Transmembrane domains (TMDs) are often flanked by Lys or Arg because they keep their aliphatic parts in the bilayer and their charged groups in the polar interface. Here we examine the relevance of this so-called " snorkeling" of a cationic amino acid, which is conserved in the outer TMD of small viral K+ channels. Experimentally, snorkeling activity is not mandatory for KcvPBCV-1 because K29 can be replaced by most of the natural amino acids without any corruption of function. Two similar channels, KcvATCV-1 and KcvMT325, lack a cytosolic N-terminus, and neutralization of their equivalent cationic amino acids inhibits their function. To understand the variable importance of the cationic amino acids, we reanalyzed molecular dynamics simulations of KcvPBCV-1 and N-terminally truncated mutants; the truncated mutants mimic KcvATCV-1 and KcvMT325. Structures were analyzed with respect to membrane positioning in relation to the orientation of K29. The results indicate that the architecture of the protein (including the selectivity filter) is only weakly dependent on TMD length and protonation of K29. The penetration depth of Lys in a given protonation state is independent of the TMD architecture, which leads to a distortion of shorter proteins. The data imply that snorkeling can be important for K+ channels; however, its significance depends on the architecture of the entire TMD. The observation that the most severe N-terminal truncation causes the outer TMD to move toward the cytosolic side suggests that snorkeling becomes more relevant if TMDs are not stabilized in the membrane by other domains.
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