Mapping the sequence specificity of heterotypic amyloid interactions enables the identification of aggregation modifiers

Nikolaos Louros,Katerina Konstantoulea,Emiel Michiels,Meine Ramakers,Nele Moonen,Joost Schymkowitz,Dietmar Rudolf Thal,Vera Goossens,Sam D’Haeyer,Frederic Rousseau,Chiara Morelli,Teresa Garcia,Dominique Audenaert

doi:10.1038/s41467-022-28955-9

Abstract

Heterotypic amyloid interactions between related protein sequences have been observed in functional and disease amyloids. While sequence homology seems to favour heterotypic amyloid interactions, we have no systematic understanding of the structural rules determining such interactions nor whether they inhibit or facilitate amyloid assembly. Using structure-based thermodynamic calculations and extensive experimental validation, we performed a comprehensive exploration of the defining role of sequence promiscuity in amyloid interactions. Using tau as a model system we demonstrate that proteins with local sequence homology to tau amyloid nucleating regions can modify fibril nucleation, morphology, assembly and spreading of aggregates in cultured cells. Depending on the type of mutation such interactions inhibit or promote aggregation in a manner that can be predicted from structure. We find that these heterotypic amyloid interactions can result in the subcellular mis-localisation of these proteins. Moreover, equilibrium studies indicate that the critical concentration of aggregation is altered by heterotypic interactions. Our findings suggest a structural mechanism by which the proteomic background can modulate the aggregation propensity of amyloidogenic proteins and we discuss how such sequence-specific proteostatic perturbations could contribute to the selective cellular susceptibility of amyloid disease progression.

Highlights

Heterotypic amyloid interactions between related protein sequences have been observed in functional and disease amyloids
While heterotypic amyloid protein interactions have been observed in different model systems, we still have no understanding on their determining structural rules beyond the observation that sequence homology favours heterotypic amyloid interactions
We limited our search to single variants of the known major aggregation prone regions (APRs) reasoning that: (i) APRs are the kinetic drivers that promote self-assembly of amyloids[41–44], (ii) individual amyloid polymorphs share energetic profiles in a sense that they depend on APRs as a common framework of high structural stability to counteract longer regions of structural frustration in their core[40] and (iii) this approach supports a deeper understanding of potential tendencies, as assignments are performed at a single residue level

Summary

Introduction

Heterotypic amyloid interactions between related protein sequences have been observed in functional and disease amyloids. Cellular predilection to toxic aggregates is conformationspecific, as recent evidence has shown that different amyloid fibril morphologies derived from the same misfolded protein can characterise other neurodegenerative disorders[33–35] Regardless of their protein of origin and self-assembly conditions, amyloid fibrils share a common structural cross-β architecture[36–39]. These regions, previously identified as aggregation prone regions (APRs)[41–45], form thermodynamically stable steric zipper interfaces that staple together amyloid fibril structures As a result, they are able to support their own self-assembly[46–50], as well as to promote heterotypic interactions dominated by sequence similarity[19,51–55] that have been shown to promote pathology[56–59] or the formation of biologically functional amyloids[60–66]. Even single disease mutations typically induce significant morphological differentiation that often raises barriers of structural incompatibility between strains[74–76]

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Conclusion