Network of hotspot interactions cluster tau amyloid folds

Cryogenic electron microscopy has revealed unprecedented molecular insight into the conformations of beta-sheet-rich protein amyloids linked to neurodegenerative diseases. It remains unknown how a protein can adopt a diversity of folds and form multiple distinct fibrillar structures. Here we develop an in silico alanine scan method to estimate the relative energetic contribution of each amino acid in an amyloid assembly. We apply our method to twenty-seven ex vivo and in vitro fibril structural polymorphs of the microtubule-associated protein tau. We uncover networks of energetically important interactions involving amyloid-forming motifs that stabilize the different fibril folds. We evaluate our predictions in cellular and in vitro aggregation assays. Using a machine learning approach, we classify the structures based on residue energetics to identify distinguishing and unifying features. Our energetic profiling suggests that minimal sequence elements control the stability of tau fibrils, allowing future design of protein sequences that fold into unique structures.

Automated summary

Cryogenic electron microscopy has provided new insights into the conformations of beta-sheet-rich protein amyloids related to neurodegenerative diseases. By using an in silico alanine scan method, the relative energetic contributions of each amino acid in amyloid assembly can be estimated. Applying this method to various fibril structural polymorphs of tau protein, networks of energetically important interactions that stabilize different fibril folds are identified. These findings have implications for the future design of protein sequences that can fold into unique structures.