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bioRxiv · 10.1101/2024.07.24.604935

Energetic portrait of the amyloid beta nucleation transition state

Arutyunyan, A.·Seuma, M.·Faure, A. J.·Bolognesi, B.·Lehner, B.
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Abstract

Amyloid protein aggregates are pathological hallmarks of more than fifty 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 beta (A{beta}42), the protein that aggregates in Alzheimers disease. In total, we quantify the nucleation rates of >140,000 variants of A{beta}42. This allows us to accurately quantify the changes in reaction activation energy for all possible amino acid substitutions in a protein for the first time and, in addition, to quantify >600 energetic interactions between mutations. The data reveal the simple and interpretable genetic architecture of an amyloid nucleation reaction. Strikingly, strong energetic couplings are rare and identify a subset of structural contacts in mature fibrils. Together with the activation energy changes, this strongly suggests that the A{beta}42 nucleation reaction transition state is structured in a short C-terminal region, providing a structural model for the reaction that may initiate Alzheimers disease. We believe this approach can be widely applied to probe the energetics and transition state structures of protein reactions.

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Arutyunyan, A., Seuma, M., Faure, A. J., Bolognesi, B., Lehner, B.. 2024-07-24. Energetic portrait of the amyloid beta nucleation transition state. https://doi.org/10.1101/2024.07.24.604935

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