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Membrane protein assembly is an extremely complex cellular process during which the translocon machinery incorporates newly synthesized membrane proteins into the lipid bilayer. Key open issues include i) what is the oligomeric state of the functioning translocon; ii) how the interaction between the membrane-embedded translocon and the signal peptide triggers a conformational change ultimately leading to the opening of the translocon; iii) what is the conformation of the open-state translocon; iv) are the hydrophobic newly synthesized peptides exposed to an aqueous milieu inside the translocon, and how do they partition into the lipid membrane; v) what determines the insertion into the lipid membrane of helices containing polar residues, and vi) how the lipid bilayer participates to membrane protein assembly.
Computer simulations are critical to understand the energetics and the pathway of newly synthesized proteins through the translocon to their final destination in the lipid membrane. Exciting recent developments from the experimental studies (e.g., crystal structures of wild-type and mutant translocon phenotypes, identification of the translocon:signal peptide contacts) challenge some of the views held on the mechanism of membrane protein assembly.