Unraveling molecular interactions in a phase-separating protein by atomistic simulations

Abstract

Membraneless organelles are dynamical cellular condensates formed by the liquid-liquid phase separation of proteins and RNA molecules. Multiple evidence suggests that disordered proteins are structural scaffolds that drive the condensation by forming a dynamic network of inter- and intra-molecular contacts. Despite the blooming research activity in this field, the structural characterization of these condensates is very limited and we still do not understand how the phase behaviour is encoded in the amino-acid sequences of the scaffolding proteins. Here we exploited explicit-solvent atomistic simulations to disentangle the molecular interactions governing the phase behaviour of the N-terminal disordered region of DEAD-box helicase 4 (NDDX4), which is a well-established model for phase separation in vitro and in vivo. Single-molecule simulations clarified the interplay between the intramolecular interactions that shape NDDX4 conformational ensemble and the known determinants of its phase behaviour, such as the attraction between oppositely-charged regions and the presence of arginine and phenylalanine. We then investigated intermolecular interactions associated with phase separation via a divide-and-conquer strategy based on the simulations of various NDDX4 fragments at high concentration. Our approach allowed us to probe conditions mimicking real condensates and revealed, in agreement with mutagenesis results, how these interactions arise from the complex interplay of diverse molecular mechanisms. Particularly, we characterized the transient formation of clusters of arginine and aromatic residues, which may stabilize the assembly of several MLOs. Overall, our results reveal the potential of atomistic simulations in the investigation of biomolecular phase separation paving the way for future studies.