Posey Ammon E, Holehouse Alex S, Pappu Rohit V
Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO, United States.
Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO, United States.
Methods Enzymol. 2018;611:1-30. doi: 10.1016/bs.mie.2018.09.035. Epub 2018 Oct 31.
There is growing interest in the topic of intracellular phase transitions that lead to the formation of biologically regulated biomolecular condensates. These condensates are membraneless bodies formed by phase separation of key protein and nucleic acid molecules from the cytoplasmic or nucleoplasmic milieus. The drivers of phase separation are referred to as scaffolds whereas molecules that preferentially partition into condensates formed by scaffolds are known as clients. Recent advances have shown that it is possible to generate physical and functional facsimiles of many biomolecular condensates in vitro. This is achieved by titrating the concentration of key scaffold proteins and solution parameters such as salt concentration, pH, or temperature. The ability to reproduce phase separation in vitro allows one to compare the relationships between information encoded in the sequences of scaffold proteins and the driving forces for phase separation. Many scaffold proteins include intrinsically disordered regions whereas others are entirely disordered. Our focus is on comparative assessments of phase separation for different scaffold proteins, specifically intrinsically disordered linear multivalent proteins. We highlight the importance of coexistence curves known as binodals for quantifying phase behavior and comparing driving forces for sequence-specific phase separation. We describe the information accessible from full binodals and highlight different methods for-and challenges associated with-mapping binodals. In essence, we provide a wish list for in vitro characterization of phase separation of intrinsically disordered proteins. Fulfillment of this wish list through key advances in experiment, computation, and theory should bring us closer to being able to predict in vitro phase behavior for scaffold proteins and connect this to the functions and features of biomolecular condensates.
细胞内相变导致生物调控的生物分子凝聚物形成这一主题正引发越来越多的关注。这些凝聚物是通过关键蛋白质和核酸分子从细胞质或核质环境中相分离而形成的无膜体。相分离的驱动因子被称为支架,而优先分配到由支架形成的凝聚物中的分子则被称为客户分子。最近的进展表明,在体外生成许多生物分子凝聚物的物理和功能模拟物是可能的。这是通过滴定关键支架蛋白的浓度以及溶液参数(如盐浓度、pH值或温度)来实现的。在体外重现相分离的能力使人们能够比较支架蛋白序列中编码的信息与相分离驱动力之间的关系。许多支架蛋白包含内在无序区域,而其他一些则完全无序。我们的重点是对不同支架蛋白,特别是内在无序的线性多价蛋白的相分离进行比较评估。我们强调共存曲线(称为双节线)对于量化相行为和比较序列特异性相分离驱动力的重要性。我们描述了从完整双节线中可获得的信息,并突出了绘制双节线的不同方法以及与之相关的挑战。实质上,我们为内在无序蛋白相分离的体外表征提供了一份愿望清单。通过实验、计算和理论方面的关键进展来实现这份愿望清单,应该会使我们更接近能够预测支架蛋白的体外相行为,并将其与生物分子凝聚物的功能和特征联系起来。