A Comprehensive Resource to Explore Protein Kinase-substrate Phosphorylation Networks

• Main Authors: Chen-Tse Ma, 馬晟哲
• Other Authors: Ting-Ying Chien
• Format: Others
• Language: en_US
• Published: 2019
• Online Access: http://ndltd.ncl.edu.tw/handle/s3b9d9

碩士 === 元智大學 === 資訊工程學系 === 107 === Protein phosphorylation is an important and reversible mechanism in post-translational modification. By adding or removing phosphate groups, it is possible to transfer information from the cell surface to the nucleus. Over the past decade, advances in mass spectrometry have enabled biologists to quickly obtain large amounts of protein phosphorylation sites, but have no way of knowing how phosphorylation occurs. For example, 46% of the more than 20,000 known human proteins are phosphorylated, but only 25% of these phosphorylated proteins know how it is phosphorylated. In addition, because the phosphorylation site may be catalyzed by various phosphatases, and the phosphorylated protein may also catalyze the phosphorylation of other proteins. Such complex and continuous regulatory mechanisms allow us to explore multiple protein kinases and substrates simultaneously when discussing phosphorylation regulation. For a comprehensive study of phosphorylation regulation, we referred to the architecture of many related research. We had collected phosphatase, phosphorylation sites, protrin-protein interaction and other data. The addition of protein dephosphorylation, crosstalk between other PTMs and phosphorylation, made the phosphorylation regulatory network more comprehensive . This study not only collated phosphorylation data of mammalian species such as humans, mouse and rats, but also several species of Yeast, Drome and Caeel. Protein regulatory networks are a recognized and widely used method of biological systems research. In order to construct a phosphorylation regulatory network, we first identify protein kinases and phosphatases as the starting point for regulatory networks. Then find and mark the phosphorylation/dephosphorylation between the protein kinase/phosphatase and the substrate. Information such as protein-protein interactions, subcellular localization and metabolic pathways are used as evidence. Finally, a graphical interface is used to display the protein phosphorylation regulatory network, allowing users to quickly and clearly understand protein phosphorylation regulation in organisms. In addition, we also used actual protein experimental data from Massachusetts General Hospital, Harvard Medical School for analysis, including protein expression data, time-course proteomics data and time-course phosphoproteomics data. The practicality of this research was demonstrated by actual protein experimental data analysis.