Quantitative real-time in-cell imaging reveals heterogeneous clusters of proteins prior to condensation DOI Creative Commons

Chenyang Lan,

Juhyeong Kim, Svenja Ulferts

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 15, 2023

Abstract Our current understanding of biomolecular condensate formation is largely based on observing the final near-equilibrium state. Despite expectations from classical nucleation theory, pre-critical protein clusters were recently shown to form under subsaturation conditions in vitro; if similar long-lived comprising more than a few molecules are also present cells, our physical basis biological phase separation may fundamentally change. Here, we combine fluorescence microscopy with photobleaching analysis quantify NELF proteins living, stressed cells. We categorise small and large their dynamics response p38 kinase inhibition. find broad distribution pre-condensate cluster sizes show that can be explained as non-classical surprisingly flat free-energy landscape for wide range an inhibition condensation unstressed

Language: Английский

The molecular basis for cellular function of intrinsically disordered protein regions DOI
Alex S. Holehouse, Birthe B. Kragelund

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 25(3), P. 187 - 211

Published: Nov. 13, 2023

Language: Английский

Citations

221
Phase separation of protein mixtures is driven by the interplay of homotypic and heterotypic interactions DOI Creative Commons
Mina Farag, Wade M. Borcherds, Anne Bremer

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 8, 2023

Prion-like low-complexity domains (PLCDs) are involved in the formation and regulation of distinct biomolecular condensates that form via phase separation coupled to percolation. Intracellular often encompass numerous proteins with PLCDs. Here, we combine simulations experiments study mixtures PLCDs from two RNA-binding proteins, hnRNPA1 FUS. Using experiments, find 1:1 A1-LCD FUS-LCD undergo more readily than either on their own due complementary electrostatic interactions. Tie line analysis reveals stoichiometric ratios different components sequence-encoded interactions contribute jointly driving forces for condensate formation. Simulations also show spatial organization within is governed by relative strengths homotypic versus heterotypic We uncover rules how interaction sequence lengths modulate conformational preferences molecules at interfaces formed proteins.

Language: Английский

Citations

90
A disordered region controls cBAF activity via condensation and partner recruitment DOI Creative Commons
Ajinkya Patil, Amy R. Strom, João A. Paulo

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(22), P. 4936 - 4955.e26

Published: Oct. 1, 2023

Intrinsically disordered regions (IDRs) represent a large percentage of overall nuclear protein content. The prevailing dogma is that IDRs engage in non-specific interactions because they are poorly constrained by evolutionary selection. Here, we demonstrate condensate formation and heterotypic distinct separable features an IDR within the ARID1A/B subunits mSWI/SNF chromatin remodeler, cBAF, establish "sequence grammars" underlying each contribution. Condensation driven uniformly distributed tyrosine residues, partner mediated non-random blocks rich alanine, glycine, glutamine residues. These concentrate specific cBAF protein-protein interaction network essential for localization activity. Importantly, human disease-associated perturbations ARID1B sequence grammars disrupt function cells. Together, these data identify contributions to remodeling explain how phase separation provides mechanism through which both genomic functional recruitment achieved.

Language: Английский

Citations

79
Expanding the molecular language of protein liquid–liquid phase separation DOI
Shiv Rekhi, Cristobal Garcia Garcia,

Mayur Barai

et al.

Nature Chemistry, Journal Year: 2024, Volume and Issue: 16(7), P. 1113 - 1124

Published: March 29, 2024

Language: Английский

Citations

76
Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient DOI Creative Commons
Matthew R. King, Kiersten M. Ruff, Andrew Z. Lin

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(8), P. 1889 - 1906.e24

Published: March 18, 2024

Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed E-rich regions, as defining features of nucleolar proteins. show that the localization preferences proteins determined their IDRs types RNA or DNA binding domains they encompass. In vitro reconstitutions studies in cells showed how condensation, which combines complex coacervation components, contributes to organization. D/E contribute lowering pH co-condensates formed with RNAs vitro. cells, this sets up a gradient between nucleoli nucleoplasm. By contrast, juxta-nucleolar bodies, have different macromolecular compositions, featuring protein very charge profiles, values equivalent higher than Our findings compositional specificities generate physicochemical properties for condensates.

Language: Английский

Citations

65
Thermodynamic forces from protein and water govern condensate formation of an intrinsically disordered protein domain DOI Creative Commons
Saumyak Mukherjee, Lars V. Schäfer

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 21, 2023

Liquid-liquid phase separation (LLPS) can drive a multitude of cellular processes by compartmentalizing biological cells via the formation dense liquid biomolecular condensates, which function as membraneless organelles. Despite its importance, molecular-level understanding underlying thermodynamics this process remains incomplete. In study, we use atomistic molecular dynamics simulations low complexity domain (LCD) human fused in sarcoma (FUS) protein to investigate contributions water and molecules free energy changes that govern LLPS. Both components are found have comparably sizeable thermodynamic FUS condensates. Moreover, quantify counteracting effects released into bulk upon condensate waters retained within droplets. Among various factors considered, solvation entropy interaction enthalpy identified most important contributions, while smaller. These results provide detailed insights on intricate interplay between protein- solvation-related forces

Language: Английский

Citations

48
Sequence-specific interactions determine viscoelasticity and ageing dynamics of protein condensates DOI
Ibraheem Alshareedah, Wade M. Borcherds, Samuel R. Cohen

et al.

Nature Physics, Journal Year: 2024, Volume and Issue: 20(9), P. 1482 - 1491

Published: July 2, 2024

Language: Английский

Citations

35
Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions DOI Creative Commons
Begoña Monterroso, William Margolin, Arnold J. Boersma

et al.

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(4), P. 1899 - 1949

Published: Feb. 8, 2024

Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, energy status, influences structure cytoplasm thereby indirectly function. Notably, also promotes formation biomolecular condensates by phase separation, initially identified eukaryotic cells but more recently discovered to play key functions Bacterial require a variety mechanisms maintain homeostasis, particular environments fluctuating conditions, is emerging one mechanism. In this work, we connect homeostasis function bacterial cell compare supramolecular structures found bacteria those cells. We focus on effects separation control chromosome replication, segregation, division, discuss contribution fitness adaptation environmental stress.

Language: Английский

Citations

30
Protein misfolding and amyloid nucleation through liquid–liquid phase separation DOI
S. Mukherjee, Manisha Poudyal, K. Dave

et al.

Chemical Society Reviews, Journal Year: 2024, Volume and Issue: 53(10), P. 4976 - 5013

Published: Jan. 1, 2024

Protein misfolding and amyloid aggregation, linked to neurodegenerative diseases, can result from liquid–liquid phase separation (LLPS) a subsequent liquid-to-solid transition. This represents LLPS as generic mechanism in nucleation.

Language: Английский

Citations

23
Fundamental Aspects of Phase-Separated Biomolecular Condensates DOI
Huan‐Xiang Zhou,

Divya Kota,

Sanbo Qin

et al.

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(13), P. 8550 - 8595

Published: June 17, 2024

Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations behaviors properties biomolecular condensates. Here we aim fill this by writing a comprehensive, critical, accessible review on fundamental aspects phase-separated We introduce relevant theoretical background, present basis for computation experimental measurement condensate properties, give mechanistic interpretations terms interactions at molecular residue levels.

Language: Английский

Citations

22