclampsia and in normotensive pregnant women","volume":"186","author":"Sasaki","year":"2002","journal-title":"Am. J. Obstet. Gynecol."},{"key":"ref_426","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/s12276-021-00719-3","article-title":"Application of QPLEX(TM) biomarkers in cognitively normal individuals across a broad age range and diverse regions with cerebral amyloid deposition","volume":"54","author":"Lee","year":"2022","journal-title":"Exp. Mol. Med."},{"key":"ref_427","doi-asserted-by":"crossref","first-page":"L1046","DOI":"10.1152\/ajplung.00139.2012","article-title":"Periostin promotes fibrosis and predicts progression in patients with idiopathic pulmonary fibrosis","volume":"303","author":"Naik","year":"2012","journal-title":"Am. J. Physiol. Lung Cell Mol. Physiol."},{"key":"ref_428","doi-asserted-by":"crossref","first-page":"4305","DOI":"10.1007\/s00018-017-2649-z","article-title":"The role of periostin in lung fibrosis and airway remodeling","volume":"74","author":"Moore","year":"2017","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_429","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1515\/med-2017-0044","article-title":"The Effective Regulation of Pro- and Anti-inflammatory Cytokines Induced by Combination of PA-MSHA and BPIFB1 in Initiation of Innate Immune Responses","volume":"12","author":"Zhou","year":"2017","journal-title":"Open Med."},{"key":"ref_430","doi-asserted-by":"crossref","first-page":"651","DOI":"10.21037\/atm-20-3462","article-title":"Molecular biology of BPIFB1 and its advances in disease","volume":"8","author":"Li","year":"2020","journal-title":"Ann. Transl. Med."},{"key":"ref_431","doi-asserted-by":"crossref","unstructured":"Pretorius, E., Page, M.J., Mbotwe, S., and Kell, D.B. (2018). Lipopolysaccharide-binding protein (LBP) can reverse the amyloid state of fibrin seen or induced in Parkinson\u2019s disease. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0192121"},{"key":"ref_432","first-page":"356","article-title":"Overexpression of BPIFB1 promotes apoptosis and inhibits proliferation via the MEK\/ERK signal pathway in nasopharyngeal carcinoma","volume":"12","author":"Xu","year":"2019","journal-title":"Int. J. Clin. Exp. Pathol."},{"key":"ref_433","doi-asserted-by":"crossref","unstructured":"Cai, J., Xiao, L., Liu, J., Wang, D., Zhou, Y., Liao, Z., and Chen, G. (2024). BPIFB1, Serving as a Downstream Effector of EBV-miR-BART4, Blocks Immune Escape of Nasopharyngeal Carcinoma via Inhibiting PD-L1 Expression. Biochem. Genet.","DOI":"10.1007\/s10528-024-10719-3"},{"key":"ref_434","doi-asserted-by":"crossref","unstructured":"Richardo, T., Prattapong, P., Ngernsombat, C., Wisetyaningsih, N., Iizasa, H., Yoshiyama, H., and Janvilisri, T. (2020). Epstein-Barr Virus Mediated Signaling in Nasopharyngeal Carcinoma Carcinogenesis. Cancers, 12.","DOI":"10.3390\/cancers12092441"},{"key":"ref_435","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/s41579-022-00846-2","article-title":"Long COVID: Major findings, mechanisms and recommendations","volume":"21","author":"Davis","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_436","doi-asserted-by":"crossref","unstructured":"Bohmwald, K., Diethelm-Varela, B., Rodr\u00edguez-Guilarte, L., Rivera, T., Riedel, C.A., Gonz\u00e1lez, P.A., and Kalergis, A.M. (2024). Pathophysiological, immunological, and inflammatory features of long COVID. Front. Immunol., 15.","DOI":"10.3389\/fimmu.2024.1341600"},{"key":"ref_437","doi-asserted-by":"crossref","first-page":"eadg7942","DOI":"10.1126\/science.adg7942","article-title":"Persistent complement dysregulation with signs of thromboinflammation in active Long Covid","volume":"383","author":"Bruningk","year":"2024","journal-title":"Science"},{"key":"ref_438","doi-asserted-by":"crossref","first-page":"103487","DOI":"10.1016\/j.jprot.2019.103487","article-title":"Plasma fibrin clot proteomics in healthy subjects: Relation to clot permeability and lysis time","volume":"208","author":"Stachowicz","year":"2019","journal-title":"J. Proteom."},{"key":"ref_439","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1136\/jcp.34.5.504","article-title":"Plasma fibronectin in normal subjects and in various disease states","volume":"34","author":"Stathakis","year":"1981","journal-title":"J. Clin. Pathol."