ArticleACS central science2025
Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates.
Article in ACS central science, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.Nature communications · 2026Article
- Progress toward linking single-molecule behavior and condensate material properties.Current opinion in structural biology · 2026Review
- Antibody-drug conjugate engineering: from design to efficacy and safety.Signal transduction and targeted therapy · 2026Review
- Article
- Capsid stabilization reprograms the nuclear fate of the HIV genome.Science advances · 2026Article
- CondenSimAdapter: A Versatile Builder for Multiscale Simulations of Protein Condensates with Broad Force-Field Compatibility and Robust Dense-Phase Relaxation.Journal of chemical information and modeling · 2026Article
- Distinguishing near- versus off-critical phase behaviors of intrinsically disordered proteins.Reports on progress in physics. Physical Society (Great Britain) · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Cooperative molecular interaction networks govern PARP1 inhibitor selectivity and binding affinity.PLoS computational biology · 2026Article
- Computational rheometry for modeling viscoelasticity and mechanical responses of biomolecular condensates.Biophysical journal · 2026Article
- Intrinsic Disorder as a Biomimetic Design Paradigm.Biomimetics (Basel, Switzerland) · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Determination of Nucleotide-Nucleotide and Nucleotide-Amino Acid Binding Interactions from All-Atom Potential-of-Mean-Force Calculations.ACS physical chemistry Au · 2026Article
- Molecular origins of viscoelasticity in biomolecular condensates.The Journal of chemical physics · 2026Article
- Scaffold-client behavior and structural organization in multicomponent protein condensates as revealed by studying tau/TDP-43 droplets.Communications chemistry · 2026Article
- A Systematic Evaluation of Protein Phase Separation Predictors across Diverse Protein Landscapes.Computational and structural biotechnology journal · 2026Article
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.bioRxiv : the preprint server for biology · 2025Article
- Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins Reveal Asymmetric Chain Compaction.Journal of chemical theory and computation · 2025Article
- Molecular insights on the mechanism of α1-antitrypsin condensate formation and maturation.PLoS computational biology · 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
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biomolecular condensates composed of highly charged biomolecules, such as DNA, RNA, chromatin, and nucleic-acid binding proteins, are ubiquitous in the cell nucleus. The biophysical properties of these charge-rich condensates are largely regulated by electrostatic interactions. Residue-resolution coarse-grained models that describe solvent and ions implicitly are widely used to gain mechanistic insights into the biophysical properties of condensates, offering transferability, computational efficiency, and accurate predictions for multiple systems. However, their predictive accuracy diminishes for charge-rich condensates due to the implicit treatment of solvent and ions. Here, we present Mpipi-Recharged, a residue-resolution coarse-grained model that improves the description of charge effects in biomolecular condensates containing disordered proteins, multidomain proteins, and/or disordered single-stranded RNAs. Mpipi-Recharged introduces a pair-specific asymmetric Yukawa electrostatic potential, informed by atomistic simulations. We show that this asymmetric coarse-graining of electrostatic forces captures intricate effects, such as charge blockiness, stoichiometry variations in complex coacervates, and modulation of salt concentration, without requiring explicit solvation. Mpipi-Recharged provides excellent agreement with experiments in predicting the phase behavior of highly charged condensates. Overall, Mpipi-Recharged improves the computational tools available to investigate the physicochemical mechanisms regulating biomolecular condensates, enhancing the scope of computer simulations in this field.
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