A Novel Coarse-Grained Model to Study Liquid-Liquid Phase Separation of Disordered Proteins

Abstract

Recent studies have led to the discovery of droplets composed of disordered protein chains in a separate liquid-like phase. Such assemblies have been found to be relevant to physiological function as membraneless compartments in living cells including the nucleolus and ribonucleoprotein (RNP) granules as well as many organelles in prokaryotic cells (1). The thermodynamic driving force for this phase separation, however, is still not well characterized. Fused in Sarcoma (FUS) is an RNA binding protein that naturally forms these droplets as RNP granules which aid with DNA repair. The low complexity domain, FUS LC is a fully disordered domain and has been observed to form these droplets on its own in vitro (2). Mutations of FUS can result in transformation of these assemblies into poorly soluble aggregates involved in the pathogenesis of Amyotrophic Lateral Sclerosis and Frontotemporal Dementia (3). As the spatiotemporal scales involved in the phase separation of proteins cannot be resolved using fully detailed all-atom models, we develop a simple Cα;-based coarse-grained model that treats each amino acid in the chain as a single interaction site. The model is parameterized to treat each of the twenty naturally occurring amino acids differently in order to capture sequence-specific effects. Development of the proposed model involves top-down comparisons with experimental data available from the recent literature as well as comparisons with atomistic simulations of a single chain. We then use this model to characterize the droplet formation for FUS LC including the proposed transition from liquid-like to solid-like aggregates. We are also able to capture known trends in FUS LC phase separation as a function of salt concentration and disease-related mutations. This model should aid in the molecular understanding of phase behavior of disordered proteins thus aiding in development of therapeutic strategies.1.Brangwynne, C. P.; Eckmann, C. R.; Courson, D. S.; Rybarska, A.; Hoege, C.; Gharakhani, J.; Julicher, F.; Hyman, A. A. Science 2009, 324, 1729-17322.Burke, K. A.; Janke, A. M.; Rhine, C. L.; Fawzi, N. L. Molecular Cell 2015, 60, 231-2413.Patel, A.; Lee H. O.; Jawerth, L.; Dechsel, D.; Hyman, A. A.; Alberti, S. and othersCell 2015, 162, 1066-1077