Ubiquitin (Ub) is ubiquitous. This small, 76-residue protein is used to mark cellular proteins for degradation by the ubiquitin proteasome system (UPS). Two key enzyme families, Ub ligases and deubiquitylation enzymes (DUBs), are responsible for putting on and taking off these Ub units and controlling the overall protein population of the cell. As you might imagine, this dynamic process is important, and dysregulation can lead to an array of bad things. Thus, understanding the relations between DUB or Ub ligase activity and specific diseases would be helpful in designing inhibitors or other therapeutic interventions. Accordingly, a number of Ub-based probes for activity-based protein profiling (ABPP) have been developed, typically involving an affinity tag, such as hemagglutinin (HA) or biotin, on the N-terminus and an electrophilic warhead on the C-terminus, such as propargylamide (PA), vinyl methyl ester (VME), or dehydroalanine (Dha). However, many of these probes are limited to experiments with purified recombinant proteins or cell lysates due to poor cell penetrance. Probes really need to be able to enter cells and react with enzymes intracellularly in order to gain the most useful information for drug targeting and other efforts.

• Ubiquitin chains of different lengths and types can be applied to biochemical functions such as interation and enzyme activity as well as structural biology study of crystals, electron microscopes and Nuclear Magnetic Resonance.
• Ubiquitin-derived cross-linking probes can be used to detect unknown interacting proteins from normal or diseased cells and new targets foe disease treatment.
• Ubiquitin-derived fluorescent probes can used to analyze the activity and specificity of deubiquitinase and high throughput screening of deubiquitinase inhibitors.