},{"key":"ref_440","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1161\/01.ATV.0000223342.15969.7a","article-title":"Plasma fibronectin concentration: A risk factor for arterial thrombosis?","volume":"26","author":"Mosher","year":"2006","journal-title":"Arterioscler. Thromb. Vasc. Biol."},{"key":"ref_441","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.cca.2016.09.024","article-title":"Plasma concentration of fibronectin is decreased in patients with hypertrophic cardiomyopathy","volume":"463","author":"Fucikova","year":"2016","journal-title":"Clin. Chim. Acta"},{"key":"ref_442","doi-asserted-by":"crossref","first-page":"1724","DOI":"10.1021\/bi0347104","article-title":"Urea-induced sequential unfolding of fibronectin: A fluorescence spectroscopy and circular dichroism study","volume":"43","author":"Patel","year":"2004","journal-title":"Biochemistry"},{"key":"ref_443","doi-asserted-by":"crossref","unstructured":"Dalton, C.J., and Lemmon, C.A. (2021). Fibronectin: Molecular Structure, Fibrillar Structure and Mechanochemical Signaling. Cells, 10.","DOI":"10.20944\/preprints202108.0010.v1"},{"key":"ref_444","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1755-1536-4-21","article-title":"Plasma and cellular fibronectin: Distinct and independent functions during tissue repair","volume":"4","author":"To","year":"2011","journal-title":"Fibrogenesis Tissue Repair."},{"key":"ref_445","doi-asserted-by":"crossref","first-page":"11901","DOI":"10.1016\/S0021-9258(20)71297-4","article-title":"Thermal stability of human plasma fibronectin and its constituent domains","volume":"259","author":"Ingham","year":"1984","journal-title":"J. Biol. Chem."},{"key":"ref_446","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1093\/protein\/gzv002","article-title":"Structural and dynamic properties that govern the stability of an engineered fibronectin type III domain","volume":"28","author":"Porebski","year":"2015","journal-title":"Protein Eng. Des. Sel."},{"key":"ref_447","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1152\/physrev.00016.2010","article-title":"Factor XIII: A coagulation factor with multiple plasmatic and cellular functions","volume":"91","author":"Muszbek","year":"2011","journal-title":"Physiol. Rev."},{"key":"ref_448","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.thromres.2011.11.040","article-title":"Factor XIII, clot structure, thrombosis","volume":"129","author":"Bagoly","year":"2012","journal-title":"Thromb. Res."},{"key":"ref_449","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1182\/blood.2020007415","article-title":"Factor XIII cross-links fibrin(ogen) independent of fibrin polymerization in experimental acute liver injury","volume":"137","author":"Poole","year":"2021","journal-title":"Blood"},{"key":"ref_450","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1182\/blood-2007-01-066837","article-title":"Functional analysis of fibrin {gamma}-chain cross-linking by activated factor XIII: Determination of a cross-linking pattern that maximizes clot stiffness","volume":"110","author":"Standeven","year":"2007","journal-title":"Blood"},{"key":"ref_451","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1006\/jsbi.2000.4253","article-title":"Probing the kinetics of beta-amyloid self-association","volume":"130","author":"Murphy","year":"2000","journal-title":"J. Struct. Biol."},{"key":"ref_452","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/S0959-440X(98)80016-X","article-title":"The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways","volume":"8","author":"Kelly","year":"1998","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_453","doi-asserted-by":"crossref","unstructured":"Rayan, B., Barnea, E., Khokhlov, A., Upcher, A., and Landau, M. (2023). Differential fibril morphologies and thermostability determine functional roles of Staphylococcus aureus PSMalpha1 and PSMalpha3. Front. Mol. Biosci., 10.","DOI":"10.3389\/fmolb.2023.1184785"},{"key":"ref_454","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1093\/protein\/gzi022","article-title":"Understanding the relationship between the primary structure of proteins and their amyloidogenic propensity: Clues from inclusion body formation","volume":"18","author":"Balaji","year":"2005","journal-title":"Protein Eng. Des. Sel."