In structural biology, a protomer is the structural unit of an oligomeric protein. It is the smallest unit composed of at least two different protein chains that form a larger hetero-oligomer by association of two or more copies of this unit.
The term was introduced by Chetverin to make nomenclature in the Na/K-ATPase enzyme unambiguous. This enzyme is composed of two subunits: a large, catalytic α subunit, and a smaller glycoprotein β subunit (plus a proteolipid, called γ-subunit). At the time it was unclear how many of each work together. In addition, when people spoke of a dimer, it was unclear whether they were referring to αβ or to (αβ)2. Chetverin suggested to call αβ a protomer and (αβ)2 a diprotomer.
Protomers usually arrange in cyclic symmetry to form closed point group symmetries.
In chemistry, a so-called protomer is a molecule which displays tautomerism due to position of a proton.
Examples
Hemoglobin is a heterotetramer consisting of four subunits (two α and two β). However, structurally and functionally hemoglobin is described better as (αβ)2, so we call it a dimer of two αβ-protomers, that is, a diprotomer.
Aspartate carbamoyltransferase has a α6β6 subunit composition. The six αβ-protomers are arranged in D3 symmetry.
Viral capsid are often composed of protomers.
Examples in chemistry include tyrosine and 4-aminobenzoic acid. The former may be deprotonated to form the carboxylate and phenoxide anions, and the later may be protonated at the amino or carboxyl groups.