KvAP is a voltage-gated tetrameric K؉ channel with six transmembrane (S1-S6) segments in each monomer from the archaeon Aeropyrum pernix. The objective of the present investigation was to understand the plausible role of the S6 segment, which has been proposed to form the inner lining of the pore, in the membrane assembly and functional properties of KvAP channel. For this purpose, a 22-residue peptide, corresponding to the S6 transmembrane segment of KvAP (amino acids 218 -239), and a scrambled peptide (S6-SCR) with rearrangement of only hydrophobic amino acids but without changing its composition were synthesized and characterized structurally and functionally. Although both peptides bound to the negatively charged phosphatidylcholine/phosphatidylglycerol model membrane with comparable affinity, significant differences were observed between these peptides in their localization, selfassembly, and aggregation properties onto this membrane. S6-SCR also exhibited reduced helical structures in SDS micelles and phosphatidylcholine/phosphatidylglycerol lipid vesicles as compared with the S6 peptide. Furthermore, the S6 peptide showed significant membrane-permeabilizing capability as evidenced by the release of calcein from the calcein-entrapped lipid vesicles, whereas S6-SCR showed much weaker efficacy. Interestingly, although the S6 peptide showed ion channel activity in the bilayer lipid membrane, despite having the same amino acid composition, S6-SCR was significantly inactive. The results demonstrated sequence-specific structural and functional properties of the S6 wild type peptide. The selected S6 segment is probably an important structural element that could play an important role in the membrane interaction, membrane assembly, and functional property of the KvAP channel.Ion channels belong to a large family of proteins that catalyze the diffusion of inorganic ions down their electrochemical gradients across the cell membranes (1-3). It is known that electric fields exist or arise in living cells and tissues affecting conductance of ion channels (1-3). These ion channel proteins are involved in versatile physiological activities and are responsible for all electrical signaling in living creatures (4 -6). Ion channels have been named according to the name of ions that they allow to diffuse through the pores they form. For example, K ϩ channels are responsible for the diffusion of K ϩ ions and constitute an important class of ion channels (7-9). K ϩ channels modulate the resting potential and action potential duration of neurons, myocytes, and endocrine cells and stabilize the membrane potential of excitable and non-excitable cells (10 -13). K ϩ channels that are activated by membrane depolarization are termed voltage-gated K ϩ (Kv) 4 channels. These Kv channels are tetramers containing six transmembrane segments and one pore region in each monomer. The first four transmembrane segments, S1-S4, form a module that somehow controls the opening and closing of the pore. The fifth (S5) and sixth (S6) transmembrane se...