},{"key":"ref_455","doi-asserted-by":"crossref","first-page":"9848","DOI":"10.1021\/bi101351c","article-title":"The critical role of the constant region in thermal stability and aggregation of amyloidogenic immunoglobulin light chain","volume":"49","author":"Klimtchuk","year":"2010","journal-title":"Biochemistry"},{"key":"ref_456","doi-asserted-by":"crossref","first-page":"22604","DOI":"10.3390\/ijms141122604","article-title":"Thermal stability threshold for amyloid formation in light chain amyloidosis","volume":"14","author":"Poshusta","year":"2013","journal-title":"Int. J. Mol. Sci."},{"key":"ref_457","doi-asserted-by":"crossref","first-page":"30300","DOI":"10.1074\/jbc.M113.467829","article-title":"Ion-specific effects on prion nucleation and strain formation","volume":"288","author":"Rubin","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_458","doi-asserted-by":"crossref","unstructured":"Proal, A.D., and VanElzakker, M.B. (2021). Long COVID or Post-acute Sequelae of COVID-19 (PASC): An Overview of Biological Factors That May Contribute to Persistent Symptoms. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.698169"},{"key":"ref_459","doi-asserted-by":"crossref","unstructured":"Nunes, J.M., Kruger, A., Proal, A., Kell, D.B., and Pretorius, E. (2022). The Occurrence of Hyperactivated Platelets and Fibrinaloid Microclots in Myalgic Encephalomyelitis\/Chronic Fatigue Syndrome (ME\/CFS). Pharmaceuticals, 15.","DOI":"10.21203\/rs.3.rs-1727226\/v1"},{"key":"ref_460","doi-asserted-by":"crossref","first-page":"101075","DOI":"10.1016\/j.blre.2023.101075","article-title":"Cardiovascular and haematological pathology in Myalgic Encephalomyelitis\/Chronic Fatigue Syndrome (ME\/CFS): A role for Viruses","volume":"60","author":"Nunes","year":"2023","journal-title":"Blood Rev."},{"key":"ref_461","doi-asserted-by":"crossref","unstructured":"Ryabkova, V.A., Gavrilova, N.Y., Fedotkina, T.V., Churilov, L.P., and Shoenfeld, Y. (2023). Myalgic Encephalomyelitis\/Chronic Fatigue Syndrome and Post-COVID Syndrome: A Common Neuroimmune Ground. Diagnostics, 13.","DOI":"10.20944\/preprints202209.0289.v1"},{"key":"ref_462","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.molmed.2024.02.003","article-title":"Unravelling shared mechanisms: Insights from recent ME\/CFS research to illuminate long COVID pathologies","volume":"30","author":"Annesley","year":"2024","journal-title":"Trends Mol. Med."},{"key":"ref_463","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1186\/s12933-024-02315-x","article-title":"Data-independent LC-MS\/MS analysis of ME\/CFS plasma reveals a dysregulated coagulation system, endothelial dysfunction, downregulation of complement machinery","volume":"23","author":"Nunes","year":"2024","journal-title":"Cardiovasc. Diabetol."},{"key":"ref_464","doi-asserted-by":"crossref","unstructured":"Komaroff, A.L., and Lipkin, W.I. (2023). ME\/CFS and Long COVID share similar symptoms and biological abnormalities: Road map to the literature. Front. Med., 10.","DOI":"10.3389\/fmed.2023.1187163"},{"key":"ref_465","doi-asserted-by":"crossref","unstructured":"Kell, D.B., Lip, G.Y.H., and Pretorius, E. (2024). Fibrinaloid Microclots and Atrial Fibrillation. Biomedicines, 12.","DOI":"10.20944\/preprints202401.1945.v1"},{"key":"ref_466","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s13024-023-00651-2","article-title":"Misfolded protein oligomers: Mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases","volume":"19","author":"Rinauro","year":"2024","journal-title":"Mol. Neurodegener."},{"key":"ref_467","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1007\/978-3-030-28151-9_16","article-title":"Amyloid Oligomers, Protofibrils and Fibrils","volume":"93","author":"Siddiqi","year":"2019","journal-title":"Subcell. Biochem."},{"key":"ref_468","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1042\/bst0300521","article-title":"Examining the structure of the mature amyloid fibril","volume":"30","author":"Makin","year":"2002","journal-title":"Biochem. Soc. Trans."