The helical hydrophobic moment: a measure of the amphiphilicity of a helix

Abstract

The spatial distribution of the hydrophobic side chains in globular proteins is of considerable interest. It was recognized previously that most of the alpha-helices of myoglobin and haemoglobin are amphiphilic; that is, one surface of each helix projects mainly hydrophilic side chains, while the opposite surface projects mainly hydrophobic side chains. To quantify the amphiphilicity of a helix, here we define the mean helical hydrophobic moment, (mu H) = [sigma Ni = 1Hi]/N, to be the mean vector sum of the hydrophobicities Hi of the side chains of a helix of N residues. The length of a vector Hi is the signed numerical hydrophobicity associated with the type of side chain, and its direction is determined by the orientation of the side chain about the helix axis. A large value of (mu H) means that the helix is amphiphilic perpendicular to its axis. We have classified alpha-helices by plotting their mean helical moment versus the mean hydrophobicity of their residues, and report that transmembrane helices, helices from globular proteins and helices which are believed to seek surfaces between aqueous and nonpolar phases, cluster in different regions of such a plot. We suggest that this classification may be useful in identifying helical regions of proteins which bind to the surface of biological membranes. The concept of the hydrophobic moment can be generalized also to non-helical protein structures.