Mass spectrometry-based methods for the comprehensive analysis of protein interactions in cells

蛋白质构成了任何类型细胞的大部分成分。毫不奇怪，它们也是负责在细胞中执行控制其形状和功能的大部分任务的主要分子组。为了使蛋白质确定其功能，它们必须与其他分子（通常是其他蛋白质）发生物理相互作用。这需要在细胞中建立一个复杂的蛋白质相互作用网络。现有的方法可以根据细胞对变化的反应来分析细胞，方法要么是识别所有相对数量变化的蛋白质，要么是识别哪些其他蛋白质与选定的蛋白质相互作用。前一种方法可以同时分析所有的蛋白质，而后一种方法只能研究在分析之前被定义为目标的蛋白质。目前，还没有一种方法能够分析所有蛋白质是如何相互作用的，或者这些相互作用是如何随着细胞内外的变化而变化的。我们之前开发了一种技术，可以研究细胞内蛋白质的相互作用。通过向活细胞中添加一种化学物质，它们被“冻结”在各自的状态，从而保留了单个蛋白质的相互作用。然后，基于串联质谱的生物分析技术可用于确定单个蛋白质相互作用和参与其中的每个分子的身份。我们现在建议改进和优化这项技术，以便它可以用于确定细胞中蛋白质相互作用的完整集合以及它们如何变化。这不仅会促进我们对细胞功能的理解，而且有一天还可以用来研究导致植物、动物和人类疾病的内部和外部影响，并测试预防这些疾病的对策。

Proteins make up the majority of the content of any type of cell. Not surprisingly, they are also the main group of molecules responsible for carrying out the majority of tasks in cells that govern their shape and functionality. In order for the proteins to ascertain their function, they have to physically interact with other molecules, most often other proteins. This requires a complex network of protein interactions to be established in cells. Methods are available that can analyze cells based on how they respond to changes brought upon them either by identifying all of the proteins that change in their relative amounts, or by identifying which other proteins interact with a selected protein. While the former method analyzes all proteins at the same time, the latter can only study the protein that has been defined as target prior to the analysis. Currently, no method exists that would be capable of analyzing how all proteins interact with each other, or how these interactions change in response to changes inside and outside of the cell. We have previously developed a technique that can study protein interactions inside cells. By adding a chemical to live cells, they are "frozen" in their respective state, which preserves individual protein interactions. Bio-analytical techniques that are based on tandem mass spectrometry can then be used to determine individual protein interactions and the identity of each molecule that participates in them. We are now proposing to refine and optimize this technique so it can be used for the determination of the complete set of protein interactions in cells and how they change. Not only would this advance our understanding of how cells function, it could also one day be used to study internal and external influences that cause diseases in plants, animals, and humans, and to test countermeasures to prevent them.