Protomer (structural biology)

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. 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

External links

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[1] 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. doi:10.1016/0014-5793(86)80225-3. PMID 3002859.

[2] 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.

[3] C. Lapthorn, T. J. Dines, B. Z. Chowdhry, G. L. Perkins and F. S. Pullen, Rapid Commun. Mass Spectrom., 2013, 27, 2399–2410.

[Bux-07-4] Buxbaum, E. (2007). Fundamentals of protein structure and function. New York: Springer. pp. 105–120. ISBN 978-0-387-26352-6.

[5] J. Am. Chem. Soc., 2009, 131 (3), pp 1174–1181

[6] J. Phys. Chem. A, 2011, 115 (26), pp 7625–7632

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