Transmembrane domains

Question

Are integral membrane proteins the only membrane proteins that have domains? How are these domains established?

Answer 1

Hi, Catherine!

All proteins have domains (though some are/have only a single domain). A 'domain' is a unit of structural organization. "Organized blob" might be another way of putting it. Domains arise because of the same kinds of interactions that cause alpha helices and beta sheets to happen, as well as some others. You likely learned that amino acid side chains can be grouped by type--positively charged ones, negatively charged ones, hydrophobic ones... each of these is 'most content' with an appropriate partner (positive with negative; hydrophobic with other hydrophobic). So while a protein is initially synthesized as a string-of-amino-acids by the ribosome, complementary amino acids will cluster together. Hydrogen bonds between elements of the BACKBONE cause alpha helices and beta sheets; side chain interactions also form reliable partnerships with other side chains. You can think of it somewhat as what happens every day in a classroom of kids before they have to take their seats--they form into small groups based on which students like each other (what their affinities are). In a protein, this is constrained because each amino acid is attached to two other through the backbone, but overall, the idea is the same.

For proteins to function, they must reliably self-assemble into precise 3D shapes. So they have evolved to consist of amino acid chains that always result in the same globs (domains), and these domains will display side chains in appropriate 3D placements to... do whatever it is the protein does!