Physical Chemistry of Cellular Liquid-Phase Separation

Abstract

Compartmentalization of biochemical processes is essential for cell function. Although membrane-bound organelles are well studied in this context, recent work has shown that phase separation is a key contributor to cellular compartmentalization through the formation of liquid-like membraneless organelles (MLOs). In this Minireview, the key mechanistic concepts that underlie MLO dynamics and function are first briefly discussed, including the relevant noncovalent interaction chemistry and polymer physical chemistry. Next, a few examples of MLOs and relevant proteins are given, along with their functions, which highlight the relevance of the above concepts. The developing area of active matter and non-equilibrium systems, which can give rise to unexpected effects in fluctuating cellular conditions, are also discussed. Finally, our thoughts for emerging and future directions in the field are discussed, including in vitro and in vivo studies of MLO physical chemistry and function.

Keywords: active matter; biophysics; liquid-liquid phase separation; membraneless organelles.

Figure 1.

A. Cation-pi interactions involved in phase separation of Ddx4. B. Sliding charge analysis of Ddx4, showing charge blocks in the WT (i) but not in a charge scrambled mutant (ii). iii shows positions of phenylalanine to alanine mutants in another mutant Ddx4. C. Images showing that the above mutants reduce phase-separation propensity in cells. B and C from Nott et al. Molecular Cell (2015) 57:936–947.^{[20a, 23]}

Figure 2.

Different NPM1 states and LLPS mechanisms. a. NPM1 has different folded and disordered regions with charge-patch interactions modulating conformational properties. b-e. Interactions with self or complementary molecules can result in different LLPS mechanisms. f. Suggested assembly-dependent partitioning of rRNA during ribosome biogenesis. See text for additional details. Figure from Mitrea et al. Nature Communications (2018) 9:842.^{[23, 30a]}

Figure 3.

Sub-compartmentalization in the nucleolus. (A) Cartoon of nucleolar substructure and (B) images of droplet within droplet structures in the nucleolus. Figure adapted with permission from Feric et al. Cell (2016) 165:1686.

Figure 4.

Cartoon of the magic number effect. When the number of valences on one of the components (here 8, green) is a multiple of those on the other (here 4, blue), a small oligomer satisfies all valences and reduces phase separation. When this condition is not satisfied, larger networks of interacting species are formed leading to LLPS.