References
1. Deleanu M, Hernandez JF, Cipelletti L, et al. Unraveling the Speciation of beta-Amyloid Peptides during the Aggregation Process by Taylor Dispersion Analysis. Anal Chem. 2021;93(16):6523-6533.
2. Urban AS, Pavlov KV, Kamynina AV, Okhrimenko IS, Arseniev AS, Bocharov EV. Structural Studies Providing Insights into Production and Conformational Behavior of Amyloid-beta Peptide Associated with Alzheimer’s Disease Development. Molecules. 2021;26(10).
3. Mroczko B, Groblewska M, Litman-Zawadzka A, Kornhuber J, Lewczuk P. Cellular Receptors of Amyloid beta Oligomers (AbetaOs) in Alzheimer’s Disease. Int J Mol Sci. 2018;19(7).
4. Gremer L, Schölzel D, Schenk C, et al. Fibril structure of amyloid-β(1–42) by cryo–electron microscopy. Science.2017;358(6359):116-119.
5. Lu JX, Qiang W, Yau WM, Schwieters CD, Meredith SC, Tycko R. Molecular structure of beta-amyloid fibrils in Alzheimer’s disease brain tissue. Cell. 2013;154(6):1257-1268.
6. Lührs T, Ritter C, Adrian M, et al. 3D structure of Alzheimer’s amyloid-β(1–42) fibrils. Proceedings of the National Academy of Sciences of the United States of America. 2005;102(48):17342-17347.
7. Petkova AT, Yau WM, Tycko R. Experimental constraints on quaternary structure in Alzheimer’s beta-amyloid fibrils. Biochemistry.2006;45(2):498-512.
8. Soldner CA, Sticht H, Horn AHC. Role of the N-terminus for the stability of an amyloid-beta fibril with three-fold symmetry. PLoS One. 2017;12(10):e0186347.
9. Ghosh U, Thurber KR, Yau WM, Tycko R. Molecular structure of a prevalent amyloid-beta fibril polymorph from Alzheimer’s disease brain tissue. Proc Natl Acad Sci U S A. 2021;118(4).
10. Qiang W, Yau WM, Luo Y, Mattson MP, Tycko R. Antiparallel beta-sheet architecture in Iowa-mutant beta-amyloid fibrils. Proc Natl Acad Sci U S A. 2012;109(12):4443-4448.
11. Mroczko B, Groblewska M, Litman-Zawadzka A, Kornhuber J, Lewczuk P. Amyloid β oligomers (AβOs) in Alzheimer’s disease. Journal of Neural Transmission. 2018;125(2):177-191.
12. Cline EN, Bicca MA, Viola KL, Klein WL. The Amyloid-beta Oligomer Hypothesis: Beginning of the Third Decade. J Alzheimers Dis.2018;64(s1):S567-S610.
13. Huang Y-r, Liu R-t. The Toxicity and Polymorphism of β-Amyloid Oligomers. International Journal of Molecular Sciences.2020;21(12):4477.
14. Fu L, Sun Y, Guo Y, et al. Comparison of neurotoxicity of different aggregated forms of Aβ40, Aβ42 and Aβ43 in cell cultures. Journal of Peptide Science. 2017;23(3):245-251.
15. Arispe N, Pollard HB, Rojas E. Zn2+ interaction with Alzheimer amyloid beta protein calcium channels. Proc Natl Acad Sci U S A.1996;93(4):1710-1715.
16. Arispe N, Rojas E, Pollard HB. Alzheimer disease amyloid beta protein forms calcium channels in bilayer membranes: blockade by tromethamine and aluminum. Proc Natl Acad Sci U S A.1993;90(2):567-571.
17. Hirakura Y, Lin MC, Kagan BL. Alzheimer amyloid abeta1-42 channels: effects of solvent, pH, and Congo Red. J Neurosci Res.1999;57(4):458-466.
18. Lin H, Bhatia R, Lal R. Amyloid beta protein forms ion channels: implications for Alzheimer’s disease pathophysiology. FASEB J.2001;15(13):2433-2444.
