Crowder induced conformational fluctuations modulate the phase separation of yeast SUP35 NM domain

Abstract

Intrinsically disordered proteins (IDPs) like Sup35NM can undergo liquid-liquid phase separation (LLPS) to form biomolecular condensates, a process influenced by their conformational flexibility and the crowded intracellular environment. This study investigates how molecular crowding, specifically the size and shape of crowders like Dextran and Ficoll, modulates the conformational states and phase separation behavior of Sup35NM. Using fluorescence correlation spectroscopy (FCS) and molecular dynamics simulations, we observed that Dextran, depending on its molecular weight, induces both compaction and expansion of Sup35NM, driving phase separation at certain thresholds. Notably, rod-like Dextran crowders promote phase separation, while spherical Ficoll does not, highlighting the impact of crowder geometry on IDP behavior. Computational modelling further revealed that the crowder shape influences Sup35NMs conformational ensemble by modulating intra- and inter-domain interactions. These findings elucidate the role of crowding agents in IDP phase behavior, suggesting that cellular crowding may regulate IDP functionality through conformational control.