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ATP-triggered stress granule formation via phase separation
18 Aug 2017-
TL;DR: It is indicated that ATP is continuously hydrolysed to deter SG formation under normal conditions, and specific predictions that can be tested experimentally are provided.
Abstract: Stress granules (SG) are droplets of proteins and RNA that form in the cell cytoplasm during stress conditions. We consider minimal models of stress granule formation based on the mechanism of phase separation regulated by ATP-driven chemical reactions. Motivated by experimental observations, we identify a minimal model of SG formation triggered by ATP depletion. Our analysis indicates that ATP is continuously hydrolysed to deter SG formation under normal conditions, and we provide specific predictions that can be tested experimentally.
Citations
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TL;DR: Two active mechanisms that can explain how cells regulate condensate formation and size are proposed and can guide studies into the many emerging roles of biomolecular condensates.
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TL;DR: It is shown that the kinetically arrested metastable multi-droplet state is a dynamic outcome of the interplay between two competing processes: a diffusion-limited encounter between proteins, and the exhaustion of available valencies within smaller clusters, resulting in metastable, long-living droplets.
Abstract: Multivalent biopolymers phase separate into membrane-less organelles (MLOs) which exhibit liquid-like behavior. Here, we explore formation of prototypical MOs from multivalent proteins on various time and length scales and show that the kinetically arrested metastable multi-droplet state is a dynamic outcome of the interplay between two competing processes: a diffusion-limited encounter between proteins, and the exhaustion of available valencies within smaller clusters. Clusters with satisfied valencies cannot coalesce readily, resulting in metastable, long-living droplets. In the regime of dense clusters akin to phase-separation, we observe co-existing assemblies, in contrast to the single, large equilibrium-like cluster. A system-spanning network encompassing all multivalent proteins was only observed at high concentrations and large interaction valencies. In the regime favoring large clusters, we observe a slow-down in the dynamics of the condensed phase, potentially resulting in loss of function. Therefore, metastability could be a hallmark of dynamic functional droplets formed by sticker-spacer proteins.
94 citations
TL;DR: A conceptual framework for rationalizing the recent experimental findings is offered and an outline of the basic thermodynamics of temperature-, pressure-, and osmolyte-dependent LLPS is presented as well as a molecular-level statistical mechanics picture in terms of solvent-mediated interactions and void volumes are presented.
Abstract: Liquid-liquid phase separation (LLPS) of proteins and other biomolecules play a critical role in the organization of extracellular materials and membrane-less compartmentalization of intra-organismal spaces through the formation of condensates. Structural properties of such mesoscopic droplet-like states were studied by spectroscopy, microscopy, and other biophysical techniques. The temperature dependence of biomolecular LLPS has been studied extensively, indicating that phase-separated condensed states of proteins can be stabilized or destabilized by increasing temperature. In contrast, the physical and biological significance of hydrostatic pressure on LLPS is less appreciated. Summarized here are recent investigations of protein LLPS under pressures up to the kbar-regime. Strikingly, for the cases studied thus far, LLPSs of both globular proteins and intrinsically disordered proteins/regions are typically more sensitive to pressure than the folding of proteins, suggesting that organisms inhabiting the deep sea and sub-seafloor sediments, under pressures up to 1 kbar and beyond, have to mitigate this pressure-sensitivity to avoid unwanted destabilization of their functional biomolecular condensates. Interestingly, we found that trimethylamine-N-oxide (TMAO), an osmolyte upregulated in deep-sea fish, can significantly stabilize protein droplets under pressure, pointing to another adaptive advantage for increased TMAO concentrations in deep-sea organisms besides the osmolyte's stabilizing effect against protein unfolding. As life on Earth might have originated in the deep sea, pressure-dependent LLPS is pertinent to questions regarding prebiotic proto-cells. Herein, we offer a conceptual framework for rationalizing the recent experimental findings and present an outline of the basic thermodynamics of temperature-, pressure-, and osmolyte-dependent LLPS as well as a molecular-level statistical mechanics picture in terms of solvent-mediated interactions and void volumes.
91 citations
References
More filters
TL;DR: Two active mechanisms that can explain how cells regulate condensate formation and size are proposed and can guide studies into the many emerging roles of biomolecular condensates.
