Disease‐linked TDP‐43 hyperphosphorylation suppresses TDP‐43 condensation and aggregation

The EMBO Journal, Journal Year: 2022, Volume and Issue: 41(8)

Published: Feb. 3, 2022

Post-translational modifications (PTMs) have emerged as key modulators of protein phase separation and been linked to aggregation in neurodegenerative disorders. The major aggregating amyotrophic lateral sclerosis frontotemporal dementia, the RNA-binding TAR DNA-binding (TDP-43), is hyperphosphorylated disease on several C-terminal serine residues, a process generally believed promote TDP-43 aggregation. Here, we however find that Casein kinase 1δ-mediated hyperphosphorylation or phosphomimetic mutations reduce aggregation, instead render condensates more liquid-like dynamic. Multi-scale molecular dynamics simulations reveal reduced homotypic interactions low-complexity domains through enhanced solvation residues. Cellular experiments show substitutions do not affect nuclear import RNA regulatory functions TDP-43, but suppress accumulation membrane-less organelles its solubility neurons. We speculate may be protective cellular response counteract

Language: Английский

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Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure

JACS Au, Journal Year: 2022, Volume and Issue: 2(3), P. 673 - 686

Published: March 1, 2022

The paradigmatic disordered protein tau plays an important role in neuronal function and neurodegenerative diseases. To disentangle the factors controlling balance between functional disease-associated conformational states, we build a structural ensemble of K18 fragment containing four pseudorepeat domains involved both microtubule binding amyloid fibril formation. We assemble 129-residue-long chains with atomic detail from extensive library constructed molecular dynamics simulations. introduce reweighted hierarchical chain growth (RHCG) algorithm that integrates experimental data reporting on local structure into assembly process systematic manner. By combining Bayesian refinement importance sampling, obtain well-defined ensembles overcome problem exponentially varying weights integrative modeling long-chain polymeric molecules. resulting capture nuclear magnetic resonance (NMR) chemical shift J-coupling measurements. Without further fitting, achieve very good agreement measurements NMR residual dipolar couplings. measures global such as single-molecule Förster energy transfer (FRET) efficiencies is improved by refinement. comparing wild-type mutant ensembles, show pathogenic single-point P301L, P301S, P301T mutations population turn-like conformations microtubule-bound state to extended fibrils. RHCG thus provides us atomically detailed view equilibrium aggregation-prone states K18, demonstrates characteristics this intrinsically emerge its structure.

Language: 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, Journal Year: 2023, Volume and Issue: 120(2)

Published: Jan. 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.

Language: Английский

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The role of biomolecular condensates in protein aggregation

Nature Reviews Chemistry, Journal Year: 2024, Volume and Issue: 8(9), P. 686 - 700

Published: Aug. 12, 2024

Language: Английский

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

Science Advances, Journal Year: 2024, Volume and Issue: 10(1)

Published: Jan. 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.

Language: Английский

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Crosstalk between protein post-translational modifications and phase separation

Cell Communication and Signaling, Journal Year: 2024, Volume and Issue: 22(1)

Published: Feb. 12, 2024

Abstract The phenomenon of phase separation is quite common in cells, and it involved multiple processes life activities. However, the current research on correlation between protein modifications interference with tendency has some limitations. Here we focus several post-translational proteins, including phosphorylation modification at sites, methylation modification, acetylation ubiquitination SUMOylation etc., which regulate formation stability structure through multivalent interactions. This regulatory role closely related to development neurodegenerative diseases, tumors, viral infections, other also plays essential functions environmental stress, DNA damage repair, transcriptional regulation, signal transduction, cell homeostasis living organisms, provides an idea explore interaction novel separation.

Language: Английский

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Direct prediction of intermolecular interactions driven by disordered regions

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

Published: June 3, 2024

ABSTRACT Intrinsically disordered regions (IDRs) are critical for a wide variety of cellular functions, many which involve interactions with partner proteins. Molecular recognition is typically considered through the lens sequence-specific binding events. However, growing body work has shown that IDRs often interact partners in manner does not depend on precise order amino acid order, instead driven by complementary chemical leading to bound-state complexes. Despite this emerging paradigm, we lack tools describe, quantify, predict, and interpret these types structurally heterogeneous from underlying sequences. Here, repurpose physics developed originally molecular simulations develop an approach predicting intermolecular between Our enables direct prediction phase diagrams, identification chemically-specific interaction hotspots IDRs, route test mechanistic hypotheses regarding IDR function context recognition. We use our examine range systems questions highlight its versatility applicability.

