Decoding Phase Separation of Prion-Like Domains through Data-Driven Scaling Laws

Abstract

Proteins containing prion-like low complexity domains (PLDs) are common drivers of the formation of biomolecular condensates and are prone to misregulation due to amino acid mutations. Here, we exploit the accuracy of our residue-resolution coarse-grained model, Mpipi, to quantify the impact of amino acid mutations on the stability of an unprecedented set of 140 PLD mutants from six proteins (hnRNPA1, TDP43, FUS, EWSR1, RBM14, and TIA1). Our simulations reveal the existence of predictive rules that quantify the range of change in the critical solution temperature of PLDs as a function of the number and type of amino acid sequence mutations. Remarkably, these rules are consistent with the physicochemical properties of the mutations and extend across the entire family tested, suggesting universal scaling laws govern PLD phase behaviour. Our work offers a quantitative lens into how the emergent behaviour of PLD solutions varies in response to physicochemical changes of single PLD molecules.

Tandem-repeat proteins introduce tuneable properties to engineered biomolecular condensates

“…3, B, C). Consistent with the in vitro and in silico findings of other research groups, our observations underline the positive role arginine residues can play in phase separation propensity of proteins (4,11,(40)(41)(42)(43). Lastly, PhaseScan analysis of LCD2-CTPR4 proteins containing two different LC3-binding loops shows that introducing these loops between repeats 3 and 4 decreases the condensate-forming propensity.…”

“… A) Predicted structure of a CTPR construct (LCD2-CTPR4) in atomistic resolution, determined using AlphaFold [Jumper 2021]. (42) B) Coarse-grained representation of the CTPR-protein. C) Simulation box for a Direct Coexistence simulation.…”

Design of intrinsically disordered protein variants with diverse structural properties

“…Building on previous work in this area ( Zeng et al, 2021 ; Lichtinger et al, 2021 ), the fourth question that we sought to answer is: Are the changes in single-chain compaction of the designed swap variants accompanied by a change in their propensity to phase separate? To examine this question we chose to study A1-LCD in more detail because the relationship between sequence and phase sep- aration of A1-LCD has been studied extensively by experiments, theory and simulations ( Martin et al, 2020 ; Tesei et al, 2021 ; Bremer et al, 2022 ; Maristany et al, 2023 ).…”