Pi interactions in monomeric and phase-separated disordered state ensembles

蛋白质是由一系列不同类型的氨基酸残基组成的。虽然许多蛋白质采用相对静态和有序的三维形状来发挥功能，但很明显，一大类“无序”蛋白质却不是这样。它们在高度灵活的状态下工作，就像一串串珠子。从病毒到植物和动物，在整个生物学中都发现了无序蛋白质，并且与控制关键的生物事件以及疾病有关。它们还会形成大的液滴，类似于沙拉酱中的油滴，在细胞组织中起着“相分离”的作用。我们最近发现，具有双键的无序蛋白质氨基酸残基（含pi基团）对相分离很重要，我们假设pi基团也显著影响分离的无序蛋白质的结构。为了更好地理解无序蛋白质的本质以及无序蛋白质在生物学中的作用，特别是在组织细胞方面，无序蛋白质及其相分离状态的原子水平描述是必不可少的。静态蛋白质需要一种结构来描述它，而无序蛋白质或液相分离状态需要许多结构（一个集合）来表示它。用标准方法是不可能进行如此广泛的系综结构计算的。因此，我们一直在开发计算机方法ENSEMBLE，计算与大量实验数据一致的结构集合，并共同代表无序蛋白质。为了实现描述无序和相分离状态的目标，我们提出了以下目标：(1)设计基于pi相互作用的无序蛋白质紧密度及其相分离倾向的预测因子。(2)为蛋白质的计算模拟创建新的参数集，使它们能够有效地模拟pi相互作用。(3)计算分离蛋白和相分离蛋白的ENSEMBLE模型，以获得详细的核磁共振数据，从而生成这些状态的结构特征的精确图像，并分析π相互作用对这些特征的贡献。我们的努力将显著提高结构社区研究这些具有挑战性的无序蛋白质的能力，这些蛋白质在细胞组织中发挥着重要的生物学作用

Proteins are made up of a chain of different types of amino acid residues. While many proteins adopt a relatively static and ordered 3-dimensional shape in order to function, it has become clear that a large class of "disordered" proteins do not. They function in a highly flexible state, like strands of beads. Disordered proteins are found throughout biology, from viruses to plants and animals, and are associated with controlling critical biological events as well as in disease. They also form large liquid droplets, similar to oil droplets in salad dressing, that function in cellular organization in a process called “phase separation”. We have recently found that disordered protein amino acid residues having double bonds (pi-containing groups) are important for phase separation and we hypothesize that pi groups also significantly affect the structure of isolated disordered proteins. In order to better understand the nature of disordered proteins and how disordered proteins function in biology, particularly in organizing cells, atomic-level descriptions of disordered proteins and their phase-separated states are essential. While a static protein needs one structure to describe it, a disordered protein or liquid phase-separated state requires many structures (an ensemble) to represent it. Such extensive ensemble structural calculations are not possible with standard approaches. Thus, we have been developing the computer approach ENSEMBLE that calculates collections of structures that together are consistent with a large amount of experimental data and together represent the disordered protein. To address our goals of describing disordered and phase-separated states, we propose the following aims: (1) Design predictors of the compactness of disordered proteins and their propensities to phase-separate based on pi interactions. (2) Create new parameter sets for computational simulations of proteins to enable them to effectively model pi interactions. (3) Calculate ENSEMBLE models for an isolated and phase-separated protein for which we can obtain detailed NMR data in order to generate precise pictures of the structural features of these states and analyze the contributions of pi interactions to these features. Our efforts will significantly enhance the ability of the structural community to study these challenging disordered proteins that play essential biological roles, including in organizing the cell.**