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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Biomolecular condensates: new opportunities for drug discovery and RNA therapeutics

Trends in Pharmacological Sciences, Journal Year: 2022, Volume and Issue: 43(10), P. 820 - 837

Published: Aug. 23, 2022

Numerous examples now exist where biomolecular condensates are mechanistically linked to disease.Small-molecule drugs used in the clinic today can interact with condensates, whether intended or not, possibly affecting their pharmacology.Recent clinical success has demonstrated utility of RNA therapeutics help patients and propelled interest this field.Endogenous is a key constituent both physiological pathological potential link between prospective emerging.Understanding interaction small molecules may improve drug discovery process. Biomolecular organize cellular functions absence membranes. These membraneless organelles form through liquid–liquid phase separation coalescing proteins into well-defined, yet dynamic, structures distinct from surrounding milieu. disease-causing processes which could impact several ways. First, disruption seeded by mutated RNAs provide new opportunities treat disease. Second, be leveraged tackle difficult-to-drug targets lacking binding pockets whose function depends on separation. Third, condensate-resident display unexpected pharmacology. We discuss therapeutics, leveraging concrete examples, towards novel opportunities. Membraneless organelles, support compartmentalization spatiotemporal regulation biochemical activities inside cells [1.Shin Y. Brangwynne C.P. Liquid condensation cell physiology disease.Science. 2017; 357: eaaf4382Crossref PubMed Scopus (1287) Google Scholar, 2.Lyon A.S. et al.A framework for understanding across scales.Nat. Rev. Mol. Cell Biol. 2021; 22: 215-235Crossref (121) 3.Banani S.F. al.Biomolecular condensates: organizers biochemistry.Nat. 18: 285-298Crossref (1891) Scholar]. (hereafter condensates), term coined represent coalescence biomolecules (see Glossary) like [3.Banani Scholar], functional, nonstoichiometric, dynamic assemblies that, membrane-bound create subcellular environments but lack enclosing membranes import/export machinery. Dynamism discriminators aggregates (Box 1). While alternative models [4.Darzacq X. Tjian R. Weak multivalent interactions: strength versus numbers tug war implications partitioning.RNA. 2022; 28: 48-51Crossref (0) Scholar,5.McSwiggen D.T. al.Evaluating live cells: diagnosis, caveats, functional consequences.Genes Dev. 2019; 33: 1619-1634Crossref (216) theoretical modeling experiments purified settings notion that separation, same phenomenon forming oil droplets water, contributes condensate formation regulation.Box 1Condensates aggregates, contextThe original definition all-inclusive, was intracellular manner does not involve membrane Phase defined as demixing two (or more) phases, while transition change molecular organization within system changing its material properties liquid-to-solid. Both phenomena at play context condensates.Biomolecular readily differentiated [9.Alberti S. Hyman A.A. nexus stress, protein aggregation disease ageing.Nat. 196-213Crossref (126) Here, we define non-native, nonfunctional assemblies, irreversible timescale without involving degradation pathways. Aggregates often misfolded (and RNA) assume non-native conformation. Importantly, case unstructured proteins, misfolding lead more ordered less-dynamic structure, causing abnormal interactions [125.Iadanza M.G. era amyloid disease.Nat. 2018; 19: 755-773Crossref (347) For further discussion about differences shared features direct reader recent review Scholar].Certain elements explained spontaneous, thermodynamically driven events. However, describing necessarily reductionistic cannot fully incorporate complexity. numerous forced undergo settings. occur under conditions [126.Alberti al.Considerations challenges studying liquid-liquid condensates.Cell. 176: 419-434Abstract Full Text PDF (766) The reference publications discussing best practices reconstitution study [2.Lyon Scholar,11.Roden C. Gladfelter contributions condensates.Nat. 183-195Crossref (119) Scholar,126.Alberti ATP-driven modulate cells. include post-translational modification [34.Su al.Phase signaling promotes T receptor signal transduction.Science. 