The molecular basis for cellular function of intrinsically disordered protein regions

Nature Reviews Molecular Cell Biology, Год журнала: 2023, Номер 25(3), С. 187 - 211

Опубликована: Ноя. 13, 2023

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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Active learning of the thermodynamics-dynamics trade-off in protein condensates

Science Advances, Год журнала: 2024, Номер 10(1)

Опубликована: Янв. 5, 2024

Phase-separated biomolecular condensates exhibit a wide range of dynamic properties, which depend on the sequences constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also changing thermodynamic properties that govern phase separation. Using coarse-grained simulations intrinsically disordered proteins, we show thermodynamics homopolymer are strongly correlated, with increased stability being coincident low mobilities high viscosities. We then apply an “active learning” strategy identify heteropolymer break this correlation. This data-driven approach accompanying analysis reveal how heterogeneous amino acid compositions nonuniform sequence patterning map independently tunable condensates. Our results highlight key molecular determinants governing physical establish design rules for development stimuli-responsive biomaterials.

Язык: Английский

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Insights into Molecular Diversity within the FUS/EWS/TAF15 Protein Family: Unraveling Phase Separation of the N-Terminal Low-Complexity Domain from RNA-Binding Protein EWS

Journal of the American Chemical Society, Год журнала: 2024, Номер 146(12), С. 8071 - 8085

Опубликована: Март 16, 2024

The FET protein family, comprising FUS, EWS, and TAF15, plays crucial roles in mRNA maturation, transcriptional regulation, DNA damage response. Clinically, they are linked to Ewing family tumors neurodegenerative diseases such as amyotrophic lateral sclerosis. fusion EWS::FLI1, the causative mutation of sarcoma, arises from a genomic translocation that fuses portion low-complexity domain (LCD) EWS (EWSLCD) with binding ETS transcription factor FLI1. This modifies programs disrupts native functions, splicing. exact role intrinsically disordered EWSLCD remains topic active investigation, but its ability phase separate form biomolecular condensates is believed be central EWS::FLI1's oncogenic properties. Here, we used paramagnetic relaxation enhancement NMR, microscopy, all-atom molecular dynamics (MD) simulations better understand self-association separation tendencies EWSLCD. Our NMR data mutational analysis suggest higher density proximity tyrosine residues amplify likelihood condensate formation. MD revealed tyrosine-rich termini exhibit compact conformations unique contact networks provided critical input on relationship between contacts formed within single molecule (intramolecular) inside condensed (intermolecular). These findings enhance our understanding proteins' condensate-forming capabilities underline differences TAF15.

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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Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex

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

Опубликована: Фев. 7, 2024

Abstract Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS EWSR1 play key roles recruiting chromatin remodeler mammalian SWI/SNF (mSWI/SNF) complex to oncogenic FET fusion condensates. Here, we show that disordered multiple subunits prion-like with a strong propensity undergo intracellular phase separation. These engage sequence-specific heterotypic interactions the PLD dilute at sub-saturation conditions, leading formation co-condensates. In dense phase, homotypic highly cooperative, resulting co-mixing individual phases forming spatially homogeneous Heterotypic PLD-mediated positive cooperativity protein-protein interaction networks is likely co-phase separation mSWI/SNF factors containing homologous domains.

Язык: Английский

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A complex network of interdomain interactions underlies the conformational ensemble of monomeric TDP‐43 and modulates its phase behavior

Protein Science, Год журнала: 2023, Номер 33(2)

