Expanding the molecular language of protein liquid–liquid phase separation

Nature Chemistry, Год журнала: 2024, Номер 16(7), С. 1113 - 1124

Опубликована: Март 29, 2024

Язык: Английский

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Sequence-dependent material properties of biomolecular condensates and their relation to dilute phase conformations

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Март 1, 2024

Abstract Material properties of phase-separated biomolecular condensates, enriched with disordered proteins, dictate many cellular functions. Contrary to the progress made in understanding sequence-dependent phase separation little is known about sequence determinants condensate material properties. Using hydropathy scale and Martini models, we computationally decipher these relationships for charge-rich protein condensates. Our computations yield dynamical, rheological, interfacial condensates that are quantitatively comparable experimentally characterized Interestingly, find model natural proteins respond similarly charge segregation, despite different compositions. Molecular interactions within closely resemble those single-chain ensembles. Consequently, strongly correlate molecular contact dynamics structural We demonstrate potential harness characteristics predicting engineering functional insights from dilute

Язык: Английский

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Heterotypic electrostatic interactions control complex phase separation of tau and prion into multiphasic condensates and co-aggregates

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(2)

Опубликована: Янв. 3, 2023

Biomolecular condensates formed via phase separation of proteins and nucleic acids are thought to perform a wide range critical cellular functions by maintaining spatiotemporal regulation organizing intracellular biochemistry. However, aberrant transitions implicated in multitude human diseases. Here, we demonstrate that two neuronal proteins, namely tau prion, undergo complex coacervation driven domain-specific electrostatic interactions yield highly dynamic, mesoscopic liquid-like droplets. The acidic N-terminal segment interacts electrostatically with the polybasic intrinsically disordered prion protein (PrP). We employed unique combination time-resolved tools encompass several orders magnitude timescales ranging from nanoseconds seconds. These studies unveil an intriguing symphony molecular events associated formation heterotypic comprising ephemeral, domain-specific, short-range nanoclusters. Our results reveal these can be tuned RNA stoichiometry-dependent manner resulting reversible, multiphasic, immiscible, ternary different morphologies core-shell nested This system exhibits typical three-regime behavior reminiscent other membraneless organelles including nucleolar condensates. also show upon aging, tau:PrP droplets gradually convert into solid-like co-assemblies sequestration persistent intermolecular interactions. vibrational Raman conjunction atomic force microscopy multi-color fluorescence imaging presence amorphous amyloid-like co-aggregates maturation. findings provide mechanistic underpinnings overlapping neuropathology involving PrP highlight broader biological role physiology disease.

Язык: Английский

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Determinants that enable disordered protein assembly into discrete condensed phases

Nature Chemistry, Год журнала: 2024, Номер 16(7), С. 1062 - 1072

Опубликована: Фев. 5, 2024

Язык: Английский

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Emerging regulatory mechanisms and functions of biomolecular condensates: implications for therapeutic targets

Signal Transduction and Targeted Therapy, Год журнала: 2025, Номер 10(1)

Опубликована: Янв. 6, 2025

Cells orchestrate their processes through complex interactions, precisely organizing biomolecules in space and time. Recent discoveries have highlighted the crucial role of biomolecular condensates-membrane-less assemblies formed condensation proteins, nucleic acids, other molecules-in driving efficient dynamic cellular processes. These condensates are integral to various physiological functions, such as gene expression intracellular signal transduction, enabling rapid finely tuned responses. Their ability regulate signaling pathways is particularly significant, it requires a careful balance between flexibility precision. Disruption this can lead pathological conditions, including neurodegenerative diseases, cancer, viral infections. Consequently, emerged promising therapeutic targets, with potential offer novel approaches disease treatment. In review, we present recent insights into regulatory mechanisms by which influence pathways, roles health disease, strategies for modulating condensate dynamics approach. Understanding these emerging principles may provide valuable directions developing effective treatments targeting aberrant behavior diseases.

Язык: Английский

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Analytical Formulation and Field-Theoretic Simulation of Sequence-Specific Phase Separation of Protein-Like Heteropolymers with Short- and Long-Spatial-Range Interactions

The Journal of Physical Chemistry B, Год журнала: 2022, Номер 126(45), С. 9222 - 9245

Опубликована: Ноя. 7, 2022

A theory for sequence-dependent liquid–liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) in the study biomolecular condensates is formulated by extending random approximation (RPA) and field-theoretic simulation (FTS) heteropolymers with spatially long-range Coulomb interactions to include fundamental effects short-range, hydrophobic-like between amino acid residues. To this end, short-range are modeled Yukawa multiple nonelectrostatic charges derived from an eigenvalue decomposition pairwise residue–residue contact energies. Chain excluded volume afforded incompressibility constraints. mean-field leads effective Flory−Huggins χ parameter, which, conjunction RPA, accounts contact-interaction composition sequence-pattern electrostatics IDP LLPS, whereas FTS based on formulation provides full sequence dependence both short- interactions. This general approach illustrated here applications variants a natural context several different amino-acid interaction schemes as well set model hydrophobic-polar sequences sharing same composition. Effectiveness methodology verified coarse-grained explicit-chain molecular dynamics simulations.

