Lorenz-Ochoa Keegan A, Cho Moonyeon, Parekh Sapun H, Baiz Carlos R
Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.
Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States.
J Am Chem Soc. 2024 Dec 11;146(49):33616-33625. doi: 10.1021/jacs.4c11226. Epub 2024 Nov 26.
Biomolecular condensates provide a mechanism for compartmentalization of biomolecules in eukaryotic cells. These liquid-like condensates are formed via liquid-liquid phase separation, by a plethora of interactions, and can mediate several biological processes in healthy cells. Expansions of dipeptide repeat proteins, DPRs, in which arginine rich DPRs like poly-proline-arginine (PR), and poly-glycine-arginine (GR), partition RNA into condensates can however induce cell toxicity. Here, we use (GR) as a model for biological poly-GR and condense it using either excluded volume interactions with polyethylene glycol (PEG) as a crowder or direct electrostatic interactions with RNA oligomers. Using two-dimensional infrared (2D IR) spectroscopy, we observe that (GR) condensed through an excluded volume forms β-sheet structures, whereas (GR) condensed with RNA forms loops. We also investigate local hydrogen-bond dynamics in the condensate and compare the measurements with molecular dynamics simulations. Hydrogen bond lifetimes undergo a marked slowdown compared to dynamics in the dilute phase. This is representative of confined water within the percolated networks inside the condensate due to the interaction present in the condensate disrupting H-bond networks. Overall, our results show that both protein structure and dynamics are inherently dependent on the type of interactions that stabilize the condensates.
生物分子凝聚物为真核细胞中生物分子的区室化提供了一种机制。这些类似液体的凝聚物通过液-液相分离，经由大量相互作用形成，并且可以在健康细胞中介导多种生物学过程。然而，富含精氨酸的二肽重复蛋白（DPR）的扩增，如多脯氨酸-精氨酸（PR）和多甘氨酸-精氨酸（GR），会将RNA分配到凝聚物中，从而诱导细胞毒性。在这里，我们使用（GR）作为生物多聚GR的模型，并通过与作为拥挤剂的聚乙二醇（PEG）的排阻体积相互作用或与RNA寡聚物的直接静电相互作用使其凝聚。使用二维红外（2D IR）光谱，我们观察到通过排阻体积凝聚的（GR）形成β-折叠结构，而与RNA凝聚的（GR）形成环。我们还研究了凝聚物中的局部氢键动力学，并将测量结果与分子动力学模拟进行比较。与稀相中的动力学相比，氢键寿命明显减慢。这代表了由于凝聚物中存在的相互作用破坏了氢键网络，凝聚物内部渗透网络内的受限水。总体而言，我们的结果表明，蛋白质结构和动力学本质上都依赖于稳定凝聚物的相互作用类型。
