物理化学学报

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生物分子液-液相分离的物理化学机制

张长胜1, 来鲁华1,2   

  1. 1 北京大学化学与分子工程学院, 物理化学研究所, 分子动态与稳态结构国家重点实验室, 北京分子科学国家研究中心, 北京 100871;
    2 北京大学定量生物学中心, 北京大学-清华大学生命科学联合中心, 北京 100871
  • 收稿日期:2019-07-19 修回日期:2019-09-09 录用日期:2019-09-10 发布日期:2019-09-24
  • 通讯作者: 张长胜, 来鲁华 E-mail:changshengzhang@pku.edu.cn;lhlai@pku.edu.cn
  • 基金资助:
    国家重点研发计划(2016YFA0502303)及国家自然科学基金(21633001)资助项目

Physiochemical Mechanisms of Biomolecular Liquid-Liquid Phase Separation

Changsheng Zhang1, Luhua Lai1,2   

  1. 1 Beijing National Laboratory for Molecular Science, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China;
    2 Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, P. R. China
  • Received:2019-07-19 Revised:2019-09-09 Accepted:2019-09-10 Published:2019-09-24
  • Contact: Changsheng Zhang, Luhua Lai E-mail:changshengzhang@pku.edu.cn;lhlai@pku.edu.cn
  • Supported by:
    The project was supported by the National Key Research and Development Program of China (2016YFA0502303) and the National Natural Science Foundation of China (21633001).

摘要: 近年来,有关生物分子通过液-液相分离机制进行组织定位、功能调控的研究发展迅速。相分离产生的聚集体在众多细胞活动事件中发挥了关键作用。这些聚集体的生物功能是以相分离的物理化学性质为基础的。本文将从相分离聚集体的基本性质、相图、微观结构,相分离的统计热力学、实验和分子模拟研究等方面阐释相分离物理化学机制研究相关进展。对于生物分子相分离的重要功能体系进行了列举和归纳,收集了相分离研究的模式体系,探讨了生物分子相分离的生物功能同物理化学机制之间的关系,总结了生物分子相分离的调控机制和调控分子的设计方法,并对生物分子相分离物理化学机制研究的未来发展方向进行了展望。

关键词: 生物分子液-液相分离, 液态聚集体, 天然无序蛋白质, 多价作用, 分子聚集的计算模拟, 相分离调控

Abstract: The discoveries about the functions of biomolecular liquid-liquid phase separation in cell have been increased rapidly in the past decade. Condensates produced by phase separation play key roles in many cellular curial events. These biological functions are based on the physicochemical properties of phase separation. This review discusses the recent progress in understanding the physical and chemical mechanisms of biological liquid-liquid phase separation. (1) We summarized the basic properties and experimental characterization methods of phase separation droplets, including the morphology, fusion, and wetting, along with the dynamic properties of molecules in droplets, which are usually described by diffusion coefficients or viscosity and permeability. (2) We discussed the conditions affecting the liquid-liquid phase separation of biological molecules, including concentration, temperature, ionic strength, pH, and crowding effects. A database for liquid-liquid phase separation, LLPSDB, was introduced, and three types of nucleic acid concentration effects on the phase separation of protein molecules are discussed. These effects depend on the relative interaction strengths of protein-nucleic acid and protein-protein interactions. The major driving force of phase separation is multivalent interactions, and molecular flexibility is necessary for the dynamic properties. We summarized the diverse sources of multivalence, including multiple tandem repetitive domains, regular oligomerization, low-complexity domains (usually intrinsically disordered with repeat motifs for binding), and nucleic acid molecules via the main chain phosphates or repeat sequences. (3) We reviewed the statistical thermodynamics theories for describing the macromolecular liquid-liquid separation, including the Flory-Huggins theory, Overbeek-Voorn correction, random phase approximation method, and field theory simulation method. We discussed the experimental and simulation methods for studying the physiochemical mechanism of liquid-liquid phase separation. Model systems with simplified sequences for experimental studies were listed, including systems for studying the effects of charge properties, residue types, sequence length, and other properties. Molecular simulation methods can provide detailed information regarding the liquid-liquid phase separation process. We introduced two coarse-grain methods, the slab molecular dynamic simulation and Monte Carlo simulation using the lattice model. (4) The physiochemical properties of liquid-liquid phase separation govern the diverse functions of reversible phase transitions in a cell. We collected and analyzed important cases of biomolecular phase separation in cell activities. These biological functions were classified into five categories, including enrichment, sequestration, biological switching cooperation, localization, and mechanical force generation. We linked these functions with the physiochemical properties of liquid-liquid phase separation. To understand the specific phase-separation processes in biological activities, three types of related molecules must be studied:scaffold molecules mainly contributing to aggregate formation, recruited functional client molecules, and molecules that regulate the formation and disassembly of aggregates. We reviewed four regulation methods for the phase separation process, including changing the charge distribution by post-translational modification, changing the molecular concentration by gene expression or degradation regulation, changing the oligomerization state, and changing the cell solution environment (such as pH). Designing compounds for phase separation regulation has attracted significant attention for treating related diseases. Methods for discovering molecules that can regulate post-translational modifications or inhibit interactions in the droplets are emerging. The recently discovered phase separation phenomena and molecules in living organisms represent only the tip of the iceberg. In the future, it will be necessary to systematically examine liquid-liquid phase separation events and related molecules in all phases of biological processes.

Key words: Biomolecular liquid-liquid phase separation, Droplet condensate, Intrinsically disordered protein, Multivalent interaction, Molecular simulation for aggregation, Phase separation regulation

MSC2000: 

  • O641