There are many methods used to identify the interaction sites between two or more proteins or protein subunits.
Proteolytic Mapping A common method used is the use of proteolytic enzymes that cleave at specific protein regions. Proteolytic mapping has several advantages, including the fact that reactions can be performed in-vitro under physiological conditions and only require a small amount of native protein. Several proteases that are highly purified and chemically modified to prevent auotlysis are offered. The proteases offered are Glutamic-C, Lysine-C, Arginine-C, Chymotrypsin and Trypsin.
Chemical Mapping In some cases, chemical reagents are used that cleave proteins at known sites.