Spectral Analysis of Amino Acid Sequence. I. Intrinsic Membrane Proteins

Primary structure of proteins occasionally shows periodic pattern of hydro-phobicity. The periodicity in the hydrophobicity of amino acid sequence was studied for intrinsic membrane proteins. Power spectral density was calculated by a maximum entropy method which shows the highest resolution or spectra from short sequences of data among various methods. Power spectral density from total amino acid sequence gave a sharp peak at the period of 40 residues, arising from the average distance between neighboring helices. Spectral analysis of every fifteen residues indicated that the helix-periodicity of 3.6 residues was significantly localized at the edges or helices. Functionally important helices had the tendency to exhibit the helix-period also at the center of the helix.