2016; 352: 595-599Crossref (511) Scholar,87.Gruijs da Silva L.A. al.Disease-linked TDP-43 hyperphosphorylation suppresses aggregation.EMBO J. 41e108443Crossref (7) Scholar,90.Qamar al.FUS modulated chaperone methylation arginine cation-π interactions.Cell. 173: 720-734.e15Abstract (384) Scholar,127.Rai A.K. al.Kinase-controlled mitosis.Nature. 559: 211-216Crossref (166) Scholar] [91.Lee J.H. al.Enhancer m6A facilitates transcriptional gene activation.Mol. Cell. 81: 3368-3385.e9Abstract Scholar,92.Ries R.J. al.m6A enhances mRNA.Nature. 571: 424-428Crossref (246) chaperones [128.Yoo H. al.Chaperones directly efficiently disperse stress-triggered condensates.Mol. 82: 741-755.e11Abstract helicases [129.Hondele M. al.DEAD-box ATPases global regulators phase-separated organelles.Nature. 573: 144-148Crossref (140) Moreover, there significant interplay promote inhibit [75.Maharana al.RNA buffers behavior prion-like proteins.Science. 360: 918-921Crossref (460) Despite complexity, nonequilibrium nature contribution heterogeneous environment they described mathematical [8.Riback J.A. al.Composition-dependent thermodynamics separation.Nature. 2020; 581: 209-214Crossref (177) Scholar,130.Jacobs W.M. Self-assembly components.Phys. Lett. 126258101Crossref (5) This allows quantitative composition cells, supports interesting properties, flux out reactions take place Scholar].Finally, only generate macromolecular instance, loading static active concentration volumes motors many ways analogous formed condensates. Certain Finally, Recent developments field have illuminated disease, action currently [6.Banani al.Genetic variation associated dysregulation disease.Dev. 57: 1776-1788.e8Abstract (15) Scholar,7.Kilgore H.R. Young R.A. Learning chemical grammar Chem. (Published online June 27, 2022)https://doi.org/10.1038/s41589-022-01046-yCrossref highlight emerging trends likely influence discovery, particularly RNA-based therapeutics. mechanistic dysregulated how therapeutic approaches. also aid modulation modalities, along pharmacology existing therapies. aim readers forward-looking insights integrates evolving fields deliver patients. Intracellular borrowing concepts polymer science, boundaries effectively substitute lipid permitting diffusion phases (Figure 1A ) Scholar,3.Banani Scholar,8.Riback energy reduction caused (by satisfying attractive repulsive intermolecular forces) opposes entropy-driven mixing all components. In simplest form, leads two-phase assumes different depending constituents' concentration, strength, valency, parameters temperature pH. result liquid, freely-fusing assemblies; present continuum 1B) Scholar,9.Alberti forces leading RNA–RNA, protein–RNA, DNA–DNA, protein–DNA, protein–protein interactions, structured domains (e.g., modules) intrinsically disordered regions (IDRs) [10.Sabari B.R. nucleus.Trends Biochem. Sci. 45: 961-977Abstract (102) 1C). [12.Molliex A. low complexity stress granule assembly drives fibrillization.Cell. 2015; 163: 123-133Abstract (1231) [13.Van Treeck B. self-assembly defining transcriptome.Proc. Natl. Acad. U. 115: 2734-2739Crossref (223) 14.Jain Vale R.D. transitions repeat expansion disorders.Nature. 546: 243-247Crossref (369) 15.Poudyal R.R. sequence structure control condensates.RNA. 27: 1589-1601Crossref been described, it copartition [14.Jain Scholar,16.Fay M.M. al.ALS/FTD-associated C9ORF72 vitro cells.Cell Rep. 21: 3573-3584Abstract (78) addition controlled spontaneous events, regulate separation-driven mesoscopic objects, differing canonical, stoichiometric complexes. Evidence exists scales, architecture 1D) structural chromatin [17.Gibson B.A. al.Organization intrinsic regulated separation.Cell. 179: 470-484.e21Abstract (351) 18.Larson A.G. al.Liquid droplet HP1α suggests role heterochromatin.Nature. 