A Computational Approach Reveals the Ability of Amyloids to Sequester RNA: the Alpha Synuclein Case

Abstract

The modulating effect of nucleic acids on protein aggregation has recently come into the spotlight, with RNA shown to either prevent or promote protein assembly depending on the molecular context. Here, we computed the biophysical properties of amyloids and observed a trend indicating that regions outside the aggregates core are highly prone to interact with nucleic acids. In the case of alpha synuclein (aS), an intrinsically disordered protein abundantly expressed in the brain, found in the nucleus and involved in Parkinson's disease, our predictions indicate that regions outside the aggregate are able to contact RNA, but the acidic C-terminal prevents the formation of stable interactions. We performed aggregation assays with both the wild type alpha-synuclein (aS140) as well as a C-terminally truncated isoform (aS103) and found that while RNA increases the aggregation rate of aS103, it decreases that of aS140, although at higher RNA concentrations the trend is inverted. To further elucidate the effects driving this behavior, we built a general dynamic model that describes the aggregation process of monomers in the presence of RNA. Our predictions indicate that RNA affects aS103 and aS140 aggregation in a non-linear manner and prioritize the interaction between RNA and aggregate as the most relevant. To confirm this, we extracted RNA from aS103 and aS140 aggregates and observed that they indeed acquire distinct RNA-sequestering abilities. Our research demonstrates that binding to transcripts can drastically alter the aggregation of a protein and represents an important gain-of-function mechanism to be further investigated.

Content-enriched fluorescence lifetime fluctuation spectroscopy to study bio-molecular condensate formation

“…Alpha-Synuclein Purification and Labeling. Wild type α-syn and α-syn with the addition C141 (α-syn C141 ) were respectively purified as described in (46). Briefly, both proteins were recombinantly produced in E. coli.…”

Transmembrane Helices 7 and 8 Confer Aggregation Sensitivity to the Cystic Fibrosis Transmembrane Conductance Regulator

“…Aggregation propensity in the unfolded state and folded state were computed as described [44]. The model we used here has served originally as a predictor of amyloid formation but has been applied successfully in alternative contexts [113]. Folding propensities and aggregation propensities often are anticorrelated quantities [44,114].…”