Mapping the acylated proteome: a chemical genetic approach

随着几个重要的基因组计划的完成，例如人类基因组计划，我们现在有了基本的密码，描述了由细胞制造的蛋白质，这些蛋白质执行生命的基本过程。然而，这只是我们全面了解细胞功能的旅程的开始：研究的重点现在已经转移到解开每种蛋白质在细胞中的作用，以及它是在何时何地进行的。让故事变得更加复杂的是，蛋白质的结构在其最初产生(从遗传密码‘翻译’)后经常被其他被称为酶的蛋白质修改，这个过程被称为‘翻译后修饰’。这些修饰在细胞中可能具有至关重要的功能；例如，它们参与了我们对疾病的免疫反应和病毒感染的机制，而缺陷的修饰与癌症等疾病有关。针对真菌和寄生虫(例如导致疟疾的单细胞寄生虫恶性疟原虫)等病原体中的翻译后酶的药物正在开发中，可能会对我们控制这些疾病的能力产生重大影响。然而，由于细胞中数千种不同蛋白质(被称为蛋白质组)的整体集合的复杂性，事实证明很难识别哪些蛋白质被修饰，以及修饰对蛋白质功能的影响。识别修饰的蛋白质组是了解翻译后修饰的作用，并发现上述药物可能对细胞产生什么影响(和副作用)的关键一步。这项拟议的研究旨在通过将有机化学的最新发现与尖端的全蛋白质组分析相结合来应对这一挑战。我们的目标是利用细胞自身的酶将一种化学“标签”引入蛋白质中，通过一种名为“酰化”的过程对蛋白质进行修饰。标签的设计不会扰乱细胞的正常功能，我们可以非常有选择地用专门设计的试剂‘捕获’和纯化标记的酰基蛋白。这将使我们能够极大地提高全蛋白质组分析对酰化修饰的敏感性，揭示迄今未识别的酰化蛋白，并开辟研究酰化在细胞中的作用的新路线。后来，我们打算利用这种标记和捕获方法来分析药物对单细胞寄生虫中修饰的蛋白质组的影响，甚至使我们能够在显微镜下看到修饰的蛋白质在细胞内移动。这项工作将把伦敦帝国理工学院的化学家和约克大学的生物学家聚集在一起，开展跨学科的合作，也就是说，在传统的化学和生物学学科之间进行合作。

With the completion of several important genome projects, such as the Human Genome Project, we now have the basic code describing the proteins made by cells which carry out the essential processes of life. However, this is only the beginning of our journey towards fully understanding how cells function: the focus of research has now moved to unravelling the role of each protein in a cell, and when and where it is carried out. To further complicate the story, the structure of a protein is frequently modified after its initial creation (its 'translation' from the genetic code) by other proteins called enzymes, a process termed 'post-translational modification'. These modifications can have critically important functions in the cell; for example, they are involved in our immune response to disease and the mechanism of infection by viruses, and defective modification is implicated in diseases such as cancer. Drugs which target the post-translational enzymes in pathogenic organisms such as fungi and parasites (for example, Plasmodium falciparum, the single-celled parasite which causes malaria) are under development, and could make a major impact on our ability to control these diseases. However, due to the complexity of the total set of thousands of different proteins in a cell (dubbed the 'proteome'), it has proven difficult to identify which proteins are modified, and what effect the modification has on a protein's function. Identifying the modified proteome is a key step towards understanding the role of post-translational modification, and to discover what effects (and side-effects) the drugs mentioned above may have in the cell. The proposed research aims to address this challenge by integrating recent discoveries in organic chemistry with cutting-edge whole-proteome analysis. We aim to exploit the cell's own enzymes to introduce a chemical 'tag' into proteins which are modified by a process termed 'acylation'. The tags are designed so as not to disrupt the cell's normal function, and we can very selectively 'capture' and purify the tagged acyl proteins with specially designed reagents. This will allow us to hugely increase the sensitivity of whole-proteome analysis towards acyl modifications, revealing hitherto unidentified acyl proteins and opening up new lines of investigation into the role of acylation in cells. Later, we intend to exploit this tag and capture methodology to analyse the effect of drugs on the modified proteome in single-celled parasites, and even to enable us to see modified proteins under a microscope as they move around the cell. This work will bring together chemists at Imperial College London and biologists at the University of York in an 'interdisciplinary' collaboration / that is, at the interface between the traditional disciplines of Chemistry and Biology.