ArticleThe journal of physical chemistry. B2016
Fast Method for Computing Chemical Potentials and Liquid-Liquid Phase Equilibria of Macromolecular Solutions.
Article in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Fundamental Aspects of Phase-Separated Biomolecular Condensates.Chemical reviews · 2024Review
- Calculating Structure Factors of Protein Solutions by Atomistic Modeling of Protein-Protein Interactions.Physica A · 2024Article
- Calculating Structure Factors of Protein Solutions by Atomistic Modeling of Protein-Protein Interactions.bioRxiv : the preprint server for biology · 2024Article
- Surface Charge Can Modulate Phase Separation of Multidomain Proteins.Journal of the American Chemical Society · 2024Article
- Atomistic modeling of liquid-liquid phase equilibrium explains dependence of critical temperature on γ-crystallin sequence.Communications biology · 2023Article
- Atomistic Modeling of Liquid-Liquid Phase Equilibrium Explains Dependence of Critical Temperature on γ-Crystallin Sequence.bioRxiv : the preprint server for biology · 2023Article
- Developments in describing equilibrium phase transitions of multivalent associative macromolecules.Current opinion in structural biology · 2023Review
- Calculating Binodals and Interfacial Tension of Phase-Separated Condensates from Molecular Simulations with Finite-Size Corrections.Methods in molecular biology (Clifton, N.J.) · 2023Article
- SpiDec: Computing binodals and interfacial tension of biomolecular condensates from simulations of spinodal decomposition.Frontiers in molecular biosciences · 2022Article
- Macromolecular regulators have matching effects on the phase equilibrium and interfacial tension of biomolecular condensates.Protein science : a publication of the Protein Society · 2021Article
- Characterizing protein kinase A (PKA) subunits as macromolecular regulators of PKA RIα liquid-liquid phase separation.The Journal of chemical physics · 2021Article
- Simple Calculation of Phase Diagrams for Liquid-Liquid Phase Separation in Solutions of Two Macromolecular Solute Species.The journal of physical chemistry. B · 2020Article
- A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes.The Journal of chemical physics · 2020Article
- Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform.The journal of physical chemistry. B · 2019Article
- LASSI: A lattice model for simulating phase transitions of multivalent proteins.PLoS computational biology · 2019Article
- Transfer Free Energies of Test Proteins Into Crowded Protein Solutions Have Simple Dependence on Crowder Concentration.Frontiers in molecular biosciences · 2019Article
- Atomistic Modeling of Intrinsically Disordered Proteins Under Polyethylene Glycol Crowding: Quantitative Comparison with Experimental Data and Implication of Protein-Crowder Attraction.The journal of physical chemistry. B · 2018Article
- Why Do Disordered and Structured Proteins Behave Differently in Phase Separation?Trends in biochemical sciences · 2018Review
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
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Abstract
Chemical potential is a fundamental property for determining thermodynamic equilibria involving exchange of molecules, such as between two phases of molecular systems. Previously, we developed the fast Fourier transform (FFT)-based method for Modeling Atomistic Protein-crowder interactions (FMAP) to calculate excess chemical potentials according to the Widom insertion. Intermolecular interaction energies were expressed as correlation functions and evaluated via FFT. Here, we extend this method to calculate liquid-liquid phase equilibria of macromolecular solutions. Chemical potentials are calculated by FMAP over a wide range of molecular densities, and the condition for coexistence of low- and high-density phases is determined by the Maxwell equal-area rule. When benchmarked on Lennard-Jones fluids, our method produces an accurate phase diagram at 18% of the computational cost of the current best method. Importantly, the gain in computational speed increases dramatically as the molecules become more complex, leading to many orders of magnitude in speed up for atomistically represented proteins. We demonstrate the power of FMAP by reporting the first results for the liquid-liquid coexistence curve of γII-crystallin represented at the all-atom level. Our method may thus open the door to accurate determination of phase equilibria for macromolecular mixtures such as protein-protein mixtures and protein-RNA mixtures, that are known to undergo liquid-liquid phase separation, both in vitro and in vivo.
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