ArticleJournal of chemical theory and computation2021
Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers.
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124 citing papers in PubMed.
- Article
- Hydrophobic interactions of FG-nucleoporins are required for dilating nuclear membrane pores into selective transport channels after mitosis.Nature structural & molecular biology · 2026Article
- Valency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Tradeoff Between Condensation and Organization.bioRxiv : the preprint server for biology · 2026Article
- Simulations show increased lipid interdigitation in transmembrane coupling of protein condensates.bioRxiv : the preprint server for biology · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate Simulations.bioRxiv : the preprint server for biology · 2026Article
- Predicting an intrinsic conformational twist in Card1: an in silico study.Journal of molecular modeling · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Structural flexibility of the human vault particle revealed by high-resolution cryo-EM and molecular dynamics simulations.Nature communications · 2026Article
- Origin of the ionic-strength dependent reentrant behavior in the liquid-liquid phase separation of uncharged intrinsically disordered proteins.Communications chemistry · 2026Article
- Oxygen depletion in biomolecular condensates is dominated by macromolecular density.Nature communications · 2026Article
- Multiscale simulations of folded and intrinsically disordered region-containing protein condensates.Biophysical journal · 2026Article
- REEP1 Accumulation Disrupts ER Integrity and Drives Spinal Motoneuron Degeneration in Distal Hereditary Motor Neuropathy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Deep learning model of post-translational modification regulating liquid-liquid phase separation.Communications chemistry · 2025Article
- Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognition.Biophysical journal · 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
- Protein language model identifies disordered, conserved motifs implicated in phase separation.eLife · 2025Article
- Simulations reveal a balance between protein-protein and protein-lipid interactions during condensation on membrane surfaces.Chemical science · 2025Article
- Accurate prediction of thermoresponsive phase behavior of disordered proteins.Protein science : a publication of the Protein Society · 2025Article
- A Hybrid UA-CG Force Field for Aggregation Simulation of Amyloidogenic Peptide via Liquid-like Intermediates.Molecules (Basel, Switzerland) · 2025Article
64 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Disordered proteins and nucleic acids can condense into droplets that resemble the membraneless organelles observed in living cells. MD simulations offer a unique tool to characterize the molecular interactions governing the formation of these biomolecular condensates, their physicochemical properties, and the factors controlling their composition and size. However, biopolymer condensation depends sensitively on the balance between different energetic and entropic contributions. Here, we develop a general strategy to fine-tune the potential energy function for molecular dynamics simulations of biopolymer phase separation. We rebalance protein-protein interactions against solvation and entropic contributions to match the excess free energy of transferring proteins between dilute solution and condensate. We illustrate this formalism by simulating liquid droplet formation of the FUS low-complexity domain (LCD) with a rebalanced MARTINI model. By scaling the strength of the nonbonded interactions in the coarse-grained MARTINI potential energy function, we map out a phase diagram in the plane of protein concentration and interaction strength. Above a critical scaling factor of α
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