Structure and Dynamics of Lipid-Stabilized Amyloid Beta Aβ_1–42 Oligomers

Abstract

The Aβ peptide contributes to Alzheimer's disease through various mechanisms, including cell membrane disruption. While the fibrillar structure of Aβ_1–42 in aqueous medium has been elucidated, its oligomer structure remains elusive. We have combined Fourier transform infrared (FTIR) spectroscopy, transmission electron microscopy (TEM), solid-state NMR (ssNMR), and molecular dynamics (MD) approaches to achieve a structural model for Aβ_1–42 octamer in lipid bilayers. FTIR data identify conformational transitions of Aβ_1–42 to a stable β-sheet structure. ssNMR analysis allows assignment of 38 out of 42 Aβ_1–42 residues, with three additional inter-residue contacts to define the tertiary fold. Combined, MD simulations produce a structural model of Aβ_1–42 octamers in a novel sushi-roll fold of in-register cross-β motif with a lipid-filled internal cavity. The membrane-embedded structure of Aβ_1–42 and the mode of peptide-lipid interactions provide a better understanding of Aβ neurotoxicity.

Keywords

Alzheimer's disease / amyloid oligomer / Aβ peptide / molecular dynamics simulations / solid-state NMR

References

[1] J. M. Long and D. M. Holtzman, “Alzheimer Disease: An Update on Pathobiology and Treatment Strategies,” Cell 179 (2019): 312–339.

[2] S. A. Tatulian, “Challenges and Hopes for Alzheimer's Disease,” Drug Discovery Today 27 (2022): 1027–1043.

[3] E. Karran and B. De Strooper, “The Amyloid Cascade Hypothesis: Are We Poised for Success or Failure?,” Journal of Neurochemistry 139 (2016): 237–252.

[4] S. I. A. Cohen, S. Linse, L. M. Luheshi, et al., “Proliferation of Amyloid-β42 Aggregates Occurs Through a Secondary Nucleation Mechanism,” Proceedings of the National Academy of Sciences of the United States of America 110 (2013): 9758–9763.

[5] B. Zott, M. M. Simon, W. Hong, et al., “A Vicious Cycle of β Amyloid-Dependent Neuronal Hyperactivation,” Science 365 (2019): 559–565.

[6] H. L. Nguyen, H. Q. Linh, P. Krupa, G. La Penna, and M. S. Li, “Amyloid β Dodecamer Disrupts the Neuronal Membrane More Strongly Than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity,” Journal of Physical Chemistry B 126 (2022): 3659–3672.

[7] G. Lalli, J. M. Schott, J. Hardy, and B. De Strooper, “Aducanumab: A New Phase in Therapeutic Development for Alzheimer's Disease?,” EMBO Molecular Medicine 13 (2021): e14781.

[8] J. Cummings, “Anti-Amyloid Monoclonal Antibodies Are Transformative Treatments That Redefine Alzheimer's Disease Therapeutics,” Drugs 83 (2023): 569–576.

[9] O. Dyer, “Donanemab: FDA Experts Recommend Approval of Alzheimer's Drug,” BMJ 385 (2024): q1327.

[10] L. Söderberg, M. Johannesson, P. Nygren, et al., “Lecanemab, Aducanumab, and Gantenerumab—Binding Profiles to Different Forms of Amyloid-Beta Might Explain Efficacy and Side Effects in Clinical Trials for Alzheimer's Disease,” Neurotherapeutics 20 (2023): 195–206.

[11] A. G. Karkisaval, R. Hassan, A. Nguyen, et al., “The Structure of Tyrosine-10 Favors Ionic Conductance of Alzheimer's Disease-Associated Full-Length Amyloid-β Channels,” Nature Communications 15 (2024): 1296.

[12] C. Peters, D. Bascuñán, C. Opazo, and L. G. Aguayo, “Differential Membrane Toxicity of Amyloid-β Fragments by Pore Forming Mechanisms,” Journal of Alzheimer's Disease 51 (2016): 689–699.

[13] J. Habchi, S. Chia, C. Galvagnion, et al., “Cholesterol Catalyses Aβ42 Aggregation Through a Heterogeneous Nucleation Pathway in the Presence of Lipid Membranes,” Nature Chemistry 10 (2018): 673–683.

