A Simple Flexible Program for the Computational Analysis of Amino Acyl Residue Distribution in Proteins: Application to the Distribution of Aromatic versus Aliphatic Hydrophobic Amino Acids in Transmembrane α-Helical Spanners of Integral Membrane Transport Proteins

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Abstract
We describe a simple, flexible program (AAD) with a primary function of depicting the distribution of aliphatic and aromatic amino acid residues along the linear aligned sequence of a family of homologous proteins and a secondary function of depicting the distribution of all amino acids along the same linear sequence. The program is used to examine the distribution of aromatic versus aliphatic residues in representative well-characterized families of polytopic membrane proteins. Many but not all such protein families are shown to exhibit a predominance of aliphatic residues in the central regions of their transmembrane spanners but a predominance of aromatic residues at the peripheries of their spanners. We propose that this distribution stabilizes the hydrophobic–hydrophilic interface and renders the centers of these integral membrane proteins more fluid than their peripheries.