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]
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.[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]
References
- ^ Chetverin, A.B. (1986). "Evidence for a diprotomeric structure of Na, K-ATPase: Accurate determination of protein concentration and quantitative end-group analysis". FEBS Lett. 196 (1): 121–125. Bibcode:1986FEBSL.196..121C. doi:10.1016/0014-5793(86)80225-3. PMID 3002859.
- ^ P. M. Lalli, B. A. Iglesias, H. E. Toma, G. F. de Sa, R. J. Daroda, J. C. Silva Filho, J. E. Szulejko, K. Araki and M. N. Eberlin, J. Mass Spectrom., 2012, 47, 712–719.
- ^ C. Lapthorn, T. J. Dines, B. Z. Chowdhry, G. L. Perkins and F. S. Pullen, Rapid Commun. Mass Spectrom., 2013, 27, 2399–2410.
- ^ Buxbaum, E. (2007). Fundamentals of protein structure and function. New York: Springer. pp. 105–120. ISBN 978-0-387-26352-6.
- ^ J. Am. Chem. Soc., 2009, 131 (3), pp 1174–1181
- ^ J. Phys. Chem. A, 2011, 115 (26), pp 7625–7632
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