Sequence determinants of the aggregation of proteins within condensates generated by liquid-liquid phase separation

The transition between the native and amyloid states of proteins can proceed via a deposition pathway via oligomeric intermediates or via a condensation pathway via liquid droplet intermediates generated through liquid-liquid phase separation. While several computational methods are available to perform sequence-based predictions of the propensity of proteins to aggregate via the deposition pathway, much less is known about the physico-chemical principles that underlie aggregation within condensates. Here we investigate the sequence determinants of aggregation via the condensation pathway, and identify three features, the droplet-promoting propensity, the aggregation-promoting propensity and the multimodal interactions quantified by the binding mode entropy. By using this approach, we predict aggregation-promoting mutations in droplet-forming proteins associated with amyotrophic lateral sclerosis (ALS). This analysis provides insights into the amino acid code for the conversion of proteins between liquid-like and solid-like condensates