ArticleThe journal of physical chemistry. B2021
A Data-Driven Hydrophobicity Scale for Predicting Liquid-Liquid Phase Separation of Proteins.
Article in The journal of physical chemistry. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
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- MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate Simulations.bioRxiv : the preprint server for biology · 2026Article
- amyloid-predict and LLPS-predict: Predicting phase separation propensities in the intrinsically disordered proteome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Molecular determinants of arginine versus lysine cation-π interactions in biomolecular condensates.Communications chemistry · 2026Article
- Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs.bioRxiv : the preprint server for biology · 2026Article
- CELF2 Promotes Tau Exon 10 Inclusion via Hinge Domain-Mediated Nuclear Condensation, Driving Cognitive Dysfunction in Tauopathy Models.Research square · 2026Article
- Protein Representation in Metric Spaces for Protein Druggability Prediction: A Case Study on Aspirin.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins Reveal Asymmetric Chain Compaction.Journal of chemical theory and computation · 2025Article
- Accurate prediction of thermoresponsive phase behavior of disordered proteins.Protein science : a publication of the Protein Society · 2025Article
- Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- In silico characterization, physiochemical analysis, and antifungal evaluation of the Zea mays PR-1 protein.Scientific reports · 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
- Prediction of Small-Molecule Partitioning into Biomolecular Condensates from Simulation.JACS Au · 2025Article
- Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL.iScience · 2025Article
- Toward understanding biomolecular materials comprising intrinsically disordered proteinsMolecular systems design & engineering · 2025Review
27 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
An accurate model for macroscale disordered assemblies of biological macromolecules such as those formed in so-called membraneless organelles would greatly assist in studying their structure, function, and dynamics. Recent evidence has suggested that liquid-liquid phase separation (LLPS) underlies the formation of membraneless organelles. While the general mechanism of exchange of macromolecule/water for macromolecule/macromolecule interactions is known to be the driving force for LLPS, the specific interactions involved are not well understood. One way that protein-water and protein-protein interactions have been understood historically is via hydrophobicity scales. However, these scales are typically optimized for describing these relative interactions in certain cases, such as protein folding or insertion of proteins into membranes. To better describe the relative interactions of proteins that undergo LLPS, we have developed a new, data-driven hydrophobicity scale. To determine the new scale, we used coarse-grained molecular dynamics simulations using the hydrophobicity scale coarse-grained model, which relates the interactions between amino acids to their hydrophobicity. Hydrophobicity values were determined via the force-balance method on a library of proteins that includes unfolded, intrinsically disordered, and phase-separating proteins (PSP). The resulting hydrophobicity scale can better predict whether a given protein will undergo LLPS at physiological conditions by using coarse-grained molecular dynamics simulations than existing hydrophobicity scales. This new scale confirms the importance of π-π interactions between amino acids as important drivers of LLPS. This new hydrophobicity scale provides a convenient and compact description of protein-protein interactions for proteins that undergo LLPS and could be used to develop new models to describe interactions between PSP and other components, such as nucleic acids.
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