The molecular mechanism of protein translocation, is the subject of a review by Rapoport in Nature.
Proteins transported across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane include soluble proteins, such as those ultimately secreted from the cell or localized to the endoplasmic reticulum lumen, and membrane proteins, such as those in the plasma membrane or in other organelles of the secretory pathway.
Soluble proteins cross the membrane completely and usually have amino-terminal, cleavable signal sequences, the major feature of which is a segment of 7-12hydrophobic amino acids.
Membrane proteins have different topologies in the lipid bilayer, with one or more transmembrane segments composed of about 20 hydrophobic amino acids; the hydrophilic regions of these proteins either cross the membrane or remain in the cytosol.
Both types of proteins are handled by the same machinery within the membrane: a protein-conducting channel. The channel allows soluble polypeptides to cross the membrane and hydrophobic transmembrane segments of membrane proteins to exit laterally into the lipid phase.
An important step in the biosynthesis of many proteins is the partial or complete translocation across the endoplasmic reticulum membrane. Most of these proteins are translocated through a protein-conducting channel that is formed by a conserved, heterotrimeric membrane-protein complex, the Sec61 or SecY complex.
Depending on channel binding partners, polypeptides are moved by different mechanisms: the polypeptide chain is transferred directly into the channel by the translating ribosome, a ratcheting mechanism is used by the endoplasmic reticulum chaperone BiP. Structural, genetic and biochemical data show how the channel opens across the membrane, releases hydrophobic segments of membrane proteins laterally into lipid, and maintains the membrane barrier for small molecules.
Rapoport 2007, Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature vol 450, 663-669.

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