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

调节细胞功能的关键分子是蛋白质，参与生命的所有过程，包括细胞对细胞外刺激的反应机制。细胞间和细胞内信号传递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(PTM)。这些PTM影响蛋白质如何执行其功能，例如，作为开关或通过启用(或阻止)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加成，称为磷酸化，据预测，这种加成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，尤其是在癌症中，关键信号蛋白的磷酸化改变是癌症进展的主要因素。负责蛋白质磷酸化的酶被称为激酶，它本身通常被磷酸盐的添加激活，这是一种“多米诺骨牌”式的级联机制。最终，这些磷酸化‘级联’导致被称为转录因子的蛋白质的激活，这些转录因子启动许多新基因的表达，从而产生新的蛋白质，从而使细胞能够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针对激酶。近半个世纪以来，我们已经知道组成蛋白质的20种氨基酸中有3种在脊椎动物中是磷酸化的。令人兴奋的是，我们现在发现另外5个氨基酸在人类细胞中被广泛的磷酸化修饰，我们称之为Px蛋白。这些新的发现完全改变了我们对人类细胞中这种类型的调节蛋白修饰的理解。关键的是，添加和移除这种“缺失的”磷酸盐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，使其他研究人员能够直接获得这些新型磷酸化的证据。我们将开发在数据库中运行的软件工具，以允许我们假设这些Px蛋白在细胞中执行什么功能，并允许我们和其他研究人员开始探索哪些激酶可能导致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，并帮助制定假说，以便在新的研究中跟进。

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.