Опубликована: Дек. 31, 2023

TAR DNA-binding protein 43 (TDP-43) is a multidomain involved in the regulation of RNA metabolism, and its aggregates have been observed neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) frontotemporal dementia (FTD). Numerous studies indicate TDP-43 can undergo liquid-liquid phase separation (LLPS) vitro component biological condensates. Homo-oligomerization via folded N-terminal domain (aa:1-77) conserved helical region (aa:319-341) disordered, C-terminal found to be an important driver separation. However, comprehensive molecular view separation, particularly regarding nature heterodomain interactions, lacking due challenges associated with stability purification. Here, we utilize all-atom coarse-grained (CG) dynamics (MD) simulations uncover network interdomain interactions implicated All-atom uncovered presence transient, involving flexible linkers, RNA-recognition motif (RRM) domains charged segment disordered (CTD). CG these inter-domain which affect conformational landscape dilute are also prevalent condensed phase. Finally, sequence surface charge distribution analysis coupled (at high salt) confirmed that transient contacts predominantly electrostatic nature. Overall, our findings from multiscale lead greater appreciation complex interaction underlying structural TDP-43.

Язык: Английский

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Genetically Fused Resilin-like Polypeptide–Coiled Coil Bundlemer Conjugates Exhibit Tunable Multistimuli-Responsiveness and Undergo Nanofibrillar Assembly

Biomacromolecules, Год журнала: 2024, Номер 25(4), С. 2449 - 2461

Опубликована: Март 14, 2024

Peptide-based materials are diverse candidates for self-assembly into modularly designed and stimuli-responsive nanostructures with precisely tunable compositions. Here, we genetically fused computationally coiled coil-forming peptides to the N- C-termini of compositionally distinct multistimuli-responsive resilin-like polypeptides (RLPs) various lengths. The successful expression these hybrid in bacterial hosts was confirmed through techniques such as gel electrophoresis, mass spectrometry, amino acid analysis. Circular dichroism spectroscopy ultraviolet–visible turbidimetry demonstrated that despite fusion disparate structural responsive units, coils remained stable polypeptides, sequence-encoded differences thermoresponsive phase separation RLPs were preserved. Cryogenic transmission electron microscopy coarse-grained modeling showed after thermal annealing solution, adopted a closed loop conformation assembled nanofibrils capable further hierarchically organizing cluster structures ribbon-like mediated by self-association tendency RLPs.

Язык: Английский

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Determinants of Disordered Protein Co-Assembly Into Discrete Condensed Phases

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

Опубликована: Март 12, 2023

Abstract Cells harbor numerous mesoscale membraneless compartments that house specific biochemical processes and perform distinct cellular functions. These protein RNA-rich bodies are thought to form through multivalent interactions among proteins nucleic acids resulting in demixing via liquid-liquid phase separation (LLPS). Proteins harboring intrinsically disordered regions (IDRs) predominate organelles. However, it is not known whether IDR sequence alone can dictate the formation of condensed phases. We identified a pair IDRs capable forming spatially condensates when expressed cells. When reconstituted vitro, these model do co-partition, suggesting condensation specificity encoded directly polypeptide sequences. Through computational modeling mutagenesis, we amino chain properties governing homotypic heterotypic direct selective condensation. results basis physicochemical principles may subcellular organization into reveal an code guide construction orthogonal compartments.

Язык: Английский

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Expanding the molecular grammar of polar residues and arginine in FUS prion-like domain phase separation and aggregation

Опубликована: Фев. 15, 2024

Abstract A molecular grammar governing low-complexity prion-like domains phase separation (PS) has been proposed based on mutagenesis experiments that identified tyrosine and arginine as primary drivers of via aromatic-aromatic aromatic-arginine interactions. Here we show additional residues make direct favorable contacts contribute to separation, highlighting the need account for these contributions in PS theories models. We find important beyond only tyrosine-tyrosine tyrosine-arginine, including arginine-arginine contacts. Among polar residues, glutamine particular contributes with sequence/position-specificity, making both well other before condensed phases. For glycine, its flexibility, not small solvation volume, favors by allowing between inhibits liquid-to-solid (LST) transition. Polar residue types also sequence-specific aggregation go simple rules, which serine positions is linked formation an amyloid-core structure FUS domain. Hence, here propose a revised expanding role domain protein aggregation.

Язык: Английский

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