scholarly journals PhaSePro: the database of proteins driving liquid–liquid phase separation

2019 ◽  
Author(s):  
Bálint Mészáros ◽  
Gábor Erdős ◽  
Beáta Szabó ◽  
Éva Schád ◽  
Ágnes Tantos ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Ribosome Biogenesis ◽  
Weak Interactions ◽  
Experimental Studies ◽  
Rna Degradation ◽  
Liquid Phase Separation ◽  
General Mechanism ◽  
Open Questions ◽  
Liquid Liquid Phase Separation

Abstract Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromolecules. Since the first discoveries of certain proteins being able to drive LLPS, it emerged as a general mechanism for the effective organization of cellular space that is exploited in all kingdoms of life. While numerous experimental studies report novel cases, the computational identification of LLPS drivers is lagging behind, and many open questions remain about the sequence determinants, composition, regulation and biological relevance of the resulting condensates. Our limited ability to overcome these issues is largely due to the lack of a dedicated LLPS database. Therefore, here we introduce PhaSePro (https://phasepro.elte.hu), an openly accessible, comprehensive, manually curated database of experimentally validated LLPS driver proteins/protein regions. It not only provides a wealth of information on such systems, but improves the standardization of data by introducing novel LLPS-specific controlled vocabularies. PhaSePro can be accessed through an appealing, user-friendly interface and thus has definite potential to become the central resource in this dynamically developing field.

scholarly journals Branching microtubule nucleation is controlled by importin-mediated inhibition of TPX2 phase separation

2020 ◽  
Author(s):  
Mohammad S. Safari ◽  
Matthew R. King ◽  
Clifford P. Brangwynne ◽  
Sabine Petry
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Weak Interactions ◽  
Spindle Assembly ◽  
Liquid Phase Separation ◽  
Nuclear Localization Sequence ◽  
Microtubule Nucleation ◽  
Importin Α ◽  
Liquid Liquid Phase Separation

AbstractThe microtubule-based mitotic spindle is responsible for equally partitioning the genome during each cell division, and its assembly is executed by several microtubule nucleation pathways. In the spindle center, Targeting Protein for XKlp2 (TPX2) promotes branching microtubule nucleation, where new microtubules are nucleated from pre-existing ones. Until the onset of spindle assembly, TPX2 is sequestered by importins-α/β, yet the molecular nature of this regulation remains unclear, particularly since TPX2 was recently found to undergo a liquid-liquid phase separation to execute its function. Here we demonstrate that TPX2 interacts with importins-α/β with nanomolar affinity as a 1:1:1 mono-dispersed trimer. We identify a new nuclear localization sequence (NLS) on TPX2, which contributes to its high-affinity interaction with importin-α. Interestingly, importin-β alone can also associate with TPX2, and does so via dispersed, weak interactions. Interactions of both importin-α and importin-β with TPX2 each inhibit its propensity for phase separation, and consequently its ability to orchestrate branching microtubule nucleation. In sum, our study explains how TPX2 is regulated in order to facilitate spindle assembly, and provides novel insight into how a protein phase separation can be inhibited via weak biomolecular interactions.Significance StatementThe discovery that proteins can undergo phase separation is revolutionizing biology. Characterization of dozens of phase separating proteins in vitro over the past several years has mainly focused on how macromolecules undergo liquid-liquid phase separation (LLPS). The next, and possibly bigger challenge is to investigate how LLPS is regulated in the cell, namely how it is inhibited to spatiotemporally control a certain cellular function. Here, we addressed this challenge by identifying how the spindle assembly factor TPX2 is inhibited by importins from undergoing LLPS and thereby turning on spindle assembly.

scholarly journals Liquid-liquid phase separation in organic particles containing one and two organic species: importance of the average O:C

2018 ◽  
Author(s):  
Mijung Song ◽  
Suhan Ham ◽  
Ryan J. Andrews ◽  
Yuan You ◽  
Allan K. Bertram
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Cloud Condensation Nuclei ◽  
Experimental Studies ◽  
Liquid Phase Separation ◽  
Inorganic Salts ◽  
Organic Species ◽  
Organic Particles ◽  
Almost All ◽  
Liquid Liquid Phase Separation

