Massively parallel genetic perturbation suggests the energetic structure of an amyloid-β transition state

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• dc.contributor.author Arutyunyan, Anna
• dc.contributor.author Seuma, Mireia
• dc.contributor.author Faure, Andre J.
• dc.contributor.author Bolognesi, Benedetta
• dc.contributor.author Lehner, Ben, 1978-
• dc.date.accessioned 2025-09-09T06:02:29Z
• dc.date.available 2025-09-09T06:02:29Z
• dc.date.issued 2025
• dc.description.abstract Amyloid aggregates are pathological hallmarks of many human diseases, but how soluble proteins nucleate to form amyloids is poorly understood. Here, we use combinatorial mutagenesis, a kinetic selection assay, and machine learning to massively perturb the energetics of the nucleation reaction of amyloid-β (Aβ42), the protein that aggregates in Alzheimer's disease. In total, we measure the nucleation rates of >140,000 variants of Aβ42 to accurately quantify the changes in free energy of activation of the reaction for all possible amino acid substitutions in a protein and, in addition, to quantify >600 energetic interactions between mutations. Strong energetic couplings suggest that the Aβ42 nucleation reaction transition state is structured in a short C-terminal region, providing a structural model for the reaction that may initiate Alzheimer's disease. Using this approach it should be possible to reveal the energetic structures of additional amyloid transition states and, in combination with additional selection assays, protein transition states more generally.
• dc.description.sponsorship This work was funded by the La Caixa Research Foundation project “DeepAmyloids” (LCF/PR/HR21/52410004). Work in the lab of B.B. was also funded by the Spanish Ministry of Science, Innovation and Universities (PID2021-127761OB-I00 and RYC2020-028861-I funded by MCIN/AEI/10.13039/501100011033, “ERDF A way of making Europe” and “ESF Investing in your future”) and by the European Union (ERC Consolidator, Glam-MAP, 101125484). Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. Work in the lab of B.L. was funded by a European Research Council (ERC) Advanced (883742) grant, the Spanish Ministry of Science and Innovation (LCF/PR/HR21/52410004, EMBL Partnership, Severo Ochoa Centre of Excellence), the Bettencourt Schueller Foundation, the AXA Research Fund, Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR, 2017 SGR 1322), the CERCA Program/Generalitat de Catalunya, and Wellcome (grant reference: 220540/Z/20/A, “Wellcome Sanger Institute Quinquennial Review 2021-2026”). M.S. was funded by a fellowship from Agencia de Gestio d’Ajuts Universitaris i de Recerca (2019FI_B 01311). A.J.F. was funded by a Ramón y Cajal fellowship (RYC2021-033375-I) financed by the Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033) and the European Union (NextGenerationEU/PRTR).
• dc.format.mimetype application/pdf
• dc.identifier.citation Arutyunyan A, Seuma M, Faure AJ, Bolognesi B, Lehner B. Massively parallel genetic perturbation suggests the energetic structure of an amyloid-β transition state. Sci Adv. 2025 Jun 13;11(24):eadv1422. DOI: 10.1126/sciadv.adv1422
• dc.identifier.doi http://dx.doi.org/10.1126/sciadv.adv1422
• dc.identifier.issn 2375-2548
• dc.identifier.uri http://hdl.handle.net/10230/71157
• dc.language.iso eng
• dc.publisher American Association for the Advancement of Science (AAAS)
• dc.relation.ispartof Sci Adv. 2025 Jun 13;11(24):eadv1422
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/883742
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2021-127761OB-I00
• dc.rights Copyright © 2025 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). This is an open-access article distributed under the terms of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.other Alzheimer, Malaltia d'
• dc.subject.other ADN
• dc.title Massively parallel genetic perturbation suggests the energetic structure of an amyloid-β transition state
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion