{"title":"生物分子凝聚物和生物地貌系统的相分离行为与质量守恒模型相统一","authors":"Cheng Li, Man-Ting Guo, Xiaoqing He, Quan-Xing Liu, Zhi Qi","doi":"10.1101/2024.08.08.607271","DOIUrl":null,"url":null,"abstract":"Recent research in biogeomorphology has shown that many macroscale systems exhibit spatiotemporal self-organized patterns with coarsening behaviors and also phase separation behaviors, successfully described by a mass-conserving dynamical model. Also recently, macromolecules, such as nucleic acids and proteins, have been found to assemble mesoscale biomolecular condensates inside living cells. Despite their significance, the fundamental biophysical properties of these biomolecular condensates remain poorly understood. Here, we selected DNA and the human transcription factor p53 as a model system to form a specific type of biomolecular condensate, DNA-protein interactive co-condensates (DPICs). We developed a mass-conserving dynamical model, with all parameters derived from direct experimental measurements. This model successfully reproduces the spatiotemporal dynamics of DPICs. Our findings reveal that both mesoscale biomolecular condensates and macroscale biogeomorphological systems exhibit cross-scale spatiotemporal self-organized patterns with coarsening behaviors, and cross-scale phase separation behavior. Both systems also exhibit emergent properties. Our theoretical framework offers a deeper understanding of the mechanisms underlying these phase-separation systems.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Biomolecular condensates and biogeomorphological systems exhibit a phase-separation behavior unified by a mass-conserving model\",\"authors\":\"Cheng Li, Man-Ting Guo, Xiaoqing He, Quan-Xing Liu, Zhi Qi\",\"doi\":\"10.1101/2024.08.08.607271\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Recent research in biogeomorphology has shown that many macroscale systems exhibit spatiotemporal self-organized patterns with coarsening behaviors and also phase separation behaviors, successfully described by a mass-conserving dynamical model. Also recently, macromolecules, such as nucleic acids and proteins, have been found to assemble mesoscale biomolecular condensates inside living cells. Despite their significance, the fundamental biophysical properties of these biomolecular condensates remain poorly understood. Here, we selected DNA and the human transcription factor p53 as a model system to form a specific type of biomolecular condensate, DNA-protein interactive co-condensates (DPICs). We developed a mass-conserving dynamical model, with all parameters derived from direct experimental measurements. This model successfully reproduces the spatiotemporal dynamics of DPICs. Our findings reveal that both mesoscale biomolecular condensates and macroscale biogeomorphological systems exhibit cross-scale spatiotemporal self-organized patterns with coarsening behaviors, and cross-scale phase separation behavior. Both systems also exhibit emergent properties. Our theoretical framework offers a deeper understanding of the mechanisms underlying these phase-separation systems.\",\"PeriodicalId\":501048,\"journal\":{\"name\":\"bioRxiv - Biophysics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-08-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"bioRxiv - Biophysics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1101/2024.08.08.607271\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"bioRxiv - Biophysics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2024.08.08.607271","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
最近的生物地貌学研究表明,许多宏观系统表现出具有粗化行为和相分离行为的时空自组织模式,并成功地用质量保证动力学模型进行了描述。最近,人们还发现核酸和蛋白质等大分子在活细胞内聚集成中尺度生物分子凝聚体。尽管这些生物分子凝聚体具有重要意义,但其基本生物物理特性仍鲜为人知。在这里,我们选择 DNA 和人类转录因子 p53 作为模型系统,以形成一种特定类型的生物分子凝聚物--DNA-蛋白质交互共凝聚物(DPICs)。我们建立了一个质量守恒动力学模型,所有参数都来自直接的实验测量。该模型成功地再现了 DPIC 的时空动态。我们的研究结果表明,中尺度生物分子凝聚物和宏观生物地貌系统都表现出具有粗化行为的跨尺度时空自组织模式和跨尺度相分离行为。这两个系统还表现出突现特性。我们的理论框架有助于深入理解这些相分离系统的内在机制。
Biomolecular condensates and biogeomorphological systems exhibit a phase-separation behavior unified by a mass-conserving model
Recent research in biogeomorphology has shown that many macroscale systems exhibit spatiotemporal self-organized patterns with coarsening behaviors and also phase separation behaviors, successfully described by a mass-conserving dynamical model. Also recently, macromolecules, such as nucleic acids and proteins, have been found to assemble mesoscale biomolecular condensates inside living cells. Despite their significance, the fundamental biophysical properties of these biomolecular condensates remain poorly understood. Here, we selected DNA and the human transcription factor p53 as a model system to form a specific type of biomolecular condensate, DNA-protein interactive co-condensates (DPICs). We developed a mass-conserving dynamical model, with all parameters derived from direct experimental measurements. This model successfully reproduces the spatiotemporal dynamics of DPICs. Our findings reveal that both mesoscale biomolecular condensates and macroscale biogeomorphological systems exhibit cross-scale spatiotemporal self-organized patterns with coarsening behaviors, and cross-scale phase separation behavior. Both systems also exhibit emergent properties. Our theoretical framework offers a deeper understanding of the mechanisms underlying these phase-separation systems.