Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Chapter 5

Analysis and Prediction of Protein Posttranslational Modification Sites

JIANJIONG GAO, QIUMING YAO, CURTIS HARRISON BOLLINGER, and DONG XU

5.1 Introduction

Protein has a wide range of essential functions in living cells, including building and repair of body tissues (structural or storage proteins), catalysis of biochemical reactions (enzymes), regulation of growth and metabolism (hormones), water balancing (membrane proteins), and nutrient transport (transporters or carriers). A protein synthesized immediately after translation from mRNA is typically called an immature protein, which is often not fully functional. In order to carry out specific functions in cells, new proteins usually undergo a process called posttranslational modification (PTM). PTM plays key roles in many cellular processes such as signaling, cellular differentiation, protein degradation, protein stability, gene expression regulation, protein function regulation, and protein interactions [1]. Irregular PTM activity is often a cause or consequence of many diseases such as cancer [2].

It has been estimated that there are more than 200 types of PTMs mediated by enzymes consisting of 5% of the proteome [3]. Many of these enzymes, such as transferases (e.g., kinases and phosphatases) and ligases, add or remove various types of chemical groups such as phosphate, acyl group, lipid, glycans, or even peptides covalently at amino acid sidechains. Many of these processes are reversible and can thereby change ...