Post-doctoral position in biophysics available to study protein phase separation in poly(A)-binding protein (Pab1), in collaboration with DA Drummond lab, also at UChicago. The individual will determine in molecular detail how Pab1 phase separates in response to physiological stress conditions, which is crucial for cell survival and growth [1, 2]. Studies of Pab1’s unique stress-triggered phase separation behavior will be conducted at multiple length scales, and investigate the influence of physiological RNA targets on phase separation. Experience in biophysics including NMR or hydrogen exchange techniques preferred. Contact firstname.lastname@example.org.
Our studies aim to determine in molecular detail the mechanism(s) by which poly(A)-binding protein Pab1 phase-separates to form hydrogel assemblies during stress. Cellular stresses cause the evolutionarily conserved, putatively adaptive formation stress granules. Pab1 is a defining marker of stress granules, and Pab1’s phase separation precedes stress granule formation. Dysregulation of phase separation of multiple RNA-binding proteins is linked to pathological protein aggregation associated with major neurodegenerative disorders. The mechanism(s) of phase separation is an area of active inquiry. The key barrier has been a lack of tractable in vitro models of biologically relevant phase separation by an RNA-binding protein.
We have broken through this barrier. In recently published work, we have established that Pab1 phase-separates into hydrogel droplets in response to physiological stress conditions, and that interfering with hydrogel droplet formation disrupts budding yeast’s ability to survive thermal and starvation stress. No previously described system combines a stress-triggered phase separation process, phenotypic consequences during stress, and the ability to reconstitute phase separation at physiological concentrations and conditions. Pab1/poly(A)-binding protein is conserved across eukaryotes and is a core marker of stress granules, making it a promising model for determining the molecular basis of stress-induced phase separation. We will study Pab1’s phase separation at multiple scales, including the influence of RNA, using a combination in vitro and in vivo approaches to determine how this unique phase separation process is encoded.
We will test specific hypotheses, such as the involvement of electrostatic interactions between RNA-binding domains and hydrophobic interactions between IDRs, using mutational approaches combined with hydrogen exchange mass spectrometry (HX-MS), NMR, dynamic light scattering, and small-angle X-ray scattering. We with further develop a mesoscale assay which provides rich information about how Pab1 interactions influence the properties of the resulting assemblies (viscosity, nucleation versus growth, changes in phase) thought to contribute to its biological functions. The project combines the expertise of two complementary investigators. Sosnick brings his expertise in protein folding and chemistry while Drummond brings his extensive experience in Pab1 and stress biology.
 J.A. Riback, C.D. Katanski, J.L. Kear-Scott, E.V. Pilipenko, A.E. Rojek, T.R. Sosnick, D.A. Drummond, Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response, Cell 168 (2017) 1028-1040 e1019.
 E.W. Wallace, J.L. Kear-Scott, E.V. Pilipenko, M.H. Schwartz, P.R. Laskowski, A.E. Rojek, C.D. Katanski, J.A. Riback, M.F. Dion, A.M. Franks, E.M. Airoldi, T. Pan, B.A. Budnik, D.A. Drummond, Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress, Cell 162 (2015) 1286-1298.