ArticleBiophysical journal2021
A predictive coarse-grained model for position-specific effects of post-translational modifications.
Article in Biophysical journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed, 81 citations in OpenAlex.
- Progress toward linking single-molecule behavior and condensate material properties.Current opinion in structural biology · 2026Review
- Ki-67 regulates heterochromatin organization in neurons and forms condensates with heterochromatic components.Nature communications · 2026Article
- The role of electrostatic interactions in the phase separation of HP1α and its protein binding partners.bioRxiv : the preprint server for biology · 2026Article
- Molecular Origins of pH Gradients in Charge-Regulated Biomolecular Condensates.bioRxiv : the preprint server for biology · 2026Article
- Phosphorylation event changes the RNA binding mode of EZH2 disordered segment.Protein science : a publication of the Protein Society · 2026Article
- Deep learning model of post-translational modification regulating liquid-liquid phase separation.Communications chemistry · 2025Article
- Current practices in the study of biomolecular condensates: a community comment.Nature communications · 2025Article
- Predicting heteropolymer phase separation using two-chain contact maps.The Journal of chemical physics · 2025Article
- Connected Chromatin Amplifies Acetylation-Modulated Nucleosome Interactions.Biochemistry · 2025Article
- Modeling biomolecular condensates across scales: Atomistic, coarse-grained, and data-driven approaches.Advances in physics: X · 2025Article
- Fundamental Aspects of Phase-Separated Biomolecular Condensates.Chemical reviews · 2024Review
- The impact of IDR phosphorylation on the RNA binding profiles of proteins.Trends in genetics : TIG · 2024Review
- Molecular dynamics simulation on regulation of liquid-liquid phase separation of repetitive peptides.Scientific reports · 2024Article
- Direct prediction of intermolecular interactions driven by disordered regions.bioRxiv : the preprint server for biology · 2024Article
- Transmembrane coupling of liquid-like protein condensates.Nature communications · 2023Article
- Single-molecule FRET unmasks structural subpopulations and crucial molecular events during FUS low-complexity domain phase separation.Nature communications · 2023Article
- Challenges in studying the liquid-to-solid phase transitions of proteins using computer simulations.Current opinion in chemical biology · 2023Review
- Surfactants or scaffolds? RNAs of varying lengths control the thermodynamic stability of condensates differently.Biophysical journal · 2023Article
- Modeling the effects of phosphorylation on phase separation of the FUS low-complexity domain.Biophysical journal · 2023Article
- Phosphorylation sites are evolutionary checkpoints against liquid-solid transition in protein condensates.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
Biomolecules undergo liquid-liquid phase separation (LLPS), resulting in the formation of multicomponent protein-RNA membraneless organelles in cells. However, the physiological and pathological role of post-translational modifications (PTMs) on the biophysics of phase behavior is only beginning to be probed. To study the effect of PTMs on LLPS in silico, we extend our transferable coarse-grained model of intrinsically disordered proteins to include phosphorylated and acetylated amino acids. Using the parameters for modified amino acids available for fixed-charge atomistic force fields, we parameterize the size and atomistic hydropathy of the coarse-grained-modified amino acid beads and, hence, the interactions between the modified and natural amino acids. We then elucidate how the number and position of phosphorylated and acetylated residues alter the protein's single-chain compactness and its propensity to phase separate. We show that both the number and the position of phosphorylated threonines/serines or acetylated lysines can serve as a molecular on/off switch for phase separation in the well-studied disordered regions of Fused in Sarcoma (FUS) and DDX3X, respectively. We also compare modified residues to their commonly used PTM mimics for their impact on chain properties. Importantly, we show that the model can predict and capture experimentally measured differences in the phase behavior for position-specific modifications, showing that the position of modifications can dictate phase separation. In sum, this model will be useful for studying LLPS of post-translationally modified intrinsically disordered proteins and predicting how modifications control phase behavior with position-specific resolution.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.