ArticleJournal of chemical theory and computation2021
Consistent Force Field Captures Homologue-Resolved HP1 Phase Separation.
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 60 papers.
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Who cites it
60 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
- Article
- Valency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Tradeoff Between Condensation and Organization.bioRxiv : the preprint server for biology · 2026Article
- HyRes: Accurate Physics-Based Simulation of Dynamic Protein Structures and Interactions in Complex Environments at Scale.bioRxiv : the preprint server for biology · 2026Article
- Folded domains impose structural heterogeneity and attenuated dynamics in biomolecular condensates.Nature communications · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- The filamentous ultrastructure of the PopZ condensate is required for its cellular function.Nature structural & molecular biology · 2026Article
- Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins Reveal Asymmetric Chain Compaction.Journal of chemical theory and computation · 2025Article
- Repulsive vs Attractive Crowding Distinctly Regulate TDP-43 Condensates through Region-specific Structural Dynamics.JACS Au · 2025Article
- Protein language model identifies disordered, conserved motifs implicated in phase separation.eLife · 2025Article
- Accurate prediction of thermoresponsive phase behavior of disordered proteins.Protein science : a publication of the Protein Society · 2025Article
- Hydrophobic interactions of FG-nucleoporins are required for dilating nuclear membrane pores into selective transport channels after mitosis.bioRxiv : the preprint server for biology · 2025Article
- Current practices in the study of biomolecular condensates: a community comment.Nature communications · 2025Article
- A coarse-grained model for disordered proteins under crowded conditions.Protein science : a publication of the Protein Society · 2025Article
- Amino acid transfer free energies reveal thermodynamic driving forces in biomolecular condensate formation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Prediction of phase-separation propensities of disordered proteins from sequence.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Microphase separation produces interfacial environment within diblock biomolecular condensates.eLife · 2025Article
- Accurate prediction of thermoresponsive phase behavior of disordered proteins.bioRxiv : the preprint server for biology · 2025Article
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2 authors.
Funding
Abstract
Many proteins have been shown to function via liquid-liquid phase separation. Computational modeling could offer much needed structural details of protein condensates and reveal the set of molecular interactions that dictate their stability. However, the presence of both ordered and disordered domains in these proteins places a high demand on the model accuracy. Here, we present an algorithm to derive a coarse-grained force field, MOFF, which can model both ordered and disordered proteins with consistent accuracy. It combines maximum entropy biasing, least-squares fitting, and basic principles of energy landscape theory to ensure that MOFF recreates experimental radii of gyration while predicting the folded structures for globular proteins with lower energy. The theta temperature determined from MOFF separates ordered and disordered proteins at 300 K and exhibits a strikingly linear relationship with amino acid sequence composition. We further applied MOFF to study the phase behavior of HP1, an essential protein for post-translational modification and spatial organization of chromatin. The force field successfully resolved the structural difference of two HP1 homologues despite their high sequence similarity. We carried out large-scale simulations with hundreds of proteins to determine the critical temperature of phase separation and uncover multivalent interactions that stabilize higher-order assemblies. In all, our work makes significant methodological strides to connect theories of ordered and disordered proteins and provides a powerful tool for studying liquid-liquid phase separation with near-atomistic details.
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