Integral membrane proteins are integrated cotranslationally into the membrane of the endoplasmic reticulum in a process mediated by the Sec61 translocon. Transmembrane α-helices in a translocating polypeptide chain gain access to the surrounding membrane through a lateral gate in the wall of the translocon channel [van den Berg B, et al. (2004) To clarify the nature of the membrane-integration process, we have measured the insertion efficiency into the endoplasmic reticulum membrane of model hydrophobic segments containing nonproteinogenic aliphatic and aromatic amino acids. We find that an amino acid's contribution to the apparent free energy of membrane-insertion is directly proportional to the nonpolar accessible surface area of its side chain, as expected for thermodynamic partitioning between aqueous and nonpolar phases. But unlike bulk-phase partitioning, characterized by a nonpolar solvation parameter of 23 cal∕ðmol · Å 2 Þ, the solvation parameter for transfer from translocon to bilayer is 6-10 cal∕ðmol · Å 2 Þ, pointing to important differences between translocon-guided partitioning and simple water-to-membrane partitioning. Our results provide compelling evidence for a thermodynamic partitioning model and insights into the physical properties of the translocon.flexizyme | hydrophobicity | nonproteinogenic amino acid | transmembrane helix I n eukaryotic cells, membrane proteins destined for the plasma membrane and the various compartments along the endo-and exocytic pathways are synthesized by endoplasmic reticulum (ER)-bound ribosomes and cotranslationally integrated into the ER membrane in a process mediated by the Sec61 translocon complex; the homologous SecYEG translocon mediates membrane-protein integration into the inner membrane of prokaryotes (1, 2). Subsequent to membrane integration, membrane proteins fold and oligomerize in the ER and are then moved further along the secretory pathway by vesicular transport.During the membrane-integration step, hydrophobic segments in the translocating nascent polypeptide chain exit the Sec61 translocon through a lateral gate and become embedded in the surrounding lipid bilayer (3-5). Cotranslational, transloconmediated integration of transmembrane α-helices into the ER membrane sets the stage for all subsequent folding and oligomerization events and hence represents a critical step in the maturation of membrane proteins.In previous studies, we have provided quantitative data on the propensities of the 20 natural amino acids to promote the integration of transmembrane helices into the ER membrane and have shown that they depend both on hydrophobicity and on position within the helix (3, 6). Although the partitioning of transmembrane helices between the Sec61 translocon and the lipid membrane bears strong similarities to partitioning of solutes between water and lipid membranes, translocon-to-bilayer partitioning may not be equivalent to water-to-bilayer partitioning (7). Insights into the differences between the two partitioning processes might be revealed i...