Schematic Representation of the Alpha Helical Peptide

Abstract

Alpha helix is a typical element in the secondary structure of proteins. Because proteins are composed of many atoms, the a helical structure have been drawn in simplified manners. Crick used the helical net projection to study the packing of the a helices [1]. The position of amino acid is projected on the cylinder paper, which wraps around the helix, and then the paper is opened up flatly. By overlaying two papers, the packing of helices was estimated. Schiffer and Edmundson used the helical wheel projection, where the names of amino acid were printed in top view of the helix [2]. It is useful for experienced researchers to image the feature, such as amphiphilicity, of the a helix. Here we report a novel method which explicitly represents the feature of the a helical structure. Figure 1 shows the schematic helical structure of melittin [3]. Melittin, a toxin of bee, interacts with lipid bilayer and finally collapses the bilayer. The action is attributed to the amphipathic a helical structure of melittin. The outer diagram in Fig. 1A is a helical wheel projection and the inner one shows the distribution of hydrophobicity. The radii of circles correspond to the hydrophobicity of amino acids. Small and large circles gather in the upper side and the lower side, respectively. This diagram explicitly reveals that the upper side is hydrophilic and lower side is hydrophobic. The diagrams in Fig. 1C and 1D are helical net projections for the distribution of hydrophobicity and