[14] C.-C. Liu, T. Kanekiyo, H. Xu, and G. Bu, “Apolipoprotein E and Alzheimer Disease: Risk, Mechanisms and Therapy,” Nature Reviews Neurology 9 (2013): 106–118.

[15] M. Kivipelto, E.-L. Helkala, M. P. Laakso, et al., “Apolipoprotein E ε4 Allele, Elevated Midlife Total Cholesterol Level, and High Midlife Systolic Blood Pressure Are Independent Risk Factors for Late-Life Alzheimer Disease,” Annals of Internal Medicine 137 (2002): 149–155.

[16] J. Egawa, M. L. Pearn, B. P. Lemkuil, P. M. Patel, and B. P. Head, “Membrane Lipid Rafts and Neurobiology: Age-Related Changes in Membrane Lipids and Loss of Neuronal Function,” Journal of Physiology 594 (2016): 4565–4579.

[17] J. Luo, H. Yang, and B. L. Song, “Mechanisms and Regulation of Cholesterol Homeostasis,” Nature Reviews Molecular Cell Biology 21 (2020): 225–245.

[18] N. Kandel, T. Zheng, Q. Huo, and S. A. Tatulian, “Membrane Binding and Pore Formation by a Cytotoxic Fragment of Amyloid β Peptide,” Journal of Physical Chemistry B 121 (2017): 10293–10305.

[19] A. Quist, I. Doudevski, H. Lin, et al., “Amyloid Ion Channels: A Common Structural Link for Protein-Misfolding Disease,” Proceedings of the National Academy of Sciences of the United States of America 102 (2005): 10427–10432.

[20] S. Ciudad, E. Puig, T. Botzanowski, et al., “Aβ₍₁₋₄₂₎ Tetramer and Octamer Structures Reveal Edge Conductivity Pores as a Mechanism for Membrane Damage,” Nature Communications 11 (2020): 3014.

[21] Y. Shafrir, S. Durell, N. Arispe, and H. R. Guy, “Models of Membrane-Bound Alzheimer's Abeta Peptide Assemblies,” Proteins: Structure, Function, and Bioinformatics 78 (2010): 3473–3487.

[22] M. Serra-Batiste, M. Ninot-Pedrosa, M. Bayoumi, M. Gairí, G. Maglia, and N. Carulla, “Aβ42 Assembles Into Specific β-Barrel Pore-Forming Oligomers in Membrane-Mimicking Environments,” Proceedings of the National Academy of Sciences of the United States of America 113 (2016): 10866–10871.

[23] B. Strodel, J. W. Lee, C. S. Whittleston, and D. J. Wales, “Transmembrane Structures for Alzheimer's Aβ₁₋₄₂ Oligomers,” Journal of the American Chemical Society 132 (2010): 13300–13312.

[24] B. Frieg, M. Han, K. Giller, et al., “Cryo-EM Structures of Lipidic Fibrils of Amyloid-β(1-40),” Nature Communications 15 (2024): 1297.

[25] W. Smeralda, M. Since, J. Cardin, et al., “β-Amyloid Peptide Interactions With Biomimetic Membranes: A Multiparametric Characterization,” International Journal of Biological Macromolecules 181 (2021): 769–777.

[26] S. A. Tatulian, “FTIR Analysis of Proteins and Protein-Membrane Interactions,” Methods in Molecular Biology 2003 (2019): 281–325.

[27] Y. Shen and A. Bax, “Protein Backbone and Sidechain Torsion Angles Predicted From NMR Chemical Shifts Using Artificial Neural Networks,” Journal of Biomolecular NMR 56 (2013): 227–241.

[28] Y. Xiao, B. Ma, D. Mcelheny, et al., “Aβ_(1–42) Fibril Structure Illuminates Self-Recognition and Replication of Amyloid in Alzheimer's Disease,” Nature Structural & Molecular Biology 22 (2015): 499–505.

[29] B. Han, Y. Liu, S. W. Ginzinger, and D. S. Wishart, “SHIFTX2: Significantly Improved Protein Chemical Shift Prediction,” Journal of Biomolecular NMR 50 (2011): 43–57.

