Protein subunit

A protein subunit is an individual polypeptide component of a protein complex. The number of protein subunits counts chain copies, whereas the number of subunit types counts distinct kinds of chain. An assembly $A_2{B}_2$ has four protein subunits of two types. A protein domain is a region within a chain and need not be a separate protein subunit; the arrangement of several chains belongs to protein quaternary structure.

The alpha/beta tubulin heterodimer illustrates the distinction: it contains two related but different polypeptides, not two domains cut out of one chain. The 1998 electron-crystallographic model resolved the alpha/beta architecture at $3.7$ angstrom resolution, using zinc-induced tubulin sheets.^[ref]

Subunit counting can also become an optical experiment. In total internal reflection fluorescence microscopy, tagged membrane proteins can be observed as isolated fluorescent spots; successive photobleaching steps reveal individual fluorescent tags disappearing. Subunit counting in membrane-bound proteins by Maximilian H. Ulbrich and Ehud Y. Isacoff used this approach on membrane proteins expressed in frog oocytes. For NR1/NR3B receptor assemblies, tagging one component type mainly gave two steps, while tagging both gave four, supporting a two-plus-two arrangement.^[ref]

A count of visible steps need not equal the true number of protein subunits: some tags fail to fluoresce, and two tags may bleach too close together to resolve. The experiment therefore combines step counts with a model of labeling and detection, rather than interpreting every two-step trace as proof of a two-chain protein complex.^[ref]