Abstract. Recently, experimental studies have shown that liquid-liquid phase separation (LLPS) can occur in organic particles free of inorganic salts. Most of these studies used organic particles consisting of secondary organic materials generated in environmental chambers. To gain additional insight into LLPS in organic particles free of inorganic salts, we studied LLPS in organic particles consisting of one and two commercially available organic species. For particles containing one organic species, three out of the six particle types investigated underwent LLPS. In these cases, LLPS was observed when the O:C was ≤ 0.44 and the RH was between ~ 97 and ~ 100 %. The mechanism of phase separation was likely nucleation and growth. For particles containing two organic species, thirteen out of the fifteen particle types investigated underwent LLPS. In these cases, LLPS was observed when the O:C was ≤ 0.58 and mostly when the RH was between ~ 90 and ~ 100 % RH. The mechanism of phase separation was likely spinodal decomposition. In almost all cases when LLPS was observed (for both one-component and two-component particles), the highest RH at which two liquids was observed was 100 ± 2.0 %, which has important implications for the cloud condensation nuclei (CCN) properties of these particles. These combined results provide additional evidence that LLPS needs to be considered when predicting the CCN properties of organic particles in the atmosphere.

scholarly journals Liquid–liquid phase separation in organic particles containing one and two organic species: importance of the average O : C

2018 ◽  
Vol 18 (16) ◽  
pp. 12075-12084 ◽  
Author(s):  
Mijung Song ◽  
Suhan Ham ◽  
Ryan J. Andrews ◽  
Yuan You ◽  
Allan K. Bertram
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Cloud Condensation Nuclei ◽  
Experimental Studies ◽  
Liquid Phase Separation ◽  
Inorganic Salts ◽  
Organic Species ◽  
Organic Particles ◽  
Almost All ◽  
Liquid Liquid Phase Separation

Abstract. Recently, experimental studies have shown that liquid–liquid phase separation (LLPS) can occur in organic particles free of inorganic salts. Most of these studies used organic particles consisting of secondary organic materials generated in environmental chambers. To gain additional insight into LLPS in organic particles free of inorganic salts, we studied LLPS in organic particles consisting of one and two commercially available organic species. For particles containing one organic species, three out of the six particle types investigated underwent LLPS. In these cases, LLPS was observed when the O : C was  ≤ 0.44 (but not always) and the relative humidity (RH) was between  ∼ 97 % and  ∼ 100 %. The mechanism of phase separation was likely nucleation and growth. For particles containing two organic species, 13 out of the 15 particle types investigated underwent LLPS. In these cases, LLPS was observed when the O : C was  ≤ 0.58 (but not always) and mostly when the RH was between  ∼ 90 % RH and  ∼ 100 % RH. The mechanism of phase separation was likely spinodal decomposition. In almost all cases when LLPS was observed (for both one-component and two-component particles), the highest RH at which two liquids was observed was 100±2.0 %, which has important implications for the cloud condensation nuclei (CCN) properties of these particles. These combined results provide additional evidence that LLPS needs to be considered when predicting the CCN properties of organic particles in the atmosphere.

scholarly journals Liquid-Liquid Phase Separation of Tau Driven by Hydrophobic Interaction Facilitates Fibrillization of Tau

2021 ◽  
Vol 433 (2) ◽  
pp. 166731
Author(s):  
Yanxian Lin ◽  
Yann Fichou ◽  
Andrew P. Longhini ◽  
Luana C. Llanes ◽  
Pengyi Yin ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Hydrophobic Interaction ◽  
Liquid Phase Separation ◽  
Liquid Liquid Phase Separation

scholarly journals Amyloid Aggregation under the Lens of Liquid–Liquid Phase Separation

2020 ◽  
pp. 368-378
Author(s):  
Yanting Xing ◽  
Aparna Nandakumar ◽  
Aleksandr Kakinen ◽  
Yunxiang Sun ◽  
Thomas P. Davis ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Liquid Phase Separation ◽  
Amyloid Aggregation ◽  
Liquid Liquid Phase Separation

scholarly journals Observation of liquid-liquid phase separation of ataxin-3 and quantitative evaluation of its concentration in a single droplet using Raman microscopy

2021 ◽  
Author(s):  
Kazuki Murakami ◽  
Shinji Kajimoto ◽  
Daiki Shibata ◽  
Kunisato Kuroi ◽  
Fumihiko Fujii ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Neurodegenerative Diseases ◽  
Protein Aggregation ◽  
Quantitative Evaluation ◽  
Raman Microscopy ◽  
Liquid Phase Separation ◽  
Biological Processes ◽  
Single Droplet ◽  
Liquid Liquid Phase Separation

