Liquid-liquid phase separation of proteins is modulated by amino acids in vitro and in vivo by regulating protein-protein interactions

Abstract: Liquid liquid phase separation (LLPS) of proteins is an intracellular process that is widely used by cells for many purposes. In living cells (in vivo), LLPS occurs in complex and crowded environments. Amino acids (AAs) are vital components of such environments, occupying a significant fraction of the cellular volume. In this work, we studied the effects of proline and other proteinogenic AAs on the LLPS of proteins, both in test tubes (in vitro) and in cells (in vivo). The effects of proline on the protein-protein interaction (PPI) and LLPS of both bovine serum albumin (BSA, a folded protein) and the low-complexity domain of fused in sarcoma (FUS267, an intrinsically disordered protein) is first established in vitro. Then, the effects of proline and other proteinogenic AAs on the formation of stress granules (SGs) by LLPS in U2OS and HeLa cells are studied. We find that the presence of AAs renders the net interaction between proteins more repulsive (i.e. stabilizes protein solution), thus suppressing protein phase separation in vitro and in vivo. We also show that the formation of SGs is suppressed by AAs using both immunofluorescence and live-cell microscopy. Our study reveals an underappreciated role of cellular AAs in modulating intracellular phase separation. It may find biomedical applications, especially in the treatment of protein aggregation diseases.