Structure-function properties in disordered condensates

Abstract

Biomolecular condensates appear throughout the cell serving a wide variety of functions. Many condensates appear to form by the assembly of multivalent molecules, which produce phase separated networks with liquid-like properties. These networks then recruit client molecules, with the total composition providing functionality. Here we use a model system of poly-SUMO and poly-SIM proteins to understand client-network interactions and find that the structure of the network plays a strong role in defining client recruitment, and thus functionality. The basic unit of assembly in this system is a zipper-like filament composed of alternating poly-SUMO and poly-SIM molecules.These filaments have defects of unsatisfied bonds that allow for both the formation of a 3D network and the recruitment of clients. The filamentous structure constrains the scaffold stoichiometries and the distribution of client recruitment sites that the network can accommodate. This results in a non-monotonic client binding response that can be tuned independently by the client valence and binding energy. These results show how the interactions within liquid states can be disordered yet still contain structural features that provide functionality to the condensate. I. INTRODUCTIONMany cellular structures have been shown to form by the spontaneous condensation of biomolecules into liquidlike states [1,2], often through liquid-liquid phase transitions. While these condensates may contain hundreds of different molecules, typically only a small number of molecules with high interaction valence and high connectivity to other molecules in the structure contribute strongly to phase separation [3][4][5]. These are said to have scaffoldlike properties depending on how strongly they promote phase separation. The remaining molecules, which exhibit client-like properties, are recruited through interactions with scaffolds [6,7]. Together, the collection of molecules in a condensate determines its functionality.Since the molecules driving phase separation are multivalent, polymer-like species, many treatments of condensate formation are based on polymer theories [8][9][10][11]. In particular, scaffold condensation can be understood as the interaction between attractive stickers separated by inert spacers [11,12]. These efforts explain universal features of condensates, such as how multivalency can amplify the effect of weak interactions to tune the phase coexistence line to within physiologically relevant regions of phase space (e.g. physiological concentrations) [8]. However, there are also many non-universal features of biomolecular condensates. Experiments are revealing a striking diversity of functions performed by condensates [2,7,[13][14][15][16], and each of these assemblies will be under evolutionary pressure to optimize its specific function. This begs the question of how the disordered network of interactions within a liquid structure can affect its properties.

Using quantitative reconstitution to investigate multicomponent condensates

“…Since condensates can either activate or inhibit RNA-decapping activity, it is clear that condensate formation does not enhance RNA decapping per se. Rather the concentration and organization of activating molecules within condensates are likely important in regulating this activity (Nissan et al 2010;Bhandari et al 2021;Peeples and Rosen 2021). Thus, adjusting stoichiometry could be a regulatory mechanism to determine the balance of RNA degradation vs storage within natural Pbodies (Fig.…”

Quantitative reconstitution of yeast RNA processing bodies

“…This example illustrates how composition can modulate enzymatic activities within condensates, and highlights the importance of efforts to mimic cellular complexity when investigating the biochemical activities of condensates. In addition to individual biochemical activities being increased within P bodies, the transfer of substrate RNA between different types of enzymes could also be enhanced, particularly if certain molecules are spatially organized within the condensates (94, 95), potentially resulting in a significant increase in the overall rate of RNA degradation. This reconstitution, which includes all highly enriched P-body proteins and many activators, is suitable for future examination of enzymatic activities and pathway flux within P bodies.…”

Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair

“…Thus, the BTB-IDR2 portion of SLX4 enables the formation of SLX4 condensates by optogenetic activation. IDR2 includes multiple SUMOylation sites as well as three SUMO-interacting motifs (SIMs) that may in principle promote the formation of biomolecular condensates (46)(47)(48).…”