Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates DOI
Shuming Liu, Cong Wang, Bin Zhang

et al.

Biochemistry, Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Phase separation is a fundamental process that enables cellular organization by forming biomolecular condensates. These assemblies regulate diverse functions creating distinct environments, influencing reaction kinetics, and facilitating processes such as genome organization, signal transduction, RNA metabolism. Recent studies highlight the complexity of condensate properties, shaped intrinsic molecular features external factors temperature pH. Molecular simulations serve an effective approach to establishing comprehensive framework for analyzing these influences, offering high-resolution insights into stability, dynamics, material properties. This review evaluates recent advancements in simulations, with particular focus on coarse-grained 1-bead-per-amino-acid (1BPA) protein models, emphasizes OpenABC, tool designed simplify streamline simulations. OpenABC supports implementation various force fields, enabling their performance evaluation. Our benchmarking identifies inconsistencies phase behavior predictions across even though models accurately capture single-chain statistics. finding underscores need enhanced field accuracy, achievable through enriched training data sets, many-body potentials, advanced optimization techniques. Such refinements could significantly improve predictive capacity bridging details emergent behaviors.

Language: Английский

Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates DOI
Shuming Liu, Cong Wang, Bin Zhang

et al.

Biochemistry, Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Phase separation is a fundamental process that enables cellular organization by forming biomolecular condensates. These assemblies regulate diverse functions creating distinct environments, influencing reaction kinetics, and facilitating processes such as genome organization, signal transduction, RNA metabolism. Recent studies highlight the complexity of condensate properties, shaped intrinsic molecular features external factors temperature pH. Molecular simulations serve an effective approach to establishing comprehensive framework for analyzing these influences, offering high-resolution insights into stability, dynamics, material properties. This review evaluates recent advancements in simulations, with particular focus on coarse-grained 1-bead-per-amino-acid (1BPA) protein models, emphasizes OpenABC, tool designed simplify streamline simulations. OpenABC supports implementation various force fields, enabling their performance evaluation. Our benchmarking identifies inconsistencies phase behavior predictions across even though models accurately capture single-chain statistics. finding underscores need enhanced field accuracy, achievable through enriched training data sets, many-body potentials, advanced optimization techniques. Such refinements could significantly improve predictive capacity bridging details emergent behaviors.

Language: Английский

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