547: 236-240Crossref (803) 19.Ahn aberrant looping cancer development.Nature. 595: 591-595Crossref (39) 20.Feric Misteli T. genome evolution.Trends 31: 671-685Abstract nucleolus [21.Feric al.Coexisting liquid underlie nucleolar subcompartments.Cell. 165: 1686-1697Abstract (822) Scholar,22.Lafontaine D.L.J. al.The multiphase condensate.Nat. 165-182Crossref (129) granules [23.Khong transcriptome reveals principles mRNA accumulation granules.Mol. 68: 808-820.e5Abstract (305) processing (P) bodies [24.Luo al.P-bodies: composition, functions.Biochemistry. 2424-2431Crossref (183) Condensates contribute large-scale suggested Golgi [25.Rebane al.Liquid-liquid matrix GM130.FEBS 594: 1132-1144Crossref (20) synaptic transmission [26.McDonald N.A. al.Assembly zones requires scaffold molecules.Nature. 588: 454-458Crossref (29) endocytosis [27.Bergeron-Sandoval L.P. al.Endocytic viscoelastic enable remodeling.Proc. 118Crossref (2) autophagy [28.Fujioka organizes site autophagosome formation.Nature. 578: 301-305Crossref (132) adhesion [29.Beutel O. zonula occludens tight junctions.Cell. 923-936.e11Abstract (107) division [30.Trivedi P. inner centromere scaffolded chromosomal passenger complex.Nat. 1127-1137Crossref (38) impacts smaller innate adaptive immune [31.Zhou W. al.cGAS inhibits TREX1-mediated DNA cytosolic sensing.Mol. 739-755.e7Abstract 32.Shen virus-induced activation NLRP6 inflammasome.Cell. 184: 5759-5774.e20Abstract 33.Du Chen Z.J. DNA-induced cGAS activates signaling.Science. 361: 704Crossref 34.Su expression [35.Henninger J.E. al.RNA-mediated feedback 207-225.e24Abstract (106) 36.Sabari al.Coactivator super-enhancers links control.Science. eaar3958Crossref 37.Boija al.Transcription factors activate genes phase-separation capacity domains.Cell. 175: 1842-1855.e16Abstract (608) 38.Cho W.K. al.Mediator polymerase II clusters associate transcription-dependent condensates.Science. 412-415Crossref (539) 39.Shrinivas K. drive 75: 549-561.e7Abstract (144) splicing [40.Guo Y.E. al.Pol phosphorylation regulates switch condensates.Nature. 572: 543-548Crossref (240) repair [41.Kilic 53BP1 determines liquid-like compartments.EMBO 38e101379Crossref (156) 42.Pessina F. al.Functional transcription promoters double-strand breaks mediate RNA-driven damage-response factors.Nat. 1286-1299Crossref (130) 43.Rhine al.Poly(ADP-ribose) FUS via transient interaction.Mol. 969-985.e11Abstract (1) even membrane-associated exemplified cascades dependent SOS Ras [44.Huang W.Y.C. kinetic proofreading SOS.Science. 363: 1098-1103Crossref (134) bFGF [45.Xue surface transduction heparan sulphate.Nat. Commun. 13: 1112Crossref tyrosine kinases (RTKs) [46.Lin C.C. al.Receptor liquid-l

Language: Английский

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Recognition of the TDP-43 nuclear localization signal by importin α1/β

Cell Reports, Journal Year: 2022, Volume and Issue: 39(13), P. 111007 - 111007

Published: June 1, 2022

Cytoplasmic mislocalization of the TAR-DNA binding protein 43 kDa (TDP-43) leads to large, insoluble aggregates that are a hallmark amyotrophic lateral sclerosis and frontotemporal dementia. Here, we study how importin α1/β recognizes TDP-43 bipartite nuclear localization signal (NLS). We find NLS makes extensive contacts with α1, especially at minor NLS-binding site. results in steric clashes C terminus α1 disrupts N-terminal domain (NTD) dimerization interface. A putative phosphorylation site proximity R83 destabilizes importins by reducing backbone dynamics. Based on these data, explain pathogenic role several post-translational modifications mutations linked disease shed light chaperone activity α1/β.

Language: Английский

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