G3BP-driven RNP granules promote inhibitory RNA-RNA interactions resolved by DDX3X to regulate mRNA translatability DOI Creative Commons

Irmela R. E. A. Trussina,

Andreas Hartmann, Christine Desroches Altamirano

et al.

Molecular Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Ribonucleoprotein (RNP) granules have been linked to translation regulation and disease, but their assembly regulatory mechanisms are not well understood. Here, we show that the RNA-binding protein G3BP1 preferentially interacts with unfolded RNA, driving of RNP granule-like condensates establish RNA-RNA interactions. These interactions limit mobility translatability sequestered mRNAs stabilize condensates. The DEAD-box RNA helicase DDX3X attenuates inside condensates, rendering dynamic enabling mRNA translation. Importantly, disease-associated catalytically inactive variants fail resolve such Inhibiting in cultured cells accelerates granule delays disassembly, indicating contribute stability cells. Our findings reveal how generate inhibitory modulated by helicases ensure availability translatability.

Language: Английский

Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates DOI Creative Commons
Andrés R. Tejedor,

Anne Aguirre Gonzalez,

Maria Julia Maristany

et al.

ACS Central Science, Journal Year: 2025, Volume and Issue: 11(2), P. 302 - 321

Published: Feb. 11, 2025

Biomolecular condensates composed of highly charged biomolecules, such as DNA, RNA, chromatin, and nucleic-acid binding proteins, are ubiquitous in the cell nucleus. The biophysical properties these charge-rich largely regulated by electrostatic interactions. Residue-resolution coarse-grained models that describe solvent ions implicitly widely used to gain mechanistic insights into condensates, offering transferability, computational efficiency, accurate predictions for multiple systems. However, their predictive accuracy diminishes due implicit treatment ions. Here, we present Mpipi-Recharged, a residue-resolution model improves description charge effects biomolecular containing disordered multidomain and/or single-stranded RNAs. Mpipi-Recharged introduces pair-specific asymmetric Yukawa potential, informed atomistic simulations. We show this coarse-graining forces captures intricate effects, blockiness, stoichiometry variations complex coacervates, modulation salt concentration, without requiring explicit solvation. provides excellent agreement with experiments predicting phase behavior condensates. Overall, tools available investigate physicochemical mechanisms regulating enhancing scope computer simulations field.

Language: Английский

Citations

2
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates DOI
Alexander I. M. Sever, Rashik Ahmed, Philip Rößler

et al.

Current Opinion in Structural Biology, Journal Year: 2025, Volume and Issue: 90, P. 102976 - 102976

Published: Jan. 20, 2025

Language: Английский

Citations

1
Evolution Driven Microscale Combinatorial Chemistry in Intracellular Mimicking Droplets to Engineer Thermostable RNA for Cellular Imaging DOI Creative Commons
Andrew B. Kinghorn, Wei Guo,

Lin Wang

et al.

Small, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 26, 2025

Abstract Fluorescent light‐up aptamer/fluorogen pairs are powerful tools for tracking RNA in the cell, however limitations thermostability and fluorescence intensity exist. Current vitro selection techniques struggle to mimic complex intracellular environments, limiting vivo biomolecule functionality. Taking inspiration from microenvironment‐dependent folding observed cells organelle‐mimicking droplets, an efficient system is created that uses microscale heated water droplets simulate conditions, effectively replicating landscape. This integrated with microfluidic droplet sorting evolve aptamers. Through this approach, aptamer engineered improved activity by exploring chemical fitness landscape under biomimetic conditions. The enhanced named eBroccoli has increased thermal stability, both bacterial mammalian cells. In cell culture a improvement of 3.9‐times biological stability up 45 °C systems. enable real‐time visualization nanoscale stress granule formation during heat shock at 42 °C. By introducing concept “biomimetic equivalence” based on folding, platform offers simple yet effective strategy complexity evolution‐based engineering.

Language: Английский

Citations

0
Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations DOI Creative Commons
Matteo Boccalini, Yelyzaveta Berezovska, Giovanni Bussi

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(15)

Published: April 9, 2025

Biomolecular condensates are currently recognized to play a key role in organizing cellular space and orchestrating biochemical processes. Despite an increasing interest characterizing their internal organization at the molecular scale, not much is known about how densely crowded environment within these affects structural properties of recruited macromolecules. Here, we adopted explicit-solvent all-atom simulations based on combination enhanced sampling approaches investigate conformational ensemble RNA hairpin reshaped highly concentrated peptide solution that mimics interior biomolecular condensate. Our indicate structure greatly perturbed by this distinctive physico-chemical environment, which weakens secondary promotes extended nonnative conformations. The resulting high-resolution picture reveals unfolding driven effective solvation nucleobases through hydrogen bonding stacking interactions with surrounding peptides. This solvent effect can be modulated amino acid composition model condensate as proven differential behavior observed case arginine-rich lysine-rich

Language: Английский

Citations

0
Using the amide 15N CEST NMR experiment to study slow exchange between ‘visible’ protein states DOI

Nihar Pradeep Khandave,

Ved Prakash Tiwari, Pramodh Vallurupalli

et al.

