Disordered proteins interact with the chemical environment to tune their protective function during drying

eLife, Год журнала: 2024, Номер 13

Опубликована: Июнь 21, 2024

The conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. inherent malleability proteins, combined with the exposure residues, accounts for this sensitivity. One context in which IDPs play important roles that concomitant massive changes intracellular environment is during desiccation (extreme drying). ability organisms survive has long been linked accumulation high levels cosolutes such as trehalose or sucrose well enrichment IDPs, late embryogenesis abundant (LEA) cytoplasmic heat-soluble (CAHS) proteins. Despite knowing co-enriched alongside endogenous, species-specific desiccation, little known mechanistically about how IDP-cosolute interactions influence tolerance. Here, we test notion protective desiccation-related enhanced through induced by endogenous cosolutes. We find derived from four different spanning two LEA protein families CAHS family synergize best drying promote protection. Yet structural parameters do not correlate synergy either further demonstrate CAHS, but related self-assembly formation a gel. Our results suggest functional between convergent protection strategy seen among IDP organisms, yet mechanisms underlying differ families.

Язык: Английский

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SOP-MULTI: A Self-Organized Polymer-Based Coarse-Grained Model for Multidomain and Intrinsically Disordered Proteins with Conformation Ensemble Consistent with Experimental Scattering Data

Journal of Chemical Theory and Computation, Год журнала: 2024, Номер 20(22), С. 10179 - 10198

Опубликована: Ноя. 5, 2024

Multidomain proteins with long flexible linkers and full-length intrinsically disordered (IDPs) are best defined as an ensemble of conformations rather than a single structure. Determining high-resolution structures such poses various challenges by using tools from experimental structural biophysics. Integrative approaches combining available low-resolution ensemble-averaged data in silico biomolecular reconstructions now often used for the purpose. However, extensive Boltzmann weighted conformation sampling large proteins, especially ones where both folded domains exist same polypeptide chain, remains challenge. In this work, we present 2-site per amino-acid resolution SOP-MULTI force field simulating coarse-grained models multidomain proteins. combines two well-established self-organized polymer models─: (i) SOP-SC systems (ii) SOP-IDP IDPs. For SOP-MULTI, introduce cross-interaction terms between beads belonging to regions generate ensembles hnRNP A1, TDP-43, G3BP1, hGHR-ECD, TIA1, HIV-1 Gag, polyubiquitin, FUS. When back-mapped all-atom resolution, trajectories faithfully recapitulate scattering over range reciprocal space. We also show that individual preserve native contacts respect solved structures, root-mean-square fluctuations residues match those obtained molecular dynamics simulation systems. is made LAMMPS-compatible user package along setup codes generating required files any protein regions.

Язык: Английский

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Molecular insights into the interaction between a disordered protein and a folded RNA

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(49)

Опубликована: Ноя. 26, 2024

Intrinsically disordered protein regions (IDRs) are well established as contributors to intermolecular interactions and the formation of biomolecular condensates. In particular, RNA-binding proteins (RBPs) often harbor IDRs in addition folded domains that contribute RBP function. To understand dynamic an IDR–RNA complex, we characterized features a small (68 residues), positively charged IDR-containing protein, Small ERDK-Rich Factor (SERF). At high concentrations, SERF RNA undergo charge-driven associative phase separation form protein- RNA-rich dense phase. A key advantage this model system is threshold for demixing sufficiently could use solution-state biophysical methods interrogate stoichiometric complexes with one-phase regime. Herein, describe our comprehensive characterization alone complex fragment HIV-1 Trans-Activation Response (TAR) complementary molecular simulations. We find binding event not accompanied by acquisition structure either molecule; however, see evidence modest global compaction ensemble when bound RNA. This behavior likely reflects attenuated charge repulsion within via polyanionic provides rationale higher-order assembly context envision SERF–RNA will lower barrier accessing details support likewise deepen understanding role contacts liquid–liquid separation.

Язык: Английский

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Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 27, 2025

Nuclear speckles are enriched in serine / arginine rich splicing factors (SRSFs), such as SRSF1. Splicing and proteins TDP-43 concentrate into distinct speckle territories to enable pre-mRNA processing. We have discovered that SRSFs block copolymers the protein-specific interplay of inter-block repulsions attractions drives spontaneous microphase separation. This gives rise size-limited, ordered assemblies, 30 - 45 nm diameter. Depending on protein, each comprises several tens hundreds molecules. The sub-micron scale observed cells shown be clusters microphases. regulatory lncRNA MALAT1 binds preferentially SRSF1 microphases enhance separation alter structures. Microphase enables concentration finite numbers assemblies with nanoscale structures can modulated by . Our findings provide a structural framework for functional organization factors.

Язык: Английский

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Sequence-based prediction of intermolecular interactions driven by disordered regions

Science, Год журнала: 2025, Номер 388(6749)

Опубликована: Май 22, 2025

Intrinsically disordered regions (IDRs) in proteins play essential roles cellular function. A growing body of work has shown that IDRs often interact with partners a manner does not depend on the precise order amino acids but is instead driven by complementary chemical interactions, leading to bound-state complexes. However, these chemically specific dynamic interactions are difficult predict. In this study, we repurposed physics developed originally for molecular simulations predict specificity between and partner using protein sequence as only input. Our approach-FINCHES-enables direct prediction phase diagrams, identification interaction hotspots IDRs, decomposition distinct domains route develop test mechanistic hypotheses regarding IDR function recognition.