[30] D. Huster, X. L. Yao, and M. Hong, “Membrane Protein Topology Probed by 1 H Spin Diffusion From Lipids Using Solid-State NMR Spectroscopy,” Journal of the American Chemical Society 124 (2002): 874–883.

[31] S. R. Hartmann and E. L. Hahn, “Nuclear Double Resonance in the Rotating Frame,” Physical Review 128 (1962): 2042–2053.

[32] E. L. Hahn, “Spin Echoes,” Physical Review 80 (1950): 580–594.

[33] O. Cruciani, L. Mannina, A. P. Sobolev, C. Cametti, and A. Segre, “An Improved NMR Study of Liposomes Using 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phospatidylcholine as Model,” Molecules 11 (2006): 334–344.

[34] M. Ji, M. Arbel, L. Zhang, et al., “Label-Free Imaging of Amyloid Plaques in Alzheimer's Disease With Stimulated Raman Scattering Microscopy,” Science Advances 4 (2018): eaat7715.

[35] J. Kiskis, H. Fink, L. Nyberg, J. Thyr, J.-Y. Li, and A. Enejder, “Plaque-Associated Lipids in Alzheimer's Diseased Brain Tissue Visualized by Nonlinear Microscopy,” Scientific Reports 5 (2015): 13489.

[36] Y. Tian, R. Liang, A. Kumar, P. Szwedziak, and J. H. Viles, “3D-visualization of Amyloid-β Oligomer Interactions With Lipid Membranes by Cryo-Electron Tomography,” Chemical Science 12 (2021): 6896–6907.

[37] C. Galvagnion, D. Topgaard, K. Makasewicz, et al., “Lipid Dynamics and Phase Transition Within α-Synuclein Amyloid Fibrils,” Journal of Physical Chemistry Letters 10 (2019): 7872–7877.

[38] H. W. Chang, C. I. Yang, and J. C. C. Chan, “Incubation of Amyloidogenic Peptides in Reverse Micelles Allow Active Control of Oligomer Size and Study of Protein–Protein Interactions,” ChemMedChem 19 (2024): e202400310.

[39] Z. Niu, W. Zhao, Z. Zhang, F. Xiao, X. Tang, and J. Yang, “The Molecular Structure of Alzheimer β-Amyloid Fibrils Formed in the Presence of Phospholipid Vesicles,” Angewandte Chemie International Edition 53 (2014): 9294–9297.

[40] M. Hong and K. Schmidt-Rohr, “Magic-Angle-Spinning NMR Techniques for Measuring Long-Range Distances in Biological Macromolecules,” Accounts of Chemical Research 46 (2013): 2154–2163.

[41] X. Kang, A. Kirui, M. C. Dickwella Widanage, F. Mentink-Vigier, D. J. Cosgrove, and T. Wang, “Lignin-Polysaccharide Interactions in Plant Secondary Cell Walls Revealed by Solid-State NMR,” Nature Communications 10 (2019): 347.

[42] H. Jang, F. T. Arce, S. Ramachandran, et al., “Truncated β-amyloid Peptide Channels Provide an Alternative Mechanism for Alzheimer's Disease and Down syndrome,” Proceedings of the National Academy of Sciences of the United States of America 107 (2010): 6538–6543.

[43] H. Jang, J. Zheng, and R. Nussinov, “Models of β-Amyloid Ion Channels in the Membrane Suggest That Channel Formation in the Bilayer Is a Dynamic Process,” Biophysical Journal 93 (2007): 1938–1949.

[44] H. Jang, F. T. Arce, R. Capone, S. Ramachandran, R. Lal, and R. Nussinov, “Misfolded Amyloid Ion Channels Present Mobile β-Sheet Subunits in Contrast to Conventional Ion Channels,” Biophysical Journal 97 (2009): 3029–3037.

[45] S. R. Durell, R. Kayed, and H. R. Guy, “The Amyloid Concentric β-Barrel Hypothesis: Models of Amyloid Beta 42 Oligomers and Annular Protofibrils,” Proteins 90 (2022): 1190–1209.

[46] A. G. Kreutzer, G. Guaglianone, S. Yoo, et al., “Probing Differences Among Aβ Oligomers With Two Triangular Trimers Derived From Aβ,” Proceedings of the National Academy of Sciences of the United States of America 120 (2023): e2219216120.

