ArticleNucleic acids research2020
Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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80 citing papers in PubMed, 143 citations in OpenAlex.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
- Insertion or deletion variants in TAF15 exon 15 are genetic factors impacting the prognosis of amyotrophic lateral sclerosis in a Japanese cohort.European journal of human genetics : EJHG · 2026Article
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Article
- Decoding nucleic acid contributions to phase separation and ordering in biomolecular condensates.Nucleic acids research · 2026Article
- Alzheimer's Aβ catalyzes Tau phase separation and aggregation via early nanocluster solubilization.Nature communications · 2026Article
- A molecular grammar for programmable multiphase protein-RNA vesicles.bioRxiv : the preprint server for biology · 2026Article
- Chromatin Binding Regulates Phase Behavior and Morphology of Condensates Formed by Prion-like Domains.Journal of molecular biology · 2025Article
- Dissecting the Molecular Determinants of α-synuclein Phase Separation and Condensate Aging: The Pivotal Role of β-Sheet-Rich Motifs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Driving forces of RNA condensation revealed through coarse-grained modeling with explicit MgProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Direct Observation of the Conformational Transitions in Tau and Their Correlation with Phase Behavior.JACS Au · 2025Article
- Current practices in the study of biomolecular condensates: a community comment.Nature communications · 2025Article
- Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL.iScience · 2025Article
- FINCHES: A Computational Framework for Predicting Intermolecular Interactions in Intrinsically Disordered Proteins.International journal of molecular sciences · 2025Review
- A disordered linker in the Polycomb protein Polyhomeotic tunes phase separation and oligomerization.Molecular cell · 2025Article
- Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates.ACS central science · 2025Article
- Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates.PLoS computational biology · 2025Article
- Modeling biomolecular condensates across scales: Atomistic, coarse-grained, and data-driven approaches.Advances in physics: X · 2025Article
- Liquid-Liquid Phase Separation Associated with Intrinsically Disordered Proteins: Experimental and Computational Tools.Current protein & peptide science · 2025Review
- Microscopic Origins of Flow Activation Energy in Biomolecular Condensates.The journal of physical chemistry. B · 2024Article
20 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Ribonucleoprotein (RNP) granules are membraneless organelles (MLOs), which majorly consist of RNA and RNA-binding proteins and are formed via liquid-liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA and other polynucleotides play a key role in modulating protein phase separation. There is currently a dearth of modelling techniques which allow one to delve deeper into how polynucleotides play the role of a modulator/promoter of LLPS in cells using computational methods. Here, we present a coarse-grained polynucleotide model developed to fill this gap, which together with our recently developed HPS model for protein LLPS, allows us to capture the factors driving protein-polynucleotide phase separation. We explore the capabilities of the modelling framework with the LAF-1 RGG system which has been well studied in experiments and also with the HPS model previously. Further taking advantage of the fact that the HPS model maintains sequence specificity we explore the role of charge patterning on controlling polynucleotide incorporation into condensates. With increased charge patterning we observe formation of structured or patterned condensates which suggests the possible roles of polynucleotides in not only shifting the phase boundaries but also introducing microscopic organization in MLOs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.