Phase Separation
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Genetics ◽  
2021 ◽  
Author(s):  
Pouria Dasmeh ◽  
Roman Doronin ◽  
Andreas Wagner

Abstract One key feature of proteins that form liquid droplets by phase separation inside a cell is multivalency—the presence of multiple sites that mediate interactions with other proteins. We know little about the variation of multivalency on evolutionary time scales. Here, we investigated the long-term evolution (∼600 million years) of multivalency in fungal mRNA decapping subunit 2 protein (Dcp2), and in the FET protein family. We found that multivalency varies substantially among the orthologs of these proteins. However, evolution has maintained the length scale at which sequence motifs that enable protein-protein interactions occur. That is, the total number of such motifs per hundred amino acids is higher and less variable than expected by neutral evolution. To help explain this evolutionary conservation, we developed a conformation classifier using machine-learning algorithms. This classifier demonstrates that disordered segments in Dcp2 and FET proteins tend to adopt compact conformations, which is necessary for phase separation. Thus, the evolutionary conservation we detected may help proteins preserve the ability to undergo phase separation. Altogether, our study reveals that the length scale of multivalent interactions is an evolutionarily conserved feature of two classes of phase-separating proteins in fungi and vertebrates.


2022 ◽  
Vol 64 (1) ◽  
pp. 79
Author(s):  
В.Ф. Гильмутдинов ◽  
М.А. Тимиргазин ◽  
А.К. Аржников

The magnetic phase diagrams of the two-dimensional Hubbard model for isotropic and anisotropic triangular lattices are constructed within the Hartree-Fock and slave boson approximations. The triangular lattice specific non-collinear and spiral magnetic states, as well as phase separation between them, are shown to be realized in a wide range of model parameters along with collinear magnetic states (stripe antiferromagnetic and ferromagnetic). Phase transitions of the first and second order are found, and the boundaries of the phase separation regions are determined. A comparison of the two approximations, Hartree-Fock and slave boson, shows that electronic correlations suppress magnetic states, the region of paramagnetism being expand, for values U/t>5. At the same time, when the Fermi level is near the van Hove singularity, electron correlations do not change the diagrams qualitatively, which is consistent with the previously obtained result for square and cubic lattices. The results are compared with the data available in the literature for other methods and approaches.


eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Mathias L Heltberg ◽  
Judith Miné-Hattab ◽  
Angela Taddei ◽  
Aleksandra M Walczak ◽  
Thierry Mora

The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of contexts, but the mechanism of their formation is not fully understood. Several competing mechanisms exist that are difficult to distinguish empirically, including liquid-liquid phase separation, and the trapping of molecules by multiple binding sites. Here we propose a theoretical framework and outline observables to differentiate between these scenarios from single molecule tracking experiments. In the binding site model, we derive relations between the distribution of proteins, their diffusion properties, and their radial displacement. We predict that protein search times can be reduced for targets inside a liquid droplet, but not in an aggregate of slowly moving binding sites. We use our results to reject the multiple binding site model for Rad52 foci, and find a picture consistent with a liquid-liquid phase separation. These results are applicable to future experiments and suggest different biological roles for liquid droplet and binding site foci.


2021 ◽  
Vol 7 (43) ◽  
Author(s):  
Xin Jin ◽  
Ji-Eun Lee ◽  
Charley Schaefer ◽  
Xinwei Luo ◽  
Adam J. M. Wollman ◽  
...  

2021 ◽  
Vol 22 (21) ◽  
pp. 11431
Author(s):  
Sinem Usluer ◽  
Emil Spreitzer ◽  
Benjamin Bourgeois ◽  
Tobias Madl

The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is the presence of poly-PR/GR dipeptide repeats, which are encoded by the chromosome 9 open reading frame 72 (C9orf72) gene. Recently, it was shown that poly-PR/GR alters chromatin accessibility, which results in the stabilization and enhancement of transcriptional activity of the tumor suppressor p53 in several neurodegenerative disease models. A reduction in p53 protein levels protects against poly-PR and partially against poly-GR neurotoxicity in cells. Moreover, in model organisms, a reduction of p53 protein levels protects against neurotoxicity of poly-PR. Here, we aimed to study the detailed molecular mechanisms of how p53 contributes to poly-PR/GR-mediated neurodegeneration. Using a combination of biophysical techniques such as nuclear magnetic resonance (NMR) spectroscopy, fluorescence polarization, turbidity assays, and differential interference contrast (DIC) microscopy, we found that p53 physically interacts with poly-PR/GR and triggers liquid–liquid phase separation of p53. We identified the p53 transactivation domain 2 (TAD2) as the main binding site for PR25/GR25 and showed that binding of poly-PR/GR to p53 is mediated by a network of electrostatic and/or hydrophobic interactions. Our findings might help to understand the mechanistic role of p53 in poly-PR/GR-associated neurodegeneration.


2021 ◽  
Author(s):  
Soumik Ray ◽  
Debdeep Chatterjee ◽  
Semanti Mukherjee ◽  
Komal Patel ◽  
Jaladhar K Mahato ◽  
...  

Liquid-liquid phase separation (LLPS) and subsequent liquid-to-solid transition is implicated in membraneless organelles formation as well as disease associated protein aggregation. However, how liquid-to-solid transition is initiated inside a liquid droplet remains unclear. Here, using studies at single droplet resolution, we show that liquid-to-solid transition of α-synuclein (α-Syn) liquid droplets is associated with significant changes in the local microenvironment as well as secondary structure of the protein, which is prominently observed at the center of the liquid droplets. With the ageing of liquid droplets, the structured core at the center gradually expands and propagates over entire droplets. Further, during droplet fusion, smaller, homogeneous droplets progressively dissolve and supply proteins to the larger, heterogeneous droplets containing solid-like core at their center. The present study will significantly help to under-stand the physical mechanism of LLPS and liquid-to-solid transition in biological compartmentalization as well as in protein aggregation associated with human neurodegenerative disorders.


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