115 citations
TL;DR: Five aspects – physical and chemical properties, hierarchical organization, uptake selectivity, formation dynamics, and maturation – that are of particular interest are reviewed and how useful coacervates are are are discussed to better understand these aspects of MLOs.
Abstract: Coacervates are condensed liquid-like droplets, usually formed with oppositely charged polymeric molecules. They have been studied extensively in colloid and interface science for their remarkable material properties. The liquid–liquid phase separation underlying coacervate formation also plays an important role in the formation of various membraneless organelles (MLOs) that are found in many living cells. Therefore, there is an increasing interest to use well-characterized coacervates as in vitro models that mimic specific aspects of MLOs. Here, we review five aspects – physical and chemical properties, hierarchical organization, uptake selectivity, formation dynamics, and maturation – that are of particular interest and discuss how useful coacervates are to better understand these aspects of MLOs.
100 citations
TL;DR: It is shown that the kinetically arrested metastable multi-droplet state is a dynamic outcome of the interplay between two competing processes: a diffusion-limited encounter between proteins, and the exhaustion of available valencies within smaller clusters, resulting in metastable, long-living droplets.
Abstract: Multivalent biopolymers phase separate into membrane-less organelles (MLOs) which exhibit liquid-like behavior. Here, we explore formation of prototypical MOs from multivalent proteins on various time and length scales and show that the kinetically arrested metastable multi-droplet state is a dynamic outcome of the interplay between two competing processes: a diffusion-limited encounter between proteins, and the exhaustion of available valencies within smaller clusters. Clusters with satisfied valencies cannot coalesce readily, resulting in metastable, long-living droplets. In the regime of dense clusters akin to phase-separation, we observe co-existing assemblies, in contrast to the single, large equilibrium-like cluster. A system-spanning network encompassing all multivalent proteins was only observed at high concentrations and large interaction valencies. In the regime favoring large clusters, we observe a slow-down in the dynamics of the condensed phase, potentially resulting in loss of function. Therefore, metastability could be a hallmark of dynamic functional droplets formed by sticker-spacer proteins.
94 citations
TL;DR: A conceptual framework for rationalizing the recent experimental findings is offered and an outline of the basic thermodynamics of temperature-, pressure-, and osmolyte-dependent LLPS is presented as well as a molecular-level statistical mechanics picture in terms of solvent-mediated interactions and void volumes are presented.
Abstract: Liquid-liquid phase separation (LLPS) of proteins and other biomolecules play a critical role in the organization of extracellular materials and membrane-less compartmentalization of intra-organismal spaces through the formation of condensates. Structural properties of such mesoscopic droplet-like states were studied by spectroscopy, microscopy, and other biophysical techniques. The temperature dependence of biomolecular LLPS has been studied extensively, indicating that phase-separated condensed states of proteins can be stabilized or destabilized by increasing temperature. In contrast, the physical and biological significance of hydrostatic pressure on LLPS is less appreciated. Summarized here are recent investigations of protein LLPS under pressures up to the kbar-regime. Strikingly, for the cases studied thus far, LLPSs of both globular proteins and intrinsically disordered proteins/regions are typically more sensitive to pressure than the folding of proteins, suggesting that organisms inhabiting the deep sea and sub-seafloor sediments, under pressures up to 1 kbar and beyond, have to mitigate this pressure-sensitivity to avoid unwanted destabilization of their functional biomolecular condensates. Interestingly, we found that trimethylamine-N-oxide (TMAO), an osmolyte upregulated in deep-sea fish, can significantly stabilize protein droplets under pressure, pointing to another adaptive advantage for increased TMAO concentrations in deep-sea organisms besides the osmolyte's stabilizing effect against protein unfolding. As life on Earth might have originated in the deep sea, pressure-dependent LLPS is pertinent to questions regarding prebiotic proto-cells. Herein, we offer a conceptual framework for rationalizing the recent experimental findings and present an outline of the basic thermodynamics of temperature-, pressure-, and osmolyte-dependent LLPS as well as a molecular-level statistical mechanics picture in terms of solvent-mediated interactions and void volumes.
91 citations