Mass spectrometric data for chaperone-ligand interactions

<p><span>The assembly of proteins and peptides into amyloid fibrils is causally linked to serious disorders such as Alzheimer's Disease. Multiple proteins have been shown to prevent amyloid formation <em>in vitro</em> and <em>in vivo</em>, ranging from highly specific chaperone-client pairs to completely non-specific binding of aggregation-prone peptides. The underlying interactions remain elusive. Here, we turn to the machine learning-based structure prediction algorithm AlphaFold2 (AF2) to obtain models for the non-specific interactions of </span><span>b</span><span>-lactoglobulin (</span><span>b</span><span>LG), transthyretin (TTR), or Thioredoxin 80 (T80) with the model amyloid peptide Amyloid </span><span>b</span><span> (A</span><span>b</span><span>), and the highly specific complex between the BRICHOS chaperone domain of lung surfactant protein C (CTC) and its polyvaline target. Using a combination of native mass spectrometry (MS) and ion mobility MS, we show that non-specific chaperoning is driven predominantly by hydrophobic interactions of A</span><span>b</span><span> with hydrophobic surfaces in </span><span>b</span><span>LG, TTR, and T80, and in part regulated by oligomer stability. For CTC, native MS and hydrogen-deuterium exchange MS reveal that a disordered region recognizes the polyvaline target by forming a complementary </span><span>b</span><span>-strand. Hence, we show that AF2 and MS can yield atomistic models of hard-to-capture protein interactions that reveal different chaperoning mechanisms based on separate ligand properties and may provide possible clues for specific therapeutic intervention.</span></p>