In structural biology, a protomer is the structural unit of an oligomeric protein. It is the smallest unit composed of at least one protein chain. The protomers associate to form a larger oligomer of two or more copies of this unit. Protomers usually arrange in cyclic symmetry to form closed point group symmetries.
The term was introduced by Chetverin[1] 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. Thus, in the work by Chetverin the term protomer was only applied to a hetero-oligomer and subsequently used mainly in the context of hetero-oligomers. Following this usage, a protomer consists of a least two different proteins chains. In current literature of structural biology, the term is commonly also applied to the smallest unit of homo-oligomers, avoiding the term "monomer".
In chemistry, a so-called protomer is a molecule which displays tautomerism due to position of a proton.[2] [3]
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.[4]
Aspartate carbamoyltransferase has a α6β6 subunit composition. The six αβ-protomers are arranged in D3 symmetry.
Viral capsids are usually composed of protomers.
HIV-1 protease forms a homodimer consisting of two protomers.
Examples in chemistry include tyrosine and 4-aminobenzoic acid. The former may be deprotonated to form the carboxylate and phenoxide anions,[5] and the later may be protonated at the amino or carboxyl groups.[6]