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Nucleation of Biomolecular Condensates from Finite-Sized Simulations.

ABSTRACT: The nucleation of protein condensates is a concentration-driven process of assembly. When modeled in the canonical ensemble, condensation is affected by finite-size effects. Here, we present a general and efficient route for obtaining ensemble properties of protein condensates in the macroscopic limit from finite-sized nucleation simulations. The approach is based on a theoretical description of droplet nucleation in the canonical ensemble and enables estimation of thermodynamic and kinetic parameters, such as the macroscopic equilibrium density of the dilute protein phase, the surface tension of the condensates, and nucleation free energy barriers. We apply the method to coarse-grained simulations of NDDX4 and FUS-LC, two phase-separating disordered proteins with different physicochemical characteristics. Our results show that NDDX4 condensate droplets, characterized by lower surface tension, higher solubility, and faster monomer exchange dynamics compared to those of FUS-LC, form with negligible nucleation barriers. In contrast, FUS-LC condensates form via an activated process over a wide range of concentrations.

SUBMITTER: Li L

PROVIDER: S-EPMC9940850 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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Nucleation of Biomolecular Condensates from Finite-Sized Simulations.

Li Lunna L Paloni Matteo M Finney Aaron R AR Barducci Alessandro A Salvalaglio Matteo M

The journal of physical chemistry letters 20230209 7

The nucleation of protein condensates is a concentration-driven process of assembly. When modeled in the canonical ensemble, condensation is affected by finite-size effects. Here, we present a general and efficient route for obtaining ensemble properties of protein condensates in the macroscopic limit from finite-sized nucleation simulations. The approach is based on a theoretical description of droplet nucleation in the canonical ensemble and enables estimation of thermodynamic and kinetic para ...[more]

PMID: 36758221

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Project description:Biomolecular condensates are important contributors to the internal organization of the cell material. While initially described as liquid-like droplets, the term biomolecular condensates is now used to describe a diversity of condensed phase assemblies with material properties extending from low to high viscous liquids, gels, and even glasses. Because the material properties of condensates are determined by the intrinsic behavior of their molecules, characterizing such properties is integral to rationalizing the molecular mechanisms that dictate their functions and roles in health and disease. Here, we apply and compare three distinct computational methods to measure the viscoelasticity of biomolecular condensates in molecular simulations. These methods are the Green-Kubo (GK) relation, the oscillatory shear (OS) technique, and the bead tracking (BT) method. We find that, although all of these methods provide consistent results for the viscosity of the condensates, the GK and OS techniques outperform the BT method in terms of computational efficiency and statistical uncertainty. We thus apply the GK and OS techniques for a set of 12 different protein/RNA systems using a sequence-dependent coarse-grained model. Our results reveal a strong correlation between condensate viscosity and density, as well as with protein/RNA length and the number of stickers vs spacers in the amino acid protein sequence. Moreover, we couple the GK and the OS technique to nonequilibrium molecular dynamics simulations that mimic the progressive liquid-to-gel transition of protein condensates due to the accumulation of interprotein β-sheets. We compare the behavior of three different protein condensates, i.e., those formed by either hnRNPA1, FUS, or TDP-43 proteins, whose liquid-to-gel transitions are associated with the onset of amyotrophic lateral sclerosis and frontotemporal dementia. We find that both the GK and OS techniques successfully predict the transition from functional liquid-like behavior to kinetically arrested states once the network of interprotein β-sheets has percolated through the condensates. Overall, our work provides a comparison of different modeling rheological techniques to assess the viscosity of biomolecular condensates, a critical magnitude that provides information on the behavior of biomolecules inside condensates.

Dataset Information

Nucleation of Biomolecular Condensates from Finite-Sized Simulations.

Publications

Nucleation of Biomolecular Condensates from Finite-Sized Simulations.

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