Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions - PubMed (original) (raw)

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Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions

Jeong-Mo Choi et al. Annu Rev Biophys. 2020.

Abstract

Many biomolecular condensates appear to form via spontaneous or driven processes that have the hallmarks of intracellular phase transitions. This suggests that a common underlying physical framework might govern the formation of functionally and compositionally unrelated biomolecular condensates. In this review, we summarize recent work that leverages a stickers-and-spacers framework adapted from the field of associative polymers for understanding how multivalent protein and RNA molecules drive phase transitions that give rise to biomolecular condensates. We discuss how the valence of stickers impacts the driving forces for condensate formation and elaborate on how stickers can be distinguished from spacers in different contexts. We touch on the impact of sticker- and spacer-mediated interactions on the rheological properties of condensates and show how the model can be mapped to known drivers of different types of biomolecular condensates.

Keywords: biomolecular condensates; phase separation; phase transition; stickers and spacers.

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Figures

Figure 1:

Figure 1:. Overview of cellular bodies that are well-described as condensates.

These bodies include large well-studied structures such as the nucleolus, nuclear speckles, and P-bodies, but also smaller assemblies including those such as signaling granules, receptor clusters and DNA damage foci. The size of assemblies in this schematic are not to scale.

Figure 2:

Figure 2:. Schematic of different types of stickers and spacers for different systems.

(a) For folded proteins we can map stickers and spacers to the patchy colloid formalism. (b) For linear multivalent proteins we can broadly map stickers as folded binding domains while spacers are flexible linkers that connected domains (c) For intrinsically disordered proteins stickers may be single residues, short linear motifs, or some combination of both.

Figure 3:

Figure 3:. Schematic of sticker patterning and effective solvation volume.

(a) Three distinct sequences with identical numbers of sticker residues distributed in different arrangements. As sticker residues are clustered together, the effective sticker identity may change, such that as the number of stickers decrease the strength of each individual sticker increases. There are likely complex non-linearities in this behavior, such that the schematic here should be taken only as a qualitative description of this phenomenon. B Physical manifestation of the effective solvation volume for linkers. A positive effective solvation volume is associated with expanded and highly expanded linkers while a negative effective solvation volume leads to a collapsed and self-interacting linker. An effective solvation volume of zero implies ideal chain behavior.

Figure 4:

Figure 4:. Four examples of multiphase assemblies formed from different components.

(a) Three-phase nucleoli assembly is readily reproduced using a simple stickers-and-spacers model, as shown by Feric et al. (b) Various distinct types of nuclear speckle architecture can also be recapitulated in a similar manner, as shown by Fei et al. (c) MEG-3 and PGL-3 form distinct phases in P-granules and in vitro, as demonstrated by Putnam et al. (d) A simple four component system (solvent, proline-arginine dipeptides, polyadenosine, polycytosine) forms two distinct dense phases due to distinct sticker-sticker strengths, as described by Boeynaems et al.

Figure 5:

Figure 5:

(a) General model for emergent stickers formed through oligomerization. Monomeric species might lack the requisite valence to drive condensates, but oligomerization through a defined interface gives rise to multivalence of emergent stickers that drive condensate formation. (b) A schematized version of condensate regulation in the context of ARF19. The PB1 oligomerization domain drives assembly via an electrostatically mediated binding surface. Neutralization of a lysine residues abrogates oligomerization and consequently prevents condensate formation. (c) For a system that gives rise to emergent stickers, condensate formation can be regulated at two levels. An effectively binary regulation that dictates whether oligomerization occurs (modulation of valence), and a second level in which the strength of emergent stickers can be altered. Note that temporally the order in which these levels of modulation occur is irrelevant. As a tangible example, in a scenario in which IDRs phosphorylation weakens the strength of emergent stickers, the act of phosphorylation could happen before or after oligomerization. The binding of ligands, which could include other proteins, nucleic acids, small molecules, may either lead to a conformational transition that allows homotypic oligomerization or itself could drive heterotypic assembly. In principle, multiple nested layers of assembly via orthogonal interaction modes provide the foundations for arbitrarily complex regulation.

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