Membrane proteins reside in cell and organelle membranes. They play significant roles in many processes vital to living cells. Receptors and ion channels are examples of membrane proteins that regulate the physiological state of the cell and are attractive targets for drug development.

In eukaryotic cells most membrane proteins insert and fold cotranslationally into the endoplasmic reticular membrane. The insertion process is mediated by the Sec61 translocon which is a hetero-oligomeric protein-conducting channel that allows transmembrane segments to exit laterally into the lipid bilayer. How the translocon recognizes the molecular characteristics of transmembrane helices and integrate them into the lipid bilayer is the focus of this thesis.

We have determined the sequence requirements for translocon-mediated integration of a transmembrane -helix into the ER membrane by challenging the Sec61 translocon with designed polypeptide segments in an in vitro expression system that permits quantitative assessment of membrane insertion efficiency. A biological hydrophobicity scale and a position-dependent free energy matrix have been developed, describing the contribution of each of the 20 amino acids in each position of a 19-residues long polypeptide segment to the overall free energy of a single transmembrane segment insertion. These studies suggest that the translocon provides direct contact between the nascent chain and the lipids in the membrane and that this protein-lipid interaction is the basis for the recognition of transmembrane helices in the translocon.