The hydrophobic moment detects periodicity in protein hydrophobicity.

Abstract

Periodicities in the polar/apolar character of the amino acid sequence of a protein can be examined by assigning to each residue a numerical hydrophobicity and searching for periodicity in the resulting 1-dimensional function. The strength of each periodic component is the quantity that has been termed the hydrophobic moment. When proteins of known 3-dimensional structure are examined, sequences that form .alpha. helices tend to have , on average, a strong periodicity in the hydrophobicity of 3.6 residues, the period of the .alpha. helix. Similarly , many sequences that form strands of .beta. sheets tend to have a periodicity in their hydrophobicity of .apprx. 2.3 residues, the period typical of .beta. structure. Also, the few sequences known to form 310 helices display a periodicity of .apprx. 2.5 residues, not far from the period of 3 for an ideal 310 helix. This means that many protein sequences tend to form the periodic structure that maximizes their amphiphilicity. The periodicity of the hydrophobicity of the protein primary structure may be a factor in the formation of secondary structures. Moreover, the observation that many protein sequences tend to form segments of maximum amphiphilicity suggests that segments of secondary structure fold at a hydrophobic surface, probably formed from other parts of the folding protein.