Язык: Английский

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The analytical Flory random coil is a simple-to-use reference model for unfolded and disordered proteins

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

Опубликована: Март 13, 2023

Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties fit simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable stand-alone reference Here we use all-atom simulations of polypeptides in conjunction with scaling theory parameterize an that behave ideal chains (ν = 0.50). The model, which call Flory Random Coil (AFRC), requires only amino acid sequence input provides direct access probability distributions global local conformational order parameters. defines a specific state computational compared normalized. As proof-of-concept, AFRC identify sequence-specific intramolecular interactions proteins. We also contextualize curated set 145 different radii gyration obtained from previously published small-angle X-ray scattering experiments is implemented software package available via Google colab notebook. In summary, simple-to-use guide intuition aid interpreting results.

Язык: Английский

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Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator

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

Опубликована: Апрель 25, 2024

Abstract Organismal physiology is widely regulated by the molecular circadian clock, a feedback loop composed of protein complexes whose members are enriched in intrinsically disordered regions. These regions can mediate protein-protein interactions via SLiMs, but contribution these to clock had not been elucidated. To determine functionality regions, we applied synthetic peptide microarray approach FRQ Neurospora crassa . We identified residues required for FRQ’s interaction with its partner FRH, mutation which demonstrated FRH necessary persistent oscillations repression transcriptional activity. Additionally, an enrichment binding peptides net positive charge. found that positively charged occurred significant “blocks” within amino acid sequence and ablation one blocks affected both core timing physiological output. Finally, charge clusters were commonly shared feature repressive proteins. Overall, our study suggests mechanistic purpose yielded insights into arm roles function.

Язык: Английский

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Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins

Bioinformatics, Год журнала: 2024, Номер 40(11)

Опубликована: Окт. 21, 2024

Abstract Motivation Characterizing the structure of flexible proteins, particularly within realm intrinsic disorder, presents a formidable challenge due to their high conformational variability. Currently, structural representation relies on (possibly large) ensembles derived from combination experimental and computational methods. The detailed analysis these is difficult task, for which existing tools have limited effectiveness. Results This study proposes an innovative extension concept contact maps ensemble framework, incorporating probabilistic nature disordered proteins. Within this characterized through weighted family maps. To achieve this, conformations are first described using refined definition that appropriately accounts geometry inter-residue interactions sequence context. Representative features naturally emerge subsequent clustering resulting contact-based descriptors. Importantly, transiently populated readily identified large ensembles. performance method illustrated by several use cases compared with other approaches, highlighting its superiority in capturing relevant highly Availability implementation An open-source provided together easy-to-use Jupyter notebook, available at https://gitlab.laas.fr/moma/WARIO.

Язык: Английский

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Structural dynamics of the intrinsically disordered linker region of cardiac troponin T

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 31, 2024

The cardiac troponin complex, composed of troponins I, T, and C, plays a central role in regulating the calcium-dependent interactions between myosin thin filament. Mutations can cause cardiomyopathies; however, it is still major challenge to connect how changes sequence affect troponin's function. Recent high-resolution structures filament revealed critical insights into structure-function relationship troponin, but there remain large, unresolved segments including troponin-T linker region that hotspot for cardiomyopathy mutations. This predicted be intrinsically disordered, with behaviors are not well described by traditional structural approaches; this proposal has been experimentally verified. Here, we used combination single-molecule Förster resonance energy transfer (FRET), molecular dynamics simulations, functional reconstitution assays investigate region. We show context both isolated fully regulated behaves as dynamic, disordered undergoes polyampholyte expansion presence high salt distinct conformational during assembly complex. also examine ΔE160 hypertrophic mutation demonstrate does linker, rather allosterically affects other complex subunits, leading increased contractility. Taken together, our data clearly importance disorder within provide new mechanisms driving pathogenesis cardiomyopathies.

Язык: Английский

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Molecular insights into the interaction between a disordered protein and a folded RNA

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 12, 2024

ABSTRACT Intrinsically disordered protein regions (IDRs) are well-established as contributors to intermolecular interactions and the formation of biomolecular condensates. In particular, RNA-binding proteins (RBPs) often harbor IDRs in addition folded domains that contribute RBP function. To understand dynamic an IDR-RNA complex, we characterized features a small (68 residues), positively charged IDR-containing protein, SERF. At high concentrations, SERF RNA undergo charge-driven associative phase separation form protein- RNA-rich dense phase. A key advantage this model system is threshold for demixing sufficiently could use solution-state biophysical methods interrogate stoichiometric complexes with one-phase regime. Herein, describe our comprehensive characterization alone complex fragment HIV-1 TAR (TAR) complementary molecular simulations. We find binding event not accompanied by acquisition structure either molecule; however, see evidence modest global compaction ensemble when bound RNA. This behavior likely reflects attenuated charge repulsion within via polyanionic provides rationale higher-order assembly context envision SERF-RNA will lower barrier accessing details support likewise deepen understanding role contacts liquid-liquid separation. SIGNIFICANCE Subcellular organization through condensates has emerged important contributor myriad cellular functions, implications homeostasis, stress response, disease. general specific principles condensate formation, must their constituent biomolecules. end, study introduces simple comprised small, charge-driven, extensive these molecules also generate new insights into mode interaction between unstructured structured

Язык: Английский

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