Toward universal models for collective interactions in biomolecular condensates

Biophysics Reviews, Journal Year: 2025, Volume and Issue: 6(1)

Published: March 1, 2025

A wide range of higher-order structures, including dense, liquid-like assemblies, serve as key components cellular matter. The molecular language how protein sequences encode the formation and biophysical properties biomolecular condensates, however, is not completely understood. Recent notion on scale invariance cluster sizes below critical concentration for phase separation suggests a universal mechanism, which can operate from oligomers to non-stoichiometric assemblies. Here, we propose model collective interactions in based context-dependent variable interactions. We provide mathematical formalism, capable describing growing dynamic clusters well changes their material properties. Furthermore, discuss consequences maximize sensitivity environmental signals increase correlation lengths.

Language: Английский

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Heterogeneous elasticity drives ripening and controls bursting kinetics of transcriptional condensates

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(12)

Published: March 15, 2024

Many biomolecular condensates, including transcriptional are formed in elastic mediums. In this work, we study the nonequilibrium condensate dynamics a chromatin-like environment modeled as heterogeneous medium. We demonstrate that ripening process such an medium exhibits temporal power-law scaling of average radius, depending on local stiffness distribution and different from Ostwald ripening. Moreover, incorporate active to model dissolution condensates upon RNA accumulation. Intriguingly, three types kinetics growth emerge, corresponding constitutively expressed, transcriptional-bursting, silenced genes. Furthermore, simulated burst frequency decreases exponentially with stiffness, through which infer lognormal living cells using transcriptome-wide frequency. Under inferred distribution, distributions bursting kinetic parameters agree reasonably well experimental data. Our findings reveal interplay between mediums, yielding far-reaching implications for gene expression.

Language: Английский

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Learning physics and biology from cytoskeletal and condensate interactions

Current Opinion in Cell Biology, Journal Year: 2025, Volume and Issue: 94, P. 102506 - 102506

Published: April 6, 2025

Two important mechanisms for self-organization in cells include condensation of biomolecules, such as proteins and nucleic acids into phase-separated droplets to form membraneless organelles organization the cytoskeletal filaments larger-scale systems actin cortex microtubule-based mitotic spindle. Recent publications highlight that these two intracellular schemes are coordinated, with condensates controlling organizations cytoskeleton organizing condensates. Here, we focus on recent progress from past 2 years at interface between cytoskeleton. We split discussion physical biological principles can learn studies.

Language: Английский

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Nanotubes Growth by Self-Assembly of DNA Strands at Room Temperature

ACS Nano, Journal Year: 2025, Volume and Issue: unknown

Published: May 8, 2025

Artificial biomolecular nanotubes are a promising approach to building materials mimicking the capacity of cellular cytoskeleton grow and self-organize dynamically. Nucleic acid nanotechnology has demonstrated variety self-assembling with programmable, robust features morphological similarities actual components. However, their production typically requires thermal annealing, which not only poses general constraint on potential applications but is also incompatible physiological conditions. Here, we demonstrate that DNA can self-assemble from simple mixture five short strands at constant room temperature, growing for extended periods time in bulk conditions as well under confinement. Assembly achieved using monovalent salt buffer, ensures faithful nanoscale arrangement avoids nanotube aggregation. We observe formation individual up 20 days diameter 22 ± 4 nm length several tens micrometers. finally encapsulate microsized compartments, such water-in-oil microdroplets giant unilamellar vesicles serving cell models. Notably, isothermally directly inside microcompartments into dynamic higher-order structures resembling rings networks. Our study provides an advantageous method situ assembly programmable scaffolds synthetic without requirements treatment.

Language: Английский

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Protein Condensates and Protein Aggregates: In Vitro, in the Cell, and In Silico

Frontiers in Bioscience-Landmark, Journal Year: 2023, Volume and Issue: 28(8), P. 183 - 183

Published: Aug. 28, 2023

Similar to other polypeptides and electrolytes, proteins undergo phase transitions, obeying physicochemical laws. They can liquid-to-gel liquid-to-liquid transitions. Intrinsically disordered are particularly susceptible separation. After a general introduction, the principles of in vitro studies protein folding, aggregation, condensation described. Numerous recent older have confirmed that process liquid-liquid separation (LLPS) leads various condensed bodies cells, which is one way cells manage stress. We review what known about aggregation cell, notwithstanding protective pathological roles aggregates. This includes membrane-less organelles cytotoxicity prefibrillar oligomers amyloid-forming proteins. then describe evaluate bioinformatic (in silico) methods for predicting aggregation-prone regions form amyloids, prions, condensates.

Language: Английский

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