19. Serra-Batiste M, Ninot-Pedrosa M, Bayoumi M, Gairí M, Maglia G, Carulla N. Aβ42 assembles into specific β-barrel pore-forming oligomers in membrane-mimicking environments. Proceedings of the National Academy of Sciences. 2016;113(39):10866-10871.
20. Bode DC, Baker MD, Viles JH. Ion Channel Formation by Amyloid-β42 Oligomers but Not Amyloid-β40 in Cellular Membranes. Journal of Biological Chemistry. 2017;292(4):1404-1413.
21. Hu Z-W, Ma M-R, Chen Y-X, Zhao Y-F, Qiang W, Li Y-M. Phosphorylation at Ser8 as an Intrinsic Regulatory Switch to Regulate the Morphologies and Structures of Alzheimer’s 40-residue β-Amyloid (Aβ40) Fibrils.Journal of Biological Chemistry. 2017;292(7):2611-2623.
22. Shafrir Y, Durell S, Arispe N, Guy HR. Models of membrane-bound Alzheimer’s Abeta peptide assemblies. Proteins.2010;78(16):3473-3487.
23. Shafrir Y, Durell SR, Anishkin A, Guy HR. Beta-barrel models of soluble amyloid beta oligomers and annular protofibrils.Proteins. 2010;78(16):3458-3472.
24. Laganowsky A, Liu C, Sawaya MR, et al. Atomic view of a toxic amyloid small oligomer. Science. 2012;335(6073):1228-1231.
25. Do TD, LaPointe NE, Nelson R, et al. Amyloid β-Protein C-Terminal Fragments: Formation of Cylindrins and β-Barrels. Journal of the American Chemical Society. 2016;138(2):549-557.
26. Harmeier A, Wozny C, Rost BR, et al. Role of amyloid-beta glycine 33 in oligomerization, toxicity, and neuronal plasticity. J Neurosci. 2009;29(23):7582-7590.
27. Bitan G, Tarus B, Vollers SS, et al. A molecular switch in amyloid assembly: Met(35) and amyloid beta-protein oligomerization.Journal of the American Chemical Society.2003;125(50):15359-15365.
28. Cerf E, Sarroukh R, Tamamizu-Kato S, et al. Antiparallel beta-sheet: a signature structure of the oligomeric amyloid beta-peptide.Biochem J. 2009;421(3):415-423.
29. Yoshiike Y, Kayed R, Milton SC, Takashima A, Glabe CG. Pore-forming proteins share structural and functional homology with amyloid oligomers. Neuromolecular medicine. 2007;9(3):270-275.
30. Vignaud H, Bobo C, Lascu I, et al. A Structure-Toxicity Study of Aß42 Reveals a New Anti-Parallel Aggregation Pathway. PLOS ONE.2013;8(11):e80262.
31. Ciudad S, Puig E, Botzanowski T, et al. Abeta(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage. Nat Commun. 2020;11(1):3014.
32. Gao Y, Guo C, Watzlawik JO, et al. Out-of-Register Parallel beta-Sheets and Antiparallel beta-Sheets Coexist in 150-kDa Oligomers Formed by Amyloid-beta(1-42). J Mol Biol. 2020;432(16):4388-4407.
33. Iacovache I, De Carlo S, Cirauqui N, Dal Peraro M, van der Goot FG, Zuber B. Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process. Nat Commun. 2016;7:12062.
34. Bokori-Brown M, Martin TG, Naylor CE, Basak AK, Titball RW, Savva CG. Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein. Nat Commun. 2016;7:11293.
35. Chou PY, Fasman GD. Empirical predictions of protein conformation.Annu Rev Biochem. 1978;47:251-276.
36. Aggarwal L, Biswas P. Hydration Thermodynamics of the N-Terminal FAD Mutants of Amyloid-beta. J Chem Inf Model. 2021;61(1):298-310.
