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Is the phrase “transmembrane segment” equivalent to the transmembrane domain of a protein?

Is the phrase “transmembrane segment” equivalent to the transmembrane domain of a protein?



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I am reading the Handbook of Neurochemistry and Molecular Neurobiology and I am learning about the cell adhesion molecule NCAM2 and I have come across the following:

The overall structure of NCAM2 is similar to that of NCAM. Thus, NCAM2 consists of five Ig‐modules (supposedly of the C2‐type) followed by two Fn3‐modules. The protein exists in a GPI‐anchored isoform and in a transmembrane isoform that contains a 20-25 amino acid transmembrane segment followed by a 106-119‐amino acid cytoplasmic tail (Alenius and Bohm, 1997; Yoshihara et al., 1997).

I know that NCAM2 is located at the cell membrane and has an extracellular, transmembrane and intracellular domain. However, for the above statement: The protein exists in a GPI‐anchored isoform and in a transmembrane isoform that contains a 20-25 amino acid transmembrane segment followed by a 106-119‐amino acid cytoplasmic tail, is the term 'transmembrane segment' equivalent to the transmembrane domain? Further is the term 'cytoplasmic tail' equivalent to the intracellular domain? Any insights are appreciated.


Yes

I'll admit defeat in trying to find the section in the text you linked - if there's any one thing Google can't do, it's search. But questions like this are better put to Uniprot, which gives quite a bit of information. Following that link, you'll see they identify 21 AA of transmembrane topology from 698 to 718, with a cytoplasmic domain afterward. So the cytoplasmic tail is the intracellular domain.

In a sense there is a second transmembrane domain - the signal peptide from 1-19 - but because it is cleaved little attention is paid to it. The extracellular domain starts at 20, with an N terminus outside the cell.

To quote Wikipedia, a transmembrane domain "usually denotes a single alpha helix of a protein". You should probably listen to them on such an issue because nobody is more fixated on semantics (it's a sort of vote). Philosophically, you can picture that multiple transmembrane segments could operate as a functional unit - but each of these segments would be separated by some region of extracellular or intracellular sequence from the next. A "domain" in a protein is a self-contained unit in the primary sequence, not just a series of helices that turn out to be near each other, so that wouldn't work. And in fact if you look at a GPCR paper they speak in standard terms of seven transmembrane domains even while analyzing how they function together.


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