Journal of Magnetic Resonance, Journal Year: 2025, Volume and Issue: unknown, P. 107883 - 107883

Published: April 1, 2025

Language: Английский

Citations

0
Client-scaffold interactions suppress aggregation of a client protein in model condensates DOI
Rashik Ahmed,

Rhea P. Hudson,

Julie D. Forman‐Kay

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 17, 2025

ABSTRACT Many studies have shown that sequestration of client proteins into condensates locally increases their concentrations and/or modulates conformational landscapes to promote aberrant aggregation. Far fewer examples emerged where the proteinaceous condensed phase environment protects clients from Here, we show a condensate scaffolded by C-terminal disordered region Cell Cycle Associated Protein 1 (CAPRIN1) suppresses aggregation Fused in Sarcoma (FUS) RNA Recognition Motif (RRM) client, both components stress granules. Although FUS RRM is mediated through unfolded ensemble, comparative NMR outside and within establish CAPRIN1 attenuate despite increasing its concentration 2-fold significantly unfolding domain. Regions transient intermolecular contacts between protomers driving been identified, including hydrophobic segments spanning I287-I308 G335-A369. Intermolecular NOE experiments recorded on RRM:CAPRIN1 indicate interacts with much RRM, regions stronger sequences 287 IFVQ 290, 296 VTIES 300, 322 INLY 325 , 351 IDWFDG 356 . These interactions collectively outcompete homotypic Our results demonstrate scaffold molecules can, some cases, shield interprotomer interactions, delaying or completely suppressing SIGNIFICANCE STATEMENT Numerous can protein cells, potentially leading disease. Here cases protect against them, using model system consisting pair are found Protection occurs even though polypeptide chains, normally associated aggregation, increase condensed-phase environment. Using solution spectroscopy, provide an atomic resolution map recognition module FUS, phase-separating protein, CAPRIN1, findings broaden our understanding mechanisms which regulate cellular homeostasis.

Language: Английский

Citations

0
Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic Simulations DOI Creative Commons
Matteo Boccalini, Yelyzaveta Berezovska, Giovanni Bussi

et al.

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

Published: Sept. 19, 2024

Biomolecular condensates are currently recognized to play a key role in organizing cellular space and orchestrating biochemical processes. Despite an increasing interest characterizing their internal organization at the molecular scale, not much is known about how densely crowded environment within these affects structural properties of recruited macromolecules. Here we adopted explicit-solvent all-atom simulations based on combination enhanced sampling approaches investigate conformational ensemble RNA hairpin reshaped highly-concentrated peptide solution that mimics interior biomolecular condensates. Our indicate structure greatly perturbed by this distinctive physico-chemical environment, which weakens secondary promotes extended non-native conformations. The resulting high-resolution picture reveals unfolding driven effective solvation nucleobases through hydrogen bonding stacking interactions with surrounding peptides. This solvent effect can be modulated aminoacid composition model condensate as proven differential behaviour observed case arginine-rich lysine-rich peptides

Language: Английский

Citations

3
Mapping and engineering RNA-controlled architecture of the multiphase nucleolus DOI Creative Commons
Sofia A. Quinodoz, Lianzhou Jiang,

AA Abu-Alfa

et al.

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

Published: Sept. 29, 2024

Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, nucleolus is a layered multiphase liquid-like structure and site ribosome biogenesis. In nucleolus, ribosomal RNAs (rRNAs) transcribed processed, undergoing multiple maturation steps that ultimately result formation small subunit (SSU) large (LSU). However, how rRNA processing coupled to nucleolar organization poorly understood due lack tools precisely monitor perturb dynamics. Here, we developed two complementary approaches spatiotemporally map engineer

Language: Английский

Citations

3
G3BP-driven RNP granules promote inhibitory RNA-RNA interactions resolved by DDX3X to regulate mRNA translatability DOI Creative Commons

Irmela R. E. A. Trussina,

Andreas Hartmann, Christine Desroches Altamirano

et al.

Molecular Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Ribonucleoprotein (RNP) granules have been linked to translation regulation and disease, but their assembly regulatory mechanisms are not well understood. Here, we show that the RNA-binding protein G3BP1 preferentially interacts with unfolded RNA, driving of RNP granule-like condensates establish RNA-RNA interactions. These interactions limit mobility translatability sequestered mRNAs stabilize condensates. The DEAD-box RNA helicase DDX3X attenuates inside condensates, rendering dynamic enabling mRNA translation. Importantly, disease-associated catalytically inactive variants fail resolve such Inhibiting in cultured cells accelerates granule delays disassembly, indicating contribute stability cells. Our findings reveal how generate inhibitory modulated by helicases ensure availability translatability.

Language: Английский

Citations

3