The European Physical Journal E, Journal Year: 2023, Volume and Issue: 46(10)
Published: Oct. 1, 2023
Language: Английский
Molecular Biology of the Cell, Journal Year: 2024, Volume and Issue: 35(5)
Published: April 10, 2024
Neurofilaments (NFs) are multisubunit, neuron-specific intermediate filaments consisting of a 10-nm diameter filament "core" surrounded by layer long intrinsically disordered protein (IDP) "tails." NFs thought to regulate axonal caliber during development and then stabilize the mature axon, with NF subunit misregulation, mutation, aggregation featuring prominently in multiple neurological diseases. The field's understanding structure, mechanics, function has been deeply informed rich variety biochemical, cell biological, mouse genetic studies spanning more than four decades. These have contributed much our collective physiology disease. In recent years, however, there resurgence interest proteins two new contexts: as potential blood- cerebrospinal fluid-based biomarkers neuronal damage, model IDPs intriguing properties. Here, we review established principles discoveries structure function. Where possible, place these findings context biophysics assembly, interaction, contributions mechanics.
Language: Английский
Citations
6
Current Opinion in Structural Biology, Journal Year: 2023, Volume and Issue: 83, P. 102722 - 102722
Published: Oct. 21, 2023
Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities of conformations can be predictors cell function. The states molecules preferentially visit viewed phenotypic determinants, and their mutations work by altering relative propensities, thus phenotype. Our examples include (i) inactive state variants harboring cancer driver present active state-like features, in K-Ras4B
Language: Английский
Citations
16
Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(30)
Published: July 17, 2023
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% eukaryotes proteome is composed intrinsically disordered proteins (IDPs) protein regions that fluctuate between ensembles numerous conformations. Therefore, to understand function, it critical depict how structural ensemble statistics correlate IDPs' amino acid sequence. Here, using small-angle X-ray scattering time-resolved Förster resonance energy transfer (trFRET), we study intramolecular heterogeneity neurofilament low tail domain (NFLt). Using theoretical results polymer physics, find Flory scaling exponent NFLt subsegments correlates linearly with net charge, ranging from ideal self-avoiding chains. Surprisingly, measuring same segments in context whole protein, regardless peptide sequence, segments' are more expanded than when measured independently. Our findings show while physics can, some level, relate IDP's sequence its conformations, distant acids play crucial role determining structures. This emphasizes necessity advanced theories fully describe IDPs hope will allow us model
Language: Английский
Citations
12
Current Opinion in Structural Biology, Journal Year: 2023, Volume and Issue: 84, P. 102734 - 102734
Published: Nov. 30, 2023
Language: Английский
Citations
11
PNAS Nexus, Journal Year: 2025, Volume and Issue: 4(2)
Published: Feb. 1, 2025
Liquid-liquid phase separation (LLPS) exhibited by intrinsically disordered proteins (IDPs) depends on the solvation state around Θ-regime, which separates good from poor solvent. Experimentally, Θ-solvent regime of finite length (N) IDPs, as probed small angle X-ray scattering (SAXS) and single molecular fluorescence resonance energy transfer (smFRET), is in disagreement. Using computer simulations a coarse-grained IDP model, we address effect chain Θ-regime IDPs with polar side chains (polyglutamine) hydrophobic (polyleucine) subject to varying concentrations cosolvents [C] , urea (denaturant) or trimethylamine N-oxide (protective osmolyte) water. Due their intrinsic stiffness, these are always expanded short-length scales, independent solvent quality. As result, for short sequences ( ≈10 25 residues), propensity exhibit LLPS cannot be inferred single-chain properties. Further, finite-size cosolvent concentration attain [CΘ] ) extracted structure factor emulating SAXS pair distances mimicking smFRET differs. They converge same only at large N, indicating that size corrections vary different We show radius gyration Rg satisfies scaling relation Rg2=Nf(cN) can exploited accurately extract c=([C]/[CΘ]-1) ). demonstrate importance aspects originating stiffness thermal blob analyzing properties identify regime.
Language: Английский
Citations
0
Advanced Science, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 14, 2025
Abstract The self‐assembly of intrinsically disordered proteins (IDPs) into condensed phases and the formation membrane‐less organelles (MLOs) can be considered as phenomenon collective behavior. conformational dynamics IDPs are essential for their interactions a phase. From physical perspective, behavior emergence phase associated with long‐range correlations. Here correlations therein analyzed, using µs‐scale atomistic molecular (MD) simulations single‐molecule Förster resonance energy transfer (smFRET) experiments. existence typical scale‐free spatio‐temporal in IDP fluctuations is demonstrated. Their evolutions exhibit “1/ f noise” power spectra accompanied by appearance residue domains following power‐law size distribution. Additionally, motions residues present behavioral correlation. These resemble those systems near critical points, suggesting that poised at state. Therefore, effectively respond to finite differences sequence compositions engender considerable structural heterogeneity which beneficial formation.
