Specificity pockets are essential in the activity of proteases, allowing them to identify specific proteins or amino acid sequences for cleavage. These are pockets in the active site of the protease, lined with specific amino acids, allowing only one specific side chain to interact. Conveying specificity is important in proteolysis, preventing bulk protein degradation. This can also be used to cleave proteins are specific locations (such as with chymotrypsinogen and trypsin to form the active form, chymotrypsin).
TEV is a highly specific protease, frequently used in research. The specificity allows for viral polyproteins to be cleaved at the desired locations, allowing the virus to replicate.
Thrombin is a protease found in blood clotting pathways. It is less specific than TEV – able to cleave any protein if incubated for a sufficiently long period of time. Due to the reduced specificity of thrombin, it is less common for it to be used in research.