37. Banchelli M, Cascella R, D’Andrea C, et al. Probing the Structure of Toxic Amyloid-beta Oligomers with Electron Spin Resonance and Molecular Modeling. ACS Chem Neurosci. 2021;12(7):1150-1161.
38. Urbanc B. Cross-Linked Amyloid beta-Protein Oligomers: A Missing Link in Alzheimer’s Disease Pathology? J Phys Chem B.2021;125(5):1307-1316.
39. Kayed R, Pensalfini A, Margol L, et al. Annular Protofibrils Are a Structurally and Functionally Distinct Type of Amyloid Oligomer.Journal of Biological Chemistry. 2009;284(7):4230-4237.
40. Murzin AG, Lesk AM, Chothia C. Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis. J Mol Biol. 1994;236(5):1369-1381.
41. Hayward S, Milner-White EJ. Geometrical principles of homomeric beta-barrels and beta-helices: Application to modeling amyloid protofilaments. Proteins. 2017;85(10):1866-1881.
42. Durell SR, Guy HR. The amyloid concentric β-barrel hypothesis: models of Synuclein oligomers, annular protofibrils, lipoproteins, and transmembrane channels. Proteins: Structure, Function, and Bioinformatics. 2021.
43. Photoshop. Adobe Photoshop, RRID:SCR_014199. Available at: https://www.adobe.com/products/photoshop.html.
44. Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605-1612.
45. UCSF Chimera. http://www.rbvi.ucsf.edu/chimera.
46. Blastp. https://blast.ncbi.nlm.nih.gov/Blast.cgi.
47. Bernstein SL, Dupuis NF, Lazo ND, et al. Amyloid-beta protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer’s disease. Nat Chem. 2009;1(4):326-331.
48. Lacor PN, Buniel MC, Chang L, et al. Synaptic targeting by Alzheimer’s-related amyloid beta oligomers. J Neurosci.2004;24(45):10191-10200.
49. Lesne S, Koh MT, Kotilinek L, et al. A specific amyloid-beta protein assembly in the brain impairs memory. Nature.2006;440(7082):352-357.
50. Stroud JC, Liu C, Teng PK, Eisenberg D. Toxic fibrillar oligomers of amyloid-beta have cross-beta structure. Proc Natl Acad Sci U S A.2012;109(20):7717-7722.
51. Sebollela A, Mustata GM, Luo K, et al. Elucidating molecular mass and shape of a neurotoxic Abeta oligomer. ACS Chem Neurosci.2014;5(12):1238-1245.
52. Gu L, Liu C, Guo Z. Structural insights into Abeta42 oligomers using site-directed spin labeling. J Biol Chem.2013;288(26):18673-18683.
53. Pham CL, Kwan AH, Sunde M. Functional amyloid: widespread in Nature, diverse in purpose. Essays Biochem. 2014;56:207-219.
54. Otzen D, Riek R. Functional Amyloids. Cold Spring Harb Perspect Biol. 2019;11(12).
55. Kumar DKV, Choi SH, Washicosky KJ, et al. Amyloid-beta peptide protects against microbial infection in mouse and worm models of Alzheimer’s disease. Sci Transl Med. 2016;8(340).
56. Ngo S, Guo Z. Key residues for the oligomerization of Abeta42 protein in Alzheimer’s disease. Biochem Biophys Res Commun.2011;414(3):512-516.
57. Valdes H, Pluhackova K, Hobza P. Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic-Aromatic Side Chain Interactions in Proteins. J Chem Theory Comput. 2009;5(9):2248-2256.
58. McClean S. Eight stranded beta -barrel and related outer membrane proteins: role in bacterial pathogenesis. Protein Pept Lett.2012;19(10):1013-1025.
59. LaLonde JM, Bernlohr DA, Banaszak LJ. The up-and-down beta-barrel proteins. FASEB J. 1994;8(15):1240-1247.
60. Nagano N, Orengo CA, Thornton JM. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol.2002;321(5):741-765.