Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom.
Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
Biophys J. 2023 Jul 25;122(14):2973-2987. doi: 10.1016/j.bpj.2023.03.006. Epub 2023 Mar 6.
Biomolecular condensates, thought to form via liquid-liquid phase separation of intracellular mixtures, are multicomponent systems that can include diverse types of proteins and RNAs. RNA is a critical modulator of RNA-protein condensate stability, as it induces an RNA concentration-dependent reentrant phase transition-increasing stability at low RNA concentrations and decreasing it at high concentrations. Beyond concentration, RNAs inside condensates can be heterogeneous in length, sequence, and structure. Here, we use multiscale simulations to understand how different RNA parameters interact with one another to modulate the properties of RNA-protein condensates. To do so, we perform residue/nucleotide resolution coarse-grained molecular dynamics simulations of multicomponent RNA-protein condensates containing RNAs of different lengths and concentrations, and either FUS or PR proteins. Our simulations reveal that RNA length regulates the reentrant phase behavior of RNA-protein condensates: increasing RNA length sensitively rises the maximum value that the critical temperature of the mixture reaches, and the maximum concentration of RNA that the condensate can incorporate before beginning to become unstable. Strikingly, RNAs of different lengths are organized heterogeneously inside condensates, which allows them to enhance condensate stability via two distinct mechanisms: shorter RNA chains accumulate at the condensate's surface acting as natural biomolecular surfactants, while longer RNA chains concentrate inside the core to saturate their bonds and enhance the density of molecular connections in the condensate. Using a patchy particle model, we additionally demonstrate that the combined impact of RNA length and concentration on condensate properties is dictated by the valency, binding affinity, and polymer length of the various biomolecules involved. Our results postulate that diversity on RNA parameters within condensates allows RNAs to increase condensate stability by fulfilling two different criteria: maximizing enthalpic gain and minimizing interfacial free energy; hence, RNA diversity should be considered when assessing the impact of RNA on biomolecular condensates regulation.
生物分子凝聚体被认为通过细胞内混合物的液-液相分离形成,是包含多种类型蛋白质和 RNA 的多组分系统。RNA 是 RNA-蛋白质凝聚体稳定性的关键调节剂,因为它诱导 RNA 浓度依赖性的重入相转变——在低 RNA 浓度下增加稳定性,在高浓度下降低稳定性。除了浓度之外,凝聚体中的 RNA 可以在长度、序列和结构上具有异质性。在这里,我们使用多尺度模拟来理解不同的 RNA 参数如何相互作用,从而调节 RNA-蛋白质凝聚体的性质。为此,我们对含有不同长度和浓度的 RNA 的多组分 RNA-蛋白质凝聚体进行了残基/核苷酸分辨的粗粒度分子动力学模拟,并且使用了 FUS 或 PR 蛋白。我们的模拟表明,RNA 长度调节 RNA-蛋白质凝聚体的重入相行为:增加 RNA 长度会敏感地提高混合物临界温度达到的最大值,以及凝聚体可以包含的 RNA 最大浓度,然后凝聚体开始变得不稳定。引人注目的是,不同长度的 RNA 在凝聚体内部是异质组织的,这使它们能够通过两种不同的机制增强凝聚体的稳定性:较短的 RNA 链在凝聚体的表面聚集,充当天然的生物分子表面活性剂,而较长的 RNA 链集中在核心内部,以饱和它们的键并增强凝聚体中分子连接的密度。使用嵌段粒子模型,我们还证明了 RNA 长度和浓度对凝聚体性质的综合影响取决于所涉及的各种生物分子的价数、结合亲和力和聚合物长度。我们的结果假设凝聚体内部 RNA 参数的多样性允许 RNA 通过满足两个不同的标准来增加凝聚体的稳定性:最大化焓增益和最小化界面自由能;因此,在评估 RNA 对生物分子凝聚体调节的影响时,应该考虑 RNA 的多样性。