[47] M. Khaled, I. Rönnbäck, L. L. Ilag, A. Gräslund, B. Strodel, and N. Österlund, “A Hairpin Motif in the Amyloid-β Peptide Is Important for Formation of Disease-Related Oligomers,” Journal of the American Chemical Society 145 (2023): 18340–18354.

[48] C. Jang, D. Portugal Barron, L. Duo, C. Ma, H. Seabaugh, and Z. Guo, “EPR Studies of Aβ42 Oligomers Indicate a Parallel in-Register β-Sheet Structure,” ACS Chemical Neuroscience 15 (2024): 86–97.

[49] S. Sahoo, T. Pal, S. Mondal, K. P. Ghanta, and S. Bandyopadhyay, “Conformational Properties of Aβ Peptide Oligomers in Aqueous Ionic Liquid Solution: Insights From Molecular Simulation Studies,” Journal of Physical Chemistry B 127 (2023): 10960–10973.

[50] Y. Guan, Y. Li, W. Gao, et al., “Aggregation Dynamics Characteristics of Seven Different Aβ Oligomeric Isoforms-Dependence on the Interfacial Interaction,” ACS Chemical Neuroscience 15 (2024): 155–168.

[51] T. D. Samdin, C. R. Jones, G. Guaglianone, et al., “A β-Barrel-Like Tetramer Formed by a β-Hairpin Derived From Aβ,” Chemical Science 15 (2023): 285–297.

[52] K. Wang and W. Cai, “Aggregation, Structure and Water Permeability of Membrane-Embedded Helical Aβ Oligomers,” Physical Chemistry Chemical Physics 26 (2024): 5128–5140.

[53] K. M. King, E. M. Cleveland, A. Pennington, S. Fuccello, and A. M. Brown, “The Influence of POPC as a Coaggregate in Amyloid-β Oligomer Formation,” ACS Chemical Neuroscience 16 (2025): 3886–3898.

[54] R. Pandey and B. Urbanc, “Oligomer Formation by Physiologically Relevant C-Terminal Isoforms of Amyloid β-Protein,” Biomolecules 14 (2024): 774.

[55] S. T. Ngo, P. H. Nguyen, and P. Derreumaux, “Cholesterol Molecules Alter the Energy Landscape of Small Aβ_1–42 Oligomers,” Journal of Physical Chemistry B 125 (2021): 2299–2307.

[56] A. E. Bennett, C. M. Rienstra, M. Auger, K. V. Lakshmi, and R. G. Griffin, “Heteronuclear Decoupling in Rotating Solids,” Journal of Chemical Physics 103 (1995): 6951–6958.

[57] K. Takegoshi, J. Mizokami, and T. Terao, “1H decoupling With Third Averaging in Solid NMR,” Chemical Physics Letters 341 (2001): 540–544.

[58] A. Pines, M. G. Gibby, and J. S. Waugh, “Proton-Enhanced Nmr of Dilute Spins in Solids,” Journal of Chemical Physics 59 (1973): 569–590.

[59] F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, and A. Bax, “NMRPipe: A Multidimensional Spectral Processing System Based on UNIX Pipes,” Journal of Biomolecular NMR 6 (1995): 277–293.

[60] W. Lee, M. Tonelli, and J. L. Markley, “NMRFAM-SPARKY: Enhanced Software for Biomolecular NMR Spectroscopy,” Bioinformatics 31 (2015): 1325–1327.

[61] C. Ader, R. Schneider, K. Seidel, M. Etzkorn, S. Becker, and M. Baldus, “Structural Rearrangements of Membrane Proteins Probed by Water-Edited Solid-State NMR Spectroscopy,” Journal of the American Chemical Society 131 (2009): 170–176.

[62] A. D. Mackerell, D. Bashford, M. Bellott, et al., “All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins,” Journal of Physical Chemistry B 102 (1998): 3586–3616.

[63] J. C. Phillips, D. J. Hardy, J. D. C. Maia, et al., “Scalable Molecular Dynamics on CPU and GPU Architectures With NAMD,” Journal of Chemical Physics 153 (2020): 044130.

RIGHTS & PERMISSIONS

2026 The Author(s). Aggregate published by SCUT, AIEI, and John Wiley & Sons Australia, Ltd.