Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates.

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Tác giả: Rosana Collepardo-Guevara, Jorge R Espinosa, Alejandro Feito, Antonio Rey, Ignacio Sanchez-Burgos, Eduardo Sanz, Andrés R Tejedor, Ignacio Tejero

Ngôn ngữ: eng

Ký hiệu phân loại: 553.453 Tin

Thông tin xuất bản: United States : PLoS computational biology , 2025

Mô tả vật lý:

Bộ sưu tập: NCBI

ID: 217189

Intracellular liquid-liquid phase separation (LLPS) of proteins and nucleic acids is a fundamental mechanism by which cells compartmentalize their components and perform essential biological functions. Molecular simulations play a crucial role in providing microscopic insights into the physicochemical processes driving this phenomenon. In this study, we systematically compare six state-of-the-art sequence-dependent residue-resolution models to evaluate their performance in reproducing the phase behaviour and material properties of condensates formed by seven variants of the low-complexity domain (LCD) of the hnRNPA1 protein (A1-LCD)-a protein implicated in the pathological liquid-to-solid transition of stress granules. Specifically, we assess the HPS, HPS-cation-π, HPS-Urry, CALVADOS2, Mpipi, and Mpipi-Recharged models in their predictions of the condensate saturation concentration, critical solution temperature, and condensate viscosity of the A1-LCD variants. Our analyses demonstrate that, among the tested models, Mpipi, Mpipi-Recharged, and CALVADOS2 provide accurate descriptions of the critical solution temperatures and saturation concentrations for the multiple A1-LCD variants tested. Regarding the prediction of material properties for condensates of A1-LCD and its variants, Mpipi-Recharged stands out as the most reliable model. Overall, this study benchmarks a range of residue-resolution coarse-grained models for the study of the thermodynamic stability and material properties of condensates and establishes a direct link between their performance and the ranking of intermolecular interactions these models consider.
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