Deciphering driving forces of biomolecular phase separation from simulations

Current Opinion in Structural Biology, Journal Year: 2025, Volume and Issue: 92, P. 103026 - 103026

Published: March 8, 2025

The formation and modulation of biomolecular condensates as well their structural dynamic properties are determined by an intricate interplay different driving forces, which down at the microscopic scale involve molecular interactions biological macromolecules surrounding solvent ions. Molecular simulations increasingly used to provide detailed insights into various processes thermodynamic forces play, thereby yielding mechanistic understanding aiding interpretation experiments level individual amino acid residues or even atoms. Here we summarize recent advances in field biocondensate with a focus on coarse-grained all-atom dynamics (MD) simulations. We highlight possible future challenges concerning computationally efficient physically accurate large complex systems.

Language: Английский

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Deciphering the Inhibitory Mechanism of ALS-Associated N352S and S352p Variants against TDP-43 Aggregation and Its Destabilization Effect on TDP-43 Protofibrils

ACS Chemical Neuroscience, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Amyotrophic lateral sclerosis (ALS) is closely related to ubiquitin-positive inclusions formed by transactive response deoxyribonucleic acid (DNA) binding protein of 43 kDa (TDP-43). Previous experiments identified that the ALS-linked familial variant, N352S (asparagine substituted serine), and subsequent phosphorylation S352 (S352p) are associated with aggregation TDP-43. However, underlying molecular mechanisms still not fully understood. By performing all-atom explicit-solvent replica exchange dynamics (REMD) simulations a total simulation time 100.8 μs, we scrutinized impact mutation its variant S352p on conformational ensembles TDP-43342-366 dimer. Our results show both variants could promote formation unstructured conformation impede β-structure helix content, inhibitive effect S352P more obvious. Further analyses suggest H-bonding hydrophobic interaction among peptides, as well R361-E362 salt bridge, attenuated variants. Additional MD reduce structural stability region lower number H-bonds contacts two clusters, thus possessing destabilization TDP-43282-360 protofibrils. unmask mechanism toward inhibition prove protofibril-destabilizing effects these variants, which may be helpful for designing drugs treatment ALS.

Language: Английский

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Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: May 19, 2025

Abstract Condensation and aggregation of disordered proteins in cellular non-equilibrium environments are shaped decisively by enzymes. Enzymes called kinases phosphorylate proteins, consuming the chemical fuel ATP. Protein phosphorylation such as Casein kinase 1 delta (CK1 δ ) determines interactions neurodegeneration-linked TDP-43. Hyperphosphorylation TDP-43 CK1 may be a cytoprotective mechanism for neurons, but how interacts with protein condensates is not known. Molecular dynamics simulations hold promise to resolve interact their condensates, this shapes dynamics. In practice, it difficult verify whether implementations chemical-fuel driven coarse-grained thermodynamically consistent, which we address generally applicable automatic Markov state modeling approach. work, thus elucidate simulations, drivers phosphorylated leads dissolution upon hyperphosphorylation.

Language: Английский

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The Regulation of TDP-43 Structure and Phase Transitions: A Review

The Protein Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 22, 2025

Language: Английский

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Hydrogen–Deuterium Exchange Mass Spectrometry Reveals Mechanistic Insights into RNA Oligonucleotide-Mediated Inhibition of TDP-43 Aggregation

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 29, 2024

Deposits of aggregated TAR DNA-binding protein 43 (TDP-43) in the brain are associated with several neurodegenerative diseases. It is well established that binding RNA/DNA to TDP-43 can prevent aggregation, but an understanding structure(s) and conformational dynamics TDP-43, TDP-43-RNA complexes, lacking, including knowledge how solution environment modulates these properties. Here, we address this challenge using hydrogen-deuterium exchange-mass spectrometry. In presence RNA olignoucleotides, observe protection from exchange recognition motif (RRM) domains linker region between RRM domains, consistent nucleic acid modulating interdomain interactions. Intriguingly, at elevated salt concentrations, extent reduced when bound sequence derived 3' UTR mRNA (CLIP34NT) compared a (UG)6 repeat sequence. Under conditions, CLIP34NT no longer able aggregation. This suggests salt-induced structural rearrangement occurs RNA, which may play role facilitating Additionally, upon binding, identify differences within short α-helical located C-terminal domain (CTD) TDP-43. These allosterically altered regions influence ability aggregate fine-tune its repertoire. Combined, data provide additional insights into intricate interplay aggregation crucial for unraveling molecular mechanisms underlying TDP-43-associated neurodegeneration.

