In some transmembrane proteins, an internal, rather than an N-terminal, signal sequence is used to start the protein transfer; this internal signal sequence, called a start-transfer sequence, is never removed from the polypeptide.

This arrangement occurs in some transmembrane proteins in which the polypeptide chain passes back and forth across the lipid bilayer. In these cases, hydrophobic signal sequences are thought to work in pairs: an internal start-transfer sequence serves to initiate translocation, which continues until a stop-transfer sequence is reached; the two hydrophobic sequences are then released into the bilayer, where they remain as membrane-spanning α helices.

In complex multipass proteins, in which many hydrophobic α helices span the bilayer, additional pairs of start- and stop-transfer sequences come into play: one sequence reinitiates translocation further down the polypeptide chain, and the other stops translocation and causes polypeptide release, and so on for subsequent starts and stops.

In this way, multipass membrane proteins are stitched into the lipid bilayer as they are being synthesized, by a mechanism resembling the workings of a sewing machine.