Liquid–liquid phase separation (LLPS) plays an important role in a variety of biological processes and is also associated with protein aggregation in neurodegenerative diseases. Quantification of LLPS is necessary to...

scholarly journals Targeting NSD2-mediated SRC-3 liquid–liquid phase separation sensitizes bortezomib treatment in multiple myeloma

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jing Liu ◽  
Ying Xie ◽  
Jing Guo ◽  
Xin Li ◽  
Jingjing Wang ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Drug Resistance ◽  
Phase Separation ◽  
Liquid Phase ◽  
Liquid Phase Separation ◽  
Acquired Drug Resistance ◽  
Bortezomib Treatment ◽  
Liquid Liquid Phase Separation

AbstractDevelopment of chemoresistance is the main reason for failure of clinical management of multiple myeloma (MM), but the genetic and epigenetic aberrations that interact to confer such chemoresistance remains unknown. In the present study, we find that high steroid receptor coactivator-3 (SRC-3) expression is correlated with relapse/refractory and poor outcomes in MM patients treated with bortezomib (BTZ)-based regimens. Furthermore, in immortalized cell lines, high SRC-3 enhances resistance to proteasome inhibitor (PI)-induced apoptosis. Overexpressed histone methyltransferase NSD2 in patients bearing a t(4;14) translocation or in BTZ-resistant MM cells coordinates elevated SRC-3 by enhancing its liquid–liquid phase separation to supranormally modify histone H3 lysine 36 dimethylation (H3K36me2) modifications on promoters of anti-apoptotic genes. Targeting SRC-3 or interference of its interactions with NSD2 using a newly developed inhibitor, SI-2, sensitizes BTZ treatment and overcomes drug resistance both in vitro and in vivo. Taken together, our findings elucidate a previously unrecognized orchestration of SRC-3 and NSD2 in acquired drug resistance of MM and suggest that SI-2 may be efficacious for overcoming drug resistance in MM patients.

scholarly journals Deciphering the Role of π-Interactions in Polyelectrolyte Complexes Using Rationally Designed Peptides

Polymers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 2074
Author(s):  
Sara Tabandeh ◽  
Cristina Elisabeth Lemus ◽  
Lorraine Leon
Keyword(s):  
Hydrogen Bonding ◽  
Phase Separation ◽  
Liquid Phase ◽  
Charge Density ◽  
Secondary Structures ◽  
Liquid Phase Separation ◽  
Polyelectrolyte Complexes ◽  
Π Interactions ◽  
Liquid Liquid Phase Separation

Electrostatic interactions, and specifically π-interactions play a significant role in the liquid-liquid phase separation of proteins and formation of membraneless organelles/or biological condensates. Sequence patterning of peptides allows creating protein-like structures and controlling the chemistry and interactions of the mimetic molecules. A library of oppositely charged polypeptides was designed and synthesized to investigate the role of π-interactions on phase separation and secondary structures of polyelectrolyte complexes. Phenylalanine was chosen as the π-containing residue and was used together with lysine or glutamic acid in the design of positively or negatively charged sequences. The effect of charge density and also the substitution of fluorine on the phenylalanine ring, known to disrupt π-interactions, were investigated. Characterization analysis using MALDI-TOF mass spectroscopy, H NMR, and circular dichroism (CD) confirmed the molecular structure and chiral pattern of peptide sequences. Despite an alternating sequence of chirality previously shown to promote liquid-liquid phase separation, complexes appeared as solid precipitates, suggesting strong interactions between the sequence pairs. The secondary structures of sequence pairs showed the formation of hydrogen-bonded structures with a β-sheet signal in FTIR spectroscopy. The presence of fluorine decreased hydrogen bonding due to its inhibitory effect on π-interactions. π-interactions resulted in enhanced stability of complexes against salt, and higher critical salt concentrations for complexes with more π-containing amino acids. Furthermore, UV-vis spectroscopy showed that sequences containing π-interactions and increased charge density encapsulated a small charged molecule with π-bonds with high efficiency. These findings highlight the interplay between ionic, hydrophobic, hydrogen bonding, and π-interactions in polyelectrolyte complex formation and enhance our understanding of phase separation phenomena in protein-like structures.

Sign in / Sign up

Export Citation Format

Share Document