Language: Английский

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Progress in the role and mechanism of TDP-43

New discovery., Journal Year: 2024, Volume and Issue: unknown, P. 1 - 8

Published: Sept. 20, 2024

Background: TAR DNA-binding protein 43 kDa (TDP-43) has been shown to play an important role in the development of neurodegenerative diseases, but mechanism is still under study. Methods: By utilizing “TDP43”, “disease”, and “mechanism” as keywords, 200 related studies were retrieved downloaded from Pubmed database, including 60 articles. We summarized progress understanding TDP-43 over past two years, focusing on disease systems classification upstream downstream, connection, improvement, formation. Results: TDP-43, when abnormally aggregated, phosphorylated, or mislocalized, plays a key pathological diseases. Additionally, its impact normal reproductive cell formation, development, quantity, activity, well insulin secretion activation intestinal epithelial necrosis, should not be overlooked. Mechanistically, we identified relationship between expression factors, Enterovirus D68 (EV-D68), Heterogeneous Nuclear Ribonucleoprotein D (HNRNPD AUF1), Endoplasmic Reticulum Protein 57 (ERp57), Progranulin (PGRN), downstream factors such Meiotic Recombination Spo11 (Spo11), AMP-Activated Kinase (AMPK), Double-Strand-Break Repair Rad21 Homolog (Rad21L), IκB (IKK), TDP-43. Conclusion: neurodegeneration, which, phosphorylation, EV-d68, HNRNPD.

Language: Английский

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Amino Acid Transfer Free Energies Reveal Thermodynamic Driving Forces in Biomolecular Condensate Formation

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

Published: Dec. 5, 2024

The self-assembly of intrinsically disordered proteins into biomolecular condensates shows a dependence on the primary sequence protein, leading to sequence-dependent phase separation. Methods investigate this separation rely effective residue-level interaction potentials that quantify propensity for residues remain in dilute versus dense phase. most direct measure these are distribution coefficients different amino acids between two phases, but due lack availability coefficients, proxies, notably hydropathy, have been used. However, recent work has demonstrated limitations assumption hydropathy-driven In work, we address fundamental gap by calculating transfer free energies associated with transferring each acid side chain analog from model condensate. We uncover an interplay favorable protein-mediated and unfavorable water-mediated contributions overall transfer. further asymmetry positive negative charges driving forces condensate formation. results presented provide explanation several non-trivial trends observed literature will aid interpretation experiments aimed at elucidating underlying formation condensates.

Language: Английский

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Short RNA chaperones promote aggregation-resistant TDP-43 conformers to mitigate neurodegeneration

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

Published: Dec. 15, 2024

Abstract Aberrant aggregation of the prion-like, RNA-binding protein TDP-43 underlies several debilitating neurodegenerative proteinopathies, including amyotrophic lateral sclerosis (ALS). Here, we define how short, specific RNAs antagonize aggregation. Short, engage and stabilize RNA-recognition motifs, which allosterically destabilizes a conserved helical region in prion-like domain, thereby promoting aggregation-resistant conformers. By mining sequence space, uncover short with enhanced activity against diverse disease-linked variants. The solubilizing RNA chaperones corrects aberrant phenotypes optogenetic models ALS patient-derived neurons. Remarkably, an chaperone mitigates proteinopathy neurodegeneration mice. Our studies reveal mechanisms pave way for development therapeutics fatal proteinopathies.

Language: Английский

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