Imaging-Based Quantitative Assessment of Biomolecular Condensates in vitro and in Cells DOI Creative Commons
Tessa Bergsma, Anton Steen, Julia Kamenz

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 22, 2024

Abstract The formation of biomolecular condensates contributes to intracellular compartmentalization, and plays an important role in many cellular processes. characterization is however challenging, requiring advanced biophysical or biochemical methods that are often less suitable for vivo studies. A particular need easily accessible yet thorough enable the across different experimental systems thus remains. To address this, we present PhaseMetrics, a semi-automated FIJI-based image analysis pipeline tailored quantifying particle properties from microscopy data. Tested using FG-domain yeast nucleoporin Nup100, PhaseMetrics accurately assesses diverse setups, including vitro , Xenopus egg extracts, systems. It reliably detects changes induced by various conditions such as presence polyethylene glycol, 1,6-hexanediol, salt gradient, molecular chaperone DNAJB6b. By enabling accurate representation variability within population detection subtle at single level, method complements conventional assays. Combined, accessible, customizable enables imaging-based quantitative assessment cells, providing valuable addition current toolbox.

Language: Английский

Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins DOI
Munishwar N. Gupta, Vladimir N. Uversky

International Journal of Biological Macromolecules, Journal Year: 2023, Volume and Issue: 257, P. 128646 - 128646

Published: Dec. 6, 2023

Language: Английский

Citations

33
The Protein Scaffolding Functions of Polyphosphate DOI
Jian Guan,

Ursula Jakob

Journal of Molecular Biology, Journal Year: 2024, Volume and Issue: 436(14), P. 168504 - 168504

Published: Feb. 27, 2024

Language: Английский

Citations

15
SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis DOI Creative Commons

Kira Breunig,

X. Lei,

Mauro Montalbano

et al.

eLife, Journal Year: 2025, Volume and Issue: 13

Published: Feb. 12, 2025

RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such stress granules nucleoli. IDR-RBPs particularly relevant nervous system their dysfunction is associated with neurodegenerative diseases brain tumor development. Serpine1 mRNA-binding protein 1 (SERBP1) a unique member this group, being mostly lacking canonical RNA-binding domains. We defined SERBP1’s interactome, uncovered novel roles splicing, cell division ribosomal biogenesis, showed its participation pathological Tau aggregates Alzheimer’s brains. SERBP1 preferentially interacts other G-quadruplex (G4) binders, implicated different stages gene expression, suggesting that G4 critical component settings. Similarly, we identified important associations between PARP1/polyADP-ribosylation (PARylation). PARP1 factors influences PARylation. Moreover, which participates contain PARylated PAR binders. Based on these results, propose feedback regulatory model PARylation, while PARylation modulates functions complexes.

Language: Английский

Citations

1
Biomolecular condensates: insights into early and late steps of the HIV-1 replication cycle DOI Creative Commons
Francesca Di Nunzio, Vladimir N. Uversky, Andrew J. Mouland

et al.

Retrovirology, Journal Year: 2023, Volume and Issue: 20(1)

Published: April 7, 2023

Abstract A rapidly evolving understanding of phase separation in the biological and physical sciences has led to redefining virus-engineered replication compartments many viruses with RNA genomes. Condensation viral, host genomic subgenomic RNAs can take place evade innate immunity response help viral replication. Divergent prompt liquid–liquid (LLPS) invade cell. During HIV there are several steps involving LLPS. In this review, we characterize ability individual partners that assemble into biomolecular condensates (BMCs). Of note, bioinformatic analyses predict models line published observations. Importantly, BMCs contribute function key retroviral For example, reverse transcription takes within nuclear BMCs, called HIV-MLOs while during late steps, nucleocapsid acts as a driver or scaffold recruit client components aid assembly progeny virions. Overall, LLPS infections represents newly described event now appreciated virology field, also be considered an alternative pharmacological target current drug therapies especially when become resistant antiviral treatment.

Language: Английский

Citations

21
The Role of Liquid–Liquid Phase Separation in Actin Polymerization DOI Open Access
Olga I. Povarova, Iuliia A. Antifeeva, Alexander V. Fonin

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(4), P. 3281 - 3281

Published: Feb. 7, 2023

To date, it has been shown that the phenomenon of liquid-liquid phase separation (LLPS) underlies many seemingly completely different cellular processes. This provided a new idea spatiotemporal organization cell. The paradigm makes possible to provide answers long-standing, but still unresolved questions facing researcher. In particular, regulation assembly/disassembly cytoskeleton, including formation actin filaments, becomes clearer. coacervates actin-binding proteins arise during type can integrate G-actin and thereby increase its concentration initiate polymerization. It also activity intensification control polymerization, such as N-WASP Arp2/3, be caused by their integration into liquid droplet formed signaling on inner side cell membrane.

Language: Английский

Citations

13
Interfacial stabilization of aqueous two-phase systems: a review DOI Creative Commons

Caitlyn Fick,

Zara Khan, Samanvaya Srivastava

et al.

Materials Advances, Journal Year: 2023, Volume and Issue: 4(20), P. 4665 - 4678

Published: Jan. 1, 2023

A review discussing aqueous two-phase systems (ATPS), their utility, and many different approaches for stabilizing water/water (w/w) emulsions.

Language: Английский

Citations

12
Functional unfoldomics: Roles of intrinsic disorder in protein (multi)functionality DOI
Vladimir N. Uversky

Advances in protein chemistry and structural biology, Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 1, 2023

Language: Английский

Citations

11
On the Roles of Protein Intrinsic Disorder in the Origin of Life and Evolution DOI Creative Commons
Vladimir N. Uversky

Life, Journal Year: 2024, Volume and Issue: 14(10), P. 1307 - 1307

Published: Oct. 15, 2024

Obviously, the discussion of different factors that could have contributed to origin life and evolution is clear speculation, since there no way checking validity most related hypotheses in practice, as corresponding events not only already happened, but took place a very distant past. However, are few undisputable facts present at moment, such existence wide variety living forms abundant presence intrinsically disordered proteins (IDPs) or hybrid containing ordered domains regions (IDRs) all forms. Since it seems currently existing originated from common ancestor, their result evolution. Therefore, one ask logical question what role(s) structureless highly dynamic vastly multifunctional IDPs/IDRs might This study represents an attempt consider various ideas pertaining potential roles protein intrinsic disorder

Language: Английский

Citations

4
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation DOI

Omar Jurado,

Marco V. José, Eugenio Frixione

et al.

Biosystems, Journal Year: 2025, Volume and Issue: unknown, P. 105405 - 105405

Published: Jan. 1, 2025

Language: Английский

Citations

0
A sequence‐based model for identifying proteins undergoing liquid–liquid phase separation/forming fibril aggregates via machine learning DOI

Shaofeng Liao,

Yujun Zhang, Xinchen Han

et al.

Protein Science, Journal Year: 2024, Volume and Issue: 33(3)

Published: Feb. 21, 2024

Liquid-liquid phase separation (LLPS) and the solid aggregate (also referred to as amyloid aggregates) formation of proteins, have gained significant attention in recent years due their associations with various physiological pathological processes living organisms. The systematic investigation differences connections between proteins undergoing LLPS those forming fibrils at sequence level has not yet been explored. In this research, we aim address gap by comparing two types across 36 features using collected data available currently. statistical comparison results indicate that, 24 selected exhibit difference protein groups. A LLPS-Fibrils binary classification model built on these random forest reveals that fraction intrinsically disordered residues (F

Language: Английский

Citations

3