Biomolecular phase separation through theoretical and computational microscope

IF 1.7 4区 化学 Bulletin of the Korean Chemical Society Pub Date : 2024-04-02 DOI:10.1002/bkcs.12840
Rajeev Kumar, Da-Hyun Koo, Yu-Gon Eom, Jeong-Mo Choi
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Abstract

Biomolecular phase separation is a vital mechanism for orchestrating biomolecules within living cells. This crucial role has spurred an intense pursuit to comprehend the molecular underpinnings governing and regulating these processes. Computational methodologies offer a unique perspective, augmenting experimental techniques by providing detailed information that cannot be obtained otherwise. In this review, we briefly overview the theoretical and computational approaches to investigate biomolecular phase separation. As a short primer, we explain the factors driving and affecting phase separation of biomolecules, and then we delve into analytical and simulation methods used to study phase separation. We explain how analytical methods like the Flory–Huggins theory, random phase approximation, and graph-based methods have been used to study phase behaviors of various proteins. We also discuss principles and applications of all-atom simulations, coarse-grained simulations, and field-theoretical approaches. Additionally, we explore the recent advances in machine learning approach to predict phase separation of biomolecules.

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通过理论和计算显微镜实现生物分子相分离
生物分子相分离是协调活细胞内生物分子的重要机制。这一关键作用激发了人们对控制和调节这些过程的分子基础的强烈追求。计算方法提供了一个独特的视角,通过提供其他方法无法获得的详细信息来增强实验技术。在本综述中,我们将简要概述研究生物分子相分离的理论和计算方法。作为一个简短的入门,我们将解释驱动和影响生物分子相分离的因素,然后深入探讨用于研究相分离的分析和模拟方法。我们将解释如何使用 Flory-Huggins 理论、随机相近似和基于图的方法等分析方法来研究各种蛋白质的相行为。我们还讨论了全原子模拟、粗粒度模拟和场理论方法的原理和应用。此外,我们还探讨了预测生物大分子相分离的机器学习方法的最新进展。
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来源期刊
Bulletin of the Korean Chemical Society
Bulletin of the Korean Chemical Society Chemistry-General Chemistry
自引率
23.50%
发文量
182
期刊介绍: The Bulletin of the Korean Chemical Society is an official research journal of the Korean Chemical Society. It was founded in 1980 and reaches out to the chemical community worldwide. It is strictly peer-reviewed and welcomes Accounts, Communications, Articles, and Notes written in English. The scope of the journal covers all major areas of chemistry: analytical chemistry, electrochemistry, industrial chemistry, inorganic chemistry, life-science chemistry, macromolecular chemistry, organic synthesis, non-synthetic organic chemistry, physical chemistry, and materials chemistry.
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