Specific interactions of membrane proteins with the membrane interfacial region potentially define protein position with respect to the lipid environment. We investigated the proposed roles of tryptophan and lysine side chains as "anchoring" residues of transmembrane proteins. Model systems were employed, consisting of phosphatidylcholine lipids and hydrophobic ␣-helical peptides, flanked either by tryptophans or lysines. Peptides were incorporated in bilayers of different thickness, and effects on lipid structure were analyzed. Induction of nonbilayer phases and also increases in bilayer thickness were observed that could be explained by a tendency of Trp as well as Lys residues to maintain interactions with the interfacial region. However, effects of the two peptides were remarkably different, indicating affinities of Trp and Lys for different sites at the interface. Our data support a model in which the Trp side chain has a specific affinity for a well defined site near the lipid carbonyl region, while the lysine side chain prefers to be located closer to the aqueous phase, near the lipid phosphate group. The information obtained in this study may further our understanding of the architecture of transmembrane proteins and may prove useful for refining prediction methods for transmembrane segments.In biological membranes, a variety of interactions can occur between lipids and proteins that affect protein as well as lipid properties and in which both the hydrophobic membrane core and the more polar membrane interfaces can be involved (1-3). Membrane proteins are able to span the lipid bilayer through interactions of their exposed hydrophobic segments with the lipid hydrocarbon acyl chains. In general, the length of these hydrophobic segments will approximately match the membrane hydrophobic thickness. However, also a mismatch between protein hydrophobic length and membrane hydrophobic thickness may occur. Such a mismatch can have considerable influence on membrane structure and function (reviewed in Ref. 4) and may, for example, be involved in protein sorting, microdomain formation, changes in protein activity, or changes in lipid structure and organization.In contrast to the hydrophobic core of a membrane, the membrane interface presents a complex and heterogeneous chemical environment, which accounts for a relatively large proportion of the total bilayer thickness (3). Specific interactions of membrane proteins with the interfacial region of the lipids may influence many functional processes, such as for instance membrane protein assembly, topology of membrane proteins, the mode of protein insertion into the membrane, and protein anchoring to the membrane. In addition, such interactions may play a determining role in hydrophobic mismatch (4).Analyses of the structure of transmembrane proteins suggest that two types of amino acids may be of special importance for interactions of membrane proteins with the interfacial region: aromatic amino acids, in particular tryptophans, which are enriched at both ends of tr...