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

The spatial distribution of the hydrophobic side chains in globular proteins is of considerable interest. It was recognized previously1 that most of the α-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, 〈μH〉 = |ΣNi=1 H⇀i/N, to be the mean vector sum of the hydrophobicities H⇀i of the side chains of a helix of N residues. The length of a vector H⇀i 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 〈μH〉 means that the helix is amphiphilic perpendicular to its axis. We have classified α-helices by plotting their mean helical moment versus the mean hydrophobicity of their residues, and report that trans-membrane helices, helices from globular proteins and helices which are believed to seek surfaces between aqueous and non-polar 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 hydrophobia moment can be generalized also to non-helical protein structures.

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