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Ion channels may be formed by bundles of amphipathic alpha-helices aligned parallel to one another and spanning a lipid bilayer membrane, with the hydrophilic faces of the helices lining a central pore. In order to provide insight into the packing of such helices in bundles, a method has been developed to evaluate hydrophilic surface maps of amphipathic alpha-helices and to display these surfaces in a readily interpretable form. The procedure is based upon empirical energy calculations of interactions of a water molecule with an amphipathic alpha-helix. The method has been applied to three channel-forming peptides: Staphylococcal delta-toxin; alamethicin; and a synthetic leucine- and serine-containing peptide. Particular emphasis is placed upon the effects of sidechain conformational flexibility on hydrophilic surface maps. A family of models of the delta-toxin helix is generated by a simulated annealing procedure. The results of hydrophilic surface map analyses provide more exact definition of the centre of the hydrophilic face of amphipathic helices, and of the variation of the position of the centre in response to changes in sidechain conformation. This information is used to define families of preliminary models for a given ion channel, as is illustrated for delta-toxin.


Journal article


Eur Biophys J

Publication Date





269 - 277


Alamethicin, Amino Acid Sequence, Bacterial Toxins, Chemical Phenomena, Chemistry, Physical, Ion Channels, Models, Chemical, Molecular Sequence Data, Peptides, Protein Conformation, Protein Structure, Secondary, Surface Properties