Multi-scale computational investigation of functions and mechanisms of protein-RNA phase separation.

项目摘要/摘要 近年来，人们逐渐意识到蛋白质和核糖核酸的液-液分离 酸是各种细胞内无膜细胞器的形成原因。细胞器的例子 核内有核仁和Cajal小体，核内有应力颗粒和P颗粒 细胞质。蛋白质-rna复合体的相分离尤其受到重视。 基因调控过程与真核生物表型复杂性之间的关系。尽管令人震惊- fi的生物学意义和广泛的实验努力，我们对其中联系的机制的理解 蛋白质-RNA与转录和催化过程的相分离仍然是缺乏的。最基本的 挑战来自(I)rna和蛋白质的分子异质性和构象fl灵活性，这 包含低复杂性无序区(II)分子和细胞尺度的并置(III)存在 由生化反应、三磷酸腺苷驱动的过程和不可逆生物聚合物flux引起的非平衡效应。 目前的理论和计算范例往往缺乏最优的时空分辨率和正确的 结合物理洞察力全面、综合地面对复杂的实验数据 举止。在这里，我建议将我们实验室开发的多尺度计算工具与 揭示蛋白质-RNA相分离及其联系的一般机理的数据驱动方法 与职能监管流程相适应。该提案包括三个方向。在fiFirst方向，我们将重点放在 用于液-液热力学驱动力研究的蛋白质和RNA分级粗粒化 通过分子动力学技术实现体外相分离。在第二个方向上，我们使用fiNite-Element 以及由分子模型和实验数据训练的反应扩散模拟，以研究连接- 具有体内特征的转录和催化反应的液-液相分离 条件。在第三个方向上，我们评估了蛋白质-RNA相分离通用基因调控的影响 网络，使用随机动力学模拟。选择用于研究的特定fic系统进行了实验。 符合良好的RNA结合蛋白FUS、TDP-43、Tau、hnrpa1和hnrpa2。这些系统是已知的 用于在通常调节的条件下形成液体蛋白质-RNA凝聚体和聚集结构 调节不当，从而导致重大的神经退行性疾病。 拟议研究计划的完成将阐明蛋白质-RNA相SEPA的性质。 定量说明其与功能生化反应的联系，并为发展干预提供亟需的见解 阻止蛋白质聚集到诱发细胞体的疾病中的策略。

PROJECT SUMMARY/ABSTRACT In recent years there has emerged a striking realization that liquid-liquid phase separation of proteins and nucleic acids is responsible for the formation of various intracellular membraneless organelles. Examples of organelles formed by phase separation are nucleoli and Cajal bodies in the nucleus and stress granules and P granules in the cytoplasm. The phase separation of protein-RNA composites, in particular, is being appreciated for crucial roles of connecting gene regulatory processes with the phenotypic complexity of eukaryotes. Despite the appar- ent biological significance and extensive experimental efforts, our understanding of the mechanisms which link protein-RNA phase separation with the transcriptional and catalytic processes is still lacking. The fundamental challenges stem from (i) The molecular heterogeneity and conformational flexibility of RNA and proteins, which contain low complexity disordered regions (ii) The juxtaposition of molecular and cellular scales (iii) Presence of non-equilibrium effects due to biochemical reactions, ATP driven processes, and irreversible bio-polymer fluxes. The current theoretical and computational paradigms often lack optimal spatio-temporal resolution and the right combination of physical insights for confronting the complex experimental data in a comprehensive and integrative manner. Here, I propose using multi-scale computational tools developed in our lab combined in conjunction with data-driven approaches for revealing general mechanistic principles of protein-RNA phase separation and its link with the functional regulatory processes. The proposal consists of three directions. In the first direction, we focus on hierarchical coarse-graining of proteins and RNA for studying thermodynamic driving forces of liquid-liquid phase separation in in vitro via molecular dynamics techniques. In the second direction, we employ finite-element and reaction-diffusion simulations trained by molecular models and experimental data for studying the connec- tion of liquid-liquid phase separation with transcriptional and catalytic reactions, which is characteristic of in vivo conditions. In the third direction, we assess the impact of protein-RNA phase separation generic gene regulatory networks by using stochastic dynamics simulations. The specific systems chosen for the study are experimen- tally well-characterized RNA binding proteins FUS, TDP-43, Tau, hnrpa1, and hnrpa2. These systems are known for forming liquid protein-RNA condensates under usually regulated conditions and aggregated structures when misregulated, thereby leading to major neurodegenerative diseases. The completion of the proposed research program will elucidate the nature of the protein-RNA phase sepa- ration its link with functional biochemical reactions and provide much-needed insights for developing intervention strategies for halting protein aggregation into diseases inducing cellular bodies.