A conceptual framework for understanding phase separation and addressing open questions and challenges

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(12), P. 2201 - 2214

Published: June 1, 2022

Language: Английский

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Phase Transitions of Associative Biomacromolecules

Chemical Reviews, Journal Year: 2023, Volume and Issue: 123(14), P. 8945 - 8987

Published: March 7, 2023

Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for formation compositional regulation of biomolecular condensates. Here, we review key concepts phase transitions aqueous solutions specifically that include folded domains intrinsically disordered regions. The these systems come under rubric coupled segregative transitions. underlying processes are presented, their relevance condensates is discussed.

Language: Английский

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Phase-separating RNA-binding proteins form heterogeneous distributions of clusters in subsaturated solutions

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(28)

Published: July 5, 2022

Macromolecular phase separation is thought to be one of the processes that drives formation membraneless biomolecular condensates in cells. The dynamics are follow tenets classical nucleation theory, and, therefore, subsaturated solutions should devoid clusters with more than a few molecules. We tested this prediction using vitro biophysical studies characterize phase-separating RNA-binding proteins intrinsically disordered prion-like domains and domains. Surprisingly, direct contradiction expectations from we find characterized by presence heterogeneous distributions clusters. cluster sizes, which dominated small species, shift continuously toward larger sizes as protein concentrations increase approach saturation concentration. As result, many encompass tens hundreds molecules, while less 1% mesoscale species several hundred nanometers diameter. supersaturated strongly coupled via sequence-encoded interactions. also can decoupled solutes well specific sets mutations. Our findings, concordant predictions for associative polymers, implicate an interplay between networks sequence-specific solubility-determining interactions that, respectively, govern above occurs.

Language: Английский

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Engineering synthetic biomolecular condensates

Nature Reviews Bioengineering, Journal Year: 2023, Volume and Issue: 1(7), P. 466 - 480

Published: April 17, 2023

Language: Английский

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Phase separation of protein mixtures is driven by the interplay of homotypic and heterotypic interactions

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

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RNA granules: functional compartments or incidental condensates?

Genes & Development, Journal Year: 2023, Volume and Issue: 37(9-10), P. 354 - 376

Published: May 1, 2023

RNA granules are mesoscale assemblies that form in the absence of limiting membranes. contain factors for biogenesis and turnover often assumed to represent specialized compartments biochemistry. Recent evidence suggests assemble by phase separation subsoluble ribonucleoprotein (RNP) complexes partially demix from cytoplasm or nucleoplasm. We explore possibility some nonessential condensation by-products arise when RNP exceed their solubility limit as a consequence cellular activity, stress, aging. describe use evolutionary mutational analyses single-molecule techniques distinguish functional "incidental condensates."

Language: Английский

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Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility

Nature Chemistry, Journal Year: 2024, Volume and Issue: 16(7), P. 1073 - 1082

Published: Feb. 21, 2024

Endogenous biomolecular condensates, composed of a multitude proteins and RNAs, can organize into multiphasic structures with compositionally distinct phases. This organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood. Here we use in vivo condensate reconstitution experiments coarse-grained molecular simulations investigate how oligomerization sequence interactions modulate condensates. We demonstrate that increasing state an intrinsically disordered protein results enhanced immiscibility formation. Interestingly, find tunes miscibility asymmetric manner, effect being more pronounced when protein, exhibiting stronger homotypic interactions, oligomerized. Our findings suggest flexible mechanism cells exploit tune internal condensates associated functions.

Language: Английский

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Local environment in biomolecular condensates modulates enzymatic activity across length scales

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 18, 2024

Abstract The mechanisms that underlie the regulation of enzymatic reactions by biomolecular condensates and how they scale with compartment size remain poorly understood. Here we use intrinsically disordered domains as building blocks to generate programmable NADH-oxidase (NOX) different sizes spanning from nanometers microns. These domains, derived three distinct RNA-binding proteins, each possessing net charge, result in formation characterized a comparable high local concentration enzyme yet within environments. We show only highest recruitment substrate cofactor exhibit an increase activity. Notably, observe enhancement rate across wide range condensate sizes, microns, indicating emergent properties can arise assemblies small nanometers. Furthermore, larger smaller condensates. Our findings demonstrate ability modulate creating effective solvent environments compared surrounding solution, implications for design protein-based heterogeneous biocatalysts.

Language: Английский

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MolPhase, an advanced prediction algorithm for protein phase separation

The EMBO Journal, Journal Year: 2024, Volume and Issue: 43(9), P. 1898 - 1918

Published: April 2, 2024

Abstract We introduce MolPhase, an advanced algorithm for predicting protein phase separation (PS) behavior that improves accuracy and reliability by utilizing diverse physicochemical features extensive experimental datasets. MolPhase applies a user-friendly interface to compare distinct biophysical side-by-side along sequences. By additional comparison with structural predictions, enables efficient predictions of new phase-separating proteins guides hypothesis generation design. Key contributing factors underlying include electrostatic pi-interactions, disorder, prion-like domains. As example, finds phytobacterial type III effectors (T3Es) are highly prone homotypic PS, which was experimentally validated in vitro biochemically vivo plants, mimicking their injection accumulation the host during microbial infection. The characteristics T3Es dictate patterns association multivalent interactions, influencing material properties droplets based on surrounding microenvironment or vitro. Robust integration MolPhase’s effective prediction validation exhibit potential evaluate explore how biomolecule PS functions biological systems.

Language: Английский

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Molecular determinants of condensate composition

Molecular Cell, Journal Year: 2025, Volume and Issue: 85(2), P. 290 - 308

Published: Jan. 1, 2025

Language: Английский

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