(770a) Studying RNA Modulated Protein Liquid-Liquid Phase Separation Using Coarse-Grained Models

Disordered proteins phase separate in biological cells creating distinct membraneless organelles coexisting with the surrounding cytosol¹. But living cells contain a multitude of proteins, nucleic acids and lipids with remarkable spatiotemporal organization controlling their interactions for specific functions. Experiments have found that some membraneless organelles such as P granules are mixtures of RNA and proteins that form via phase separation². Hence, it is essential to study biomolecular phase separation, taking into account the presence of RNA for a deeper understanding of the in vivo formation and function of membraneless organelles. We have successfully studied protein phase separation via molecular dynamics³, using a coarse grained modeling approach where we effectively capture protein-protein interactions on the amino acid level.

In this work we extend our coarse graining approach to incorporate RNA and determine how it modulates protein phase separation. We directly simulate the co-phase separation of both the disordered domain of DEAD-box helicase protein LAF-1 and polyA RNA condensed together in a slab geometry using standard molecular dynamics simulations which are conducted over a range of temperatures. RNA-protein interactions lead to formation of condensed phases containing both RNA and protein. The presence of RNA lowers the concentration of protein in the dense phase and RNA-protein interactions also change the dynamics of proteins inside the condensed phase.

1. Boeynaems, S., Alberti, S., Fawzi, N. L., Mittag, T., Polymenidou, M., Rousseau, F., ... Fuxreiter, M. (2018). Protein Phase Separation: A New Phase in Cell Biology. Trends in Cell Biology, 28(6), 420–435.
2. Wei, M. T., Elbaum-Garfinkle, S., Holehouse, A. S., Chen, C. C. H., Feric, M., Arnold, C. B., ... Brangwynne, C. P. (2017). Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles. Nature Chemistry, 9(11).
3. Dignon, G. L., Zheng, W., Kim, Y. C., Best, R. B., & Mittal, J. (2018). Sequence determinants of protein phase behavior from a coarse-grained model. PLoS Computational Biology, 14(1), e1005941.