Язык: Английский

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A synergy between site-specific and transient interactions drives the phase separation of a disordered, low-complexity domain

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(34)

Опубликована: Авг. 14, 2023

TAR DNA-binding protein 43 (TDP-43) is involved in key processes RNA metabolism and frequently implicated many neurodegenerative diseases, including amyotrophic lateral sclerosis frontotemporal dementia. The prion-like, disordered C-terminal domain (CTD) of TDP-43 aggregation-prone, can undergo liquid-liquid phase separation (LLPS) isolation, critical for (PS) the full-length under physiological conditions. While a short conserved helical region (CR, spanning residues 319-341) promotes oligomerization essential LLPS, aromatic flanking regions (QN-rich, IDR1/2) are also found to play role PS aggregation. Compared with other phase-separating proteins, CTD has notably distinct sequence composition aliphatic such as methionine leucine. Aliphatic were previously suggested modulate apparent viscosity resulting phases, but their direct contribution toward been relatively ignored. Using multiscale simulations coupled vitro saturation concentration (csat) measurements, we identified importance while suggesting an promoting single-chain compaction LLPS. Surprisingly, NMR experiments showed that transient interactions involving phenylalanine directly enhance site-specific, CR-mediated intermolecular association. Overall, our work highlights underappreciated mode biomolecular recognition, wherein both site-specific hydrophobic act synergistically drive disordered, low-complexity domain.

Язык: Английский

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Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding

Nucleic Acids Research, Год журнала: 2022, Номер 50(22), С. 12702 - 12722

Опубликована: Дек. 9, 2022

Abstract Heterochromatin protein 1α (HP1α) is a crucial element of chromatin organization. It has been proposed that HP1α functions through liquid-liquid phase separation (LLPS), which allows it to compact into transcriptionally repressed heterochromatin regions. In vitro, can undergo upon phosphorylation its N-terminus extension (NTE) and/or interactions with DNA and chromatin. Here, we combine computational experimental approaches elucidate the molecular drive these processes. phosphorylation-driven LLPS, exchange intradimer hinge-NTE interdimer contacts, also leads structural change from compacted an extended dimer conformation. This process be enhanced by presence positively charged peptide ligands disrupted addition negatively or neutral peptides. DNA-driven both perturb separation. Our findings demonstrate importance electrostatic in LLPS where binding partners modulate overall charge droplets screen enhance hinge region specific non-specific effects. study illuminates complex framework fine-tune properties contribute regulation function.

Язык: Английский

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Expanding the molecular language of protein liquid-liquid phase separation

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Март 3, 2023

Abstract Understanding the relationship between an amino acid sequence and its phase separation has important implications for analyzing cellular function, treating disease, designing novel biomaterials. Several features have been identified as drivers protein liquid-liquid (LLPS), leading to development of a “molecular grammar” LLPS. In this work, we further probed how modulates material properties resulting condensates. Specifically, used model intrinsically disordered polypeptide composed 8-residue repeat unit performed systematic manipulations targeting previously overlooked in literature. We generated sequences with no charged residues, high net charge, glycine or devoid aromatic arginine residues. report that all but one twelve variants designed undergo LLPS, albeit different extents, despite significant differences composition. These results support hypothesis multiple interactions diverse residue pairs work tandem drive separation. Molecular simulations paint picture underlying molecular details involving various atomic mediated by not just handful types, most characterized changes inter-residue contacts variants, thereby developing more complete understanding contributions such hydrophobicity, aromaticity Further, find condensates formed behave like viscous fluids, large their viscosities. The presented study significantly advance current sequence-phase behavior sequence-material relationships help interpret, model, design assembly.

Язык: Английский

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Role of Strong Localized vs Weak Distributed Interactions in Disordered Protein Phase Separation

The Journal of Physical Chemistry B, Год журнала: 2023, Номер 127(17), С. 3829 - 3838

Опубликована: Апрель 20, 2023

Interaction strength and localization are critical parameters controlling the single-chain condensed-state properties of intrinsically disordered proteins (IDPs). Here, we decipher these relationships using coarse-grained heteropolymers comprised hydrophobic (H) polar (P) monomers as model IDPs. We systematically vary fraction P XP employ two distinct particle-based models that include either strong localized attractions between only H–H pairs (HP model) or weak distributed both H–P (HP+ model). To compare different sequences models, first carefully tune attraction for all to match radius gyration. Interestingly, find this procedure produces similar conformational ensembles, nonbonded potential energies, chain-level dynamics single chains almost in with some deviations HP at large XP. However, observe a surprisingly rich phase behavior deviates from expectation similarity level will translate phase-separation propensity. Coexistence dilute dense phases is observed up model-dependent XP, despite presence favorable interchain interactions, which quantify second virial coefficient. Instead, limited number attractive sites (H monomers) leads self-assembly finite-sized clusters sizes depending on Our findings strongly suggest interactions favor formation liquid-like condensates over much larger range sequence compositions compared interactions.

Язык: Английский

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