Expanding the molecular grammar of polar residues and arginine in FUS phase separation

Nature Chemical Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Language: Английский

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Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model Intrinsically Disordered Proteins

The Journal of Physical Chemistry Letters, Journal Year: 2024, Volume and Issue: 15(32), P. 8248 - 8256

Published: Aug. 6, 2024

Conformational properties of intrinsically disordered proteins (IDPs) are governed by a sequence-ensemble relationship. To differentiate the impact sequence-local versus sequence-nonlocal features an IDP's charge pattern on its conformational dimensions and phase-separation propensity, "blockiness" κ nonlocality-weighted sequence decoration (SCD) parameters compared for their correlations with isolated-chain radii gyration (Rgs) upper critical solution temperatures (UCSTs) polyampholytes modeled random phase approximation, field-theoretic simulation, coarse-grained molecular dynamics. SCD is superior to in predicting Rg because accounts effects contact order, i.e., nonlocality, isolated chains. In contrast, comparably good, though nonideal, predictors UCST frequencies interchain contacts multiple-chain condensed less sensitive positions than intrachain chain, as reflected correlating better condensed-phase interaction energy SCD.

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

Published: Feb. 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.

Language: Английский

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Unlocking the electrochemical functions of biomolecular condensates

Nature Chemical Biology, Journal Year: 2024, Volume and Issue: 20(11), P. 1420 - 1433

Published: Sept. 26, 2024

Language: Английский

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Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates

PLoS Computational Biology, Journal Year: 2025, Volume and Issue: 21(1), P. e1012737 - e1012737

Published: Jan. 13, 2025

Intracellular liquid–liquid phase separation (LLPS) of proteins and nucleic acids is a fundamental mechanism by which cells compartmentalize their components perform essential biological functions. Molecular simulations play crucial role in providing microscopic insights into the physicochemical processes driving this phenomenon. In study, we systematically compare six state-of-the-art sequence-dependent residue-resolution models to evaluate performance reproducing behaviour material properties condensates formed seven variants low-complexity domain (LCD) hnRNPA1 protein (A1-LCD)—a implicated pathological liquid-to-solid transition stress granules. Specifically, assess HPS, HPS-cation– π , HPS-Urry, CALVADOS2, Mpipi, Mpipi-Recharged predictions condensate saturation concentration, critical solution temperature, viscosity A1-LCD variants. Our analyses demonstrate that, among tested models, Mpipi-Recharged, CALVADOS2 provide accurate descriptions temperatures concentrations for multiple tested. Regarding prediction its variants, stands out as most reliable model. Overall, study benchmarks range coarse-grained thermodynamic stability establishes direct link between ranking intermolecular interactions these consider.

Language: 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, Journal Year: 2023, Volume and Issue: 33(2)

Published: Dec. 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.

Language: Английский

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Structural details of helix-mediated TDP-43 C-terminal domain multimerization

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

Published: July 6, 2024

Abstract The primarily disordered C-terminal domain (CTD) of TAR DNA binding protein-43 (TDP-43), a key nuclear protein in RNA metabolism, forms neuronal inclusions several neurodegenerative diseases. A conserved region (CR, spanning residues 319-341) CTD transient helix-helix contacts important for its higher-order oligomerization and function that are disrupted by ALS-associated mutations. However, the structural details CR assembly explanation variants’ impact on phase separation remain unclear due to challenges analyzing dynamic association TDP-43 using traditional biology approaches. By employing an integrative approach, combining biophysical experiments, biochemical assays, AlphaFold2-Multimer (AF2-Multimer), atomistic simulations, we generated models helical CR. Using NMR, first established native state under physiological conditions is α-helical. Next, alanine scanning mutagenesis revealed while hydrophobic assembly, retention function, polar down regulate these processes. Finally, pairing AF2-Multimer modeling with AAMD simulations indicated dynamic, oligomeric assemblies stabilized methionine-rich core specific contributions from tryptophan/leucine pair. In conclusion, our results advance understanding mechanisms driving provide window into initial stages conversion pathogenic aggregates.

Language: Английский

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

Published: Feb. 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.

Language: Английский

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A guide to selecting high-performing antibodies for TAF15 (UniProt ID: Q92804) for use in western blot, immunoprecipitation, and immunofluorescence

F1000Research, Journal Year: 2025, Volume and Issue: 14, P. 37 - 37

Published: Jan. 6, 2025

TAF15 (TATA-box binding protein-associated factor 15) is a member of the FET protein family, known for their roles in transcriptional regulation and RNA metabolism. Here we have characterized five TAF15 commercial antibodies western blot, immunoprecipitation, immunofluorescence using standardized experimental protocol based on comparing read-outs knockout cell lines isogenic parental controls. These studies are part larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available human proteins publishing results openly as resource scientific community. While use protocols vary between laboratories, encourage readers this report guide select most appropriate specific needs.

Language: Английский

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Deciphering the role of liquid-liquid phase separation in sarcoma: Implications for pathogenesis and treatment

Cancer Letters, Journal Year: 2025, Volume and Issue: 616, P. 217585 - 217585

Published: Feb. 23, 2025

Language: Английский

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