Visualizing the disordered nuclear transport machinery in situ

Nature, Год журнала: 2023, Номер 617(7959), С. 162 - 169

Опубликована: Апрель 26, 2023

Abstract The approximately 120 MDa mammalian nuclear pore complex (NPC) acts as a gatekeeper for the transport between nucleus and cytosol 1 . central channel of NPC is filled with hundreds intrinsically disordered proteins (IDPs) called FG-nucleoporins (FG-NUPs) 2,3 Although structure scaffold has been resolved in remarkable detail, actual machinery built up by FG-NUPs—about 50 MDa—is depicted an 60-nm hole even highly tomograms and/or structures computed artificial intelligence 4–11 Here we directly probed conformations vital FG-NUP98 inside NPCs live cells permeabilized intact using synthetic biology-enabled site-specific small-molecule labelling approach paired time-resolved fluorescence microscopy. Single cell measurements distance distribution segments combined coarse-grained molecular simulations allowed us to map uncharted environment nanosized channel. We determined that provides—in terminology Flory polymer theory 12 —a ‘good solvent’ environment. This enables FG domain adopt expanded thus control cytoplasm. With more than 30% proteome being formed from IDPs, our study opens window into resolving disorder–function relationships IDPs situ, which are important various processes, such cellular signalling, phase separation, ageing viral entry.

Язык: Английский

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Sequence-specific interactions determine viscoelasticity and ageing dynamics of protein condensates

Nature Physics, Год журнала: 2024, Номер 20(9), С. 1482 - 1491

Опубликована: Июль 2, 2024

Язык: Английский

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Fundamental Aspects of Phase-Separated Biomolecular Condensates

Chemical Reviews, Год журнала: 2024, Номер 124(13), С. 8550 - 8595

Опубликована: Июнь 17, 2024

Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations behaviors properties biomolecular condensates. Here we aim fill this by writing a comprehensive, critical, accessible review on fundamental aspects phase-separated We introduce relevant theoretical background, present basis for computation experimental measurement condensate properties, give mechanistic interpretations terms interactions at molecular residue levels.

Язык: Английский

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

Science Advances, Год журнала: 2024, Номер 10(1)

Опубликована: Янв. 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.

Язык: Английский

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Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution

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

Опубликована: Авг. 5, 2024

Multidomain proteins with flexible linkers and disordered regions play important roles in many cellular processes, but characterizing their conformational ensembles is difficult. We have previously shown that the coarse-grained model, Martini 3, produces too compact solution, may part be remedied by strengthening protein–water interactions. Here, we show decreasing strength of protein–protein interactions leads to improved agreement experimental data on a wide set systems. 'symmetry' between rescaling breaks down when studying or within membranes; protein-protein better preserves binding specificity lipid membranes, whereas protein-water oligomerization transmembrane helices. conclude improves accuracy 3 for IDPs multidomain proteins, both solution presence membrane. authors generated molecular dynamics simulations

Язык: Английский

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A coarse‐grained model for disordered and multi‐domain proteins

Protein Science, Год журнала: 2024, Номер 33(11)

Опубликована: Окт. 16, 2024

Many proteins contain more than one folded domain, and such modular multi-domain help expand the functional repertoire of proteins. Because their larger size often substantial dynamics, it may be difficult to characterize conformational ensembles by simulations. Here, we present a coarse-grained model for that is both fast provides an accurate description global properties in solution. We show accuracy one-bead-per-residue depends on how interaction sites domains are represented. Specifically, find excessive domain-domain interactions if located at position C

Язык: Английский

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Molecular determinants of condensate composition

Molecular Cell, Год журнала: 2025, Номер 85(2), С. 290 - 308

Опубликована: Янв. 1, 2025

Язык: Английский

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COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Journal of Chemical Theory and Computation, Год журнала: 2025, Номер unknown

Опубликована: Фев. 5, 2025

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, enable more realistic modeling involving domains without additional costs. COCOMO2 was parametrized directly solubility data improve performance predicting concentration-dependent broader range biomolecular systems compared original version. enables new applications study condensates involve IDPs together assembly also provides expanded foundation development multiscale approaches span residue-level atomistic resolution.

Язык: Английский

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Martini3-IDP: improved Martini 3 force field for disordered proteins

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Март 24, 2025

Coarse-grained (CG) molecular dynamics (MD) is widely used for the efficient simulation of intrinsically disordered proteins (IDPs). The Martini model, one most popular CG force fields in biomolecular simulation, was reported to yield too compact IDP conformations, limiting its applications. Addressing this, we optimized bonded parameters based on fitting reference simulations a diverse set IDPs at atomistic resolution, resulting Martini3-based protein model coined Martini3-IDP. This leads expanded greatly improving reproduction experimentally measured radii gyration. Moreover, contrary ad-hoc fixes scaling protein-protein or protein-water interactions, Martini3-IDP keeps overall interaction balance underlying 3. To validate that, perform comprehensive testing including full-length multidomain proteins, IDP-lipid membrane binding and IDP-small molecule binding, confirming ability successfully capture complex interplay between components. Finally, recently emerging concept condensate, through liquid-liquid phase separation, also reproduced by number both homotypic heterotypic systems. With improved expand simulate processes involving environments, spatio-temporal scales inaccessible with all-atom models. Here, authors introduce Martini3-IDP, refined that addresses prior over-compact structures. Validated across systems, it captures interactions condensates.

Язык: Английский

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Prediction of phase-separation propensities of disordered proteins from sequence

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(13)

Опубликована: Март 25, 2025

Phase separation is one possible mechanism governing the selective cellular enrichment of biomolecular constituents for processes such as transcriptional activation, mRNA regulation, and immune signaling. mediated by multivalent interactions macromolecules including intrinsically disordered proteins regions (IDRs). Despite considerable advances in experiments, theory, simulations, prediction thermodynamics IDR phase behavior remains challenging. We combined coarse-grained molecular dynamics simulations active learning to develop a fast accurate machine model predict free energy saturation concentration directly from sequence. validate using computational previously measured experimental data, well new data six proteins. apply our all 27,663 IDRs chain length up 800 residues human proteome find that 1,420 these (5%) are predicted undergo homotypic with transfer energies < −2 k B T . use understand relationship between single-chain compaction changes charge- hydrophobicity-mediated can break symmetry intra- intermolecular interactions. also provide proof principle how be used force field refinement. Our work refines quantifies established rules connection sequence features phase-separation propensities, models will useful interpreting designing experiments on role separation, design specific propensities.

Язык: Английский

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