Identification and characterization of modular domains that bind ubiquitin

To receive and transmit the information carried by ubiquitin signals, cells have evolved an array of modular ubiquitin-binding domains. These domains bind directly and noncovalently to monoubiquitin and polyubiquitin chains and are found within proteins that function in diverse biological processes. Ubiquitin-binding domains characterized thus far are generally small and structurally diverse, yet they all interact with the same hydrophobic patch on the surface of ubiquitin. The rapid identification and characterization of ubiquitin-binding domains has been accomplished through the extensive use of bioinformatics, biochemistry, molecular biology, and biophysics. Here, we discuss the strategies and tools that have been most successful in the identification and characterization of ubiquitin-binding domains.