The hydropathy plot of the inwardly rectifying ROMKI K+ channel, which reveals two transmembrane and a pore region domains, also reveals areas of intermediate hydrophobicity in the N terminus (MO) and in the C terminus (post"2). Peptides that correspond to MO, post"2, and a control peptide, pre-MO, were synthesized and characterized for their structure, affinity to phospholipid membranes, organizational state in membranes, and ability to self-assemble and coassemble in the membrane-bound state. CD spectroscopy revealed that both MO and post-M2 adopt highly a-helical structures in 1% SDS and 40% TWwater, whereas pre-MO is not a-helical in either 1% SDS or 40% TFEYwater. Binding experiments with NBD-labeled peptides demonstrated that both MO and post-M2, but not pre-MO, bind to zwitterionic phospholipid membranes with partition coefficients of 103-105 M". A surface localization for both post-M2 and MO was indicated by NBD shift, tryptophan quenching experiments with brominated phospholipids, and enzymatic cleavage. Resonance energy transfer measurements between fluorescently labeled pairs of donor (NBD)/ acceptor (rhodamine) peptides revealed that MO and post-M2 can coassemble in their membrane-bound state, but cannot self-associate when membrane-bound. The results are in agreement with recent data indicating that amino acids in the carboxy terminus of inwardly rectifying K+ channels have a major role in specifying the pore properties of the channels (Taglialatela M, Wible BA, Caporaso R, Brown AM, 1994, Science 264:844847; Pessia M, Bond CT, Kavanaugh MP, Adelman JP, 1995, Neuron 14:1039-1045). The relevance of the results presented herein to the suggested model for the structure of the ROMKI channel and to general aspects of molecular recognition between membrane-bound polypeptides are also discussed.Keywords: channel structure; fluorescence; K+ channels; synthetic peptides Inwardly rectifying K+ channels conduct an inward K+ current at hyperpolarizing membrane potentials. These channels, because of their rectification properties, play an important role in regulating Reprint requests to: Yechiel Shai, Department of Membrane Research and Biophysics, Weizmann Institute of Science, Rehovot, 76100 Israel; e-mail: bmshai@weizmann.weizmann.ac.il.Abbreviufions: BOC, butyloxycarbonyl; 6,7-BrPC, l-palmitoyl-2-stearoyl(6-7) dibromo-sn-glycero-3 phosphocholine; 9,IO-BrPC. l-palmitoyl-2-stearoyl(9-IO) dibromo-sn-glycero-3 phosphocholine; 11,12-BrPC, l-palmitoyl-2-stearoyl( 1 1-12) dibromo-sn-glycero-3 phosphocholine; DCC, dicyclohexylcarbodiimide; DIEA, diisopropylethylamine; DMF, dimethyl formamide; HF, hydrogen fluoride; HOBT, 1-hydroxybenzotriazole; LUV, large unilamellar vesicles; NBD, 7-nitrobenz-2-oxa-l,3-diazole, 4-yl; Pam, (pheny1acetamido)methyl; NBD-F, 4-fluoro-7-nitrobenz-2-oxa-1,3-diazole; PC, egg phosphatidylcholine; Rho, tetramethylrhodamine; Rho-Su, 5-(and-6)-carboxytetramethylrhodamine succinimidyl ester; RP-HPLC, reversephase HPLC; SUV, small unilamellar vesicles; TFA, trifluoroacetic acid; TFE, tri...