},{"key":"ref_469","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1002\/jemt.20190","article-title":"Structure and morphology of the Alzheimer\u2019s amyloid fibril","volume":"67","author":"Stromer","year":"2005","journal-title":"Microsc. Res. Tech."},{"key":"ref_470","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/s42004-020-00372-3","article-title":"Quantification of amyloid fibril polymorphism by nano-morphometry reveals the individuality of filament assembly","volume":"3","author":"Aubrey","year":"2020","journal-title":"Commun. Chem."},{"key":"ref_471","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.3324\/haematol.2013.102764","article-title":"Clinical diagnosis and typing of systemic amyloidosis in subcutaneous fat aspirates by mass spectrometry-based proteomics","volume":"99","author":"Vrana","year":"2014","journal-title":"Haematologica"},{"key":"ref_472","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1080\/13506129.2022.2147636","article-title":"Amyloid nomenclature 2022: Update, novel proteins, and recommendations by the International Society of Amyloidosis (ISA) Nomenclature Committee","volume":"29","author":"Buxbaum","year":"2022","journal-title":"Amyloid"},{"key":"ref_473","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1002\/jms.3264","article-title":"Shotgun-proteomics-based clinical testing for diagnosis and classification of amyloidosis","volume":"48","author":"Theis","year":"2013","journal-title":"J. Mass. Spectrom."},{"key":"ref_474","first-page":"526","article-title":"Potential role of apolipoprotein-E in fibrillogenesis","volume":"145","author":"Gallo","year":"1994","journal-title":"Am. J. Pathol."},{"key":"ref_475","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1369\/0022155415595264","article-title":"MALDI-mass spectrometry imaging identifies vitronectin as a common constituent of amyloid deposits","volume":"63","author":"Winter","year":"2015","journal-title":"J. Histochem. Cytochem."},{"key":"ref_476","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1080\/13506129.2022.2120800","article-title":"Binding of serum-derived amyloid-associated proteins to amyloid fibrils","volume":"30","author":"Misumi","year":"2023","journal-title":"Amyloid"},{"key":"ref_477","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1039\/c4ib00173g","article-title":"The simultaneous occurrence of both hypercoagulability and hypofibrinolysis in blood and serum during systemic inflammation, and the roles of iron and fibrin(ogen)","volume":"7","author":"Kell","year":"2015","journal-title":"Integr. Biol."},{"key":"ref_478","doi-asserted-by":"crossref","unstructured":"Grobbelaar, L.M., Venter, C., Vlok, M., Ngoepe, M., Laubscher, G.J., Lourens, P.J., Steenkamp, J., Kell, D.B., and Pretorius, E. (2021). SARS-CoV-2 spike protein S1 induces fibrin(ogen) resistant to fibrinolysis: Implications for microclot formation in COVID-19. Biosci. Rep., 41.","DOI":"10.1042\/BSR20210611"},{"key":"ref_479","doi-asserted-by":"crossref","first-page":"3302","DOI":"10.1091\/mbc.e07-04-0317","article-title":"Modulation of proteinase K-resistant prion protein in cells and infectious brain homogenate by redox iron: Implications for prion replication and disease pathogenesis","volume":"18","author":"Basu","year":"2007","journal-title":"Mol. Biol. Cell"},{"key":"ref_480","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1080\/14737159.2017.1368389","article-title":"Applications of the real-time quaking-induced conversion assay in diagnosis, prion strain-typing, drug pre-screening and other amyloidopathies","volume":"17","author":"Candelise","year":"2017","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"ref_481","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s40478-018-0534-0","article-title":"Prion infectivity is encoded exclusively within the structure of proteinase K-resistant fragments of synthetically generated recombinant PrP(Sc)","volume":"6","author":"Wang","year":"2018","journal-title":"Acta Neuropathol. Commun."