structural biology Structural biology deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries we ...

, 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 In chemistry and biochemistry, an oligomer () is a molecule that consists of a few repeating units which could be derived, actually or conceptually, from smaller molecules, monomers.Quote: ''Oligomer molecule: A molecule of intermediate relativ ...

of two or more copies of this unit. Protomers usually arrange in

cyclic symmetry In abstract algebra, a cyclic group or monogenous group is a group, denoted C_n (also frequently \Z_n or Z_n, not to be confused with the commutative ring of -adic numbers), that is generated by a single element. That is, it is a set of invertib ...

to form closed

point group In geometry, a point group is a group (mathematics), mathematical group of symmetry operations (isometry, isometries in a Euclidean space) that have a Fixed point (mathematics), fixed point in common. The Origin (mathematics), coordinate origin o ...

symmetries Symmetry () in everyday life refers to a sense of harmonious and beautiful proportion and balance. In mathematics, the term has a more precise definition and is usually used to refer to an object that is invariant under some transformations ...

. The term was introduced by Chetverin to make nomenclature in the Na/K-ATPase

enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

unambiguous. This enzyme is composed of two subunits: a large, catalytic α subunit, and a smaller glycoprotein β subunit (plus a

proteolipid A proteolipid is a protein covalently linked to lipid molecules, which can be fatty acids, isoprenoids or sterols. The process of such a linkage is known as protein lipidation, and falls into the wider category of acylation and post-translationa ...

, 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 A monomer ( ; ''mono-'', "one" + '' -mer'', "part") is a molecule that can react together with other monomer molecules to form a larger polymer chain or two- or three-dimensional network in a process called polymerization. Classification Chemis ...

". In

chemistry Chemistry is the scientific study of the properties and behavior of matter. It is a physical science within the natural sciences that studies the chemical elements that make up matter and chemical compound, compounds made of atoms, molecules a ...

, a so-called protomer is a molecule which displays

tautomerism In chemistry, tautomers () are structural isomers (constitutional isomers) of chemical compounds that readily interconvert. The chemical reaction interconverting the two is called tautomerization. This conversion commonly results from the reloca ...

due to position of a proton.

Examples

Hemoglobin Hemoglobin (haemoglobin, Hb or Hgb) is a protein containing iron that facilitates the transportation of oxygen in red blood cells. Almost all vertebrates contain hemoglobin, with the sole exception of the fish family Channichthyidae. 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 Aspartate carbamoyltransferase (also known as aspartate transcarbamoylase or ATCase) catalyzes the first step in the pyrimidine biosynthetic pathway (). In '' E. coli'', the enzyme is a multi- subunit protein complex composed of 12 subunits ( ...

has a α₆β₆ subunit composition. The six αβ-protomers are arranged in D₃ symmetry. Viral

capsids A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called Protomer (structural biology), protomers. The observable 3-dimensional morpholog ...

are usually composed of protomers.

HIV-1 protease HIV-1 protease or PR is a retroviral aspartyl protease (retropepsin), an enzyme involved with peptide bond hydrolysis in retroviruses, that is essential for the life-cycle of HIV, the retrovirus that causes AIDS. HIV-1 PR cleaves newly synthesized ...

forms a

homodimer In biochemistry, a protein dimer is a macromolecular complex or protein multimer, multimer formed by two protein monomers, or single proteins, which are usually Non-covalent interaction, non-covalently bound. Many macromolecules, such as proteins ...

consisting of two protomers. Examples in

include

tyrosine -Tyrosine or tyrosine (symbol Tyr or Y) or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins. It is a conditionally essential amino acid with a polar side group. The word "tyrosine" is ...

and

4-aminobenzoic acid 4-Aminobenzoic acid (also known as ''para''-aminobenzoic acid or PABA because the two functional groups are attached to the benzene ring across from one another in the ''para'' position) is an organic compound with the formula H2NC6H4CO2H. PABA ...

. The former may be deprotonated to form the carboxylate and phenoxide anions, and the later may be protonated at the amino or carboxyl groups.J. Phys. Chem. A, 2011, 115 (26), pp 7625–7632

References

External links

Structural biology Polymer chemistry {{biophysics-stub