PhosphoX-db: A web-based bioinformatics platform for studying non-canonical phosphorylation

介导细胞功能的关键分子是蛋白质，它参与生命的所有过程，包括细胞对细胞外刺激的反应机制。细胞间和细胞内传递信号的主要方法之一是通过蛋白质的化学修饰，即所谓的翻译后修饰（PTMs）。这些ptm影响蛋白质如何发挥其功能，例如作为开关或通过启用（或阻断）与其他蛋白质的相互作用。也许最重要的PTM是化学磷酸基团的可逆添加，称为磷酸化，预计会发生在大约一半的人类蛋白质上。蛋白质磷酸化的改变或错误与许多疾病有关，特别是在癌症中，关键“信号”蛋白磷酸化的改变是癌症进展的主要促成因素。负责蛋白质磷酸化的酶被称为激酶，它们本身通常被磷酸盐的添加激活，以“多米诺效应”类型的级联机制。最终，这些磷酸化“级联反应”导致了转录因子蛋白质的激活，转录因子开启了许多新基因的表达，从而产生了新的蛋白质，这样细胞就可以对接收到的信号做出反应。因此，目前市场上或正在开发的大多数抗癌药物都直接或间接地靶向激酶。近半个世纪以来，我们已经知道，在脊椎动物中，构成蛋白质的20种氨基酸中有3种被磷酸化。令人兴奋的是，我们现在已经发现了另外5种氨基酸在人类细胞中被磷酸化广泛修饰，我们称之为pX蛋白。这些新发现完全改变了我们对人类细胞中这类调节蛋白修饰的理解。至关重要的是，这种“缺失”磷酸盐的添加和去除背后的生物学功能和调节机制尚未得到解释。在这个项目中，我们将开发一个基于网络的数据库，使这些新型磷酸化的证据直接提供给其他研究人员。我们将开发软件工具在数据库中运行，以允许我们假设这些pX蛋白在细胞中发挥什么功能，并允许我们和其他研究人员开始探索哪些激酶可能负责pX磷酸化。这些工具还将允许其他研究人员将这些新发现应用于他们自己的研究问题，并帮助制定假设，以便在新的研究中进行后续研究。

The key molecules that mediate cellular functions are proteins, involved in all processes of Life, including the mechanisms by which cells respond to extracellular stimuli. One of the primary methods by which signals are passed between and within cells is via chemical modification of proteins, so called post-translational modifications (PTMs). These PTMs affect how a protein performs it function, for example acting as an on-off switch or by enabling (or blocking) interactions with other proteins. Perhaps the most important PTM is the reversible addition of chemical phosphate groups, termed phosphorylation, which is predicted to occur on around half of all human proteins. Changes or mistakes in protein phosphorylation are implicated in many diseases, and particularly in cancer, where altered phosphorylation of key 'signalling' proteins is a major contributing factor to cancer progression. The enzymes responsible for protein phosphorylation are called kinases, which themselves are often activated by the addition of phosphate, in a 'domino-effect' type cascade mechanism. Ultimately, these phosphorylation 'cascades' result in the activation of proteins called transcription factors, which switch on the expression of lots of new genes, thus making new proteins so the cell can respond to the signal received. As a result, the majority of current cancer drugs on the market or in development, target kinases directly or indirectly. For nearly half a century, we have known that three of the 20 amino acids that make up proteins are phosphorylated in vertebrates. Excitingly, we have now discovered that an additional 5 amino acids are extensively modified by phosphorylation in human cells, which we call pX proteins. These novel findings completely change our understanding of the landscape of this type of regulatory protein modification in human cells. Critically, the biological functions and regulatory mechanisms that underlie the addition and removal of this 'missing' phosphate have not yet been explained. In this project, we will develop a web-based database to make the evidence for these new types of phosphorylation straightforwardly available to other researchers. We will develop software tools to run within the database to allow us to hypothesise what functions these pX proteins perform in cells, and to allow us and other researchers to start exploring which kinases may be responsible for pX phosphorylation. These tools will also allow other researchers to apply these new findings to their own research questions, and help formulate hypotheses to be followed up in new studies.