Language: Английский
Citations
0
Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 27, 2025
All-atom molecular dynamics (MD) simulations based on physics-based force fields, serve as an essential complement to experiments for investigating protein structure, dynamics, and interactions. Despite significant advances in field development, achieving a consistent balance of interactions that stabilize folded proteins protein-protein complexes while simultaneously capturing the conformational intrinsically disordered polypeptides (IDPs), remains challenging. In this work, we systematically evaluated two current state-of-the-art fields (i) AMBER ff03ws, (ii) ff99SBws, by comprehensively assessing their performance both domains IDPs. By selectively scaling side chain-water uncharged residues, refined ff03w-sc demonstrated improved stability maintaining accurate representations However, failed correct discrepancies NMR-derived ps-ns timescale backbone associated with flexible loops. Interestingly, ff99SBws retained its structural despite application upscaled water sidechain atoms displayed robust agreement dynamics. Further, targeted refinement glutamine torsion parameters, yielded ff99SBws-STQ', which effectively resolved α-helicity predictions. Extensive validation against small angle X-ray scattering (SAXS) NMR chemical shifts, revealed accurately reproduced chain dimensions secondary structure propensities peptides prion-like domains. Importantly, reliably maintained over microsecond timescales. Our systematic strategies provide accuracy transferability simulating diverse systems, from IDPs complexes.
Language: Английский
Citations
0
Journal of Structural Biology, Journal Year: 2023, Volume and Issue: 215(4), P. 108029 - 108029
Published: Sept. 22, 2023
Language: Английский
Citations
7
Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(49)
Published: Nov. 27, 2024
Neurofilaments (NFs) are multisubunit, bottlebrush-shaped intermediate filaments abundant in the axonal cytoskeleton. Each NF subunit contains a long intrinsically disordered tail domain, which protrudes from core to form “brush” surrounding each NF. Precisely how tails’ variable charge patterns and repetitive phosphorylation sites mediate their conformation within brush remains an open question biology. We address this problem by grafting recombinant protein constructs NF-Light, -Medium, -Heavy (NFL, NFM, NFH) surfaces, yielding brushes of defined stoichiometry that can be phosphorylated vitro. Atomic force microscopy measurements reveal height depends on composition monotonically but not always linearly for binary NFL:NFM or NFL:NFH systems, NFM-based highly extended, while incorporating much larger NFH surprisingly compact even after multisite phosphorylation. Complementary self-consistent field theory (SCFT) predicts multilayer morphologies NFM brushes. Further experiments SCFT analysis with designed mutants N-terminal negative charges repel residues generate morphology, C-terminal charge-neutral region contributes morphology total height. Charge-shuffled variants show segregation promotes collapse near physiological ionic strengths. Collectively, study supports role establishing dynamic range conformation, lending insight into previous vitro vivo findings. More broadly, work establishes platform dissecting contributions sequence at interfaces.
Language: Английский
Citations
2
Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(50)
Published: Dec. 6, 2024
Intrinsically disordered proteins (IDPs) adopt ensembles of rapidly fluctuating heterogeneous conformations, influencing their binding capabilities and supramolecular transitions. The primary conformational descriptors for understanding IDP ensembles—the radius gyration ( R G ), measured by small-angle X-ray scattering (SAXS), the root mean square (rms) end-to-end distance E probed fluorescent resonance energy transfer (FRET)—are often reported to produce inconsistent results regarding expansion as a function denaturant concentration in buffer. This ongoing debate surrounding FRET-SAXS discrepancy raises questions about overall reliability either method quantitatively studying properties. To address this discrepancy, we introduce genetically encoded anomalous SAXS (ASAXS) ruler, enabling simultaneous direct measurements without assuming specific structural model. ruler utilizes noncanonical amino acid with two bromine atoms, providing an signal precise measurements. Through approach, experimentally demonstrate that ratio between varies under different denaturing conditions, highlighting intrinsic properties IDPs source observed SAXS-FRET rather than shortcomings established methods. developed ASAXS emerges versatile tool both folded proteins, unified approach obtaining complementary site-specific information experiments, thereby contributing deeper protein functions.
Language: Английский
Citations
2