The alpha-helical bundle is the most common type of fold for membrane proteins. Their diverse functions include transport, signalling, and catalysis. While structure determination is much more difficult for membrane proteins than it is for soluble proteins, it is accelerating and there are now 586 unique proteins in the database of Membrane Proteins of Known 3D Structure. However, we still have quite a poor understanding of how membrane proteins fold. There is increasing evidence that it is more complicated than the two-stage model proposed in 1990 by Popot and Engelman.
The machinery that inserts most alpha-helical membrane proteins is the Sec apparatus. In prokaryotes, it is located in the plasma membrane, while eukaryotic Sec is found in the ER. Sec itself is an alpha-helical bundle in the shape of a pore, and its structure is able both to allow peptides to pass fully across the membrane, and also to open laterally to insert transmembrane helices into the membrane. In both cases, this occurs co-translationally, with translation halted by the signal recognition particle until the ribosome is associated with the Sec complex.
If helices are inserted during the process of translation, does folding only begin after translation is finished? On what timescale are these folding processes occuring? There is evidence that a hairpin of two transmembrane helices forms on a timescale of miliseconds in vitro. Are helices already interacting during translation to form components of the native structure? It has also been suggested that helices may insert into the membrane in pairs, via the Sec apparatus.
There are still many aspects of the insertion process which are not fully understood, and even the topology of an alpha-helical membrane protein can be affected by the last part of the protein to be translated. I am starting to investigate some of these questions by using computational tools to learn more about the membrane proteins whose structures have already been solved.