},{"key":"ref_482","doi-asserted-by":"crossref","unstructured":"Hailemariam, D., Goldansaz, S.A., Daude, N., Wishart, D.S., and Ametaj, B.N. (2021). Mice Treated Subcutaneously with Mouse LPS-Converted PrP(res) or LPS Alone Showed Brain Gene Expression Profiles Characteristic of Prion Disease. Vet. Sci., 8.","DOI":"10.3390\/vetsci8090200"},{"key":"ref_483","doi-asserted-by":"crossref","first-page":"27972","DOI":"10.1074\/jbc.M113.477547","article-title":"Analyses of protease resistance and aggregation state of abnormal prion protein across the spectrum of human prions","volume":"288","author":"Saverioni","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_484","doi-asserted-by":"crossref","first-page":"35284","DOI":"10.18632\/oncotarget.6074","article-title":"Viscoelastic and ultrastructural characteristics of whole blood and plasma in Alzheimer-type dementia, and the possible role of bacterial lipopolysaccharides (LPS)","volume":"6","author":"Bester","year":"2015","journal-title":"Oncotarget Gerontol."},{"key":"ref_485","doi-asserted-by":"crossref","unstructured":"de Waal, G.M., Engelbrecht, L., Davis, T., de Villiers, W.J.S., Kell, D.B., and Pretorius, E. (2018). Correlative Light-Electron Microscopy detects lipopolysaccharide and its association with fibrin fibres in Parkinson\u2019s Disease, Alzheimer\u2019s Disease and Type 2 Diabetes Mellitus. Sci. Rep., 8.","DOI":"10.1038\/s41598-018-35009-y"},{"key":"ref_486","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1039\/c5ib00158g","article-title":"On the translocation of bacteria and their lipopolysaccharides between blood and peripheral locations in chronic, inflammatory diseases: The central roles of LPS and LPS-induced cell death","volume":"7","author":"Kell","year":"2015","journal-title":"Integr. Biol."},{"key":"ref_487","doi-asserted-by":"crossref","unstructured":"Pretorius, E., Bester, J., Page, M.J., and Kell, D.B. (2018). The potential of LPS-binding protein to reverse amyloid formation in plasma fibrin of individuals with Alzheimer-type dementia. Front. Aging Neurosci., 10.","DOI":"10.3389\/fnagi.2018.00257"},{"key":"ref_488","doi-asserted-by":"crossref","unstructured":"Kruger, A., Joffe, D., Lloyd-Jones, G., Khan, M.A., \u0160alamon, \u0160., Laubscher, G.J., Putrino, D., Kell, D.B., and Pretorius, E. (Semin. Throm Hemost., 2024). Vascular pathogenesis in acute and long covid: Current insights and therapeutic outlook, Semin. Throm Hemost., online ahead of print.","DOI":"10.1055\/s-0044-1790603"},{"key":"ref_489","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.rvsc.2022.01.016","article-title":"Combination of mouse prion protein with detoxified lipopolysaccharide triggers colon genes related to inflammatory, antibacterial, and apoptotic responses","volume":"144","author":"Hailemariam","year":"2022","journal-title":"Res. Vet. Sci."},{"key":"ref_490","doi-asserted-by":"crossref","first-page":"221","DOI":"10.4161\/pri.28939","article-title":"Lipopolysaccharide induced conversion of recombinant prion protein","volume":"8","author":"Saleem","year":"2014","journal-title":"Prion"},{"key":"ref_491","first-page":"S24","article-title":"Subcutaneously administered LPS-converted recombinant mouse prion protein alone or in combination with LPS modulates the content of prion-related proteins in the brain of FVB\/N mice","volume":"9","author":"Zwierzchowski","year":"2015","journal-title":"Prion"},{"key":"ref_492","first-page":"A2247","article-title":"Evidence Circulating Microclots and Activated Platelets Contribute to Hyperinflammation within Pediatric Post Acute Sequala of COVID","volume":"209","author":"Okuducu","year":"2024","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_493","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1111\/jth.12785","article-title":"Visualization of fibrinogen alphaC regions and their arrangement during fibrin network formation by high-resolution AFM","volume":"13","author":"Protopopova","year":"2015","journal-title":"J. Thromb. Haemost."},{"key":"ref_494","doi-asserted-by":"crossref","first-page":"27789","DOI":"10.1021\/acsami.3c06460","article-title":"Biophysical Properties of the Fibril Structure of the Toxic Conformer of Amyloid-beta42: Characterization by Atomic Force Microscopy in Liquid and Molecular Docking","volume":"15","author":"Biyani","year":"2023","journal-title":"ACS Appl. Mater. 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